2011-07-20
Trish Whetzel
Chris Stoeckert
Elisabetta Manduchi
Jeffrey Grethe
Philip Lord
Philippe Rocca-Serra
Jie Zheng
Pierre Grenon
Mervi Heiskanen
Chris Mungall
Tina Hernandez-Boussard
Lawrence Hunter
Allyson Lister
Holger Stenzhorn
The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific.
John Westbrook
Richard Bruskiewich
Bill Bug
Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester
free, no license required.
Frank Gibson
Kevin Clancy
Robert Stevens
2011-07-20
Barry Smith
Dawn Field
Ontology for Biomedical Investigation
Helen C. Causton
en
Eric Deutsch
Gilberto Fragoso
OWL-DL
Dirk Derom
Daniel Rubin
Carlo Torniai
Jessica Turner
Ryan R. Brinkman
Melissa Haendel
Alan Ruttenberg
Monnie McGee
Helen Parkinson
Susanna-Assunta Sansone
James Malone
Daniel Schober
An ontology for the annotation of biomedical and functional genomics experiments.
This file is based on checkout of our SVN repository revision $Revision: 3272 $
Jennifer Fostel
Richard Scheuermann
Cristian Cocos
Bjoern Peters
Liju Fan
Yongqun He
Melanie Courtot
Matthew Pocock
Tanya Gray
Chris Taylor
Larisa Soldatova
Joe White
Jay Greenbaum
Norman Morrison
Luisa Montecchi
Stefan Wiemann
ICBO 2011 Release
SVN Revision: 3175
Thermobifida fusca
Thermobifida fusca
T cell proliferation by 3H-thymidine incorporation
IEDB
IEDB
T cell epitope (3H-Thymidine) cell proliferation assay
T cell epitope (3H-Thymidine) cell proliferation assay
T cell epitope specific proliferation assay that measures T cell proliferation utilizing the Thymidine incorporation assay.
graeco latin square design
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
Greco-Latin square design is a study design which relates to Latin square design
PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes.
Philippe Rocca-Serra
graeco latin square design
Coniferopsida
Coniferopsida
PERSON:Daniel Schober
A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing.
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01055
column cartridge
column cartridge
person:Jennifer Fostel
eMedical record
An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11.
eMedical record
article-without-pmid-or-doi:CDISCglossary
A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive.
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
Philippe Rocca-Serra
Monnie McGee
2011-03-31: [PRS].
creating a defined class by specifying the necessary output of dt
allows correct classification of FWER dt
family wise error rate correction method
family wise error rate correction method
FWER correction
error correction objective
Application of a multiple testing correction method
PERSON: James Malone
An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself.
James Malone, Helen Parkinson
error correction objective
Sciurognathi
Sciurognathi
An assay which uses a flow cytometer to detect pairs of cells that are interacting by staining them with different fluorescent labels.
cell:cell conjugate detection assay
PERSON:Bjoern Peters
cell-cell binding detection by flow cytometry assay
cell-cell binding by FACS
cell-cell binding detection by flow cytometry assay
Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates.
monocyte chemotactic protein-1 production
The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
monocyte chemotactic protein-1 production
Viruses
Viruses
mast cell
A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development.
mast cell
curve fitting data transformation
curve fitting data transformation
James Malone
A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints.
Elisabetta Manduchi
Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Curve_fitting
hyper graeco latin square design
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
PRS to do
Philippe Rocca-Serra
hyper graeco latin square design
macrophage inflammatory protein-1 gamma production
The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
macrophage inflammatory protein-1 gamma production
Paxilineae
Paxilineae
Macropus eugenii
Macropus eugenii
PERSON:Daniel Schober
GROUP:<http://msi-ontology.sourceforge.net>
The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:\n Significant S/N gains (with moderately salty samples also)\n Short pulse widths\n Short ring down times\n Linear behavior in power response\n Gradient capability\n CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and higher\n All high resolution probes have a lock circuit\n All high resolution probes have Z-gradient.
Bruker CryoProbe
Bruker CryoProbe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400191
chemokine (C-C motif) ligand 4 production
The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-C motif) ligand 4 production
scaling data transformation
A scaling data transformation is a data transformation that has objective scaling.
James Malone
PERSON: James Malone
scaling data transformation
PERSON:Alan Ruttenberg
handedness categorical measurement datum
left handed
left handed
right handed
right handed
ambidexterous
ambidexterous
A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally
handedness categorical measurement datum
PERSON:Jessica Turner
culture medium role
OBI
culture medium role
a role that inheres in a material entity and is realized in the use of that material entity by an organism grown in vitro to provide all needed nourishment.
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
culture medium
Person: Jennifer Fostel
reverse transcription polymerase chain reaction assay
reverse transcription polymerase chain reaction assay
an assay that evaluates the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR.
PERSON: Chris Stoeckert, Jie Zheng
GROUP: Penn Group
Streptophyta
Streptophyta
Staphylococcaceae
Staphylococcaceae
half life datum (t 1/2)
The time it takes for 50% of a class of stochastic processes to occur.
Bjoern Peters
t 1/2
half life datum (t 1/2)
Bjoern Peters
PERSON: Daniel Schober
microtome
PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
microtome
A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
PERSON: Phillippe Rocca-Serra
Zinnia
Zinnia
Thlaspi caerulescens
Thlaspi caerulescens
ethylenediaminetetraacetic acid
A tetracarboxylic acid that has formula C10H16N2O8.
ethylenediaminetetraacetic acid
MO_699
reference design
Philippe Rocca-Serra on behalf of MO
reference design
PMID: 12933549
A reference experiment design type is where all samples are compared to a common reference.
epitope specific T cell proliferation
epitope specific T cell proliferation
A biological process where T cells proliferate resulting from the recognition of a T cell epitope.
IEDB
IEDB
unplanned occurrence effecting an investigation
OBI
PERSON: Bjoern Peters
unplanned occurrence effecting an investigation
Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used
a process which is external in origin to the investigation that has an impact on the outcome.
Cryptopygus antarcticus
Cryptopygus antarcticus
Elisabetta Manduchi
A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows.
James Malone
Melanie Courtot
PERSON: Melanie Courtot
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set.
row submatrix extraction
row submatrix extraction
PERSON: Elisabetta Manduchi
PERSON: James Malone
Person:Chris Stoeckert
sequence data
example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search.
GROUP: OBI
A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement.
sequence data
cross validation objective
WEB: http://en.wikipedia.org/wiki/Cross_validation
A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
James Malone
cross validation objective
rotation estimation objective
An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications.
WEB:<http://www.bruker-biospin.com/nmr_magnets_usplus.html>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400190
PERSON:Daniel Schober
Bruker UltraShield Plus NMR magnet
Bruker UltraShield Plus NMR magnet
Haemosporida
Haemosporida
Bartonella grahamii
Bartonella grahamii
Rhabditoidea
Rhabditoidea
Desulfovibrio desulfuricans
Desulfovibrio desulfuricans
Euacanthopterygii
Euacanthopterygii
dose response curve
A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve.
Bjoern Peters; Randi Vita
dose response curve
IEDB
T cell epitope (BrdU) cell proliferation assay
T cell proliferation by BrdU incorporation
IEDB
T cell epitope specific proliferation assay that measures T cell proliferation utilizing the BrdU incorporation assay.
T cell epitope (BrdU) cell proliferation assay
latin square design
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
Philippe Rocca-Serra
latin square design
obsolete_right handedness
obsolete_right handedness
ribonuclease T2
A protein that is a translation product of the RNASET2 gene or a 1:1 ortholog thereof.
ribonuclease T2
James Malone
submatrix extraction
submatrix extraction
Melanie Courtot
A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.)
WEB: http://en.wikipedia.org/wiki/Submatrix
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set.
Elisabetta Manduchi
Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix.
transforming growth factor-beta production
The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3.
transforming growth factor-beta production
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01086
PERSON:Daniel Schober
Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element.
WEB:<http://elchem.kaist.ac.kr/vt/chem-ed/sep/gc/detector/aed.htmt>
atomic emission detector
AED
atomic emission detector
sequence analysis data transformation
EDITOR
A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns.
James Malone
sequence analysis data transformation
Actinobacteria (class)
Actinobacteria (class)
pressure
A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts.
pressure
Monacrosporium haptotylum
Monacrosporium haptotylum
Triticeae
Triticeae
IEDB
EL-4 cell culture
http://www.biotech.ist.unige.it/cldb/cl1160.html
EL-4 cell culture
IEDB
A cell line derived from mouse (C57BL/6N) lymphoma cells.
cell culture analyte detection bioassay of epitope specific interleukin-4 production by T cells
cell culture analyte detection bioassay of epitope specific interleukin-4 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A cell culture analyte detection bioassay that measures epitope specific interleukin-4 production by T cells
IL-4 release by bioassay
IEDB (QTT)
life cycle stage
A spatiotemporal region encompassing some part of the life cycle of an organism.
life cycle stage
Stolidobranchia
Stolidobranchia
Bartonella henselae
Bartonella henselae
PERSON: Jie Zheng
fresh specimen
fresh specimen
PERSON: Chris Stoeckert
a liver freshly removed from a rat
a specimen that is output of a specimen creation process used for an investigation without storage.
MO_730 fresh_sample
Mycobacterium
Mycobacterium
Methylophilaceae
Methylophilaceae
Streptomyces avermitilis
Streptomyces avermitilis
data set of features
PERSON: James Malone
PERSON: Monnie McGee
data set of features
A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set.
experimental infection of cell culture
experimental infection of cell culture
IEDB
IEDB
is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture
Apicomplexa
Apicomplexa
PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
microscope
microscope
A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
wikipedia
PERSON: Phillippe Rocca-Serra
intracellular cytokine staining assay of epitope specific interleukin-6 production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-6 production by T cells
intracellular cytokine staining assay of epitope specific interleukin-6 production by T cells
IL-6 release by ICS
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Thermoplasmataceae
Thermoplasmataceae
Vibrio cholerae
Vibrio cholerae
Penaeus
Penaeus
merging of columns from two different data sets
combining objective
James Malone
PERSON: Data Transformation Branch
merging objective
A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets.
merging objective
obsolete_electrically powered device
a processed material created to have a function and which requires electrical power to execute
obsolete_electrically powered device
diagnosis textual entity
Jennifer Fostel
diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
diagnosis textual entity
Mycobacteriaceae
Mycobacteriaceae
PERS:Philippe Rocca-Serra
A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant.
To compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level.
q-value
Adapted from several sources, including
http://.en/wikipedia.org/wiki/False_discovery_rate
http://svitsrv25.epfl.ch/R-doc/library/qvalue.html
q-value
PMID: 20483222. Comp Biochem Physiol Part D Genomics Proteomics. 2008 Sep;3(3):234-42. Analysis of Sus scrofa liver proteome and identification of proteins differentially expressed between genders, and conventional and genetically enhanced lines.
"After controlling the false discovery rate (FDR</=0.1) using the Storey q value only four proteins (EPHX1, CAT, PAH, ST13) were shown to be differentially expressed between genders (Males/Females) and two proteins (SELENBP2, TAGLN) were differentially expressed between two lines (Transgenic/Conventional pigs)"
FDR adjusted p-value
Thiomonas
Thiomonas
Cryptopygus
Cryptopygus
A cell line derived from mouse dendritic cells.
IEDB
IEDB
JAWS II cell culture
JAWS II cell culture
http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-11904&Template=cellBiology
A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels.
A clustered data set is the output of a K means clustering data transformation
clustered data set
PERSON: Monnie McGee
PERSON: James Malone
data set with assigned discovered class labels
clustered data set
macrophage inflammatory protein-1 alpha production
The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
macrophage inflammatory protein-1 alpha production
loess transformation
loess transformation
Philippe Rocca-Serra
James Malone
A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves.
OTHER: Editor's generalization based on MGED Ontology term
Melanie Courtot
Elisabetta Manduchi
Cyanothece
Cyanothece
Macropus
Macropus
Desulfovibrionaceae
Desulfovibrionaceae
Pinaceae
Pinaceae
Desulfovibrio
Desulfovibrio
Person: Chris Stoeckert, Jie Zheng
Group: ArrayExpress production team
A study design in which proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology
proteomic profiling by array design
proteomic profiling by array design
http://www.biotech.ist.unige.it/cldb/cl1597.html
A cell line derived from human cervical cancer cells.
HeLa cell culture
HeLa cell culture
IEDB
IEDB
chemokine (C-C motif) ligand 5 production
The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-C motif) ligand 5 production
editor
edge weighting
Tina Hernandez-Boussard
edge weighting
Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network.
Staphylococcus aureus subsp. aureus
Staphylococcus aureus subsp. aureus
Stegomyia
Stegomyia
Coccidia
Coccidia
A study design in which all specimens are compared to every other specimen.
MO_565 all_pairs
all pairs design
Person: Chris Stoeckert, Jie Zheng
all pairs design
scalar score from composite inputs
questionaire score
scalar score from composite inputs
PlanAndPlannedProcess Branch
sample preparation for assay
study
OBI branch derived
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
Magnaporthaceae
Magnaporthaceae
Actinomyces
Actinomyces
Coffea arabica
Coffea arabica
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope.
epitope specific granulocyte colony stimulating factor production by T cells
epitope specific granulocyte colony stimulating factor production by T cells
IEDB (QTT)
glucose molecules
glucose in solution
Glucose present in blood
glucose in solution
A scattered aggregate of glucose molecules in a liquid
PERSON: Jie Zheng
Brucellaceae
Brucellaceae
soil
Any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m.
soil
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
detection of specific nucleic acids with complementary probes of epitope specific perforin production
detection of specific nucleic acids with complementary probes of epitope specific perforin production
perforin release by RNA/DNA detection
A detection of specific nucleic acids with complementary probes that measures epitope specific perforin production
glucose metabolic process
The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
glucose metabolic process
Vibrio
Vibrio
Corynebacteriaceae
Corynebacteriaceae
Pipoidea
Pipoidea
An assay that measures epitope specific macrophage inflammatory protein-1 alpha production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells
assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells
MIP-1a release
alive
A viability quality inhering in a bearer by virtue of the bearer's condition before death.
alive
Sulfolobaceae
Sulfolobaceae
ELISA of epitope specific interleukin-23 production by T cells
An ELISA that measures epitope specific interleukin-23 production by T cells
ELISA of epitope specific interleukin-23 production by T cells
IEDB (QTT)
IL-23 release by ELISA
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Liliopsida
Liliopsida
epitope specific IL-10 release by T cells
A biological process where T cells produce IL-10 resulting from the recognition of a T cell epitope.
epitope specific IL-10 release by T cells
IEDB
IEDB
DNA methylation profiling by array assay
Person: James Malone
An assay in which the methylation state of DNA is determined and is compared between samples using array technology
DNA methylation profiling by array assay
EFO_0002759 methylation profiling by array
liquid chemical solution
PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution.
A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute.
PERSON: Philippe Rocca-Serra
GROUP: OBI Biomaterial Branch
chemical solution
chemical solution
PERSON: Bjoern Peters
Paracoccidioides brasiliensis
Paracoccidioides brasiliensis
IEDB (QTT)
cytometric bead array assay of epitope specific monocyte chemotactic protein-1 production by T cells
MCP-1 release by cytometric bead array
cytometric bead array assay of epitope specific monocyte chemotactic protein-1 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A cytometric bead array assay that measures epitope specific monocyte chemotactic protein-1 production by T cells
Mycobacterium leprae
Mycobacterium leprae
Poeae
Poeae
PERSON:Daniel Schober
imaging NMR probe
imaging NMR probe
GROUP:<http://msi-ontology.sourceforge.net>
An NMR probe that is designed for generating pictures from sample states via NMR imaging.
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400244
Awaiting English definition from Monnie McGee
Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean
spread calculation objective
spread calculation objective
Person:Helen Parkinson
James Malone
is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set
transcription profiling identification objective
A molecular feature identification objective that aims to characterize the abundance of transcripts
Group: Penn Group
Person: Chris Stoeckert, Jie Zheng
transcription profiling identification objective
Philippe Rocca-Serra
copy number variation profiling
copy number variation profiling
CNV analysis
Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array.
de Ståhl TD, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjöld M, Upadhyaya M, Komorowski J, Bruder CE, Dumanski JP.
Hum Mutat. 2008 Mar;29(3):398-408. PMID: 18058796
copy number variation profiling is a process which aims to provide information about lost or amplified genomic regions of DNA by comparing genomic DNA originated from tissues from same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping.
Staphylococcus aureus
Staphylococcus aureus
Estrildidae
Estrildidae
Polytrichum juniperinum
Polytrichum juniperinum
IEDB (QTT)
A detection of specific nucleic acids with complementary probes that measures epitope specific tumor necrosis factor production by T cells
TNFa release by RNA/DNA detection
detection of specific nucleic acids with complementary probes of epitope specific tumor necrosis factor production by T cells
detection of specific nucleic acids with complementary probes of epitope specific tumor necrosis factor production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Actinomyces naeslundii
Actinomyces naeslundii
in-line filter
in-line filter
PERSON:Daniel Schober
WEB:<http://www.appliedporous.com/frits-chromatography.htm>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01123
A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity.
Drosophila simulans
Drosophila simulans
JEOL ECA NMR spectrometer
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400228
JEOL ECA NMR spectrometer
PERSON:Daniel Schober
The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world.
WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECA/tabid/146/Default.aspx>
James Malone
PERSON: Ryan Brinkman
Ryan Brinkman
Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry.
PERSON: Richard Scheuermann
gating
gating
PERSON:Melanie Courtot
Richard Scheuermann
Josef Spidlen
Melanie Courtot
PERSON: James Malone
PERSON: Josef Spidlen
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An ELISA that measures epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
ELISA of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
IEDB (QTT)
ELISA of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
chemokine (C-X-C motif) ligand 9 (MIG) release by ELISA
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01073
WEB:<http://www.chromatography-online.org/topics/fraction/collector.html>
A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing.
fraction collector
PERSON:Daniel Schober
fraction collector
data vector reduction data transformation
A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where j<k.
James Malone
PERSON: James Malone
data vector reduction data transformation
Cyprinus carpio
Cyprinus carpio
epitope specific T cell tolerance induction
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
A process of T cell tolerance induction resulting from the recognition of a T cell epitope.
epitope specific T cell tolerance induction
IEDB
epitope specific GM-CSF release by T cells
epitope specific GM-CSF release by T cells
IEDB
A biological process where T cells produce GM-CSF resulting from the recognition of a T cell epitope.
Ciona savignyi
Ciona savignyi
lymphotoxin A production
TNF beta production
The appearance of lymphotoxin A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
lymphotoxin A production
left cerebral hemisphere
left cerebral hemisphere
indirect detection probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400281
An NMR probe designed to allow the indirect detection of acquisition nuclei.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
indirect detection probe
Leishmania braziliensis species complex
Leishmania braziliensis species complex
amino acids
Carboxylic acids containing one or more amino groups.
amino acids
Synechococcus
Synechococcus
PERSON: Elisabetta Manduchi
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set.
Elisabetta Manduchi
PERSON: Melanie Courtot
A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns.
column submatrix extraction
Melanie Courtot
PERSON: James Malone
James Malone
column submatrix extraction
gel filtration column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104
A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
gel filtration column
ChIP-chip assay
ChIP-on-chip assay
Person: James Malone
an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis.
WEB: http://en.wikipedia.org/wiki/ChIP-on-chip
ChIP-chip assay
center calculation data transformation
James Malone
A center calculation data transformation is a data transformation that has objective of center calculation.
PERSON: James Malone
center calculation data transformation
Eumalacostraca
Eumalacostraca
Oryzeae
Oryzeae
Pancrustacea
Pancrustacea
right cerebral hemisphere
right cerebral hemisphere
An NMR instrument that is manufactured by tecmag.
PERSON:Daniel Schober
tecmag NMR instrument
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400250
GROUP:<http://msi-ontology.sourceforge.net>
tecmag NMR instrument
descriptive statistical calculation data transformation
A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
James Malone
PERSON: James Malone
descriptive statistical calculation data transformation
Viannia
Viannia
PERSON: Monnie McGee
A mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
James Malone
PERSON: James Malone
Philippe Rocca-Serra
mean calculation
mean calculation
Monnie McGee
Trichoderma reesei QM6a
Trichoderma reesei QM6a
Person: James Malone
genotyping by high throughput sequencing assay
An assay in which high througput sequencer is used to detect polymorphisms in DNA samples
EFO_0002771: genotyping by high throughput sequencing
genotyping by high throughput sequencing assay
Mandibulata
Mandibulata
dead
A viability quality inhering in a bearer by virtue of the cessation of the bearer's life.
dead
scaling objective
is a data transformation objective where all, or some of a data set is adjusted by some data transformation according to some scale, for example a user defined minimum or maximum
Person:Helen Parkinson
Awaiting English definition from Monnie McGee
Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13
scaling objective
James Malone
PERSON: Elisabetta Manduchi
PERSON: Monnie McGee
descriptive statistical calculation objective
PERSON: James Malone
Elisabetta Manduchi
Monnie McGee
PERSON: Melanie Courtot
James Malone
A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
Melanie Courtot
descriptive statistical calculation objective
An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention.
affinity column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094
PERSON:Daniel Schober
affinity column
GROUP:<http://msi-ontology.sourceforge.net>
Fabaceae
Fabaceae
Coffea
Coffea
epitope specific IFN-g release by T cells
A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope.
IEDB
IEDB
epitope specific IFN-g release by T cells
Trifolium
Trifolium
Cyprinus
Cyprinus
ELISA of epitope specific tumor necrosis factor superfamily cytokine production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
TNF release by ELISA
IEDB (QTT)
ELISA of epitope specific tumor necrosis factor superfamily cytokine production by T cells
An ELISA that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
tumor necrosis factor production
TNF alpha production
The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
tumor necrosis factor production
Pyuridae
Pyuridae
Triticum
Triticum
NMIA RNA structure mapping assay
single nucleotide resolution mapping assay using NMIA probe
a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses NMIA as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
NMIA RNA structure mapping assay
RNA ontology
Person:Philippe Rocca-Serra
SHAPE mapping assay
PMID: 15796531
length unit
A unit which is a standard measure of the distance between two points.
length unit
substance detection
the detection of phycoerytherin by means of flow cytometry
substance detection
PERSON:Kevin Clancy
any protocol which results in the detection of a specified substance
OBI branch derived
Archaeoglobus
Archaeoglobus
recombinant YAC cloning
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611
Isolation of a YAC clone covering a cluster of nine S100 genes on human chromosome 1q21
recombinant YAC cloning
Helen Parkinson
Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material
PMID:19696660#The thrombin time was determined using thromboclotin assay kit.
thrombin time assay
A thrombin time assay is on in which after liberating the plasma from whole blood by centrifugation, bovine Thrombin is added to the sample of plasma. The clot is formed and is detected optically or mechanically by a coagulation instrument. The time between the addition of the thrombin and the clot formation is recorded as the thrombin clotting time
WEB:http://en.wikipedia.org/wiki/Thrombin_time@2009/10/06
2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
thrombin time assay
Person:Alan Ruttenberg
Pisum sativum
Pisum sativum
Drosophila erecta
Drosophila erecta
family history design
A study design in which the family history such as traits, characteristics, susceptibility to disease is studied.
family history design
MO_544 family_history_design
Person: Chris Stoeckert, Jie Zheng
left side of
A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity.
left side of
Xanthomonas campestris
Xanthomonas campestris
Veillonella parvula
Veillonella parvula
Triticum aestivum
Triticum aestivum
Pisum
Pisum
Archaeoglobus fulgidus
Archaeoglobus fulgidus
PMID:10772868
RNA ontology
Person:Philippe Rocca-Serra
Terbium RNA structure mapping assay
Terbium RNA structure mapping assay
single nucleotide resolution mapping assay using Terbium probe
a single-nucleotide-resolution nucleic acid structure mapping assay which uses Terbium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
DNA polymerase activity
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and primer.
DNA polymerase activity
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
maintaining cell culture
maintaining cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
PlanAndPlannedProcess Branch
OBI branch derived
single blind study execution
A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated
Person:Alan Ruttenberg
http://clinicaltrials.gov/ct2/info/glossary#single
single blind study execution
Thraupini
Thraupini
Campylobacter jejuni
Campylobacter jejuni
Actinobacillus
Actinobacillus
Veillonella
Veillonella
Streptococcus agalactiae
Streptococcus agalactiae
Sphingobacteriales
Sphingobacteriales
a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAase U2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
RNA ontology
PMID:409999
RNASE U2 structure mapping assay
single nucleotide resolution mapping assay using RNAse U2
RNASE U2 structure mapping assay
Person:Philippe Rocca-Serra
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
ELISA of epitope specific interleukin-9 production by T cells
IL-9 release by ELISA
ELISA of epitope specific interleukin-9 production by T cells
An ELISA that measures epitope specific interleukin-9 production by T cells
IEDB (QTT)
Hypodermis
Hypodermis
Halobacteriales
Halobacteriales
---\nThere is a more general 'membrane lysis', which could apply to artificial membranes etc. For this general membrane encapsulated objects would need to be defined.
artificially induced cell membrane lysis
a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate
PlanAndPlannedProcess Branch
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent.
OBI branch derived
artificially induced cell membrane lysis
nuclear magnetic resonance assay
www.nature.com/nrd/journal/v2/n5/glossary/nrd1086_glossary.html
OBI branch derived
nuclear magnetic resonance assay
an assay used to identify the chemical structure of a compound or biological macromolecule using an NMR instrument.
PlanAndPlannedProcess Branch
filled capsule
A pill in the form of a small rounded gelatinous container with medicine inside.
Person:Alan Ruttenberg
filled capsule
http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n
Pasteurellaceae
Pasteurellaceae
An assay that measures epitope specific lymphotoxin A production by T cells
lymphotoxin A (TNFb) release
IEDB (QTT)
assay of epitope specific lymphotoxin A production by T cells
assay of epitope specific lymphotoxin A production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Cercopithecinae
Cercopithecinae
Triticum turgidum subsp. durum
Triticum turgidum subsp. durum
CD8-positive, alpha-beta cytotoxic T cell
A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive.
CD8-positive, alpha-beta cytotoxic T cell
Halobacteriaceae
Halobacteriaceae
binding constant determination assay
Determination of KD value for an antibody binding a protein using a BIACORE assay.
A binding assay where the specified output is a binding constant
PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
binding constant determination assay
OBI branch derived
Helen Parkinson
longitudinal mass measurement assay
longitudinal mass measurement assay
A process in which the mass of a material is measured at two or more time points
The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection
A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance
transcription profiling by high thoughput sequencing design
Person: Chris Stoeckert, Jie Zheng
transcription profiling by high thoughput sequencing design
Group: ArrayExpress production team
activated partial thromboplastin time (aPTT) assay
An activated partial thromboplastin time (aPTT) assay is a an assay measuring the efficacy of both the 'intrinsic' (now referred to as the contact activation pathway) and the common coagulation pathways. In order to activate the intrinsic pathway, phospholipid, an activator (such as silica, celite, kaolin, ellagic acid), and calcium (to reverse the anticoagulant effect of the oxalate) are mixed into the plasma sample . The time is measured until a thrombus (clot) forms.
2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
WEB:http://en.wikipedia.org/wiki/Partial_thromboplastin_time@2008/10/06
activated partial thromboplastin time (aPTT) assay
PMID:19696660#The activated partial thromboplastin time (aPTT) was determined using Dade Actin FSL activated PTT reagent.
Person:Alan Ruttenberg
population
PERSON: Philippe Rocca-Serra
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
adapted from Oxford English Dictionnary
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
population
Streptococcus pneumoniae
Streptococcus pneumoniae
phage display library
PERSON: Bjoern Peters
a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
display library
WEB: http://www.immuneepitope.org/home.do
PERSON: Philippe Rocca-Serra
phage display library
A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state.
Person: Chris Stoeckert, Jie Zheng
MO_892 development_or_differentiation_design
organism development design
organism development design
Bacillus subtilis
Bacillus subtilis
Cellia
Cellia
isolation of cell culture supernatant
isolation of cell culture supernatant
OBI branch derived
PlanAndPlannedProcess Branch
Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube.
a protocol which results in the separation of supernatant material from a cell culture
This does not apply to the case where the cells are lysed
research organization
An organization formed with a goal to have its members conduct investigations
Person:Bjoern Peters
The SALK institute is a research organization.
research organization
eluate
eluate
a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase
PERSON: Philippe Rocca-Serra
OBI Bionaterial
need to add restriction to indicate: has_part some (material entity has_role mobile phase)
need to add mobile phase as role
Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263
eluted material
Mucosa of oropharynx
Mucosa of oropharynx
ssDNA viruses
ssDNA viruses
Linum
Linum
Streptococcus pyogenes
Streptococcus pyogenes
Deinococcaceae
Deinococcaceae
IEDB
MHC tetramer/multimer staining
An assay that measures MHC:epitope complex binding to TCR utilizing flow cytometry. The MHC molecules are prepared into multimers, loaded with epitope, and are fluorescently labeled in order to visualize the T cells that bind. The data that is generated provides information on the presence of epitope specific T cells in the cell population that was tested.
T cell epitope MHC tetramer/multimer staining assay
IEDB
T cell epitope MHC tetramer/multimer staining assay
Catarrhini
Catarrhini
detection of specific nucleic acids with complementary probes of epitope specific RANTES production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific RANTES production by T cells
RANTES/CCL5 release by RNA/DNA detection
IEDB (QTT)
detection of specific nucleic acids with complementary probes of epitope specific RANTES production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
Philippe Rocca-Serra
syringe
a processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
OBI Instrument adapted from Wikipedia
syringe
portion of tissue
Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.
portion of tissue
role of pathology review board
pathology review board
role of pathology review board
Person: Jennifer Fostel
a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation
Thlaspi
Thlaspi
material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process
Role Branch
drug added to a buffer contained in a tube; substance injected into an animal;
material to be added role
material to be added role
OBI
Sordariales
Sordariales
OBI branch derived
The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA
artificially induced reverse transcription
PERSON:Kevin Clancy
a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)
artificially induced reverse transcription
We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope
It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process.
Linum usitatissimum
Linum usitatissimum
pill
A dose of medicine or placebo in the form of a small pellet.
Person:Alan Ruttenberg
http://www.golovchenko.org/cgi-bin/wnsearch?q=pill#2n
pill
Solanum tuberosum
Solanum tuberosum
Plasmodium berghei
Plasmodium berghei
Ferroplasma acidarmanus
Ferroplasma acidarmanus
Cercopithecidae
Cercopithecidae
cytometric bead array assay of epitope specific interleukin-4 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
IL-4 release by cytometric bead array
A cytometric bead array assay that measures epitope specific interleukin-4 production by T cells
cytometric bead array assay of epitope specific interleukin-4 production by T cells
extracted material
GROUP: OBI Biomatrial Branch
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
PERSON: Philippe Rocca-Serra
extract
extract
an extract is a material entity which results from an extraction process
Neognathi
Neognathi
Festuca rubra subsp. littoralis
Festuca rubra subsp. littoralis
treatment portion of study execution
09/28/2009 Alan Ruttenberg. Needed because we have to have a process to scope blinding over
A planned process, part of a study design execution, during which the treatment of subjects is ongoing
Person:Alan Ruttenberg
treatment portion of study execution
A planed process with objective of obtaining quantified values from an image.
PERSON: Jie Zheng
MO_928: feature_extraction
feature extraction
feature extraction
Methanobacteria
Methanobacteria
Plasmodium
Plasmodium
microRNA profiling by array design
Person: Chris Stoeckert, Jie Zheng
A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome.
Group: ArrayExpress production team
microRNA profiling by array design
Drosophila orena
Drosophila orena
protocol optimization objective
Jennifer Fostel
Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol.
protocol optimization objective
Halobacterium
Halobacterium
obsolete_trypsinized material
A trypsinized suspension of cells
A material entity that has undergone a process of digestion with trypsin
decided to be deprecated on Aug 2, 2010 dev call
obsolete_trypsinized material
Person:Bjoern Peters
Felidae
Felidae
single nucleotide resolution mapping assay using OH-radical probe
MOHCA assay
RNA ontology
OH-radical structure mapping assay
a single-nucleotide-resolution nucleic acid structure mapping assay which uses hydroxyl radical as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
PMID:2501870
OH-radical structure mapping assay
Person:Philippe Rocca-Serra
OH footprinting assay
to be treated with placebo role
A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo
Person:Alan Ruttenberg
to be treated with placebo role
Festuca rubra subsp. fallax
Festuca rubra subsp. fallax
Linaceae
Linaceae
cytotoxic T cell degranulation
The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell.
cytotoxic T cell degranulation
Campylobacter
Campylobacter
Thermoprotei
Thermoprotei
Nicotiana
Nicotiana
assay of T cell epitope specific tolerance induction
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
assay of T cell epitope specific tolerance induction
An assay that measures epitope specific tolerance induction by T cells
tolerance induction
Actinobacillus pleuropneumoniae
Actinobacillus pleuropneumoniae
glucose
glucose
An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
PlanAndPlannedProcess Branch
OBI branch derived
imaging assay
imaging assay
Felis
Felis
OBI Biomaterial
decapitated organism
decapitated organism
Philippe Rocca-Serra
Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids.
J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172
decapitated organism is an organism which has had it's head removed
OBI Biomaterial
Philippe Rocca-Serra
injection
injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712
injection
quantitative confidence value
quantitative confidence value
A data item which is used to indicate the degree of uncertainty about a measurement.
group:OBI
person:Chris Stoeckert
PERSON: Helen Parkinson
GROUP: OBI Biomaterial Branch
GROUP: CEBS
A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension
cell pellet
cell pellet
PERSON: Philippe Rocca-Serra
Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214
Trichodesmium
Trichodesmium
Spermatophyta
Spermatophyta
efficacy of epitope intervention experiment
An experiment that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or excarbate diseases in the organism.
efficacy of treatment
Bjoern Peters
efficacy of epitope intervention experiment
loop design
A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design
Philippe Rocca-Serra on behalf of MO
MO_912
loop design
PMID: 12933549
is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes.
adaptive immune receptor
IEDB
IEDB
adaptive immune receptor
Acidithiobacillales
Acidithiobacillales
Lactobacillaceae
Lactobacillaceae
Sapindales
Sapindales
Chlamydophila
Chlamydophila
Spirurida
Spirurida
Anabaena variabilis
Anabaena variabilis
IEDB
Bjoern Peters
Enrollment of patients in a study.
Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902
enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules
enrollment
enrollment
Drosophila melanogaster
Drosophila melanogaster
(protein or rna) or has_part (protein or rna) and
has_function some GO:0003824 (catalytic activity)
enzyme
person: Melanie Courtot
MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything
that has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more.
GROUP:OBI
enzyme
GROUP: IEDB
Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell.
cell culture supernatant
PERSON: Bjoern Peters
solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1.
Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615
cell culture supernatant
Picea
Picea
Person: Chris Stoeckert, Jie Zheng
A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology.
DNA methylation profiling by high throughput sequencing design
GROUP: ArrayExpress production team
DNA methylation profiling by high throughput sequencing design
a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument
microscope slide
PERSON: Phillippe Rocca-Serra
OBI biomaterial branch
PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay.
microscope slide
Bjoern Peters
RNA sequencing
RNA sequencing
BP 12/21:Created based on a request from Melanie
RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact
Bjoern Peters
Trichodesmium erythraeum
Trichodesmium erythraeum
Tracheophyta
Tracheophyta
immunogen
immunogen
IEDB
IEDB
a material entity bearing the immunogen role
Nidovirales
Nidovirales
balanced incomplete block design
PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice.
Philippe Rocca-Serra
balanced incomplete block design
balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i'
http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html
Acidithiobacillaceae
Acidithiobacillaceae
scientific observation
assay
Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house.
measuring
OBI branch derived
assay
A planned process with the objective to produce information about some evaluant
PlanAndPlannedProcess Branch
any method
glial cell line-derived neurotrophic factor
A protein that is a translation product of the GDNF gene or a 1:1 ortholog thereof.
glial cell line-derived neurotrophic factor
Pyretophorus
Pyretophorus
Drosophila mauritiana
Drosophila mauritiana
OBI
Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
transcription profiling assay
transcription profiling assay
Philippe Rocca-Serra
gene expression profiling
trancription profiling is a process which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
denatured polymer
http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29
Is a polymer which has lost secondary or tertiary structure
PERSON: Alan Ruttenberg
denatured polymer
Drosophila pseudoobscura
Drosophila pseudoobscura
operon identification design
Person: Chris Stoeckert, Jie Zheng
A study design that identifies locations and members of operons in a genome.
operon identification design
MO_772 operon_identification_design
B cell
A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
B cell
animal cage
laboratory cage
a processed material which has the function to define a bounded habitat which is amenable to keeping animals.
PERSON: Phillippe Rocca-Serra
animal cage
OBI biomaterial branch
PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice.
randomized complete block design
A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.
Philippe Rocca-Serra
http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd))
http://www.tufts.edu/~gdallal/ranblock.htm
randomized complete block design
environmental exposure to infectious agent
environmental exposure to infectious agent
IEDB
IEDB
Is a process in which an infectious agent is in direct contact with a potential host organism in its habitat. This is preceded by proximity to the infectious agent
Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interrogation point.
arc lamp
The Jablochkoff Candle
http://en.wikipedia.org/wiki/Arc_lamp
arc lamp
John Quinn
Pleuronectoidei
Pleuronectoidei
averaging objective
Elisabetta Manduchi
A mean calculation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment.
PERSON: Elisabetta Manduchi
averaging objective
James Malone
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
substance unit
A unit which is a standardised quantity of an element or compound with uniform composition.
substance unit
Drosophila sechellia
Drosophila sechellia
MHC protein complex
A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen.
MHC protein complex
macrophage
A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells.
macrophage
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IFNg release by RIA
radio immuno assay of epitope specific interferon-gamma production by T cells
radio immuno assay of epitope specific interferon-gamma production by T cells
A radio immuno assay that measures epitope specific interferon-gamma production by T cells
Anurophorinae
Anurophorinae
Aconoidasida
Aconoidasida
FACS Calibur, Luminex 100
flow cytometer analyzer
An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis.
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
flow cytometer analyzer
John Quinn
Bjoern Peters
epitope protection from infectious challenge experiment
epitope protection from infectious challenge experiment
protection from infectious challenge
An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed.
Rosoideae
Rosoideae
A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.
parallel group design
independent measure design
http://www.holah.karoo.net/experimentaldesigns.htm
parallel group design
Philippe Rocca-Serra
IEDB (QTT)
ELISA of epitope specific macrophage inflammatory protein-1 gamma production by T cells
An ELISA that measures epitope specific macrophage inflammatory protein-1 gamma production by T cells
MIP-1g release by ELISA
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
ELISA of epitope specific macrophage inflammatory protein-1 gamma production by T cells
Drosophilini
Drosophilini
Nostoc
Nostoc
cell fixation
should include capturing what qualities are being preserved
OBI branch derived
a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time
http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16080188&dopt=AbstractPlus
cell fixation
PERSON:Bjoern Peters
temperature unit
A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter.
temperature unit
Magnetospirillum
Magnetospirillum
matched pairs design
PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs.
Philippe Rocca-Serra
http://www.holah.karoo.net/experimentaldesigns.htm
matched pairs design
A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment.
Embryophyta
Embryophyta
Melanie Courtot
The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection.
An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal.
John Quinn
A-D
A2D
http://en.wiktionary.org/wiki/Analog-to-Digital_Converter
analog-to-digital converter
analog-to-digital converter
Paxillus involutus
Paxillus involutus
gene dosage assay
David Osumi Sutherland
PERSON: Bjoern Peters
an assay of changes in phenotype due to increased or decreased
dosage of a single allele of a gene.
gene dosage assay
A mouse that is vaccinated with a peptide and develops protective immunity. A human exposed to bacteria that are killed by pre-existing immune responses.
host of immune response
In immune response processes in the context of infectious diseases and allergy, there are often multiple organisms involved, which requires calling out the 'host'. This terminology is expanded to allergy, cancer and transplantation.
IEDB
host of immune response
An organism in which an immune response process occurs.
IEDB
rhodium
A cobalt group element that has formula Rh.
rhodium
adoptive transfer
passive immunization
PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
passive immunization
The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens.
Giving VIG (concentrated antibodies from vaccinated donors) to a patient that is infected with smallpox.
Transferring epitope specific T cells from one mouse into another.
Mollicutes
Mollicutes
Brugia
Brugia
A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope.
IEDB (QTT)
epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Philippe Rocca-Serra
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
observation design
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
observation design
OBI branch derived
Pasteuria
Pasteuria
histopathology
PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
OBI branch derived
histology
histology
the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated
the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement
adverse event trigger
OBI branch derived
PERSON:Alan Ruttenberg
adverse event trigger
revisit?
Chlamydophila pneumoniae
Chlamydophila pneumoniae
n-to-1 design
Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm)
N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993).
Philippe Rocca-Serra
n-to-1 design
A40-MiniFCM
A40-MiniFCM
http://www.apogeeflow.com/flow_cytometry_products.htm
A A40-MiniFCM is a flow_cytometer_analyser that allows for the choice of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus.
John Quinn
CD4
A protein that is a translation product of the CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence.
CD4
RNA ontology
Person:Philippe Rocca-Serra
single nucleotide resolution mapping assay using Fe-BABE probe
a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-BABE as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Fe-BABE RNA structure mapping assay
PMID: 7862644
Fe-BABE RNA structure mapping assay
providing a training course for UCSD employees how to run a DNA sequencer; sequencing a DNA sample provided by a service consumer restricted to non-human samples; giving access to tissue samples in a biobank within OHSU; JAX shipping mice from their colony
service
Carlo; Matt
A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer.
OBI workshop San Diego 2011
service
Campylobacterales
Campylobacterales
An assay that measures epitope specific granzyme B production by T cells
assay of epitope specific granzyme B production by T cells
assay of epitope specific granzyme B production by T cells
granzyme B release
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
Drosophilina
Drosophilina
sequential design
Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does
MUSC
PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs.
Philippe Rocca-Serra
sequential design
Brugia malayi
Brugia malayi
time unit
A unit which is a standard measure of the dimension in which events occur in sequence.
time unit
transcription factor binding site identification
OBI
Philippe Rocca-Serra
transcription factor binding site identification
Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.
Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031
a planned process with objective to find DNA region specifically recognized by proteins that function as transcription factors
Carnivora
Carnivora
Skeletal muscle tissue
Skeletal muscle tissue
Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm.
John Quinn
A10-Analyzer
A10-Analyzer
A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells.
http://www.apogeeflow.com/flow_cytometry_products.htm
PERSON:Kevin Clancy
OBI branch derived
The use of agarase to digest an agar gel
non specific enzymatic cleavage
a protocol application to digest the fraction of input material that is susceptible to that enzyme
non specific enzymatic cleavage
Archaeoglobales
Archaeoglobales
cross over design
(source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
Philippe Rocca-Serra
a repeated measure design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
cross over design
The administration of a substance into the peritoneum of an organism
intraperitoneal administration
Person:Bjoern Peters
intraperitoneal administration
Rats were injected intraperitoneally with either rrIL-6 (250 ng/0.5 ml) or equal-volume sterile saline twice within an interval of 24 h
Individual epitope immunization in vivo
3/16/11 BP: This should have as a logical definition the exclusion that the immunogen cannot be something beyond the epitope itself. I don't know if that is possible to do here.
An immunization in which an individual epitope is administered into a host organism.
Individual epitope immunization in vivo
Injection of a peptide T cell epitope into a mouse
PERSON:Bjoern Peters, Jason Greenbaum, Randi Vita
erythrocyte
A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen.
erythrocyte
Lead structure mapping assay
a single-nucleotide-resolution nucleic acid structure mapping assay which uses lead as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
RNA ontology
PMID:2686708
single nucleotide resolution mapping assay using Lead probe
Lead structure mapping assay
Person:Philippe Rocca-Serra
293-T cell culture
293-T cell culture
http://www.biotech.ist.unige.it/cldb/cl5008.html
IEDB
A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication.
IEDB
right side of
A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity.
right side of
Xanthomonas
Xanthomonas
chemokine (C-X-C motif) ligand 9 (MIG) release by ICS
IEDB (QTT)
intracellular cytokine staining assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
intracellular cytokine staining assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
An intracellular cytokine staining assay that measures epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
validated information
OBI
Person:Philippe Rocca-Serra
an information content entity which results from a validation process aimed at confirming a claim, a finding or a predicted information entity about a material entity or a process by experimental means.
PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..."
validated information
a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage
PERSON: Jie Zheng
paraffin storage
UPenn Group
paraffin storage
need to specify paraffin or wax is one of specified input of the process
PERSON: Chris Stoeckert
repeated measure design
PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
PlanAndPlannedProcess Branch
a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
http://www.holah.karoo.net/experimentaldesigns.htm
repeated measure design
in container assay
an assay in which a measurement is made by observing entities located in a container.
in container assay
the use physical means to remove a portion of a substance from the rest
excision
excision
Cutting out the portion of a gel which contains a DNA fragment
Alan Ruttenberg, Kevin Clancy
www.crohnsresource.com/glossary.jsp (via google define:resection)
Archaeoglobaceae
Archaeoglobaceae
mass unit
A unit which is a standard measure of the amount of matter/energy of a physical object.
mass unit
RNA ontology
Person:Philippe Rocca-Serra
a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T2 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
PMID:6207483
RNASE T2 structure mapping assay
single nucleotide resolution mapping assay using RNAse T2
RNASE T2 structure mapping assay
C1R cell culture
IEDB
C1R cell culture
IEDB
A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)).
selective organism creation objective
PERSON: Chris Stoeckert, Jie Zheng
WEB: wikipedia
http://en.wikipedia.org/wiki/Cultivar
http://en.wikipedia.org/wiki/Ecotype
http://en.wikipedia.org/wiki/Strain_%28biology%29
an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms.
selective organism creation objective
Saccharomyces mikatae
Saccharomyces mikatae
An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion.
PERSON: Erik Segerdell
electron paramagnetic resonance spectrometer
electron paramagnetic resonance spectrometer
http://en.wikipedia.org/wiki/Electron_paramagnetic_resonance
Rhizobiaceae
Rhizobiaceae
IL-10 release by ELISPOT
T cell epitope ELISPOT IL-10 assay
IEDB
A T cell epitope specific cytokine production assay that measures production of IL-10 by T cells utilizing the ELISPOT methodology.
IEDB
T cell epitope ELISPOT IL-10 assay
quality of a single physical entity
A physical object quality which inheres in a single-bearer.
quality of a single physical entity
Gallus
Gallus
epitope protection from tumor challenge experiment
An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed.
Bjoern Peters
epitope protection from tumor challenge experiment
tumor burden after challenge
Cryptosporidium parvum
Cryptosporidium parvum
Gallus gallus
Gallus gallus
Proteobacteria
Proteobacteria
characteristic path length calculation
characteristic path length calculation
Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices
PERSON: Tina Hernandez-Boussard
PERSON: Tina Hernandez-Boussard
solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution
adapted from wikipedia (http://en.wikipedia.org/wiki/Solute)
PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure.
solute role
solute role
Philippe Rocca-Serra
positive reference substance role
positive reference substance role
MMS mutagen
a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "100%" response
positive reference substance
Person: Jennifer Fostel
specimen labeling function
specimen labeling function
Varian MERCURY spectrometer
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400235
MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation.
PERSON:Daniel Schober
Varian MERCURY spectrometer
WEB:<http://www.varianinc.com/cgi-bin/nav?varinc/docs/products/NMR/spectromet/mercury/index&cid=975JINLIKLRMPGLMNOILJ>
Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests.
WEB:http://mathworld.wolfram.com/FishersExactTest.html
Fisher's exact test
James Malone
Fisher's exact test
electronic repeater pipette
A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations.
PERSON: Erik Segerdell
electronic repeater pipette
http://www.faqs.org/patents/app/20090196797
A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure).
water bath
A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
Daniel Schober
water bath
PERSON: Daniel Schober
Bjoern Peters
an epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host.
epitope protection experiment
epitope protection experiment
protection from challenge
Cyprinoidea
Cyprinoidea
Philippe Rocca-Serra
adapted from Wikipedia before possible import from CHEBI
polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties
polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles.
PERSON: Tina Hernandez-Boussard
PERSON: James Malone
continuum mass spectrum
continuum mass spectrum
A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion.
PERSON: Tina Boussard
unsupervised classification data transformation
PERSON: James Malone
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
class discovery data transformation
class discovery data transformation
clustering data transformation
James Malone
A training objective is fulfilled by e.f. a bioconductor tutorial which instructs the user in the use of a package
OBI
Helen Parkinson
An training objective which is fulfilled by the provision of some training
training objective
training objective
hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments
hematology
hematology
blood analysis, haematology
Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology.
Godsland IF, Johnston DG.
Metabolism. 2008 Sep;57(9):1190-7.
PMID: 18702943
Philippe Rocca-Serra
OBI branch derived
study design
study design
PERSON: Chris Stoeckert
a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design.
experimental design
Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available.
A study design is a plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution.
analytical balance
A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy.
PERSON: Erik Segerdell
analytical balance
http://en.wikipedia.org/wiki/Weighing_scale
Monnie McGee
data imputation
Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm.
ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60.
data imputation
tumor necrosis factor superfamily cytokine production
The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
tumor necrosis factor superfamily cytokine production
Pinus resinosa
Pinus resinosa
Cricetinae
Cricetinae
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
Joseph Spliden
Ryan Brinkman
This type of transformation is typically used in flow cytometry.
A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization.
b transformation
Elisabetta Manduchi
b transformation
Enterogona
Enterogona
binding datum
A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is.
Bjoern Peters; Randi Vita
binding datum
Spirochaetes (class)
Spirochaetes (class)
detection of analyte in blood sample
clinical chemistry assay
a process which uses analytical methods to produce measurements and data on the concentration of a chemical parameters (analytes) present in a bodily fluid collected from an organism.
3/26/09: There needs to be a restriction set that specifies which type of evaluants are used in the assay, somewhere along the lines of 'sample derived of bodily fluid'
clinical chemistry assay
Person: Philippe Rocca-Serra
adapted from Wikipedia
chemical pathology
Influence of hydroxyethyl starch (6% HES 130/0.4) administration on hematology and clinical chemistry parameters.
Mueller T, Schimetta W, Dieplinger B, Loeffler P, Rehm M, Kreimeier U, Poelz W, Haltmayer M.
Clin Chem Lab Med. 2008;46(4):558-62.
PMID: 18605936
B cell tolerance induction
A process involving any mechanism for tolerance induction in B cells.
B cell tolerance induction
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
assay of epitope specific interleukin-6 production by T cells
An assay that measures epitope specific interleukin-6 production by T cells
assay of epitope specific interleukin-6 production by T cells
IL-6 release
column heater
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01040
PERSON:Daniel Schober
The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure.
WEB:<http://www.chromatography-online.org/GC/Injection-Devices/Open-Tubular-Column/rs15.html>
column heater
a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s).
investigation
Bjoern Peters
OBI branch derived
investigation
Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation
James Malone
curve fitting objective
Elisabetta Manduchi
curve fitting objective
A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints.
PERSON: Elisabetta Manduchi
Escherichia coli
Escherichia coli
4/10/2011 BP: This is not worded well, and was thrown together quickly to allow this term into the release, as several other terms are depending on it. The example is better than the definition.
categorical label
categorical label
Bjoern Peters
A label that is part of a categorical datum and that indicates the category of that datum
The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels.
Bjoern Peters
PlanAndPlannedProcess Branch
PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale.
Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]
The definition needs to be extended to other things than simply patients
clinical study design
clinical study design
Clinical Research Glossary Version 4.0 CDICS glossary group
t cell epitope prediction
A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope.
t cell epitope prediction
PERSON: Helen Parkinson
Helen Parkinson
PERSON: Erik Segerdell
rocker
PERSON: Erik Segerdell
rocker
A device that provides three-dimensional motion for biomedical applications (e.g., gel trays).
Actinobacteridae
Actinobacteridae
negative binding datum
A binding datum that states that there is no significant disposition of two or more entities to form a complex
negative binding datum
quality of related physical entities
A physical entity quality which exists in relation towards some other entity.
quality of related physical entities
OBI Instrument branch
A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original
sample for particles of interest based on qualities determined by gating) or disposal.
droplet sorter
droplet sorter
OBI Instrument branch
Bruker Metabolic Profiler
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400199
An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis.
Bruker Metabolic Profiler
PERSON:Daniel Schober
WEB:<http://www.bruker-biospin.com/metabolicprofiler.html>
Escherichia
Escherichia
Spirochaetes
Spirochaetes
single cell gel electrophoresis assay
a comet assay is an assay which utilizes gel electrophoresis on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions.
SCGE assay
comet assay
PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review.
PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay.
Philippe Rocca-Serra
comet assay
in live cell assay
An assay in which a measurement is made by observing entities located in a live cell.
in live cell assay
background correction objective
background correction objective
James Malone
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation.
GROUP: Role Branch
When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role.
OBI
evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
evaluant role
a role that inheres in an entity that is realized in an assay in which data is generated about the bearer of the evaluant role
assay of epitope specific interleukin-4 production by T cells
IL-4 release
assay of epitope specific interleukin-4 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An assay that measures epitope specific interleukin-4 production by T cells
IEDB (QTT)
Aculeata
Aculeata
IL-13 release
An assay that measures epitope specific interleukin-13 production by T cells
assay of epitope specific interleukin-13 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific interleukin-13 production by T cells
IEDB (QTT)
Bifidobacteriales
Bifidobacteriales
infection
infection
IEDB
IEDB
the detrimental process in which an infectious agent colonizes or replicates in a host environment
Populus deltoides
Populus deltoides
Rosales
Rosales
lymphotoxin A (TNFb) release by ICS
An intracellular cytokine staining assay that measures epitope specific lymphotoxin A production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
intracellular cytokine staining assay of epitope specific lymphotoxin A production by T cells
intracellular cytokine staining assay of epitope specific lymphotoxin A production by T cells
Coregonus
Coregonus
JEOL CapNMR probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400233
JEOL CapNMR probe
PERSON:Daniel Schober
The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 µl flowcell with an NMR active volume of 2.5 µl, and a 10 µl flowcell with an NMR active volume of 5 µl. The fluidic connections are 75 µm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility.
WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/CapNMRProbe/tabid/396/Default.aspx>
trial monitor role
trial monitor
trial monitor role
Person:Jennifer Fostel
a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study
Onchocercidae
Onchocercidae
Rubus idaeus
Rubus idaeus
partial least square discriminant analysis
PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information.
WEB: http://www.camo.com/rt/Resources/pls-da.html
James Malone
PLS-DA
partial least square discriminant analysis
An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
T cell degranulation by intracellular staining
intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation
mitosporic Trichocomaceae
mitosporic Trichocomaceae
Actinomycineae
Actinomycineae
Populus trichocarpa x Populus deltoides
Populus trichocarpa x Populus deltoides
IEDB
IEDB
Immunization in vitro
Process of administering an object playing the role of immunogen to a cell culture
Immunization in vitro
Mycoplasma
Mycoplasma
TNFa release by bioassay
cell culture analyte detection bioassay of epitope specific tumor necrosis factor production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cell culture analyte detection bioassay of epitope specific tumor necrosis factor production by T cells
IEDB (QTT)
A cell culture analyte detection bioassay that measures epitope specific tumor necrosis factor production by T cells
DNA methylation profiling assay
Philippe Rocca-Serra
OBI branch derived
DNA methylation profiling assay
an assay which aims to provide information about state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion.
Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J.
Genome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979
Rosaceae
Rosaceae
Filarioidea
Filarioidea
IEDB
PERSON: Bjoern Peters
a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion
Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin
A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617
peptide construct
peptide construct
PERSON: Elisabetta Manduchi
classification objective
class prediction objective
supervised classification objective
A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and
class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
James Malone
PERSON: James Malone
class prediction objective
Bjoern Peters; Randi Vita
half maximal effective concentration (EC50)
half maximal effective concentration (EC50)
wikipedia
The term half maximal effective concentration (EC50) refers to the concentration of a drug, antibody or toxicant which induces a response halfway between the baseline and maximum after some specified exposure time. It is commonly used as a measure of drug's potency. The EC50 of a graded dose response curve therefore represents the concentration of a compound where 50% of its maximal effect is observed. The EC50 of a quantal dose response curve represents the concentration of a compound where 50% of the population exhibit a response, after a specified exposure duration.
eh transformation
Joseph Spliden
Ryan Brinkman
This type of transformation is typically used in flow cytometry.
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
eh transformation
Elisabetta Manduchi
An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization.
Vitales
Vitales
A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound.
PERSON: Daniel Schober
digital-to-analog converter
Daniel Schober
A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal.
digital-to-analog converter
assay of epitope specific interleukin-9 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An assay that measures epitope specific interleukin-9 production by T cells
IEDB (QTT)
IL-9 release
assay of epitope specific interleukin-9 production by T cells
microcentrifuge
A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Laboratory_centrifuge
microcentrifuge
gas purifier
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01036
Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems.
PERSON:Daniel Schober
WEB:<http://www.sigmaaldrich.com/Area_of_Interest/Analytical__Chromatography/Gas_Chromatography/Accessories/SGT_Gas_Purifier.html>
gas purifier
Mycoplasmataceae
Mycoplasmataceae
Cannabaceae
Cannabaceae
Populus trichocarpa
Populus trichocarpa
class discovery objective
A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
PERSON: James Malone
discriminant analysis objective
clustering objective
class discovery objective
unsupervised classification objective
James Malone
PERSON: Elisabetta Manduchi
Xanthomonas campestris pv. campestris
Xanthomonas campestris pv. campestris
Herdmania
Herdmania
ELISPOT assay of epitope specific interleukin-5 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
ELISPOT assay of epitope specific interleukin-5 production by T cells
IL-5 release by ELISPOT
An ELISPOT assay that measures epitope specific interleukin-5 production by T cells
OBI
A buffer of carbonic acid (H2CO3) and bicarbonate (HCO3−) is present in blood plasma, to maintain a pH between 7.35 and 7.45. http://en.wikipedia.org/wiki/Buffer_solution
buffer
buffer role
Person:Philippe Rocca-Serra
Person:Helen Parkinson
a role which inheres in some molecular entity realized during the process of buffering
buffer role
partial least square regression analysis
ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263.
PLS-RA
Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that
Y = b0 + b1X1 + b2X2 + ... + bpXp
In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data.
Tina Hernandez-Boussard
partial least square regression analysis
oil bath
Daniel Schober
PERSON: Daniel Schober
An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample).
An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period.
oil bath
Person: Chris Stoeckert, Jie Zheng
array platform variation design
A study design in which the array platform is compared, e.g. Agilent versus Affymetrix.
array platform variation design
MO_899 array_platform_variation_design
Corynebacterineae
Corynebacterineae
Cannabis
Cannabis
gas chromatography detector
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
gas chromatography detector
A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01083
FID
Saccharomyces kudriavzevii
Saccharomyces kudriavzevii
Dictyostelium
Dictyostelium
Tetraodontoidei
Tetraodontoidei
reagent application function
4/10/2011: It is unclear if we need / want this, or what this is supposed to be for. Lots of the functions we have are reagent specific. Will this only confuse people?
reagent application function
center calculation objective
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
James Malone
center calculation objective
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
PERSON: James Malone
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400013
PERSON:Daniel Schober
acquisition computer
acquisition computer
GROUP:<http://msi-ontology.sourceforge.net>
A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers.
solvent role
Philippe Rocca-Serra
solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation
solvent role
adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation)
PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors.
pathogenicity design
pathogenicity design
MO_807 pathogenicity_design
A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed.
Person: Chris Stoeckert, Jie Zheng
Herdmania momus
Herdmania momus
WEB: http://www.statsoft.com/textbook/stdiscan.html
discriminant analysis
discriminant analysis
Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
Tina Hernandez-Boussard
mitosporic Onygenales
mitosporic Onygenales
multiple linear regression analysis
Tina Hernandez-Boussard
multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as
Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon
where \beta_0 = 0 is the intercept ("constant" term), the \beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression.
WEB:http://en.wikipedia.org/wiki/Linear_regression
multiple linear regression analysis
ELISA of epitope specific monocyte chemotactic protein-1 production by T cells
IEDB (QTT)
ELISA of epitope specific monocyte chemotactic protein-1 production by T cells
An ELISA that measures epitope specific monocyte chemotactic protein-1 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
MCP-1 release by ELISA
preparative autosampler
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01062
For preparative LC with injection of sample volumes ranging from L to mL ranges.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
preparative autosampler
Hypocreaceae
Hypocreaceae
Triticum turgidum
Triticum turgidum
flow HR-probe
flow high resolution probe
Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes.
GROUP:<http://msi-ontology.sourceforge.net>
flow high resolution probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400195
PERSON:Daniel Schober
Collembola
Collembola
Solanum lycopersicum
Solanum lycopersicum
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-5 production by T cells
IEDB (QTT)
IL-5 release by RNA/DNA detection
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
detection of specific nucleic acids with complementary probes of epitope specific interleukin-5 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-5 production by T cells
anterior to
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity.
anterior to
frontal
IEDB
T cell epitope intracellular cytokine staining (ICS) IL-17 assay
IL-17 release by ICS
T cell epitope intracellular cytokine staining (ICS) IL-17 assay
A T cell epitope specific cytokine production assay that measures production of IL-17 by T cells utilizing the ICS methodology.
IEDB
WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html
The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores.
principal component regression
Tina Hernandez-Boussard
principal component regression
Salmoniformes
Salmoniformes
detection of specific nucleic acids with complementary probes of epitope specific monocyte chemotactic protein-1 production by T cells
MCP-1 release by RNA/DNA detection
IEDB (QTT)
A detection of specific nucleic acids with complementary probes that measures epitope specific monocyte chemotactic protein-1 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
detection of specific nucleic acids with complementary probes of epitope specific monocyte chemotactic protein-1 production by T cells
PERSON:Daniel Schober
Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent.
WEB:<http://en.wikipedia.org/wiki/Gas_chromatography>
splitless GC injector
splitless GC injector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01060
Ustilaginomycetidae
Ustilaginomycetidae
Felis catus
Felis catus
Mycoplasma genitalium
Mycoplasma genitalium
Brassicales
Brassicales
A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-3 production by T cells
epitope specific interleukin-3 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
T cell epitope intracellular cytokine staining (ICS) IL-10 assay
IEDB
IL-10 release by ICS
T cell epitope intracellular cytokine staining (ICS) IL-10 assay
A T cell epitope specific cytokine production assay that measures production of IL-10 by T cells utilizing the ICS methodology.
IEDB
Polytrichopsida
Polytrichopsida
ELISA of epitope specific interleukin-21 production by T cells
IEDB (QTT)
IL-21 release by ELISA
ELISA of epitope specific interleukin-21 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An ELISA that measures epitope specific interleukin-21 production by T cells
Peloderinae
Peloderinae
Papilionoideae
Papilionoideae
linear discriminant functional analysis
Tina Hernandez-Boussard
Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective.
PERSON: Tina Hernandez-Boussard
linear discriminant functional analysis
First subject treated
First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study
first subject treated. First subject who receives the test article or placebo in a clinical trial.
obsolete_role of being first subject treated
OBI
Rat 1A; first enrolled patient to receive treatment
Role Branch
Listeria innocua
Listeria innocua
A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-1 alpha production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
epitope specific interleukin-1 alpha production by T cells
Neosartorya fennelliae
Neosartorya fennelliae
JEOL NMR probe
PERSON:Daniel Schober
An NMR probe that is manufactured by JEOL.
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400232
GROUP:<http://msi-ontology.sourceforge.net>
JEOL NMR probe
acquisition
Bjoern Peters
IEDB
acquisition
the process of obtaining a continuant from a source.
Culicini
Culicini
chemokine (C-C motif) ligand 4 (MIP-1b) release
assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells
assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
An assay that measures epitope specific chemokine (C-C motif) ligand 4 production by T cells
regression analysis method
regression analysis method
BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048
Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data.
Tina Hernandez-Boussard
Streptomyces coelicolor
Streptomyces coelicolor
Thermoanaerobacter
Thermoanaerobacter
epitope specific lymphotoxin A production by T cells
IEDB (QTT)
epitope specific lymphotoxin A production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope.
WEB:<http://www.chromatography-online.org/EC-Dispersion/HPLC-Sample-Valves/rs16.html>
PERSON:Daniel Schober
liquid chromatography valve
liquid chromatography valve
A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01110
T cell epitope intracellular cytokine staining (ICS) IL-4 assay
A T cell epitope specific cytokine production assay that measures production of IL-4 by T cells utilizing the ICS methodology.
IL-4 release by ICS
IEDB
IEDB
T cell epitope intracellular cytokine staining (ICS) IL-4 assay
exposure of material to environment
Bjoern Peters
IEDB
Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber.
a planned process in which an input material is exposed to a defined set of conditions in a controlled environment. The environment is a specified input.
exposure of material to environment
Chroococcales
Chroococcales
A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
partitioning objective
James Malone
partitioning objective
A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene?
PMID: 18219595.Mol Biotechnol. 2008 Feb;38(2):155-63.PCR-SSCP: a method for the molecular analysis of genetic diseases.
polymerase chain reaction-single strand conformation polymorphism assay
PCR-SSCP assay
PERSON: Philippe Rocca-Serra
a PCR-SSCP assay is an assay that identifies DNA sequence variation (mutation, deletion, insertions) using gel electrophoresis technique and denaturating conditions on target DNA sequences amplified using polymerase chain reaction procedure.
PCR-SSCP assay
PERSON:Daniel Schober
vial
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01117
vial
A vial is a cylindrical container often made from glass tubing.
dorsal to
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity.
dorsal to
a study personnel role played by a party who reports the outcome of a study component
MO:submitter mapped to this term. So, alternative term 'submitter' was added.
reporting party role
OBI
reporting party
The first section has been pre-designated as the 'Reporting Party' section and should be filled with the Reporting Party's personal information. http://www.mercedsheriff.com/SelfReporting.htm
submitter
Person who prepares microarray data in MAGE-TAB format and submits to a database, such as ArrayExpress.
Jennifer Fostel
reporting party role
Ovis
Ovis
chi square test
PERSON: Tina Boussard
chi square test
PERSON: James Malone
The chi-square test is a data transformation with the objective of statistical hypothesis testing, in which the sampling distribution of the test statistic is a chi-square distribution when the null hypothesis is true, or any in which this is asymptotically true, meaning that the sampling distribution (if the null hypothesis is true) can be made to approximate a chi-square distribution as closely as desired by making the sample size large enough.
Festuca rubra
Festuca rubra
injection function
PERSON: Alan Ruttenberg
adapted from WEB: http://www.dictionary.net/injection
PERSON: Melanie Courtot
injection function
The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc.
IEDB
T cell epitope intracellular cytokine staining (ICS) TNF assay
TNFa release by ICS
T cell epitope intracellular cytokine staining (ICS) TNF assay
IEDB
A T cell epitope specific cytokine production assay that measures production of TNF by T cells utilizing the ICS methodology.
MO_939 translational_bias_design
A study design that characterizes the association of transcripts and translation machinery.
Person: Chris Stoeckert, Jie Zheng
translational bias design
translational bias design
flame ionization detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01197
A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample.
PERSON:Daniel Schober
WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
flame ionization detector
FID
t-tests were used with the type I error adjusted for multiple comparisons, Holm's correction (HOLM 1979), and false discovery rate, http://www.genetics.org/cgi/content/full/172/2/1179
WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_method
Philippe Rocca-Serra
Person:Helen Parkinson
Holm-Bonferroni family-wise error rate correction method
2011-03-14: [PRS]. Class Label has been changed to address the conflict with the definition
Also added restriction to specify the output to be a FWER adjusted p-value
The 'editor preferred term' should be removed
Holm-Bonferroni family-wise error rate correction method
a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction
canonical variate analysis
canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form.
CVA
WEB: http://en.wikipedia.org/wiki/Canonical_analysis
Tina Hernandez-Boussard
canonical variate analysis
ANOVA
ANOVA
ANOVA or analysis of variance is a data transformation in which a statistical test of whether the means of several groups are all equal.
James Malone
T cell receptor co-receptor CD8
A protein complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction.
T cell receptor co-receptor CD8
Culicimorpha
Culicimorpha
A T cell epitope specific cytokine production assay that measures production of IL-2 by T cells utilizing the ICS methodology.
T cell epitope intracellular cytokine staining (ICS) IL-2 assay
IL-2 release by ICS
IEDB
IEDB
T cell epitope intracellular cytokine staining (ICS) IL-2 assay
Filicophyta
Filicophyta
ChIP-seq design
ChIP-seq design
http://en.wikipedia.org/wiki/Chip-Sequencing
A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications.
Person: Chris Stoeckert, Jie Zheng
partitioning data transformation
James Malone
A partitioning data transformation is a data transformation that has objective partitioning.
PERSON: James Malone
partitioning data transformation
Leishmania infantum
Leishmania infantum
Varian VXR spectrometer
WEB:<http://www.scs.uiuc.edu/NMR/instruments/vxr500.php>
A Varian NMR spectrometer.
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400238
PERSON:Daniel Schober
Varian VXR spectrometer
IEDB (QTT)
intracellular cytokine staining assay of epitope specific interleukin-21 production by T cells
IL-21 release by ICS
intracellular cytokine staining assay of epitope specific interleukin-21 production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-21 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
frequency unit
A unit which is a standard measure of the number of repetitive actions in a particular time.
frequency unit
Emberizinae
Emberizinae
eudicotyledons
eudicotyledons
Isotomidae
Isotomidae
T cell epitope intracellular cytokine staining (ICS) IFN-g assay
T cell epitope intracellular cytokine staining (ICS) IFN-g assay
IFNg release by ICS
A T cell epitope specific cytokine production assay that measures production of IFN-g by T cells utilizing the ICS methodology.
IEDB
IEDB
averaging data transformation
James Malone
An averaging data transformation is a data transformation that has objective averaging.
PERSON: James Malone
averaging data transformation
T cell tolerance induction
A process involving any mechanism for tolerance induction in T cells.
T cell tolerance induction
Pulmonata
Pulmonata
Cyanobacteria
Cyanobacteria
Macropodidae
Macropodidae
A cell culture analyte detection bioassay that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
cell culture analyte detection bioassay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
IEDB (QTT)
GM-CSF release by bioassay
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cell culture analyte detection bioassay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400130
A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle.
PERSON:Daniel Schober
magic angle spinning rotor
WEB:<http://www.freepatentsonline.com/4352066.html>
MAS rotor
magic angle spinning rotor
Dechloromonas
Dechloromonas
Person:Tina Hernandez-Boussard
centroid mass spectrum calculation
centroiding
centroid mass spectrum
centroid mass spectrum
centroid mass spectrum
A centroid mass spectrum is a data transformation in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data.
Cryptosporidium
Cryptosporidium
IEDB
A T cell epitope specific cytokine production assay that measures production of IL-13 by T cells utilizing the ELISPOT methodology.
T cell epitope ELISPOT IL-13 assay
IEDB
T cell epitope ELISPOT IL-13 assay
IL-13 release by ELISPOT
band pass filter
530/30 BP filter, 585/42 BP filter
Person:John Quinn
band pass filter
http://en.wikipedia.org/wiki/Band_pass_filter
A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 band-pass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others.
Coregonus clupeaformis
Coregonus clupeaformis
Coprinopsis cinerea
Coprinopsis cinerea
Mycosphaerella
Mycosphaerella
e.g the function of a bar code reader used to read slide bar codes
specimen fixation function
a function that allows specific identification of individual speciment from one another.
specimen fixation function
EAGLE-I
group assignment
Assigning' to be treated with active ingredient role' to an organism during group assignment. The group is those organisms that have the same role in the context of an investigation
group assignment
group assignment is a process which has an organism as specified input and during which a role is assigned
OBI Plan
cohort assignment
study assignment
Philippe Rocca-Serra
Rhodospirillum
Rhodospirillum
IEDB (QTT)
detection of specific nucleic acids with complementary probes of epitope specific interleukin-4 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-4 production by T cells
IL-4 release by RNA/DNA detection
detection of specific nucleic acids with complementary probes of epitope specific interleukin-4 production by T cells
polyploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes.
polyploid
material component separation
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification
a material processing in which components of an input material become segregated in space
Bjoern Peters
IEDB
material component separation
obsolete_specimen fixation function
A specimen
fixation function is a function that holds or fastens an entity in a fixed position.
EAGLE-I
duplicate term
obsolete_specimen fixation function
Bactiflow
http://www.chemunex.com/products/chemframe.htm
A Bactiflow is a flow_cytometer_analyser manufactured by Chemunex SA. It is a cell counter for bacteria and other micro organisms. Bacteria are stained with a fluorochrome and the number of particles that fluoresce are counted. The system uses digital electronics, a single laser and a single detector. An ALS version is available as well - Automatic Labeling System. The Bactiflow is specialized cytometer used exclusively for counting microbes.
Bactiflow
John Quinn
occurrence of infectious disease
IEDB
IEDB
Is an occurrence of a disease caused by an infection
occurrence of infectious disease
Solanum
Solanum
Percomorpha
Percomorpha
Picea glauca
Picea glauca
Filicales
Filicales
Jennifer Fostel
Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.
methodology testing objective
methodology testing objective
health care provider role
health care provider
health care provider role
Person:Jennifer Fostel
a worker role of providing medical care either within or outside the study timeline
Gerbera
Gerbera
RNAOntology
Person:Philippe Rocca-Serra
is a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhutenium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Ruthenium structure mapping assay
PMID:3016894
Ruthenium structure mapping assay
data acquisition
data acquisition
Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC
data collection
OBI branch derived
Bjoern Peters
an acquisition in which information acquisition from an organization that provides information. This is not an assay. It consists of specifiying a query what information is desired, putting this query to an organization, and retrieveing the requested information from the organization.
John Quinn
BioSorter2000
BioSorter 2000 at TSRI Flow Cytometry Core Facility
http://www.unionbio.com/products/BioSorter.html
A BioSorter2000 is a sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter.
BioSorter2000
a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely
living in endemic area
IEDB
IEDB
living in endemic area
administration in vivo with infectious agent
administration in vivo with infectious agent
IEDB
IEDB
is an administration of an infectious agent to a host organism
catalytic activity
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
catalytic activity
Drosophila teissieri
Drosophila teissieri
Novosphingobium aromaticivorans
Novosphingobium aromaticivorans
primary structure of DNA macromolecule
BP et al
a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues.
placeholder for SO
primary structure of DNA macromolecule
Caulobacteraceae
Caulobacteraceae
0.01, 0.03
A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role
parameter threshold
parameter threshold
person:Kevin Clancy
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
RNA ontology
inline probing RNA structure mapping
is a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses intromolecular reactivity to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
PMID:10573122 and PMID: 18369975
inline probing RNA structure mapping
Person: Philippe Rocca-Serra
Haloferax volcanii
Haloferax volcanii
Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
environmental material collection
environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
IEDB
Bjoern Peters, Alan Ruttenberg
environmental material collection
BioSorter 1000 at TSRI Flow Cytometry Core Facility
http://www.unionbio.com/products/BioSorter.html
A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter.
BioSorter1000
John Quinn
BioSorter1000
pathogen release in laboratory accident
a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent
pathogen release in laboratory accident
IEDB
IEDB
Chlamydomonas reinhardtii
Chlamydomonas reinhardtii
Zea mays
Zea mays
curated information
PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6.
2010-01-31 Philippe Rocca-Serra: restriction now changed to be the output of a digital curation process + reflected in example of usage and reference
OBI
2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions.
A information content entity that has undergone a digital curation performed by a curator for accuracy checks and compliance with curation requirements. Information which has been assessed for accuracy by domain experts.
curated information
Person:Bjoern Peters
Person:Philippe Rocca-Serra
Melanie Courtot
A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement
solid support function
Frank Gibson
solid support function
Taped, glued, pinned, dried or molecularly bonded to a solid support
Daniel Schober
cytometer sample tube
A particle delivery vessel. The cytometer sample tube is a vessel in which the sample is introduced to the cytometer. Frequently the tube is placed on the cytometer in such a manner that a seal is formed between the tube and cytometer, and gas is used to create enough pressure to push the sample out of the tube and into the cytometer.
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
cytometer sample tube
sample tube in a cytometer
Person:Alan Ruttenberg
09/28/2009 Alan Ruttenberg: This is made a subclass of the higher level processual entity in BFO because I don't want to take a stand on whether it is a process aggregate. Analogous to the situation with Material entity.
informed consent process
http://clinicaltrials.gov/ct2/info/glossary#informed
a planned process in which subject is taught key facts about a clinical trial both before deciding whether or not to participate, and throughout the study. Agents of the investigation, such as doctors and nurses involved in the trial, explain the details of the study.
informed consent process
autotransplantation
OBI branch derived
PlanAndPlannedProcess Branch
autotransplantation
is the transplantation of tissue from one part of \nthe body to another in the same individual. )
Herminiimonas
Herminiimonas
Trifolium repens
Trifolium repens
pressure unit
A unit which is a standard measure of the force applied to a given area.
pressure unit
Rhodospirillum rubrum
Rhodospirillum rubrum
PlanAndPlannedProcess Branch
non-specific labeling
The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies.
non-specific labeling
OBI branch derived
guar gum
Helen Parkinson
guar gum
Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder.
http://en.wikipedia.org/wiki/Guar_gum
The group of randomized participants that are assigned to a treatment arm of the trial
Jennifer Fostel
a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol
study group role
study group role
study group population
Mouth
Mouth
image acquisition device
Frank Gibson
sep:00096
An image acquisition device is a device which captures a digitized image of an object
image acquisition device
Drosophila yakuba
Drosophila yakuba
PERSON: James Malone
An assay in which a microRNA array is used to analyse the microRNA component of the transcriptome.
microRNA profiling by array assay
EFO_0000753 microRNA profiling by array
microRNA profiling by array assay
Zea
Zea
PERSON: Helen Parkinson
A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient
to be treated with active ingredient role
to be treated with active ingredient role
Person:Alan Ruttenberg
Role of a patient in a group treated with an active substance in a clinical trial
Hypocreales
Hypocreales
material portioning
a material processing in which the input substance is partitioned into a number of portions that are similar in composition.
OBI branch derived
pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
PERSON:Bjoern Peters
apportioning
aliquoting
material portioning
Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038
GROUP: OBI Biomaterial Branch
precipited material
precipitate
a precipitate is a material entity which is output of a precipitation process
precipitate
PERSON: Philippe Rocca-Serra
mononuclear cell
A leukocyte with a single non-segmented nucleus in the mature form.
mononuclear cell
unfolds_in
Example: oocyte axis determination : The establishment, maintenance and elaboration of an axis in the oocyte. This process unfolds_in the oocyte
P unfolds_in C : the execution of P is spatially contained by C. forall pP, forall c' partipates_in p, c' located_in C at t, for some t in P
unfolds_in
Jessica Turner, NIF, Dirk Derom, OBI
The process of measuring neural activity in the caudate nucleus
measuring neural activity in the caudate nucleus
Helen Parkinson
measuring neural activity in the caudate nucleus
An SU micro-electrode was used to measure neural activity in the form of spike trains in the caudate nucleus of monkeys in response to a flashing light stimulus
quality control testing design
MO_981 quality_control_testing_design
A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance.
Person: Chris Stoeckert, Jie Zheng
quality control testing design
image acquisition function
Frank Gibson
An image acquisition function is a function to acquire an image of a material
image acquisition function
ploidy
A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism.
ploidy
Fabales
Fabales
Nicotiana benthamiana
Nicotiana benthamiana
Capsicum annuum
Capsicum annuum
relational spatial quality
A quality of related physical entities inhering in a bearer by virtue of the bearer's pertaining to or involving or having the nature of space in relation to another entity.
relational spatial quality
T cell epitope ELISPOT IL-4 assay
IEDB
IL-4 release by ELISPOT
T cell epitope ELISPOT IL-4 assay
IEDB
A T cell epitope specific cytokine production assay that measures production of IL-4 by T cells utilizing the ELISPOT methodology.
the detection of the amount of a label which is a proxy for the detection of the labeled biomaterial
detection of label
detection of label
OBI branch derived
Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present
PERSON:Bjoern Peters
avalanche photodiode
An avalanche photodiode is typically used to collect photons emitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode with high quantum efficiency and a mechanism for producing gains as high as a few thousand.
C30644E - InGaAs Avalanche Photodiode
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
avalanche photodiode
micro electrode
Jessica Turner, Dirk Derom
A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus
micro electrode measuring device
Helen Parkinson, Jessica Turner, Dirk Derom
An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system.
micro electrode
Gibberella
Gibberella
Chlamydomonas
Chlamydomonas
recombinant plasmid
recombinant plasmid
PERSON: Bjoern Peters
PERSON: Melanie Courtot
GROUP: OBI Biomaterial Branch
PERSON: Kevin Clancy
a plasmid in which extraneous DNA has been inserted.
multi-tissue structure
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
multi-tissue structure
Saccharophagus
Saccharophagus
Enterococcaceae
Enterococcaceae
sheath tank
LSR2 sheath tank
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
sheath tank
Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid.
John Quinn
haploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes.
haploid
Person: Chris Stoeckert, Jie Zheng
A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied.
MO_832 clinical_history_design
clinical history design
clinical history design
Estrildinae
Estrildinae
Capsicum
Capsicum
IEDB
A T cell epitope specific cytokine production assay that measures production of TNF by T cells utilizing the ELISPOT methodology.
T cell epitope ELISPOT TNF assay
T cell epitope ELISPOT TNF assay
TNFa release by ELISPOT
IEDB
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
PlanAndPlannedProcess Branch
OBI branch derived
2
sample pooling
physical combination of several instances of like material
pooling specimens
pooling specimens
John Quinn
argon ion laser in a cytometer
Daniel Schober
http://en.wikipedia.org/wiki/Laser#Gas_lasers
argon ion laser
argon ion laser
An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes.
Chlamydomonadaceae
Chlamydomonadaceae
Berichrom(r) Antithrombin III (A) Kit
Berichrom(r) Antithrombin III (A) Kit
For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution
Person:Alan Ruttenberg
WEB:http://www.dadebehring.com/edbna2/ebusiness/products/productDetail.jsp?sDiscipline=Hemostasis&FirstLevelOID=-13075&sCategory_Name=BCS&SecondLevelOID=-13895&ThirdLevelOID=-13904&selectedProductType=H-Assays+-+non+US&sProductName=OWWR15&PROD_OID=44198@2009/08/06
PERSON: Helen Parkinson
a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
cloning vector role
cloning vector role
pBluescript plays the role of a cloning vector
short pass filter
620 SP filter
A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm.
John Quinn
http://en.wikipedia.org/wiki/Low-pass_filter
short pass filter
May be outside the scope of OBI long term, is needed so is retained
PMID:19696660
in contrast to the in-vivo data AT-III increased significantly from
113.5% at baseline to 117% after 4 days (n = 10, P-value= 0.02; Table 2).
PERSON:Alan Ruttenberg
PERSON:Chris Stoeckert
A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
WEB: http://en.wikipedia.org/wiki/P-value
p-value
p-value
Phyllobacteriaceae
Phyllobacteriaceae
protein-protein interaction detection
20091101, Bjoern Peters: This class may be overly broad. Lot's of assays would seem to classify under it, and I have the feeling that the intend would be to limit this to determining protein-protein interactions as they occur within an organism, rather than e.g. peptide:MHC binding assays.
An assay with the objective to determine interactions between proteins, such as protein-protein binding.
protein-protein interaction detection
Macaca
Macaca
Lycopersicon
Lycopersicon
signal amplification function
A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal.
Daniel Schober
signal amplification function
Frank Gibson
Bill Bug
Melanie Courtot
genotyping design
Person: Chris Stoeckert, Jie Zheng
genotyping design
MO_560 genotyping_design
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs.
blot module
blot module
Frank Gibson
A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised
sep:00092
Brucella
Brucella
Anabaena
Anabaena
Leuconostocaceae
Leuconostocaceae
solid state laser
A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby crystal solid state laser.
Daniel Schober
Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command
http://en.wikipedia.org/wiki/Solid-state_laser
solid state laser
Drosophilidae
Drosophilidae
methylated polymer
methylated polymer
A methylated polymer which has artificially acquired one or more methyl groups
OBI Biomaterial
Binding and penetration of methylated DNA into primary and transformed human cells.
Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922
Philippe Rocca-Serra
ssRNA positive-strand viruses, no DNA stage
ssRNA positive-strand viruses, no DNA stage
PPPB branch
material separation objective
The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood.
material separation objective
PPPB branch
is an objective to transform a material entity into spatially separated components.
calibration
the process of using pH buffer adjust a pH meter
calibration
GROUP: OBI Philly workshop
WEB:http://en.wikipedia.org/wiki/calibration
A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements.
Desulfitobacterium hafniense
Desulfitobacterium hafniense
Tetraodontiformes
Tetraodontiformes
The process of an allergic disease occurring in an organism.
occurrence of allergy
IEDB
occurrence of allergy
IEDB
adaptive immune response
An immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).
adaptive immune response
epitope
epitope
IEDB
IEDB
a material entity bearing the epitope role
Brucella abortus
Brucella abortus
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IL-2 release
An assay that measures epitope specific interleukin-2 production by T cells
assay of epitope specific interleukin-2 production by T cells
assay of epitope specific interleukin-2 production by T cells
IEDB (QTT)
Bill Bug
Frank Gibson
signal conversion function
Daniel Schober
Melanie Courtot
A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon.
transduction function
signal conversion function
a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle
Bjoern Peters and Nicole Washington
cell cycle synchronization
OBI PA
cell cycle synchronization
Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs.
Nostocaceae
Nostocaceae
randomized group participant role
randomized group participant role
Philippe Rocca-Serra
Person:Helen Parkinson
A person enrolled in a randomized clinical trial bears a randomized group participant role
a role that borne by an organism and realized by some group randomization process
Eurotiales
Eurotiales
volume unit
A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas.
volume unit
Cannabis sativa
Cannabis sativa
Somacount
A Somacount is a flow_cytometer_analyser manufactured by Bently Instruments. It is a specialized tool for counting somatic cells in milk by specifically staining them with Ethidium Bromide and counting the cells that fluoresce. It has one laser, and the filters and a PMT for the single parameter. There are three sizes available, the 150, 300, and 500 with the number indicating the maximum number of cells that can be analysed per hour. The Somacount is an example of a very specific use cytometer; it exclusively counts somatic cells in milk.
John Quinn
Somacount
http://www.bentleyinstruments.com/somacount.html#Anchor-Bentley-49575
fucoidan
Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber).
Helen Parkinson
fucoidan
http://en.wikipedia.org/wiki/Fucoidan
T cell epitope ELISPOT IL-2 assay
IEDB
IL-2 release by ELISPOT
T cell epitope ELISPOT IL-2 assay
IEDB
A T cell epitope specific cytokine production assay that measures production of IL-2 by T cells utilizing the ELISPOT methodology.
Citrus
Citrus
The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932
lysate
cell lysate
a cell lysate is a material entity which is output of a cell lysis process
cell lysate
lysed material
GROUP: PSI
PRS:22-02-2008: is a material which has output_role during lysis protocol-application.
old defintion: A mixture (collection) of cell components created by rupturing of the cell wall resulting from a lysis process
PERSON: Susanna Sansone
An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
information processor function
Frank Gibson
information processor function
data processor function
IEDB (QTT)
epitope specific interleukin-15 production by T cells
A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-15 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Sparidae
Sparidae
Nostocales
Nostocales
disposition to cause an allergic reaction
disposition to cause an allergic reaction
allergenic disposition
IEDB
IEDB
The role borne by a material entity that is realized when it is recognized by the immune system and results in the occurrence of an allergic disease.
SomaScope
"http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10"
Josef Spidlen
SomaScope
SomaScope Mark II Automatic Economical
The SomaScope is an instrument to quantify somatic cells in milk.
Pteridaceae
Pteridaceae
a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse T1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Person:Philippe Rocca-Serra
RNA ontology
RNASE T1 structure mapping assay
RNASE T1 structure mapping assay
single nucleotide resolution mapping assay using RNAse T1
PMID:114514
Cyanothece sp. ATCC 51142
Cyanothece sp. ATCC 51142
Frank Gibson
An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy
energy supply function
energy supply function
IEDB (QTT)
epitope specific macrophage inflammatory protein-1 gamma production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope.
epitope specific macrophage inflammatory protein-1 gamma production by T cells
Measurment of the radioactivity of a supernatant, as in chromium_release_assay.
An assay in which a material's radioactivity is measured.
radioactivity detection
OBI branch derived
PlanAndPlannedProcess Branch
radioactivity detection
polymerase chain reaction
adapted from wikipedai
PCR
Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
OBI Plan
polymerase chain reaction
PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
Drosophila
Drosophila
Storage of a blood specimen in a tube with anticoagulant
anticoagulant tube storage of blood specimen
anticoagulant tube storage of blood specimen
Person:Alan Ruttenberg
allergic reaction
IEDB
allergic reaction
an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen)
IEDB
flow cytometer sorter
Melanie Courtot
A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during analysis) to collect cells of interest.
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
John Quinn
flow cytometer sorter
BioSorter2000, LSR2
PERSON: Jie Zheng
array image acquisition
array image acquisition
An image acquisition process that generate an image from the array.
MO_929: image_acquisition
epitope protection experiment based on survival
Bjoern Peters
an epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host.
epitope protection experiment based on survival
host survival after challenge
Asteraceae
Asteraceae
Bifidobacteriaceae
Bifidobacteriaceae
cloning insert role
OBII and Wikipedia
cloning insert role
Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just "cloning process"
cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process.
GROUP: Role branch
PERSON:Bjoern Peters
in vivo assay
in live organism assay
in live organism assay
Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells.
An assay in which a measurement is made by observing entities located in an organism.
Frank Gibson
thermostatic circulator
thermostatic circulator
sep:00098
A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid
individual genetic characteristics comparison design
individual genetic characteristics comparison design
Person: Chris Stoeckert, Jie Zheng
A study design where genotype, haplotype, or other individual genetic characteristics are compared.
MO_527 individual_genetic_characteristics_design
investigation agent role
GROUP: Role Branch
The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress.
investigator
Implementing a study means carrying out or performing the study and providing reagents or other materials used in the study and other tasks without which the study would not happen.
Investigation agent role is a role borne by a person or organization which is realized in a process that is part of an investigation in which an objective is achieved. These processes include: planning, overseeing, funding, reviewing.
OBI
investigation agent role
Person:Helen Parkinson
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)
a device which has a function to emit light.
OBI
light emission device
light emission device
Saccharophagus degradans
Saccharophagus degradans
Schistosomatoidea
Schistosomatoidea
A function realized as an immune response, which inheres in a T cell, B cell or antibody which derives from or is produced by a cell with prior antigen experience.
adaptive immune effector function
adaptive immune effector function
IEDB
IEDB
John Quinn
A BioSorter500 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length.
BioSorter500
http://www.unionbio.com/products/BioSorter.html
BioSorter500
BioSorter 500 at TSRI Flow Cytometry Core Facility
Bjoern Peters
epitope disease exacerbation experiment
exacerbation assay
epitope disease exacerbation experiment
an epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host.
acclimatization
A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment.
CEBS, Biomaterial_branch
Jennifer Fostel
acclimatization
placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress
Archaeoglobi
Archaeoglobi
Halobacterium sp.
Halobacterium sp.
container
03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)
A device that can be used to restrict the location of material entities over time
PERSON: Bjoern Peters
container
Bjoern Peters, Alan Ruttenberg, Helen Parkinson
Acquiring 50 C57BL/6 mice in the investigators animal facilities. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI.
object acquisition
material acquisition
object acquisition
IEDB
Bjoern is concerned that information such as model number and serial number are to be associated with the process. Others contend that these are associated, perhaps as labels, to the instances that are the participants.
The assumption is that the object already exists in its current state, e.g, an available mouse strain purchased from the Jackson Lab, this is the differentia from speciment creation
an acquisition of an object from an investigator, institution or vendor.
PERSON: Chris Stoeckert
MO_589 freeze_dried_sample
freezing dried DNA
lyophilized specimen
PERSON: Jie Zheng
lyophilized specimen
a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage.
Salmonoidei
Salmonoidei
Hymenoptera
Hymenoptera
antigen binding
Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
antigen binding
Staphylococcus
Staphylococcus
An assay that measures epitope specific interleukin-1 beta production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific interleukin-1 beta production by T cells
IL-1b release
assay of epitope specific interleukin-1 beta production by T cells
IEDB (QTT)
OBI Vancouver workshop 2010
A homogenizer is a perturbation device.
perturbation device
PERSON: Helen Parkinson
Helen Parkinson
perturbation device
A perturbation device is a device which is designed to perform a perturb function
IEDB
living with infected household contact
living with infected household contact
a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent
IEDB
infectious agent detection assay
2/22/2011, BP: This should probably be an analyte assay, but the logical definition of those is currently restricted to 'scattered molecular aggregates', which excludes using infectious agents as analytes. See below
(realizes some
('evaluant role'
and (role_of some material_entity)))
and (realizes some
('analyte role'
and (role_of some 'infectious agent')))
and (achieves_planned_objective some 'analyte measurement objective')
An assay in which the presence or amount of an infectious agent in an input material is detected in an evaluant
Bjoern Peters, Randi Vita, Jason Greenbaum
Culturing a sputum sample on agar medium to detect bacterial growth; Stain slices of liver from a mouse to count presence of infectious centers.
infectious agent detection assay
Tetradontoidea
Tetradontoidea
BioSorter250
John Quinn
BioSorter250
http://www.unionbio.com/products/BioSorter.html
BioSorter 250 at TSRI Flow Cytometry Core Facility
A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter.
Rubrobacter
Rubrobacter
An assay that determines the concentration of glucose molecules in a blood serum sample
Person:Bjoern Peters
measuring glucose concentration in blood serum
measuring glucose concentration in blood serum
is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe
BP
intraperitoneal injection
intraperitoneal injection
Betulaceae
Betulaceae
GROUP: Role branch
nutrient role
a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment.
nutrient role
nutrient
Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.
Wikipedia, feb 29, 2008
host exposure to infectious agent
host exposure to infectious agent
IEDB
IEDB
a process in which an infectious agent comes into physical contact with a host organism.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
LSR2 charge plate
John Quinn
charge plate
Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting.
charge plate
epitope protection from infectious challenge experiment based on pathogen burden
An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls.
Bjoern Peters
epitope protection from infectious challenge experiment based on pathogen burden
pathogen burden after infectious challenge
epitope binding by adaptive immune receptor
epitope binding by adaptive immune receptor
IEDB
IEDB
is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding.
Helen Parkinson
An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity.
environmental control device
OBI
environmental control device
A growth chamber is an environmental control device.
Pinus
Pinus
reverse transcriptase
group:OBI
person:Melanie Courtot
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase
activity)
reverse transcriptase
Thermotogae
Thermotogae
dose specification
a directive information entity that describes the dose that will be administered to a target
a protocol specifying to administer 1 ml of vaccine to a mouse
dose specification
peptide antigen binding
Interacting selectively and non-covalently with an antigen peptide.
peptide antigen binding
Role Branch
Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role.
obsolete_dropout role
Dropout
Will be modelled as defined material, ouput of some 'dropout or withdrawal
process' instead of role
OBI
Escaped rat; human who moved to another city. Rat which escapes part way through a study; a human study participant who moved to another city before the study was completed (and stopped participating in the study)
John Quinn
A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 fluorescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of individual cells.
Cell Lab Quanta SC
http://www.beckmancoulter.com/cell-lab
Cell Lab Quanta SC
IEDB
occurrence of disease
IEDB
occurrence of disease
An occurrence of disease is a process involving pathologic changes within an organism
strain
Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert
selectively maintained organism
An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms
MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar
ecotype
cultivar
selectively maintained organism
PMID:363143
a single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Nuclease S1 structure mapping assay
single nucleotide resolution mapping assay using Nuclease S1
Nuclease S1 structure mapping assay
Person: Philippe Rocca-Serra
RNA ontology
Immunization in vivo
Immunization in vivo
IEDB
IEDB
Process of administering an object playing the role of immunogen to a living organism
Halobacterium salinarum
Halobacterium salinarum
PERSON: Helen Parkinson
A device is a processed material which is designed to perform some function or functions
food should not classify as a device - counter example for using manufacturer and not device. macroscopic only
would include reagents
instrument
A voltmeter is a measurement device which is intended to perform some measure function.
if we keep this exploratory term we could reinstate the old device class which is obsolete_device. didn't work before as we had manufacturing as part of the definition. device was needed, but couldn't define in Philadelphia. If we decide that in addition to function there are also capabilities for which a device is created we will include these in the definition.
device
device
OBI Vancouver workshop 2010
Schistosomatidae
Schistosomatidae
disease symptom exacerbation
T cell epitope disease exacerbation experiment
T cell epitope disease exacerbation experiment
PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB
An epitope disease exacerbation experiment in which the evaluated response is made by T cells
liver
liver is an anatomical entity which constituent are mainly hepatocytes, which has a function of detoxification, hematopoietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates
GROUP: OBI Biomaterial Branch
liver
PERSON: Philippe Rocca-Serra
PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology.
AJR Am J Roentgenol. 1990 Jan;154(1):87-93.
mode calculation
James Malone
PERSON: Monnie McGee
A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data.
mode calculation
PERSON: James Malone
Monnie McGee
Diptera
Diptera
Person: Helen Parkinson
vital dye role
The role of a dye that is realized when used in an experiment to stain live cells
Person: Jennifer Fostel
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893048&group_id=177891&atid=886178
vital dye
typtan blue has a vital dye
vital dye role
Coronaviridae
Coronaviridae
blood coagulation
The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
blood coagulation
Bacillus cereus group
Bacillus cereus group
disease
disease
IEDB
IEDB
placeholder to be imported from disease ontology
A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents.
autoclave
J. Black, Microbiology, Prentice Hall (1993) pg. 334; http://en.wikipedia.org/wiki/Autoclave
autoclave
PERSON: Erik Segerdell
Monnie McGee
quantile calculation
quantile calculation
WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html
A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details.
An intracellular cytokine staining assay that measures epitope specific interleukin-12 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
intracellular cytokine staining assay of epitope specific interleukin-12 production by T cells
intracellular cytokine staining assay of epitope specific interleukin-12 production by T cells
IL-12 release by ICS
epitope treatment experiment
Bjoern Peters
an epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host.
decreased disease symptoms after treatment
epitope treatment experiment
a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference
reference subject role
Saline treated rat; one of three identically-treated subjects
Jennifer Fostel
reference subject role
reference participant
OBI
Coronavirus
Coronavirus
Fusobacterium nucleatum
Fusobacterium nucleatum
autoimmune disease
autoimmune disease
IEDB
IEDB
Is a disease characterized by an immune response of an organism against parts of itself
Noctuoidea
Noctuoidea
A device that is used for the warming of paraffin embedding medium.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
paraffin oven
paraffin oven
half maximal inhibitory concentration (IC50)
The half maximal inhibitory concentration (IC50) is a measure of the effectiveness of a compound in inhibiting biological or biochemical function. This quantitative measure indicates how much of a particular drug or other substance (inhibitor) is needed to inhibit a given biological process (or component of a process, i.e. an enzyme, cell, cell receptor or microorganism) by half. In other words, it is the half maximal (50%) inhibitory concentration (IC) of a substance (50% IC, or IC50).
half maximal inhibitory concentration (IC50)
Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited.
Bjoern Peters; Randi Vita
wikipedia
IEDB (QTT)
An assay that measures epitope specific monocyte chemotactic protein-1 production by T cells
assay of epitope specific monocyte chemotactic protein-1 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
MCP-1 release
assay of epitope specific monocyte chemotactic protein-1 production by T cells
Monnie McGee
A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values.
James Malone
PERSON: James Malone
median calculation
median calculation
PERSON: Monnie McGee
Vertebrata
Vertebrata
Xanthomonadaceae
Xanthomonadaceae
Galliformes
Galliformes
protocol testing objective
Jennifer Fostel
Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
protocol testing objective
laboratory animal care
a process that realizes an animal care protocol that specifies how animals are kept and maintained
laboratory animal care
real-time PCR machine
An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
real-time PCR machine
Schizotrypanum
Schizotrypanum
MHC:epitope complex binding to TCR
IEDB
MHC:epitope complex binding to TCR
a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule.
IEDB
epitope specific immune intervention
An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope
Person: Bjoern Peters, Randi Vita, Jason Greenbaum
epitope specific immune intervention
GROUP: Role Branch
study subject role
study subject role
Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study.
Parasite example
people infected, then extract parasite which are then tested = observation study of the parasite
1 study in which we observe people and 1 study in which subject is parasite is one way to split this. the true definition will come from the study design specification.
OBI
study subject role inheres in an entity and realized through the execution of a study design in which the entity participates by being that which the results are about.
MO_462 strain_or_line_design
strain comparison design
strain comparison design
A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species.
Person: Chris Stoeckert, Jie Zheng
double-stranded DNA
double-stranded DNA
YAC
Kevin Clancy, Bjoern Peters
this should be a child of 'chromosome' if we import that from another source
yeast artificial chromosome vector
yeast artificial chromosome vector
a double-stranded DNA that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences
Portion of blood
Body substance which consists of plasma and blood cells
Portion of blood
IEDB
epitope specific IL-2 release by T cells
epitope specific IL-2 release by T cells
A biological process where T cells produce IL-2 resulting from the recognition of a T cell epitope.
IEDB
an intervention design in which the treatment is the administration of a compound
compound treatment design
MO_555 compound_treatment_design
PERSON: Bjoern Peters
This is meant to include all kinds of material administrations, including vaccinations, chemical compounds etc.
compound treatment design
decapitation
OBI-Branch
Philippe Rocca-Serra
decapitation
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
decapitation is a process by which the head of a living organism is physically removed from the body, usually resulting in rapid death (in the case of Rhodnius prolixus, it might take a bit longer..)
Ostariophysi
Ostariophysi
EFO_0002768: transcription profiling by array
transcription profiling by array assay
Person: James Malone
transcription profiling by array assay
An assay in which the transcriptome of a biological sample is analysed using array technology.
tritiated thymidine incorporation assay
3H-thymidine incorporation
IEDB
tritiated thymidine incorporation assay
IEDB
The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity.
2/26/09: RESOLVE: need to replace 'molecular entities' in the logical definition with 'tritiated thymidine'
A tritiated thymidine incorporation assay is an assay to detect actively replicating cells. Tritiated thymidine is incorporated into the newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine can then be detected thus indicating cells that were actively replicating their DNA.
Platyrrhini
Platyrrhini
Parvovirinae
Parvovirinae
epitope specific cytokine production by T cells
A process of cytokine production by T cells resulting from the recognition of a T cell epitope.
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific cytokine production by T cells
temperature
A physical quality of the thermal energy of a system.
temperature
Bacillus halodurans
Bacillus halodurans
CD8- T cell culture
A T cell population characterized by not expressing the CD8 molecule on its surface.
CD8- T cell culture
IEDB
IEDB
Eurotiomycetes
Eurotiomycetes
A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
vacuum manifold
vacuum manifold
circular
A quality of a nucleotide polymer that has no terminal nucleotide residues.
circular
lethal injection
intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death
OBI Biomaterial
Philippe Rocca-Serra
intentional overdosing
In vivo measurement of tumor blood oxygenation by near-infrared spectroscopy: immediate effects of pentobarbital overdose or carmustine treatment.
J Neurooncol. 1994;22(3):209-20. PMID: 7760097
intentional overdosing
error correction data transformation
James Malone
Monnie McGee
An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation.
error correction data transformation
EDITORS
oral administration
PERSON: Melanie Courtot
The administration of a substance into the mouth of an organism
oral administration
IEDB (QTT)
epitope specific IP-10 production by T cells
epitope specific IP-10 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A process of IP-10 production by T cells resulting from the recognition of a T cell epitope.
Paracanthopterygii
Paracanthopterygii
Ceratopteris
Ceratopteris
Phaeophyceae
Phaeophyceae
Rubus
Rubus
from http://cvi.asm.org/cgi/content/full/11/2/255 (and slightly simplified)\nAutologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target (5 x 10E4 cells/ml) and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1 (9). Spontaneous release of 51Cr was assessed by the incubation of target cells in medium alone, and maximum release of 51Cr was determined by the incubation of target cells in 0.1% Triton X-100 (Sigma-Aldrich).\nAfter a 4-h incubation of the effector cells with the target cells at 37 degrees C in 6% CO2, supernatants were collected following brief centrifugation. The supernatant was collected into filters of supernatant collection system harvesting frames (Molecular Devices Skatron, Sunnyvale, Calif.) and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac).\nPercent specific was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
PlanAndPlannedProcess Branch
An assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died.
OBI branch derived
chromium release assay
chromium release assay
51 chromium release
TGFb release by ELISPOT
ELISPOT assay of epitope specific transforming growth factor-beta production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
ELISPOT assay of epitope specific transforming growth factor-beta production by T cells
IEDB (QTT)
An ELISPOT assay that measures epitope specific transforming growth factor-beta production by T cells
Aquifex
Aquifex
ELISA microplate washer
A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA).
ELISA microplate washer
PERSON: Erik Segerdell
PERSON: Erik Segerdell
Brassica rapa
Brassica rapa
CD4- T cell culture
A T cell population characterized by not expressing the CD4 molecule on its surface.
CD4- T cell culture
IEDB
IEDB
protein
antithrombin III is a protein
An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA.
protein
Listeria
Listeria
adipose tissue
GROUP: OBI Biomaterial derived
PERSON: Philippe Rocca-Serra
PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4.
adipose tissue
adipose tissue is a tissue which main constituents are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates.
principal components analysis dimensionality reduction
principal components analysis dimensionality reduction
PERSON: Elisabetta Manduchi
PERSON: Melanie Courtot
PERSON: James Malone
James Malone
pca data reduction
Elisabetta Manduchi
Philippe Rocca-Serra
Melanie Courtot
A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
granzyme B release by ELISA
ELISA of epitope specific granzyme B production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
ELISA of epitope specific granzyme B production by T cells
An ELISA that measures epitope specific granzyme B production by T cells
IEDB (QTT)
IEDB
MHC tetramer/multimer staining
An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer
IEDB
MHC multimer staining assay
MHC tetramer assay
MHC multimer staining assay
Measuring T cells that are specific for the SYFPEITHI peptide when presented by the murine MHC molecule H-2 Kd by staining them with a tetramer of peptide loaded MHC complexes.
ribonuclease CL3
A protein with ribonuclease activity that is purified from chicken liver.
ribonuclease CL3
Ceratopteris thalictroides
Ceratopteris thalictroides
Person: Chris Stoeckert, Jie Zheng
operator variation design
operator variation design
A study design that assesses the operator performance and relation to data consistency and quality.
MO_519 operator_variation_design
Pseudomonas aeruginosa group
Pseudomonas aeruginosa group
cancer
cancer
A disease characterized by abnormal and uncontrolled cell division
IEDB
IEDB
Dothideomycetes et Chaetothyriomycetes incertae sedis
Dothideomycetes et Chaetothyriomycetes incertae sedis
PERSON: Erik Segerdell
A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis.
nucleic acid extraction/purification instrument
PERSON: Erik Segerdell
nucleic acid extraction/purification instrument
A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
homogenizer
mortar, blender
Trish Whetzel
http://en.wikipedia.org/wiki/Homogenizer
Melanie Courtot
homogenizer
background correction data transformation
James Malone
A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction.
PERSON: James Malone
background correction data transformation
genetic modification design
MO_447 genetic_modification_design
A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out.
Person: Chris Stoeckert, Jie Zheng
genetic modification design
Nematocera
Nematocera
liver tissue embedded in paraffin
paraffin specimen
a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin
paraffin specimen
PERSON: Jie Zheng
PERSON: Chris Stoeckert
MO_990 paraffin_sample
ribonuclease V1
A protein with ribonuclease activity that is a constituent of cobra venom.
ribonuclease V1
Rodentia
Rodentia
Citrus sinensis
Citrus sinensis
cytometric bead array assay of epitope specific IP-10 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
cytometric bead array assay of epitope specific IP-10 production by T cells
A cytometric bead array assay that measures epitope specific IP-10 production by T cells
IP-10 release by cytometric bead array
Listeria monocytogenes
Listeria monocytogenes
CD4-/CD8- T cell culture
CD4-/CD8- T cell culture
IEDB
IEDB
A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface.
PERSON: James Malone
dimensionality reduction
Melanie Courtot
data projection
PERSON: Melanie Courtot
dimensionality reduction
Elisabetta Manduchi
A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m.
PERSON: Elisabetta Manduchi
Philippe Rocca-Serra
James Malone
Rickettsieae
Rickettsieae
A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY??
microplate washer
PERSON: Erik Segerdell
http://www.articlesnatch.com/Article/Microplate-Readers-And-Washers-For-Laboratories/948037
microplate washer
platelet activating factor production
The synthesis or release of platelet activating factor following a stimulus, resulting in an increase in its intracellular or extracellular levels.
platelet activating factor production
IL-12 release by ELISA
A T cell epitope specific cytokine production assay that measures production of IL-12 by T cells utilizing the ELISA methodology.
IEDB
T cell epitope ELISA IL-12 assay
IEDB
T cell epitope ELISA IL-12 assay
genetic population background information
genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information
Group: OBI group
proposed and discussed on San Diego OBI workshop, March 2011
Group: OBI group
genetic population background information
a genetic characteristics information which is a part of genotype information that identifies the population of organisms
frozen
A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point.
frozen
Acanthopterygii
Acanthopterygii
Dicondylia
Dicondylia
Pseudomonas fluorescens group
Pseudomonas fluorescens group
Pasteurella
Pasteurella
normalized data set
PERSON: James Malone
PERSON: Melanie Courtot
normalized data set
A data set that is produced as the output of a normalization data transformation.
IEDB
intracellular cytokine staining assay
intracellular cytokine staining (ICS)
intracellular cytokine staining assay
IEDB
ICCS
ICS
The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
Permeabilizing T cells and staining them with fluorescent labeled anti-IFN-gamma antibodies
self-organizing map
SOM
A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these.
self-organizing map
James Malone
Ryan Brinkman
PERSON: Ryan Brinkman
removing CD4+ cells from PBMCs using magnetic beads.
a process in which a population of cells with certain characteristics is isolated from a larger population
isolation of cell population
isolation of cell population
Person: Bjoern Peters
Frank Gibson
Daniel Schober
http://en.wikipedia.org/wiki/Mechanical_work
mechanical function
Bill Bug
mechanical function
Melanie Courtot
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force).
expectation maximization
EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function.
James Malone
PERSON: James Malone
expectation maximization
informing subject of study arm
09/28/2009 Alan Ruttenberg. This and the class informing-investigator-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of blinding pertaining to subjects (happens in single and double blinding) we say that that the study execution doesn't include any processes of this sort
A process in which the subject is made aware of which study arm they are participating in, for example whether they are receiving a placebo or a treatment with an investigational compound.
Person:Alan Ruttenberg
informing subject of study arm
rosids
rosids
Illumina Genome Analyzer II
Philippe Rocca-Serra
Illumina Corporation
Illumina
Illumina
Philippe Rocca-Serra
Illumina Genome Analyzer II
is a DNA sequence which is manufactured by Illumina (Solexa) corporation. it support sequencing of single or paired end clone libraries relying on sequencing by synthesis technology
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57.
Populus
Populus
Streptococcus mutans UA159
Streptococcus mutans UA159
Magnoliaceae
Magnoliaceae
Filobasidiales
Filobasidiales
Epsilonproteobacteria
Epsilonproteobacteria
A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government.
regulatory agency
WEB: en.wikipedia.org/wiki/Regulator
The US Environmental Protection Agency
GROUP: OBI Biomaterial Branch
regulatory agency
ribonuclease U2
A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof.
ribonuclease U2
GROUP:<http://msi-ontology.sourceforge.net>
A lubricant used in liquid chromatography that eases sample injector penetration.
injector lubricant
PERSON:Daniel Schober
injector lubricant
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01118
Elisabetta Manduchi
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
This type of transformation is typically used in flow cytometry.
s transformation
Ryan Brinkman
s transformation
Joseph Spliden
An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization.
IEDB
BrdU incorporation assay
wiki http://en.wikipedia.org/wiki/BrdU
BrdU incorporation
The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU.
A BrdU incorporation assay is an assay to detect actively replicating cells. BrdU is incorporated into the newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication. Antibodies specific for BrdU can then be used to detect the incorporated chemical, thus indicating cells that were actively replicating their DNA.
BrdU incorporation assay
The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays
Sysmex CA-6000 Coagulation Analyzer
Sysmex CA-6000 Coagulation Analyzer
Person:Alan Ruttenberg
Sysmex Corporation, Kobe, Japan
Sysmex Corporation, Kobe, Japan
WEB:http://www.sysmex.com/@2009/08/06
web:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06
A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data.
PERSON: James Malone
James Malone
probabilistic algorithm
probabilistic algorithm
Methanosarcina mazei
Methanosarcina mazei
Roche
Philippe Rocca-Serra
Roche
454 Genome Sequencer FLX
adapted from https://www.roche-applied-science.com/servlet/RCProductDisplay?langId=-1&storeId=10202&productId=3.8.8.1.1.3&catalogId=10202&krypto=mgV8a0Sdps6%2BCXU8IoddmzNEyGgjde9j8MOFCiMzRsduELeenAlVZ%2FE1QR%2BxLpzNlqMZPLRHqaI%3D&ddkey=https:RCProductDisplay
454 Genome Sequencer FLX
Philippe Rocca-Serra
454 GS FLX
PMID: 18616967. The Genome Sequencer FLX System--longer reads, more applications, straight forward bioinformatics and more complete data sets. Droege M, Hill B.
J Biotechnol. 2008 Aug 31;136(1-2):3-10.
is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are
controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
GS-FLX
Vitaceae
Vitaceae
T cell epitope ELISA IL-17 assay
T cell epitope ELISA IL-17 assay
IEDB
A T cell epitope specific cytokine production assay that measures production of IL-17 by T cells utilizing the ELISA methodology.
IL-17 release by ELISA
IEDB
cytometric bead array assay of epitope specific interleukin-1 beta production by T cells
cytometric bead array assay of epitope specific interleukin-1 beta production by T cells
A cytometric bead array assay that measures epitope specific interleukin-1 beta production by T cells
IEDB (QTT)
IL-1b release by cytometric bead array
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Magnoliales
Magnoliales
Pseudomonas putida group
Pseudomonas putida group
Aspergillus terreus
Aspergillus terreus
Vitis
Vitis
Chloroflexaceae
Chloroflexaceae
PERSON: Melanie Courtot
James Malone
PERSON: James Malone
Melanie Courtot
PERSON: Elisabetta Manduchi
data visualization
PERSON: Tina Boussard
Tina Boussard
An planned process that creates images, diagrams or animations from the input data.
visualization
Generation of a heatmap from a microarray dataset
data encoding as image
Elisabetta Manduchi
data visualization
unblinding process
Person:Alan Ruttenberg
The part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials
unblinding process
PERSON:Daniel Schober
reversed phase column
GROUP:<http://msi-ontology.sourceforge.net>
reversed phase column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01106
A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column.
PERSON: James Malone
class prediction data transformation
class prediction data transformation
James Malone
supervised classification data transformation
A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction.
James Malone
dye swap merge
PERSON: James Malone
PERSON: Elisabetta Manduchi
Elisabetta Manduchi
A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met.
dye swap merge
mitosporic Filobasidiales
mitosporic Filobasidiales
IEDB
A T cell epitope specific cytokine production assay that measures production of IL-1b by T cells utilizing the ELISA methodology.
IEDB
T cell epitope ELISA IL-1b assay
IL-1b release by ELISA
T cell epitope ELISA IL-1b assay
An ELISA that measures epitope specific RANTES production by T cells
RANTES/CCL5 release by ELISA
ELISA of epitope specific RANTES production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
ELISA of epitope specific RANTES production by T cells
Ryan Brinkman
PERSON: Ryan Brinkman
SVM
support vector machine
A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space.
support vector machine
James Malone
global modularity calculation
A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network.
PERSON: Richard Scheuermann
Richard Scheuermann
global modularity calculation
Chloroflexus
Chloroflexus
error corrected data set
PERSON: James Malone
PERSON: Monnie McGee
error corrected data set
A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for).
subject agrees they understand informed consent document
09/28/2009 Alan Ruttenberg. There's a need for a general process like this in IAO - document and person in, signed document (and associated obligations, rights, out
A process in which a subject receives an informed consent document and agrees that they have understood it
Person:Alan Ruttenberg
subject agrees they understand informed consent document
Anura
Anura
Ralstonia syzygii
Ralstonia syzygii
Ferroplasma
Ferroplasma
nuclease S1
A protein that is a translation product of the Aspergillus oryzae nucS gene or a 1:1 ortholog thereof.
nuclease S1
tandem mass spectrometer
A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge.
PERSON: Erik Segerdell
http://goldbook.iupac.org/T06250.html
tandem mass spectrometer
Sylvia
Sylvia
EFO_0002764 ChIP-chip by SNP array
An assay where chromatin immunoprecipitation (ChIP) is used in combination with SNP microarray technology
ChIP-chip by SNP array assay
ChIP-chip by SNP array assay
Group: ArrayExpress production team
Philippe Rocca-Serra
is a DNA sequencing which allows sequence identification by relying on the following steps:
1. Primers hybridize to the P1 adapter sequence within the library template.
2. A set of four fluorescently labeled di-base probes compete for ligation to the sequencing primer. Specificity of the di-base probe is achieved by interrogating every 1st and 2nd base in each ligation reaction.
3. Multiple cycles of ligation, detection and cleavage are performed with the number of cycles determining the eventual read length.
4. Following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles
SOLiD sequencing
PMID: 19119315. High-resolution analysis of the 5'-end transcriptome using a next generation DNA sequencer. Hashimoto S, Qu W, Ahsan B, Ogoshi K, Sasaki A, Nakatani Y, Lee Y, Ogawa M, Ametani A, Suzuki Y, Sugano S, Lee CC, Nutter RC, Morishita S, Matsushima K. PLoS One. 2009;4(1):e4108.
adapted from Wikipedia and Applied Biosystems web site
SOLiD sequencing
A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.\n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss.
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400185
NMR magnet
NMR magnet
GROUP:<http://msi-ontology.sourceforge.net>
Methanosarcinaceae
Methanosarcinaceae
PERSON: Helen Parkinson
Helen Parkinson
Elisabetta Manduchi
replicate analysis
Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data.
replicate analysis
A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc.
PERSON:Elisabetta Manduchi
PERSON: Elisabetta Manduchi
similarity calculation
A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are.
Elisabetta Manduchi
similarity calculation
Chloroflexus aurantiacus
Chloroflexus aurantiacus
Salmonidae
Salmonidae
species comparison design
Person: Chris Stoeckert, Jie Zheng
MO_675 species_design
A study design that assays differences between distinct species.
species comparison design
cellular quality
A monadic quality of continuant that exists at the cellular level of organisation.
cellular quality
ELISA
Enzyme-Linked ImmunoSorbent Assay
ELISA is an assay where an enzyme linked antibody is used to detect a plate bound material in a liquid (the evaluant) utilizing a chemiluminescent reaction. The detected signal is proxy for the concentration of an analyte in the evaluant.
ELISA
IEDB
It is possible to add further restrictions, such as utilizing a plate as part of the assay.
IEDB
ELISA
1) Detection of IL-2 (analyte) in a cell supernatant (evaluant), using plate bound anti IL-2 antibodies, and a reporter enzyme linked reporter antibody. 2) Measurement of IgG antibody (analyte) titer in a serum sample (evaluant) using plate bound antigen and a reporter anti-IgG antibody.
Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material
recombinant BAC cloning
http://en.wikipedia.org/wiki/Bacterial_artificial_chromosome
recombinant BAC cloning
microhardness tester
microhardness tester
United States Patent 4611487
PERSON: Erik Segerdell
A hardness testing device that is used in light-optical microscopes.
cell culture analyte detection bioassay of epitope specific interleukin-10 production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A cell culture analyte detection bioassay that measures epitope specific interleukin-10 production by T cells
cell culture analyte detection bioassay of epitope specific interleukin-10 production by T cells
IL-10 release by bioassay
NMR probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400014
NMR probe
PERSON:Daniel Schober
Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.\n alt The instrument that transmits and receives radiofrequency to and from the NMR sample.
GROUP:<http://msi-ontology.sourceforge.net>
decision tree building data transformation
James Malone
A decision tree building data transformation is a data transformation that has objective decision tree induction.
PERSON: James Malone
decision tree building data transformation
IEDB
T cell epitope ELISA IL-18 assay
T cell epitope ELISA IL-18 assay
IL-18 release by ELISA
A T cell epitope specific cytokine production assay that measures production of IL-18 by T cells utilizing the ELISA methodology.
IEDB
Helen Parkinson
moving average
Philippe Rocca-Serra
PERSON: Helen Parkinson
Elisabetta Manduchi
A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set.
PERSON: Elisabetta Manduchi
moving average
The moving average is often used to handle data from tiling arrays.
A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind.
PERSON:Daniel Schober
chromatofocusing column
chromatofocusing column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01209
WEB:<http://www.bioprocessintl.com/default.asp?page=glossary&TopicID=1>
Oncorhynchus
Oncorhynchus
euclidean distance calculation
An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
euclidean distance calculation
background corrected data set
PERSON: James Malone
PERSON: Melanie Courtot
background corrected data set
A data set that is produced as the output of a background correction data transformation.
Salicaceae
Salicaceae
Paxillus filamentosus
Paxillus filamentosus
James Malone
decision tree induction objective
A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made.
decision tree induction objective
Archosauria
Archosauria
Bruker AMX series NMR instrument
A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe.
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400240
WEB:<http://www.tufts.edu/med/biochemistry/NMR/amx500.html>
Bruker AMX series NMR instrument
Methanosarcina barkeri
Methanosarcina barkeri
pearson correlation coefficient calculation
A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
WEB: http://en.wikipedia.org/wiki/Correlation
pearson correlation coefficient calculation
Vitis vinifera
Vitis vinifera
mhc binding prediction
PERSON: Helen Parkinson
mhc binding prediction
Helen Parkinson
An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule.
Ellipura
Ellipura
diploid
A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father.
diploid
Bos
Bos
Mycoplasmatales
Mycoplasmatales
adapted from Wikipedia (http://en.wikipedia.org/wiki/Edman_degradation)
Edman degradation
PMID 4773306. Niall HD (1973). "Automated Edman degradation: the protein sequenator". Meth. Enzymol. 27: 942-1010
is a process which produces a sequence from an input peptide or protein. In this process, the amino-terminal (N-terminal) residue is labeled and cleaved from the peptide without disrupting the peptide bonds between other amino acid residues.
Edman degradation
DISCOVERY console
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400247
DISCOVERY console
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network.
Methanosarcina
Methanosarcina
A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope.
PERSON: Helen Parkinson
Helen Parkinson
b cell epitope prediction
b cell epitope prediction
ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101.
Monnie McGee
loess fitting
A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda).
Philippe Rocca-Serra
loess fitting
Cricetidae
Cricetidae
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cell culture analyte detection bioassay of epitope specific interleukin-16 production by T cells
A cell culture analyte detection bioassay that measures epitope specific interleukin-16 production by T cells
IL-16 release by bioassay
cell culture analyte detection bioassay of epitope specific interleukin-16 production by T cells
IEDB (QTT)
Leymus triticoides
Leymus triticoides
power supply
electricity supply function
the function of supplying current during a neuroscience experiment.
Melanie Courtot
Frank Gibson
Daniel Schober
electricity supply function
An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment.
GROUP: PSI
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
ALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
PMID:6110205. collection of cDNA derived from mouse splenocytes.
cDNA library
cDNA library
PERSON: Luisa Montecchi
PERSON: Philippe Rocca-Serra
identification
Alan Ruttenberg 2010/11/22: After OBI call. A specific identification objective should be used instead, as necessary
Philippe Rocca-Serra
identification
DNA cleavage assay for the identification of topoisomerase I inhibitors.
Nat Protoc. 2008;3(11):1736-50. PMID: 18927559
a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval
Coelomata
Coelomata
photodetector
John Quinn
photodetector
http://einstein.stanford.edu/content/glossary/glossary.html
A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye.
A photomultiplier tube, a photo diode
WEB:<http://sangerhinxtongbr.library.ingentaconnect.com/content/els/00219673/1999/00000842/00000001/art00177>
Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01088
PERSON:Daniel Schober
ozone-induced chemiluminescence detector
ozone-induced chemiluminescence detector
Rubrobacteraceae
Rubrobacteraceae
RNA ontology
a single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
PMID:2422386 and PMID:2446263
CMCT structure mapping assay
Person: Philippe Rocca-Serra
CMCT structure mapping assay
single nucleotide resolution mapping assay using CMCT probe
interleukin-22 production
The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-22 production
An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects.
radiography instrument
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Medical_radiography
radiography instrument
chemokine (C-X-C motif) ligand 9 production
The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-X-C motif) ligand 9 production
http://www.answers.com/topic/syringe, 2007-05-11
Person:John Quinn
syringe pump
NE-1000 Single Syringe Pump
Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates.
syringe pump
hepatocyte
The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated.
hepatocyte
T cell epitope ELISA TNF assay
IEDB
T cell epitope ELISA TNF assay
IEDB
TNFa release by ELISA
A T cell epitope specific cytokine production assay that measures production of TNF by T cells utilizing the ELISA methodology.
Leymus cinereus
Leymus cinereus
A transfer function is a function to displace a material from one location to another.
transfer function
Daniel Schober
transfer function
Bill Bug
Melanie Courtot
Frank Gibson
ELISA of epitope specific macrophage inflammatory protein-1 alpha production by T cells
ELISA of epitope specific macrophage inflammatory protein-1 alpha production by T cells
IEDB (QTT)
MIP-1a release by ELISA
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An ELISA that measures epitope specific macrophage inflammatory protein-1 alpha production by T cells
Protostomia
Protostomia
intra cellular electrophysiology recording
intra cellular electrophysiology recording
PERSON: Frank Gibson
PERSON: Frank Gibson
An intracellular electrophysiology recording is a process where the recording location of the electrode is intracellular
photodiode
A photodiode is a semiconductor photodetector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer.
Avalanche photodiode
John Quinn
http://cyto.mednet.ucla.edu/Protocols/flow.htm
photodiode
Jennifer Fostel
radiolabel role
radiolabel role
radiolabel
radiolabel role is a role which inheres in a material entity which is realized by the
process of radioactivity detection
Bruker NMR magnet
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400186
An NMR magnet that is manufactured by Bruker.
Bruker NMR magnet
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
A planned process that captures an image of an object.
image acquisition
PERSON: Jie Zheng
image acquisition
Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel
A device that is used to effect the transition of a substance into a glass.
vitrification apparatus
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Glass_transition
vitrification apparatus
Onygenales
Onygenales
IL-10 release by ELISA
IEDB
IEDB
T cell epitope ELISA IL-10 assay
A T cell epitope specific cytokine production assay that measures production of IL-10 by T cells utilizing the ELISA methodology.
T cell epitope ELISA IL-10 assay
interleukin-21 production
The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-21 production
aneuploid
A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes.
aneuploid
complete nutrient role
A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment.
complete nutrient
complete nutrient role
Person: Jennifer Fostel
Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm
a device or part of a device that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emitted or scattered by those particles.
DS: Is 'subsystem' necessary or is 'optical_system' enough. Not sure its graph position since an optical subsystem is not necessarily an instrument, but more likely part of one.
Person: Daniel Schober
optical subsystem
John Quinn
optical subsystem
optical subsystem of a cytometer
target of material addition role
target of material addition role
OBI
GROUP: Role Branch
target of material addition role is a role realized by an entity into which a material is added in a material addition process
From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role.
peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application.
Agaricales
Agaricales
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector.
trap column
trap column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01261
An assay that measures epitope specific interleukin-8 production by T cells
IEDB (QTT)
assay of epitope specific interleukin-8 production by T cells
assay of epitope specific interleukin-8 production by T cells
IL-8 release
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Callithrix
Callithrix
interleukin-20 production
The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-20 production
GM-CSF release by ELISA
T cell epitope ELISA GM-CSF assay
T cell epitope ELISA GM-CSF assay
IEDB
IEDB
A T cell epitope specific cytokine production assay that measures production of GM-CSF by T cells utilizing the ELISA methodology.
http://en.wikipedia.org/wiki/Freeze_drying
A device that is used to freeze dry material.
lyophilizer
PERSON: Erik Segerdell
lyophilizer
transforming growth factor-beta2 production
The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
transforming growth factor-beta2 production
Melanie Courtot
http://en.wikipedia.org/wiki/Ionization
The ion source in amass spectrometer
Daniel Schober
ionization function
An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
ionization function
Bill Bug
Frank Gibson
IEDB (QTT)
IL-2 release by cytometric bead array
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A cytometric bead array assay that measures epitope specific interleukin-2 production by T cells
cytometric bead array assay of epitope specific interleukin-2 production by T cells
cytometric bead array assay of epitope specific interleukin-2 production by T cells
Passeroidea
Passeroidea
tecmag NMR console
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400246
An NMR console manufactured by tecmac.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
tecmag NMR console
Pleuronichthys verticalis
Pleuronichthys verticalis
particle delivery vessel
FC 500 particle delivery vessel
John Quinn
Part of the fluidics subsystem. A particle delivery vessel is used to introduce either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
particle delivery vessel
epithelium
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina.
epithelium
mass measurement assay
mass measurement assay
The patients was weighed and mass was determined to be 47 kilograms
Helen Parkinson
a process to determine the mass of an evaluant
OBI
bromophenol blue
A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe.
bromophenol blue
crossover population role
crossover population role
a role realized when a participant serves as reference to itself
crossover population
Person: Jennifer Fostel
WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/accessory/auto_samplers/vast/index&cid=HFIH>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400131
An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes.
flow probe
flow probe
PERSON:Daniel Schober
Cryptococcus [NCBITaxon:107441]
Cryptococcus [NCBITaxon:107441]
Person: Jie Zheng
A RNA extraction process in which the desired output material is RNA in the organelle(s).
organellar RNA extraction
Person: Chris Stoeckert
organellar RNA extraction
UPenn Group
Callitrichinae
Callitrichinae
A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific chemokine (C-C motif) ligand 1 production by T cells
IEDB (QTT)
epitope specific chemokine (C-C motif) ligand 1 production by T cells
RNASE CL3 structure mapping assay
PMID:16453415
RNASE CL3 structure mapping assay
a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse CL3 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
single nucleotide resolution mapping assay using RNAse CL3
Person:Philippe Rocca-Serra
RNA ontology
Noctuinae
Noctuinae
interleukin-2 production
The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-2 production
transforming growth factor-beta3 production
The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
transforming growth factor-beta3 production
IEDB
T cell epitope ELISA IL-6 assay
A T cell epitope specific cytokine production assay that measures production of IL-6 by T cells utilizing the ELISA methodology.
IEDB
T cell epitope ELISA IL-6 assay
IL-6 release by ELISA
PERSON: Erik Segerdell
radiation measurement device
radiation measurement device
PERSON: Erik Segerdell
A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector.
MC: should be imported
heart
Person:Bjoern Peters
http://en.wikipedia.org/wiki/Heart
unused class. decided to be deprecated on Aug 2, 2010 dev call. Will be imported when need.
The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions
obsolete_heart
Alan Ruttenberg's heart
Bill Bug
Daniel Schober
An electricity cable
Frank Gibson
A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another.
connection function
Melanie Courtot
connection function
Clostridium botulinum
Clostridium botulinum
Pipidae
Pipidae
PERSON: Alan Ruttenberg
PERSON: Chris Stoeckert
controlled variable specification
PERSON: Bjoern Peters
controlled variable specification
2/2/2009 Original definition: Controlled variables are also important to identify in experiments. They are the variables that are kept constant to prevent their influence on the effect of the independent variable on the dependent. Every experiment has a controlling variable, and it is necessary to not change it, or the results of the experiment won't be valid
WEB: http://en.wikipedia.org/wiki/Control_variable
Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent.
Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information
genotype information
discussed on San Diego OBI workshop, March 2011
a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc.
Group: OBI group
Group: OBI group
genotype information
Moraxellaceae
Moraxellaceae
Salmonella typhi
Salmonella typhi
PERSON: Erik Segerdell
gel imaging system
A device that is used to acquire images of laboratory gels.
PERSON: Erik Segerdell
gel imaging system
IL-13 release by ELISA
IEDB
T cell epitope ELISA IL-13 assay
IEDB
T cell epitope ELISA IL-13 assay
A T cell epitope specific cytokine production assay that measures production of IL-13 by T cells utilizing the ELISA methodology.
Faraday cage
Wikipedia http://en.wikipedia.org/wiki/Faraday_cage
Faraday cage
PERSON:Bjoern Peters
A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields.
Faraday shield
helper T cell enhancement of adaptive immune response
Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell.
helper T cell enhancement of adaptive immune response
interleukin-19 production
The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-19 production
IEDB (QTT)
cell culture analyte detection bioassay of epitope specific interleukin-2 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cell culture analyte detection bioassay of epitope specific interleukin-2 production by T cells
A cell culture analyte detection bioassay that measures epitope specific interleukin-2 production by T cells
IL-2 release by bioassay
DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input
The use of taq polymerase to amplify a DNA fragment during a PCR.
PERSON:Kevin Clancy
Philippe Rocca-Serra
OBI branch derived
DNA polymerase amplification
DNA polymerase amplification
Person: Jie Zheng
polyA RNA extraction
Person: Chris Stoeckert
UPenn Group
A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA.
polyA RNA extraction
A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted.
organellar RNA extract
organellar RNA extract
PERSON: Chris Stoeckert
UPenn Group
PERSON: Jie Zheng
Extraction of organellar RNA from plant cells using organellar RNA binding protein.
Pan
Pan
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material.
Frank Gibson
cool function
cool function
Daniel Schober
Melanie Courtot
analyte assay
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum
and
('has measurement unit label' some 'measurement unit label') and
('is quality measurement of' some 'molecular concentration'))
An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant.
PERSON:Bjoern Peters
PERSON:Helen Parkinson
PERSON:Philippe Rocca-Serra
PERSON:Alan Ruttenberg
GROUP:OBI Planned process branch
analyte assay
Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg
Xenopus
Xenopus
A study design that examines the stability and/or decay of RNA transcripts.
Person: Chris Stoeckert, Jie Zheng
RNA stability design
RNA stability design
MO_553 RNA_stability_design
Acinetobacter
Acinetobacter
patch clamp device
patch clamp device
A device used in electrophysiology that allows the study of single or multiple ion channels in cells.
http://en.wikipedia.org/wiki/Patch_clamp
PERSON: Erik Segerdell
interleukin-18 production
The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-18 production
transforming growth factor-beta1 production
The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
transforming growth factor-beta1 production
UPenn Group
agar stab storage
need to specify that agar is one of input for this process
PERSON: Chris Stoeckert
a storage process with input cell culture and agar and output agar stab for long time storage
PERSON: Jie Zheng
agar stab storage
vector mediated amplification
E coli expressing the gene for M avium p35 were cultured in order to produce p35.
OBI branch derived
The process of creating a copy of some biological entity in cell culture
PERSON:Kevin Clancy
vector mediated amplification
assay of epitope specific interleukin-22 production by T cells
An assay that measures epitope specific interleukin-22 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IL-22 release
IEDB (QTT)
assay of epitope specific interleukin-22 production by T cells
A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation
test substance role
Group:OBI
test substance role
fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally
Person:Alan Ruttenberg
region
primary structure of sequence macromolecule
sequence
A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids.
region
Oncorhynchus mykiss
Oncorhynchus mykiss
secondary structure of RNA molecule
2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO
PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA.
Person: Philippe Rocca-Serra
secondary structure of RNA molecule
Pongo
Pongo
primary structure of RNA molecule
Person:Bjoern Peters
The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together
primary structure of RNA molecule
investigation results report
group:OBI
An investigation report is a report on the results of an investigation.
investigation results report
person:Chris Stoeckert
intracellular cytokine staining assay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
intracellular cytokine staining assay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
IEDB (QTT)
An intracellular cytokine staining assay that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
GM-CSF release by ICS
helper T cell enhancement of B cell mediated immune response
Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell.
helper T cell enhancement of B cell mediated immune response
questionaire
Need to clarify if this is a document or a directive information entity (or what their connection is))
questionaire
Moniliformopses
Moniliformopses
Endopterygota
Endopterygota
interleukin-17 production
The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-17 production
cellular feature identification objective
Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.
Jennifer Fostel
cellular feature identification objective
multichannel electronic pipette
A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations.
PERSON: Erik Segerdell
http://www.faqs.org/patents/app/20090196797
multichannel electronic pipette
normalization testing design
A study design that tests different normalization procedures.
normalization testing design
Person: Chris Stoeckert, Jie Zheng
MO_729 normalization_testing_design
Rubrobacteridae
Rubrobacteridae
anticoagulant-containing test tube
Person:Alan Ruttenberg
A 'blue top' test tube that contains anticoagulant for storing blood specimens'
anticoagulant-containing test tube
RNA ontology
DEPC structure mapping assay
PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28.
is a single-nucleotide-resolution nucleic acid structure mapping assay which uses DEPC as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Person: Philippe Rocca-Serra
DEPC structure mapping assay
hospital
hospital
http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n
A medical organization at which sick or injured people are given clinical care
modified from the wording of the wordnet definition
Person:Helen Parkinson
human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660]
Person:Alan Ruttenberg
Pan troglodytes
Pan troglodytes
Frank Gibson
An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated.
isoelectric focusing unit
isoelectric focusing device
isoelectric focusing device
sep:00097
PPPB branch
is the specification of an objective to determine a specified type of information about an evaluated entity (independent continuant bearing evaluant role)
assay objective
PPPB branch
assay objective
the objective to determine the weight of a mouse.
PERSON: Erik Segerdell
protein separation apparatus
protein separation apparatus
A device that is used for the separation of proteins.
PERSON: Erik Segerdell
An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression.
EFO_0001030 RNAi profiling by array
RNAi profiling by array assay
PERSON: James Malone
RNAi profiling by array assay
helper T cell enhancement of T cell mediated immune response
Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell.
helper T cell enhancement of T cell mediated immune response
typhus group
typhus group
The Edinburgh Handedness Inventory is a set of questions used to assess the dominance of a person's right or left hand in everyday activities.
Edingburgh handedness inventory
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
PERSON:Jessica Turner
WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html
Edingburgh handedness inventory
PERSON:Alan Ruttenberg
Edinburgh handedness assay
Person:Alan Ruttenberg
Edinburgh handedness assay
PERSON:Jessica Turner
The Edinburgh Handedness assay is an assay in which a set of questions = the Edinburgh Handedness inventory - is asked and the answers to these questions are turned into a score, used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand.
WEB:http://en.wikipedia.org/wiki/Edinburgh_Handedness_Inventory
intracellular staining assay of epitope specific perforin production
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
perforin release by intracellular staining
intracellular staining assay of epitope specific perforin production
An intracellular staining assay that measures epitope specific perforin production
Rubrobacterales
Rubrobacterales
A device that is used to perform paraffin embedding of tissue specimens.
tissue embedding station
PERSON: Erik Segerdell
tissue embedding station
PERSON: Erik Segerdell
detector reagent role
19feb2009. not clear we need this term. originally if came from microarrays -- the probes on the array are termed detectors in some instances
One that detects, especially a mechanical, electrical, or chemical device that automatically identifies and records or registers a stimulus, such as an environmental change in pressure or temperature, an electric signal, or radiation from a radioactive material. http://www.answers.com/topic/detector 19feb2009
a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus.
detector reagent role
MO
heating block
heating block
An instrument used to heat and/or maintain material at a set temperature.
Daniel Schober
A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay
Ustilaginales
Ustilaginales
The use of NMR Spectroscopy to determine the 3D-Structure of the binding of an epitope to an MHC molecule
PERSON:Kevin Clancy
structure determination assay
OBI branch derived
structure determination assay
a process that resulting in information on the 3-dimensional qualities of a biomaterial
self reported handedness assessment
An assay in which a person makes a statement that indicates what handedness he has from a choice of different categories.
self reported handedness assessment
assay of epitope specific interleukin-27 production by T cells
IEDB (QTT)
assay of epitope specific interleukin-27 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An assay that measures epitope specific interleukin-27 production by T cells
IL-27 release
Fagales
Fagales
cell lysis
cell lysis
BP, JG, RV: There is also a need for the unplanned cell lysis, which is probably not in the scope of OBI, but should be linked to from this process.
PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41.
adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis]
cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock.
Philippe Rocca-Serra
Ditrysia
Ditrysia
Heteroderinae
Heteroderinae
Oliver He
adapted from wikipedia
http://en.wikipedia.org/wiki/Survival_rate
survival rate
A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring.
survival rate
protein extract
protein extract
a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation,
OBI & wikipedia
PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE.
J Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23.
Person: Philippe Rocca-Serra
exclusion rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
PRS
an exclusion rule (criterion) is_a *eligibility rule* prospective subjects should not meet to be eligible for participation in a study
exclusion rule
PERSON: Erik Segerdell
An device that is used to determine the order of nucleotides in nucleic acid sequences.
nucleic acid sequencer
PERSON: Erik Segerdell
nucleic acid sequencer
http://en.wikipedia.org/wiki/Computer
Melanie Courtot
Trish Whetzel
computer
A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
computer
Apple PowerBook, Dell OptiPlex
Ustilaginaceae
Ustilaginaceae
obsolete_handedness
obsolete_handedness
lavage
OBI branch derived
lavage
This is not washing, in which case the material of interest is not the resulting fluid
PlanAndPlannedProcess Branch
the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
comparative genome hybridization by array design
A study design that detects genomic copy number variations using microarray technology.
comparative genome hybridization by array design
Person: Chris Stoeckert, Jie Zheng
MO_856 comparative_genome_hybridization_design
phosphorus-32
The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days.
phosphorus-32
electrocution
electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process.
OBI branch
PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376.
Philippe Rocca-Serra
electrocution
electrode puller
A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube.
electrode puller
http://faculty.plattsburgh.edu/donald.slish/Puller1.html
PERSON:Bjoern Peters
total RNA extract
Extraction of total RNA from cells with Qiagen mini RNeasy kit.
UPenn Group
PERSON: Jie Zheng
total RNA extract
PERSON: Chris Stoeckert
A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen.
Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
A protein that is a translation product of the ligA gene or a 1:1 ortholog thereof.
DNA ligase
DNA ligase
ligase
http://en.wikipedia.org/wiki/Scanning_probe_microscopy
PERSON: Erik Segerdell
A microscope that forms images of surfaces using a physical probe that scans the specimen.
scanning force microscope
scanning force microscope
has_output should be sequence of input; we don't have sequence well defined yet
the use of a chemical or biochemical means to infer the sequence of a biomaterial
sequencing assay
sequencing assay
PlanAndPlannedProcess Branch
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
OBI branch derived
quartz cuvette flow chamber
A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells.
CVF-Q-10 flow chamber, CV-Q-10 flow chamber
John Quinn
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
quartz cuvette flow chamber
Trish Whetzel
Melanie Courtot
http://en.wikipedia.org/wiki/Centrifuge
A device with a rapidly rotating container that applies centrifugal force to its contents
Person: Jennifer Fostel
centrifuge
centrifuge
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
inclusion rule
PMID: 17599746-RESULTS: Fifteen trials met our inclusion criteria. The summary effect size was 0.35 (95% confidence interval 0.14, 0.56). I(2) was 0.80.
inclusion rule
an inclusion rule (criterion) is_ rule* in a protocol that prospective subjects must meet to be eligible for participation in a study
PRS
assay of epitope specific IP-10 production by T cells
An assay that measures epitope specific IP-10 production by T cells
IP-10 release
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
assay of epitope specific IP-10 production by T cells
Sordariomycetes
Sordariomycetes
Pinus radiata
Pinus radiata
Tylenchoidea
Tylenchoidea
Festuca arundinacea
Festuca arundinacea
Caulobacter
Caulobacter
Southern blot analysis
Southern blot analysis
Southern blot analysis is a an assay used in molecular biology to assert the presence/absence status of a specific DNA sequence in DNA samples. DNA samples to be assayed are first digested by restriction enzymes, fragments are then resolved by gel electrophoresis following by a blotting ensuring transfer to nitrocellulose or nylon membrane. Immobilization of DNA fragments to the membrane is achieved by UV crosslinking and/or baking. Probes raised against the specific sequences are then hybridized to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager.
PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerström G, Nordenskjöld M, Bergerheim US. Hum Mutat. 1998;Suppl 1:S31-3.
Person: Philippe Rocca-Serra
2010-01-31: Philippe Rocca-Serra:
departure from naming convention as the assay is named after Edwin Southern.
OBI & Wikipedia
Southern blot
2010-01-31: Philippe Rocca-Serra:
need extra work on 'labeled probe'
tiling microarray
EFO_0002704: tiling array
Person: Helen Parkinson
a DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions.
genome tiling array
tiling microarray
phosphorus-33
The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2.
phosphorus-33
Felinae
Felinae
Bombycoidea
Bombycoidea
negative reference substance role
a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a "no effect" response
negative reference substance role
Person: Jennifer Fostel
negative reference substance
Saline solution
Philippe Rocca-Serra
PRS:21102008: Input must be restricted to Vertebrates (requires import from NCBI tax)
OBI branch
cervical dislocation is a process by which a Vertebrate organism has its life terminated by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion
cervical dislocation
cervical dislocation
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-3
Person:Alan Ruttenberg
PMID:19696660#The antithrombin-III (AT-III) was determined using a Berichrom(r) Antithrombin-III (A) kit.
human antithrombin-III (AT-III) in blood assay
WEB:http://www.muschealth.com/lab/content.aspx?id=150006@2009/08/06
human antithrombin-III (AT-III) in blood assay
An assay to measure the amount of antithrombin III in blood.
subcutaneous injection
subcutaneous injection
is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe
PERSON: Melanie Courtot
chromatography
Jay/Bjoern think this is problematic. There are so many different types of chromatography. This term may be overloaded. May be best to define each type separately underneath material_separation. Also, example seems to be an assay.
the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity
OBI branch derived
The use of gas chromatography in order to identify the presence of pesticides in a sample of eggs
PERSON:Kevin Clancy
chromatography
a device which deposits biological material onto a substrate in a defined pattern.
MO_697 arrayer
arrayer
Trish Whetzel
BioRobotics Microgrid II TAS, Affymetrix GMS 417
arrayer
eligibility rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
PRS
an eligibility rule (criterion) is_a *rule* which defines the positive and negative criteria decide an entity to enter a study and that will define the population of the study
eligibility rule
pulsed-field gel electrophoresis system
A gel electrophoresis system that is used to separate very large molecules of DNA.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Pulsed_field_gel_electrophoresis
pulsed-field gel electrophoresis system
Sordariomycetes incertae sedis
Sordariomycetes incertae sedis
Reflection
A Reflection is a sorter manufactured by iCyte. It uses digital signal processing, and can be configured with lasers of the users choice from among these excitation wavelengths: 355, 405,488, 532, 635nm. It accommodates up to 48 traditional PMTs. Options include an acousto-optical tunable filter (AOTF) and 16 channel spectrometer (370 to 730 nm). The various detection components can be uniquely configured across multiple Highly Automated Parallel Sorting (HAPS) modules. The Reflection can be used to analyse, sort, and collect cells.
John Quinn
Reflection
Reflection at TSRI Flow Cytometry Core Facility
http://www.i-cyt.com/reflection.htm
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
intracellular cytokine staining assay of epitope specific interleukin-13 production by T cells
intracellular cytokine staining assay of epitope specific interleukin-13 production by T cells
IL-13 release by ICS
An intracellular cytokine staining assay that measures epitope specific interleukin-13 production by T cells
IEDB (QTT)
in vivo design
in vivo design
Person: Chris Stoeckert, Jie Zheng
MO_454 in_vivo_design
A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model.
5-bromo-2-deoxyuridine
5-bromo-2-deoxyuridine
Festuca
Festuca
Tylenchina
Tylenchina
GROUP: OBI
whole mount tissue
whole mount sample
whole mount tissue
PERSON: Philippe Rocca-Serra
PERSON: Helen Parkinson
A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide
Person:Helen Parkinson
Parent of minor patient; Definition of legally acceptable representative
An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE
role of legally acceptable representative
Person: Jennifer Fostel
role of legally acceptable representative
OBI, CDISC
legally acceptable representative. An individual or juridical or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject's participation in the clinical trial. [ICH, E6 Glossary]
legally acceptable representative
a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial.
asphyxiation
asphyxiation
asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms.
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
OBI branch
Philippe Rocca-Serra
placebo role
a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance
placebo
placebo role
Person:Jennifer Fostel
Pill consisting of inert materials
WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction
Q-PCR
real time polymerase chain reaction assay
A laboratory technique based on the PCR, which is used to
amplify and simultaneously quantify a specific DNA
molecule based on the use of complementary probes/primers. It enables
both detection and quantification (as absolute number of copies or relative
amount when normalized to DNA input or additional normalizing genes) of one
or more specific sequences in a DNA sample.
quantitative real time polymerase chain reaction
person: Bjoern Peters
real time polymerase chain reaction assay
person: Melanie Courtot
kinetic polymerase chain reaction
qPCR
A specimen that has been intentionally physically modified.
Bjoern Peters
processed specimen
processed specimen
Bjoern Peters
fluorescently labeled MHC multimer
A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand
fluorescently labeled MHC multimer
Magnaporthe grisea
Magnaporthe grisea
GenePix 4200A, GenePix4000B
array scanner
Trish Whetzel
array scanner
GROUP: MGED Ontology
An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip
organ harvesting
organ harvesting
IEDB
IEDB
The process of removing an organ from its source organism
http://www.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf
plate loader
plate loader
measurement function is not corret as discussed on April 26 dev call. Will add new function such as positioning function. Add to tracker will discuss in the future.
Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications.
FC 500 plate loader
John Quinn
Mycoplasma pneumoniae
Mycoplasma pneumoniae
RNA extraction
A RNA extraction is a nucleic acid extraction where the desired output material is RNA
OBI branch derived
PlanAndPlannedProcess Branch
RNA extraction
concentrate
Evaporation of the solution containing DNA to increase the concentration of the DNA molecules
PERSON:Kevin Clancy
a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material
concentrate
OBI branch derived
gas filter function
Frank Gibson
A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture
gas filter function
PERSON: Bjoern Peters
a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it
PERSON: Philippe Rocca-Serra
GROUP:IEDB
transgenic organism
transgenic organism
PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application
HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein
Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162
polymerization
PRS:22102008: need to import catalyst from CHEBI 35223
Philippe Rocca-Serra
polymerization
polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight
PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3.
OBI-Branch
Rhodobacteraceae
Rhodobacteraceae
Trish Whetzel
DNA sequencer
DNA sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
MO
CD3+ T cell culture
A T cell population characterized by expressing the CD3 molecule on its surface.
CD3+ T cell culture
IEDB
IEDB
Tetrapoda
Tetrapoda
interleukin-25 production
The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-25 production
preamplifier
A preamplifier is part of the electronics subsystem. It converts the current output from its associated detector to a voltage. The preamplifier is the first stage in analog electronics signal processing.
Built in preamplifier in a Hamamatsu H9656 PMT
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
preamplifier
PlanAndPlannedProcess Branch
OBI branch derived
nucleic acid extraction
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
a material separation to recover the nucleic acid fraction of an input material
nucleic acid extraction
Lotus japonicus
Lotus japonicus
Metazoa
Metazoa
This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription
synthesize
synthesis
synthesis
making cDNA from nucleotides using RNA as a template
OBI branch derived
the construction of a biomaterial from simpler biomaterials
PERSON:Kevin Clancy
PERSON: Jennifer Fostel
A planned process which results in physical changes in a specified input material
material transformation
PERSON: Bjoern Peters
PERSON: Philippe Rocca Serra
PERSON: Frank Gibson
material processing
OBI branch derived
A cell lysis, production of a cloning vector, creating a buffer.
PERSON: Melanie Courtot
material processing
Pleuronichthys
Pleuronichthys
Callithrix jacchus
Callithrix jacchus
Brachycera
Brachycera
electronic case report form
CDISC glossary
An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11.
person:Jennifer Fostel
electronic case report form
((1.053096, -0.22476), (-0.24877, 1.053096))
person:Chris Stoeckert
A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix.
fluorescence compensation matrix
group:Flow Cytometry community
fluorescence compensation matrix
Note that cell proliferation assays can often be a part of another assay. For example, to detect an analyte with a cell culture bioassay.
cell proliferation assay
An assay which measures the rate of proliferation of input cells
Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation.
PERSON:Bjoern Peters
cell proliferation assay
An assay that measures epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
IEDB (QTT)
chemokine (C-X-C motif) ligand 9 (MIG) release
assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
assay of epitope specific chemokine (C-X-C motif) ligand 9 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Chloroflexi
Chloroflexi
trypsination
OBI PA
Philippe Rocca-Serra
trypsination
The use of mild trypsinization conditions in the detachment of endothelial cells to promote subsequent endothelialization on synthetic surfaces. Biomaterials. 2007 Sep;28(27):3928-35. PMID: 17570483
trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity
CD3- T cell culture
A T cell population characterized by not expressing the CD3 molecule on its surface.
CD3- T cell culture
IEDB
IEDB
waste tank
waste tank
Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
LSR2 waste tank
Person:John Quinn
vibrotome
vibrotome
A preparation device that uses a vibrating razor blade to cut
through tissue.
Ustilago
Ustilago
bead array reader
A device that is used to acquire and image bead array data.
bead array reader
PERSON: Erik Segerdell
PERSON: Erik Segerdell
Amniota
Amniota
interleukin-24 production
The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-24 production
http://cyto.mednet.ucla.edu/Protocols/flow.htm
John Quinn
photomultiplier tube
photomultiplier tube
R9647 by manufactured by Hamamatsu
A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and fluorescent parameters. Cytometers have a PMT for each color they can collect.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01218
packed column
WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
packed column
PERSON:Daniel Schober
A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube.
Paracoccidioides
Paracoccidioides
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
patient
a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider
GROUP:Role Branch
OBI, CDISC
patient role
patient role
A digital entity intended to capture data in analytical cytology domain.
FCS file, ACS file, foo.fcs, foo.asc
group:Flow Cytometry community
analytical cytology data file
analytical cytology data file
person:Chris Stoeckert
OBI branch derived
genetic transformation
genetic modification
genetic transformation
the introduction. alteration or integration of genetic material into a cell or organism
PERSON:Kevin Clancy
The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35
OBI-Branch
enzymatic ligation
An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity
Philippe Rocca-Serra
PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202.
enzymatic ligation
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An assay that measures epitope specific macrophage inflammatory protein-1 gamma production by T cells
assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells
assay of epitope specific macrophage inflammatory protein-1 gamma production by T cells
IEDB (QTT)
MIP-1g release
Betula
Betula
http://en.wiktionary.org/wiki/amplifier
Linear amplifier, log amplifier, microwave amplifier
Frank Gibson
voltage amplifier
A voltage amplifier is a device that amplifies the voltage signal.
voltage amplifier
John Quinn
IEDB
allergy
IEDB
is a disease in which an abnormally strong inflammatory immune response is triggered against non-self entities, and the immune response has no protective effect
allergy
Theria
Theria
dendritic cell
A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation.
dendritic cell
interleukin-23 production
The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-23 production
CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional
certified IRB professional
a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA
Person:Jennifer Fostel
WEB: http://en.wikipedia.org/wiki/Certified_IRB_Professional
role of certified IRB professional
Person:Helen Parkinson
role of certified IRB professional
Oscillatoriales
Oscillatoriales
Mycoplasma pulmonis
Mycoplasma pulmonis
Apparatus in the fluidic subsystem of sorters that vibrates to break up the stream coming out of the flow chamber into droplets for sorting. The peizo electric crystal vibrates in a manner that breaks off droplets at regular intervals. Not all droplets contain a cell.
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
John Quinn
piezo electric crystal
quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar
piezo electric crystal
The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35.
PERSON:Kevin Clancy
recombinant plasmid cloning
the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial
recombinant plasmid cloning
OBI branch derived
A cytometric bead array assay that measures epitope specific interleukin-8 production by T cells
cytometric bead array assay of epitope specific interleukin-8 production by T cells
cytometric bead array assay of epitope specific interleukin-8 production by T cells
IL-8 release by cytometric bead array
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
OBI-Branch
Philippe Rocca-Serra
storage
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
storage is a process by which material entities are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
storage
liquid filter function
Frank Gibson
A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture
liquid filter function
proxy respondent role
proxy respondent
proxy respondent role
Jennifer Fostel
Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel
Betula pendula
Betula pendula
Fusobacterium
Fusobacterium
immune response
Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
immune response
PERSON: Chris Stoeckert
Polystyrene tubes can be used to contain tissue culture cells during centrifgation
polystyrene tube
polystyrene tube
PERSON: Chris Stoeckert
a polystyrene tube is a test tube made of polystyrene
enzymatic cleavage
enzymatic cleavage
PlanAndPlannedProcess Branch
enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme
OBI branch derived
Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828
Culicidae
Culicidae
Person: Elisabetta Manduchi
MO_720 lowess_normalization
A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria.
lowess transformation
lowess transformation
http://en.wikipedia.org/wiki/Diffractometer
diffractometer
PERSON: Erik Segerdell
diffractometer
A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it.
IEDB
epitope disposition
Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor.
disposition to be bound by an adaptive immune receptor
disposition to be bound by an adaptive immune receptor
IEDB
Herminiimonas arsenicoxydans
Herminiimonas arsenicoxydans
Lactobacillus salivarius
Lactobacillus salivarius
phylogenetic tree
Melanie Courtot
data representational model
data structure
Data representational model is an information content entity of the relationships between data items. A data representational model is encoded in a data format specification such as for cytoscape or biopax.
data representational model
data structure specification
gene regulatory graph model
protein interaction network
GROUP: OBI
Synechococcus elongatus
Synechococcus elongatus
Enterobacteriaceae
Enterobacteriaceae
Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB
phage display binding assay
Selecting phages from a commercial library that produce peptides binding to an antibody of interest, sequencing those peptides.
An assay in which a phage display library is panned to select phages that bind a molecule of interest, the phage encoded peptide/proteins are sequenced.
phage display binding assay
electrophoresis system
PERSON: Erik Segerdell
gel electrophoresis system
http://en.wikipedia.org/wiki/Category:Electrophoresis
gel electrophoresis system
A device that moves charged particles through a medium by using an electric field induced by electrodes.
Magnaporthe
Magnaporthe
PBMC cell culture
A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types).
PBMC cell culture
IEDB
IEDB
specimen creation
Bjoern Peters
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
a planned process with the objective of obtaining specimen.
specimen creation
Aedes aegypti
Aedes aegypti
Saccharomycotina
Saccharomycotina
Zymomonas mobilis
Zymomonas mobilis
reagent
GROUP: Role Branch
reagent role
www.answers.com/topic/reagent; November 2008
reagent role
a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances
Buffer, dye, a catalyst, a solvating agent.
cytokine production involved in inflammatory response
The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels.
cytokine production involved in inflammatory response
time series design
Groups of assays that are related as part of a time series.
MO_887
PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.
Philippe Rocca-Serra on behalf of MO
time series design
Culicinae
Culicinae
node quality calculation
PERSON: Richard Scheuermann
Richard Scheuermann
node quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network.
A specimen that derives from an anatomical part or substance arising from an organism. Examples of tissue specimen include tissue, organ, physiological system, blood, or body location (arm).
MO_954 organism_part
PERSON: Chris Stoeckert, Jie Zheng
tissue specimen
tissue specimen
A device that is used to fabricate glass micropipettes.
micropipette puller
micropipette puller
http://en.wikipedia.org/wiki/Micropipette
PERSON: Erik Segerdell
adherent cell culture
A mixed cell population that is characterized by its ability to bind to tissue culture flasks or plates. This population typically contains macrophages and other cells capable of playing the antigen presenting cell role.
adherent cell culture
IEDB
IEDB
Aedes
Aedes
hardware optimization objective
Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.
Jennifer Fostel
hardware optimization objective
Ralstonia
Ralstonia
Deinococcales
Deinococcales
Zymomonas
Zymomonas
Anophelinae
Anophelinae
mass spectrometry of eluted MHC ligands
The identification of ligands eluted from MHC molecules using mass spectrometry
IEDB
IEDB
mass spectrometry of eluted MHC ligands
Neosartorya
Neosartorya
microdissection instrument
http://medical-dictionary.thefreedictionary.com/microdissection
A device that is used for the dissection of tissues under magnification.
PERSON: Erik Segerdell
microdissection instrument
Moorella
Moorella
IEDB
T cell epitope protection from tumor challenge
An epitope protection experiment in which the ability of T cell epitope responses to protect the host from developing tumors is assessed.
T cell epitope protection from tumor challenge
tumor burden after challenge
PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
Bjoern Peters
Bjoern Peters
a material entity derived from a portion of blood collected from an organism
blood specimen
blood specimen
blood drawn from a human for glucose assay
Mycobacterium tuberculosis
Mycobacterium tuberculosis
lateral to
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity.
lateral to
Candida albicans
Candida albicans
IEDB
lymph node cell
lymph node cell
A mixed cell population obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types.
IEDB
PRS
a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen
PRS
stopping rule
stopping rule
PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy.
digital microscope
A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor.
PERSON: Erik Segerdell
digital microscope
http://en.wikipedia.org/wiki/Digital_microscope
Luminex 100
The Luminex 100 is a flow_cytometer_analyser manufactured by Luminex. It is a single laser system (575 nm) with avalanche photodiodes in red and infrared and a single PMT for fluorescence. The flow chamber is a square quartz cuvette.
http://www.luminexcorp.com/products/luminex_100IS.html
Luminex 100
John Quinn
response to stimulus
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
response to stimulus
Ectocarpus siliculosus
Ectocarpus siliculosus
regulator of chemical manufacture
OBI
Person: Jennifer Fostel
role of regulator of chemical manufacturer
role of regulator of chemical manufacturer
EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm
a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture
specimen with known storage state
A specimen for which it is known whether it has been subjected to storage of a specified type.
MO_95 BiosourceType
PERSON: Chris Stoeckert, Jie Zheng
specimen with known storage state
Gas chromatography mass spectrometry is a data transformation combining mass spectrometry and
gas chromatography for the qualitative as well as quantitative
determinations of compounds.
PERSON: Tina Boussard
PERSON: James Malone
gas chromatography mass spectrometry
gas chromatography mass spectrometry
PERSON: Tina Boussard
device setting
Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification
PERSON: Frank Gibson
a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device
device setting
Candida
Candida
compliance rule
PRS
PRS
a compliance rule is a rule which ensures a compliance process occurs
compliance rule
LSR2 at TSRI Flow Cytometry Core Facility
John Quinn
http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/live/web_enabled/SJ-0142-00LSR2.pdf
A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 fluorescent parameters. The LSR II is one of the most common sorters in use.
LSR2
LSR2
infectious disease
IEDB
is a disease caused by an infectious agent
IEDB
infectious disease
laser scanning confocal microscope
A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Confocal_laser_scanning_microscopy
laser scanning confocal microscope
Tandem mass spectrometry is a data transformation that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules).
PERSON: James Malone
tandem mass spectrometry
PERSON: Tina Boussard
PERSON: Tina Boussard
tandem mass spectrometry
A precursor ion is selected in the first stage, allowed to fragment and then all resultant masses are scanned in the second mass analyzer and detected in the detector that is positioned after the second mass analyzer. This experiment is commonly performed to identify transitions used for quantification by tandem MS.
PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB
An epitope protection from infectious challenge experiment in which T cell responses are induced and the readout is a reduction in the presence of pathogens in the host compared to controls.
T cell epitope protection from infectious challenge based on pathogen burden
pathogen burden after infectious challenge
T cell epitope protection from infectious challenge based on pathogen burden
standard compliance rule
PRS
PRS
a standard compliance rule is a compliance rule which defines conformity to a representation standard
standard compliance rule
http://www.answers.com/topic/micropipette
micropipette
micropipette
PERSON: Erik Segerdell
A microinjection device that is used to measure very small volumes of liquids.
Candida glabrata
Candida glabrata
Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm
Person:Helen Parkinson
the role of a human being that is realized by enforcing regulations to ensure consumer safety
role of being consumer safety officer
OBI, CDISC
Jennifer Fostel
role of being consumer safety officer
Person charged with serving as CSO, FDA official who coordinates the review
optical microscope
PERSON:Bjoern Peters
optical microscope
A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range
lowess group transformation
A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed.
MO_861 lowess_group_normalization
Person: Elisabetta Manduchi
lowess group transformation
spectrum analysis objective
Calculation of characteristic path length in mass spectrometry
PERSON: Tina Boussard
Person:Helen Parkinson
is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process.
spectrum analysis objective
data set of predicted values according to fitted curve
PERSON: James Malone
PERSON: Monnie McGee
data set of predicted values according to fitted curve
A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints.
freeze substitution system
doi:10.1017/S143192760707866X
freeze substitution system
PERSON: Erik Segerdell
A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins.
ethical standard compliance rule
PRS
PRS
an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur
ethical standard compliance rule
quality of a solid
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable.
quality of a solid
IEDB
A biological process where T cells produce TNF resulting from the recognition of a T cell epitope.
epitope specific TNF release by T cells
epitope specific TNF release by T cells
IEDB
Phodopus sungorus
Phodopus sungorus
IEDB
IEDB
T cell epitope chromium release assay
T cell epitope chromium release assay
Is a T cell epitope specific killing assay which utilizes radiolabeled chromium in order to measure T cell mediated lysis of antigen presenting cells that occurs in response to TCR on that T cell binding an epitope:MHC complex on the APC.
cytotoxicity by 51 chromium release
transcription profiling by tiling array assay
EFO_0002769 transcription profiling by tiling array
transcription profiling by tiling array assay
An assay in which the transcriptome of a biological sample is analysed using a tiling path array.
Person: James Malone
An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster.
average linkage hierarchical clustering
PERSON: Elisabetta Manduchi
Elisabetta Manduchi
average linkage hierarchical clustering
correlation study objective
A data transformation objective in which correlation is obtained (often measured as a correlation coefficient, ρ) which indicates the strength and direction of a relationship between two random variables.
PERSON: Tina Boussard
correlation study objective
is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors.
library construction
PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120.
library preparation
Philippe Rocca-Serra
library preparation
Vein
Subdivision of venous tree (organ) which consists of branching sets of tubes (venous trunks) that form a tree; together with other venous trees (organ part), it constitutes a venous tree (organ). Examples: subclavian venous tree, jugular tree, extrahepatic portal tree, common iliac venous tree.
Vein
Legionellales
Legionellales
Melanie Courtot
magnify function
Daniel Schober
magnify function
A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
Bill Bug
Frank Gibson
Monnie McGee
WEB: http://www.riskglossary.com/link/skewness.htm
A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment
skewness calculation
skewness calculation
Xenopus laevis
Xenopus laevis
urine specimen
are we happy calling collection of urine a material separation?
This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active
urine specimen
4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant.
a portion of urine collected from an organism
Salmonella typhimurium
Salmonella typhimurium
An IFN-g ELISPOT is an assay detecting ifn-gamma production
PERSON: Bjoern Peters
an assay that determines information about the production of the cytokine interferon gamma
IEDB
assay detecting IFN-gamma production
IFNg release
assay detecting IFN-gamma production
Lactococcus
Lactococcus
Bruker Efficient Sample Transfer NMR
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400206
Bruker BEST NMR system
PERSON:Daniel Schober
Bruker BEST NMR system
The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data.
WEB:<http://www.bruker-biospin.com/automation.html>
Eucoccidiorida
Eucoccidiorida
epigenetic modification identification objective
A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications.
Chris Stoeckert, Jie Zheng
Person: Chris Stoeckert
epigenetic modification identification objective
direct submission to IEDB
A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB)
IEDB
PERSON: Bjoern Peters
The report on "Identification of a dominant CD4 T cell epitope in the membrane lipoprotein Tul4 from Francisella tularensis LVS. " submitted by Valentino et al to the IEDB.
The content of that report on the IEDB website is here: http://iedb.org/refId/1013357
direct submission to IEDB
Phodopus
Phodopus
pathogen challenge
A pathogen challenge is the administration of a live pathogenic organism to a host
pathogen challenge
PERSON: James Malone
proportional hazards model estimation
Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system.
Cox model
PERSON: Tina Boussard
Cox proportional hazards model
WEB: http://en.wikipedia.org/wiki/Cox_proportional_hazards_model
proportional hazards model estimation
Acinetobacter baumannii
Acinetobacter baumannii
hierarchical clustering
James Malone
A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
hierarchical clustering
WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering
A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html
kurtosis calculation
kurtosis calculation
WEB: http://davidmlane.com/hyperstat/A53638.html
Monnie McGee
PERSON:Daniel Schober
GROUP:<http://msi-ontology.sourceforge.net>
chromatography detector filter
chromatography detector filter
An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01121
differential expression analysis data transformation
Melanie Courtot
A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
WEB:
Monnie McGee
James Malone
differential expression analysis data transformation
Sylviidae
Sylviidae
epitope specific killing by T cells
epitope specific killing by T cells
A biological process where T cells lyse antigen presenting cells resulting from the recognition of a T cell epitope on MHC molecules of the antigen presenting cell.
IEDB
IEDB
graph of vertices
graph of vertices
WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html
For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities.
James Malone
Bjoern Peters
Chris Stoeckert
A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific interleukin-21 production by T cells
assay of epitope specific interleukin-21 production by T cells
An assay that measures epitope specific interleukin-21 production by T cells
IEDB (QTT)
IL-21 release
obsolete_primary structure of sequence macromolecule
replaced by SO_0000001 region
These are all placeholders and should be replaced by SO terms
A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds
obsolete_primary structure of sequence macromolecule
Person:Bjoern Peters
2010-06-28 Alan Ruttenberg. This term and its children to be replaced by sequence ontology terms once we figure out what the right terms are .
T cell epitope specific immune intervention
An epitope specific immune intervention in which the induced response targets a T cell epitope
IEDB
Injecting a mouse with peptide SIINFEKL to induce a T cell response against the peptide
PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
T cell epitope specific immune intervention
Monnie McGee
PERSON: Monnie McGee
standard deviation calculation
standard deviation calculation
A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean.
A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori.
PERSON: James Malone
fuzzy clustering objective
PERSON: Ryan Brinkman
James Malone
fuzzy clustering objective
dual loop autosampler
WEB:<http://www.chem.agilent.com/scripts/pds.asp?lpage=17149>
A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate).
PERSON:Daniel Schober
dual loop autosampler
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01063
light emission function
Daniel Schober
Frank Gibson
Bill Bug
A light emission function is an excitation function to excite a material to a specific excitation state that it emits light.
Melanie Courtot
light emission function
survival analysis data transformation
A data transformation which has the objective of performing survival analysis.
James Malone
PERSON: James Malone
survival analysis data transformation
GenePattern software
GenePattern software
James Malone
Person:Helen Parkinson
WEB: http://www.broadinstitute.org/cancer/software/genepattern/
a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks.
Philippe Rocca-Serra
A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
k-means clustering
James Malone
Elisabetta Manduchi
k-means clustering
WEB: http://en.wikipedia.org/wiki/K-means
stramenopiles
stramenopiles
interleukin-26 production
The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-26 production
animal care protocol
An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes
Bjoern Peters
Bjoern Peters
Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
animal care protocol
ELISA of epitope specific interleukin-22 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
ELISA of epitope specific interleukin-22 production by T cells
An ELISA that measures epitope specific interleukin-22 production by T cells
IL-22 release by ELISA
James Malone
Monnie McGee
A data visualization which has input of a background corrected data set and produces an output of a report graph which is capable of rendering data of this type.
background corrected data visualization
background corrected data visualization
Trypanosoma cruzi
Trypanosoma cruzi
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IFNb release
IEDB (QTT)
assay of epitope specific interferon-beta production by T cells
assay of epitope specific interferon-beta production by T cells
An assay that measures epitope specific interferon-beta production by T cells
bp
material combination
material combination
Mixing two fluids. Adding salt into water. Injecting a mouse with PBS.
created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes.
bp
is a material processing with the objective to combine two or more material entities as input into a single material entity as output.
epitope specific interleukin-17F production by T cells
epitope specific interleukin-17F production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope.
interquartile-range calculation
PERSON: Monnie McGee
interquartile-range calculation
The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data.
Monnie McGee
Mesoplasma
Mesoplasma
DNA residue methylation
DNA residue methylation
a quality of a DNA residue that has a methyl group attached to it
modular decomposition
editor
modular decomposition
Tina Hernandez-Boussard
Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins.
record function
Bill Bug
record function
Daniel Schober
Melanie Courtot
A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation
Frank Gibson
Bruker 1mm MicroProbe
Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:\n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)\n excellent solvent suppression properties\n virtually no salt effect\n discrete samples in tubes that can be sealed and stored\n automation accessory for sample preparation and handling available.
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400194
Bruker 1mm MicroProbe
PERSON:Daniel Schober
GROUP:<http://msi-ontology.sourceforge.net>
Metatheria
Metatheria
Eremothecium gossypii
Eremothecium gossypii
ventral to
A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity.
ventral to
T cell epitope ELISA IL-5 assay
IEDB
T cell epitope ELISA IL-5 assay
A T cell epitope specific cytokine production assay that measures production of IL-5 by T cells utilizing the ELISA methodology.
IEDB
IL-5 release by ELISA
chromatin immunoprecipitation sequencing assay
an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
adapted from Wikipedia
PMID: 19275939
ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.
Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT.
Methods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9.
Philippe Rocca-Serra
ChIP-seq assay
ChIP-seq assay
binding detection assay
A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context.
PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
binding detection assay
Cypriniformes
Cypriniformes
A data visualization which has input of a classified data set and produces an output of a report graph which is capable of rendering data of this type.
James Malone
classified data visualization
classified data visualization
Hordeum
Hordeum
ELISA of epitope specific transforming growth factor-beta production by T cells
IEDB (QTT)
An ELISA that measures epitope specific transforming growth factor-beta production by T cells
ELISA of epitope specific transforming growth factor-beta production by T cells
TGFb release by ELISA
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Neopterygii
Neopterygii
IEDB
IEDB
A biological process where T cells produce IL-5 resulting from the recognition of a T cell epitope.
epitope specific IL-5 release by T cells
epitope specific IL-5 release by T cells
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01240
pulsed amperometric detector
pulsed amperometric detector
WEB:<http://adsabs.harvard.edu/abs/2004SPIE.5261..103L>
PERSON:Daniel Schober
A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC).
PAD
weighted network graph construction
A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph.
PERSON: Richard Scheuermann
Richard Scheuermann
weighted network graph construction
Bos indicus
Bos indicus
A T cell epitope specific cytokine production assay that measures production of IL-4 by T cells utilizing the ELISA methodology.
IEDB
IL-4 release by ELISA
T cell epitope ELISA IL-4 assay
T cell epitope ELISA IL-4 assay
IEDB
MPE-Fe(II) structure mapping assay
RNA ontology
a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses Fe-MP as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
single nucleotide resolution mapping assay using Fe-MP probe
MPE-Fe(II) structure mapping assay
PMID:6209709
Person: Philippe Rocca-Serra
Trypanosoma brucei
Trypanosoma brucei
Cyprinidae
Cyprinidae
HeliScope Single Molecule Sequencer
Helicos
Helicos
Philippe Rocca-Serra
HeliScope Single Molecule Sequencer
Philippe Rocca-Serra
is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry
James Malone
Adata visualization which has input of a gene list and produces an output of a report graph which is capable of rendering data of this type.
gene list visualization
gene list visualization
Hordeum vulgare
Hordeum vulgare
IEDB
epitope specific IL-6 release by T cells
A biological process where T cells produce IL-6 resulting from the recognition of a T cell epitope.
epitope specific IL-6 release by T cells
IEDB
IEDB (QTT)
An assay that measures epitope specific interleukin-5 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific interleukin-5 production by T cells
IL-5 release
assay of epitope specific interleukin-5 production by T cells
Pyrococcus horikoshii
Pyrococcus horikoshii
directed network graph construction
A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph.
PERSON: Richard Scheuermann
Richard Scheuermann
directed network graph construction
Enterococcus faecium
Enterococcus faecium
Plantaginaceae
Plantaginaceae
Pezizomycotina
Pezizomycotina
GROUP:<http://msi-ontology.sourceforge.net>
variable wavelength detector
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01079
A chromatography detector, that can detect signals within a certain range at user-defined wavelengths.
variable wavelength detector
GROUP:<http://msi-ontology.sourceforge.net>
Bruker NMR instrument
An NMR instrument that is manufactured by Bruker.
Bruker NMR instrument
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400198
PERSON:Daniel Schober
A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type.
James Malone
clustered data visualization
clustered data visualization
multiple wavelength detector
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01078
multiple wavelength detector
GROUP:<http://msi-ontology.sourceforge.net>
A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile.
Homo/Pan/Gorilla group
Homo/Pan/Gorilla group
Trypanosoma
Trypanosoma
pathogen role
GROUP: Role Branch
Pathogen: An agent of disease. A disease producer. The term pathogen most commonly is used to refer to infectious organisms. These include bacteria (such as staph), viruses (such as HIV), and fungi (such as yeast). Less commonly, pathogen refers to a noninfectious agent of disease such as a chemical. http://www.medterms.com/script/main/art.asp?articlekey=6383
pathogen role is a role which inheres in an organism and realized in the process of disease course in the organism bearing host role caused by the organism bearing pathogen role
pathogen role
OBI
Danio
Danio
IEDB
T cell epitope ELISA IL-2 assay
A T cell epitope specific cytokine production assay that measures production of IL-2 by T cells utilizing the ELISA methodology.
IEDB
T cell epitope ELISA IL-2 assay
IL-2 release by ELISA
An assay that measures epitope specific granulocyte macrophage colony stimulating factor production by T cells
assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells
IEDB (QTT)
GM-CSF release
assay of epitope specific granulocyte macrophage colony stimulating factor production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
portable fluorometer
A compact fluorometer that can be carried or moved with ease.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
portable fluorometer
An ELISPOT assay that measures epitope specific granzyme B production by T cells
ELISPOT assay of epitope specific granzyme B production by T cells
granzyme B release by ELISPOT
ELISPOT assay of epitope specific granzyme B production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
Bos taurus
Bos taurus
editor
data pooling
data combination
data combination
A data transformation in which individual input data elements and values are merged together into a output set of data elements and values.
Richard Scheuermann
Enterococcus faecalis
Enterococcus faecalis
cation trap column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01278
A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
cation trap column
single linkage hierarchical clustering
Elisabetta Manduchi
A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster.
PERSON: Elisabetta Manduchi
single linkage hierarchical clustering
Alveolata
Alveolata
PERSON:Daniel Schober
sample injection system
An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility.
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01057
sample injection system
A T cell epitope specific cytokine production assay that measures production of IFNg by T cells utilizing the ELISA methodology.
T cell epitope ELISA IFN-g assay
IFNg release by ELISA
T cell epitope ELISA IFN-g assay
IEDB
IEDB
Danio rerio
Danio rerio
vaccine preparation
The production of B. pertussis vaccine.
OBI
vaccine preparation is a planned process with specified output a vaccine
vaccine preparation
Rhodobacter sphaeroides
Rhodobacter sphaeroides
A material entity bearing the disposition to cause an allergic reaction
allergen
IEDB
IEDB
Birch pollen is an allergen
allergen
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An assay that measures epitope specific RANTES production by T cells
RANTES/CCL5 release
assay of epitope specific RANTES production by T cells
assay of epitope specific RANTES production by T cells
Salmo
Salmo
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01113
column adapter
column adapter
PERSON:Daniel Schober
GROUP:<http://msi-ontology.sourceforge.net>
An Adapter that enabled the connection of a column to additional devices.
Burkholderiales
Burkholderiales
Enterococcus
Enterococcus
PERSON: Richard Scheuermann
network graph construction
A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph.
Richard Scheuermann
network graph construction
complete linkage hierarchical clustering
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster.
complete linkage hierarchical clustering
Coxiellaceae
Coxiellaceae
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400276
The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup.
PERSON:Daniel Schober
Bruker LC-NMR platform
Bruker LC-NMR platform
WEB:<http://www.bruker-biospin.com/hyphenation_lcnmr_ms.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01091
FPD
WEB:<http://www.shsu.edu/~chemistry/FPD/FPD.html>
The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected.
flame photometric detector
PERSON:Daniel Schober
flame photometric detector
Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
PERSON: Jie Zheng
a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution
polyacrylamide gel
PERSON: Philippe Rocca-Serra
polyacrylamide gel
GROUP: OBI Biomaterial Branch
MO_568 stimulus_or_stress_design
A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc.
stimulus or stress design
stimulus or stress design
Person: Chris Stoeckert, Jie Zheng
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
excitation function
excitation function
Bill Bug
Melanie Courtot
Daniel Schober
Frank Gibson
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
A X-ray crystallography assay that measures MHC:epitope complex binding to TCR
epitope binding to TCR by crystallography
X-ray crystallography assay of MHC:epitope complex binding to TCR
X-ray crystallography assay of MHC:epitope complex binding to TCR
Neognathae
Neognathae
multiple testing correction objective
A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously
Application of the Bonferroni correction
http://en.wikipedia.org/wiki/Multiple_Testing_Correction
multiple comparison correction objective
multiple testing correction objective
Eremothecium
Eremothecium
interleukin-7 production
The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-7 production
immunoblot scanner
A device that is used for the imaging of immunoblots.
immunoblot scanner
PERSON: Erik Segerdell
PERSON: Erik Segerdell
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01090
PERSON:Daniel Schober
The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis.
PID
photoionization detector
photoionization detector
WEB:<http://www.chemistry.adelaide.edu.au/external/soc-rel/content/pid.htm>
material maintenance
a process with that achieves the objective to maintain some or all of the characteristics of an input material over time
material maintenance
a single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
single nucleotide resolution mapping assay using DNAse I
PMID:3773731
DNASE 1 structure mapping assay
RNA ontology
Person:Philippe Rocca-Serra
DNAse footprinting assay
DNASE 1 structure mapping assay
Obtectomera
Obtectomera
right handedness
Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
right handedness
mitosporic Saccharomycetales
mitosporic Saccharomycetales
left handedness
Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot.
left handedness
genotyping using an Affymetrix chip
OBI
DNA sequence feature detection
should be a defined class where interpretation of data generated by assay qualifies a DNA sequence
Philippe Rocca-Serra
DNA sequence feature detection
An assay with the objective to determine a sequence feature of DNA
Person:Bjoern Peters
detection of specific nucleic acids with complementary probes of epitope specific interleukin-23 production by T cells
IL-23 release by RNA/DNA detection
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
detection of specific nucleic acids with complementary probes of epitope specific interleukin-23 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-23 production by T cells
IEDB (QTT)
ionize process
a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation.
ionize process
Person:Bjoern Peters
Electrospray ionization in mass spectrometry
2009-11-10. Tracker: http://en.wikipedia.org/wiki/Ionize
statistical model validation
http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29
statistical model validation
A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set.
Helen Parkinson
Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia
Haemophilus influenzae
Haemophilus influenzae
Ectocarpus
Ectocarpus
http://en.wikipedia.org/wiki/Sonography
A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs.
PERSON: Erik Segerdell
ultrasound machine
ultrasound machine
biological sex
An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved.
biological sex
interleukin-6 production
The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-6 production
gas generator
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01033
An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century.
WEB:<http://www.chromatography-online.org/GC/Gas-Supplies/Pure-Air-Generators./rs5.html>
gas generator
PERSON:Daniel Schober
oral ingestion of pill
An adding a material entity to target with the entity is a pill and the target is the mouth
Person:Alan Ruttenberg
oral ingestion of pill
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
Person: Philippe Rocca-Serra
RNAO and OBI
a single-nucleotide-resolution nucleic acid structure mapping assay which relies on small chemical compounds acting as chemical probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study.
single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing
Xenopodinae
Xenopodinae
http://www.luminexcorp.com/support/faqs.html
Luminex 200
Luminex 200
A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation
John Quinn
adding material objective
BP
adding material objective
creating a mouse infected with LCM virus
is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity
Alphaproteobacteria
Alphaproteobacteria
protein and DNA interaction identification objective
A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites.
MO_933 binding_site_identification_design
Person: Chris Stoeckert, Jie Zheng
protein and DNA interaction identification objective
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01108
plunger column
GROUP:<http://msi-ontology.sourceforge.net>
plunger column
A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column.
PERSON:Daniel Schober
handedness
A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet.
handedness
double blind study execution
A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated
Person:Alan Ruttenberg
double blind study execution
http://clinicaltrials.gov/ct2/info/glossary#double
Muroidea
Muroidea
material separation function
A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
Bill Bug
Melanie Courtot
Daniel Schober
Frank Gibson
material separation function
transcription profiling by RT-PCR design
Group: ArrayExpress production team
A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR).
transcription profiling by RT-PCR design
Person: Chris Stoeckert, Jie Zheng
liquid extraction robot
A liquid handling device that provides automatic liquid extraction.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
liquid extraction robot
Selaginellaceae
Selaginellaceae
canis group
canis group
interleukin-9 production
The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-9 production
Methanococcoides
Methanococcoides
PMID:2843807
single nucleotide resolution mapping assay using Rhodium probe
Person:Philippe Rocca-Serra
a single-nucleotide-resolution nucleic acid structure mapping assay which uses Rhodium as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
Rhodium DNA structure mapping assay
RNA ontology
Rhodium DNA structure mapping assay
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01276
A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment.
GROUP:<http://msi-ontology.sourceforge.net>
column jacket
PERSON:Daniel Schober
column jacket
a device manufacture with the intent to provide a porous unsized paper used for filtering.
sep:00107
filter paper
filter paper
Frank Gibson
IEDB (QTT)
G-CSF release by cytometric bead array
cytometric bead array assay of epitope specific granulocyte colony stimulating factor production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A cytometric bead array assay that measures epitope specific granulocyte colony stimulating factor production by T cells
cytometric bead array assay of epitope specific granulocyte colony stimulating factor production by T cells
transcription factor binding site
PLace_holder for sequence ontology term
SO:0000235
transcription factor binding site
MACS Quant
John Quinn
A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and detectors to collect 7 fluorescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications.
MACS Quant
http://www.miltenyi.com
genotype profiling, SNP genotyping
genotyping assay
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
Philippe Rocca-Serra
an assay which generates data about a genotype from a specimen of genomic DNA. A variety of
techniques and instruments can be used to produce information about sequence variation at particular genomic positions.
OBI Biomaterial
genotyping assay
Benjamini and Yekutieli false discovery rate correction method
The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli)
Helen Parkinson
Helen Parkinson
A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate
Philippe Rocca-Serra
Benjamini and Yekutieli false discovery rate correction method
2011-03-31: [PRS].
specified input and output of dt which were missing
Bill Bug
Melanie Courtot
heat function
A heat function is a function that increases the internal kinetic energy of a material
heat function
Daniel Schober
Frank Gibson
epitope specific T cell enhancement of B cell mediated immune response
A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope.
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific T cell enhancement of B cell mediated immune response
Synechocystis sp. PCC 6803
Synechocystis sp. PCC 6803
Selaginella
Selaginella
Plasmodium falciparum
Plasmodium falciparum
http://www.answers.com/topic/laser-capture-microdissection-microscope-in-medicine
laser capture microdissection microscope
PERSON: Erik Segerdell
laser capture microdissection microscope
A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue.
Rhodobacter
Rhodobacter
phagocytophilum group
phagocytophilum group
interleukin-8 production
The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-8 production
labeled oligonucleotide
2010-01-31: Philippe Rocca-Serra
placeholder
Person: Philippe Rocca-Serra
a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide
labeled oligonucleotide
WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
ECD
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01085
electron capture detector
PERSON:Daniel Schober
The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes.
electron capture detector
a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNA adenosine deaminase I as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
PMID:7527340
Person: Philippe Rocca-Serra
RNA ADA I RNA structure mapping assay
RNA ADA I RNA structure mapping assay
RNA ontology
single nucleotide resolution mapping assay using RNA adenosine deaminase I
Magnetospirillum magnetotacticum
Magnetospirillum magnetotacticum
Ralstonia pickettii
Ralstonia pickettii
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
ELISA of epitope specific chemokine (C-C motif) ligand 1 production by T cells
IEDB (QTT)
TCA-3 release by ELISA
ELISA of epitope specific chemokine (C-C motif) ligand 1 production by T cells
An ELISA that measures epitope specific chemokine (C-C motif) ligand 1 production by T cells
Haemophilus
Haemophilus
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
in vivo T cell killing
in vivo cell mediated cell killing assay of epitope specific T cell mediated cytotoxicity
An in vivo cell mediated cell killing assay that measures epitope specific T cell mediated cytotoxicity
in vivo cell mediated cell killing assay of epitope specific T cell mediated cytotoxicity
glucose meter
http://en.wikipedia.org/wiki/Glucose_meter
PERSON:Frank Gibson
glucometer
Diabetic patients use glucometers to determine their glucose levels
PERSON:Helen Parkinson
A measurement device with the function to measure and record the level/amount of glucose in a blood sample
glucometer
filter function
Frank Gibson
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through
filter function
A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment.
PERSON: Monnie McGee
variance calculation
variance calculation
Monnie McGee
Hypocrea
Hypocrea
environmental history design
A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc.
environmental history design
Person: Chris Stoeckert, Jie Zheng
MO_698 environmental_history_design
artificially induced methylation
artificially induced methylation
A planned process of adding methyl groups to polymers
the use of enzymes to add methyl groups to DNA molecules
PERSON:Kevin Clancy
OBI branch derived
Methylophilales
Methylophilales
RNASE V1 structure mapping assay
Person:Philippe Rocca-Serra
RNASE V1 structure mapping assay
RNA ontology
a single-nucleotide-resolution ribonucleic acid structure mapping assay which uses RNAse V1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
PMID:7031604
single nucleotide resolution mapping assay using RNAse V1
Solaneae
Solaneae
Isoetopsida
Isoetopsida
interleukin-3 production
The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-3 production
coagulation analyzer
A device for automatically analyzing blood coagulation in a clinical laboratory.
PERSON: Erik Segerdell
United States Patent 5439646
coagulation analyzer
gene expression
The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
gene expression
Deinococcus radiodurans
Deinococcus radiodurans
Oxalobacteraceae
Oxalobacteraceae
IEDB (QTT)
A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-21 production by T cells
epitope specific interleukin-21 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Mutisioideae
Mutisioideae
BP
purification objective
The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
PERSON:Bjoern Peters
isolation objective
the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides.
purification objective
IL-12 release
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific interleukin-12 production by T cells
An assay that measures epitope specific interleukin-12 production by T cells
IEDB (QTT)
assay of epitope specific interleukin-12 production by T cells
Frank Gibson
A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function.
http://en.wikipedia.org/wiki/Perturbation_biology
perturb function
Daniel Schober
perturb function
Melanie Courtot
Bill Bug
Rickettsia sibirica subgroup
Rickettsia sibirica subgroup
Silurana
Silurana
measurement device
A ruler, a microarray scanner, a Geiger counter.
a processed material created to have the function to measure
GROUP:OBI Philly workshop
measurement device
OBI
asterids
asterids
the addition of a labeling reagent to an input biomaterial in order to detect the labeled material in the future
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
PERSON:Kevin Clancy
labeling
labeling
OBI branch derived
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
ELISPOT assay of epitope specific interleukin-6 production by T cells
ELISPOT assay of epitope specific interleukin-6 production by T cells
An ELISPOT assay that measures epitope specific interleukin-6 production by T cells
IL-6 release by ELISPOT
Neisseriales
Neisseriales
is a single-nucleotide-resolution nucleic acid structure mapping assay which uses kethoxal as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
single nucleotide resolution mapping assay using Kethoxal probe
RNA ontology
Person: Philippe Rocca-Serra
kethoxal structure mapping assay
kethoxal structure mapping assay
Selaginellales
Selaginellales
plate shaker
A device that provides shaking motion for microplates.
PERSON: Erik Segerdell
plate shaker
PERSON: Erik Segerdell
interleukin-27 production
The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-27 production
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cell-cell binding detection by flow cytometry assay of MHC:epitope complex binding to TCR
A cell-cell binding detection by flow cytometry assay that measures MHC:epitope complex binding to TCR
IEDB (QTT)
cell-cell binding detection by flow cytometry assay of MHC:epitope complex binding to TCR
epitope binding to TCR by cell-cell binding using FACS
hydrogensulfite
A sulfur oxoanion that has formula HO3S.
hydrogensulfite
Deinococcus
Deinococcus
A device that is used to sharpen knives used in microtomy.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
microtome knife sharpener
microtome knife sharpener
plasmid
group:OBI
person:Melanie Courtot
plasmid
plasmid = DNA and has_quality circular and has_function
(is_realized_as some gene expression) GO:0010467
is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing
Philippe Rocca-Serra
OBI and Li-Cor
Li-Cor
Li-Cor
Philippe Rocca-Serra
Li-Cor 4300 DNA Analysis System
Li-Cor 4300 DNA Analysis System
Daniel Schober
Frank Gibson
A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
synthesizing function
Melanie Courtot
synthesizing function
Bill Bug
Xenopus tropicalis
Xenopus tropicalis
obsolete_primary structure of protein
Person:Bjoern Peters
SIINFEKL' is the primary structure of a peptide
The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together
obsolete_primary structure of protein
replaced by SO_0000104 polypeptide
epitope specific cytotoxic T cell degranulation
A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope.
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific cytotoxic T cell degranulation
Salmo trutta
Salmo trutta
assay of epitope specific T cell enhancement of B cell mediated immune response
IEDB (QTT)
T cell help for antibody response
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An assay that measures epitope specific T cell enhancement of B cell mediated immune response
assay of epitope specific T cell enhancement of B cell mediated immune response
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
Person: Philippe Rocca-Serra
RNAO and OBI
a single-nucleotide-resolution nucleic acid structure mapping assay which relies on proteins acting as enzymatic probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study.
single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing
cell culture splitting
The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
cell culture splitting
PlanAndPlannedProcess Branch
OBI branch derived
test tube
sample tube
http://en.wikipedia.org/wiki/Test_tube
Bjoern Peters
collection tube
A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material
test tube
interleukin-5 production
The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-5 production
gambiae species complex
gambiae species complex
Deinococcus-Thermus
Deinococcus-Thermus
Platyhelminthes
Platyhelminthes
EFO_0002765 proteomic profiling by array
proteomic profiling by array assay
An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology
proteomic profiling by array assay
Person: James Malone
Daniel Schober
Melanie Courtot
Frank Gibson
Bill Bug
A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
freeze function
freeze function
computer cluster
A group of linked computers, working together closely so that in many respects they form a single computer.
PERSON: Erik Segerdell
computer cluster
http://en.wikipedia.org/wiki/Cluster_(computing)
Zinnia elegans
Zinnia elegans
capsule shell
http://www.golovchenko.org/cgi-bin/wnsearch?q=capsule#2n
capsule shell
Person:Alan Ruttenberg
a small rounded gelatinous container
Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology
A process in which an input substance is injected into a organ section.
injection into organ section
Person:Bjoern Peters
injection into organ section
chromatography pump system
WEB:<http://en.wikipedia.org/wiki/Column_chromatography>
PERSON:Daniel Schober
chromatography pump system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01046
Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
high molecular weight DNA extract
Extraction of chromosomal DNA from mammalian cells by first isolating nucei
OBI
PERSON:Chris Stoeckert
The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas.
high molecular weight DNA extract
comparative genomic hybridization by array assay
Person: James Malone
An assay in which changes in DNA sequence copy number are analysed using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria.
array CGH
comparative genomic hybridization by array assay
EFO_0000749: comparative genomic hybridization by array
Portion of body substance
Material anatomical entity in a gaseous, liquid, semisolid or solid state, with or without the admixture of cells and biological macromolecules; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures. Examples: saliva, semen, cerebrospinal fluid, respiratory air, urine, feces, blood, plasma, lymph.
Portion of body substance
DMS structure mapping assay
RNA Ontology
a single-nucleotide-resolution nucleic acid structure mapping assay which uses DMS as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
single nucleotide resolution mapping assay using DMS probe
Person: Philippe Rocca-Serra
PMID:6159633 and PMID:2446263
DMS structure mapping assay
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
epitope binding to TCR by surface plasmon resonance [Kd in nM]
A surface plasmon resonance assay that measures MHC:epitope complex binding to TCR
surface plasmon resonance assay of MHC:epitope complex binding to TCR
surface plasmon resonance assay of MHC:epitope complex binding to TCR
manufacturer
A person or organization that has a manufacturer role
manufacturer
Effects of establishing cell cultures and cell culture conditions on the proliferative life span of human fibroblasts isolated from different tissues and donors of different ages.
Exp Cell Res. 2002 Apr 1;274(2):275-87. PMID: 11900488
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the establishing_cell_culture step comprises preparing the cells at a certain dilution and plating them in a container with growth medium.
PlanAndPlannedProcess Branch
establishing cell culture
OBI branch derived
establishing a cell culture is a process which results in creating an in vitro environment in which cells are sustained from input material containing cells. input: cell-containing material, output cell culture, part of cell culturing. Cells are originally plated at a certain concentration referred to as seeding density.
establishing cell culture
Buchnera sp.
Buchnera sp.
Leymus
Leymus
Lycopodiophyta
Lycopodiophyta
interleukin-4 production
The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-4 production
cell culture analyte detection bioassay of epitope specific interferon-gamma production by T cells
IEDB (QTT)
IFNg release by bioassay
cell culture analyte detection bioassay of epitope specific interferon-gamma production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A cell culture analyte detection bioassay that measures epitope specific interferon-gamma production by T cells
quality of a liquid
A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape.
quality of a liquid
2x2 factorial design
2x2 factorial design
PMID: 17561240
PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed.
Philippe Rocca-Serra
a factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors
DNA extraction/purification instrument
A device that is used to isolate and collect DNA for subsequent molecular analysis.
DNA extraction/purification instrument
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/DNA_extraction
FG this is synonymous with microtiter plate
A particle deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader.
multi-well plate
96 well plate, 48 multiwell plate
multi-well plate
John Quinn
http://www.nuncbrand.com/page.aspx?ID=301
Salmo salar
Salmo salar
IP-10 production
IP-10 production
The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
recombinant phage cloning
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.section.1611
recombinant phage cloning
Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro.
Helen Parkinson
Insert selection by BamHI methyltransferase protection in P1 phage-based cloning
intradermal injection
PERSON: Melanie Courtot
intradermal injection
is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe
mechanical balance
A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight).
PERSON: Erik Segerdell
http://www.britannica.com/EBchecked/topic/49765/balance
mechanical balance
Suina
Suina
Geospiza fortis
Geospiza fortis
article-without-pmid-or-doi:CDISCglossary
eSource document
an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures
eSource document
person:Jennifer Fostel
Synechocystis sp.
Synechocystis sp.
quality of a gas
A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape.
quality of a gas
CD3 subunit with immunoglobulin domain
A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response.
CD3 subunit with immunoglobulin domain
a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate)
The use of ethanol to precipitate DNA molecules from a solution containing DNA
PERSON:Kevin Clancy
precipitation
precipitation
OBI branch derived
A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
multichannel pipette
multichannel pipette
neodymium-YAG laser
A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystalline material pumped by a flash lamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer.
Daniel Schober
John Quinn
Neodymium-YAG Laser in DURIP99 System
neodymium-YAG laser
factorial design
PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
Philippe Rocca-Serra
factorial design
factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.
http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)
granulocyte colony-stimulating factor production
The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
granulocyte colony-stimulating factor production
Insulin resistance
Insulin resistance
`Increased resistance` (PATO:0001650) towards `insulin` (PRO:000009054).
Person:Helen Parkinson
A biologist who uses a sequencing services fulfills the role of a service consumer
service consumer role
OBI
a role which inheres in a person who uses a service
service consumer role
storage of measurement results from an assay into a text file, such as
a documenting process to encode an information entity into a digital document
PlanAndPlannedProcess Branch
OBI branch derived
data encoding
data encoding
multimode microplate reader
A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
multimode microplate reader
Clostridiaceae
Clostridiaceae
Geospiza conirostris
Geospiza conirostris
Synechocystis
Synechocystis
IEDB
RMA cell culture
IEDB
A cell line derived from a mouse lymphoma, specifically a Rauscher virus-induced tumor.This cell ine is antigen processing-defective and expresses a very low level of MHC molecules on its surface.
RMA cell culture
nucleic acid extract
nucleic acid extract
An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen.
PERSON: Jie Zheng
UPenn Group
obscuration bar in a flow cytometer
An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.
obscuration bar
Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249
obscuration bar
John Quinn
Daniel Schober
Philippe Rocca-Serra on behalf of MO
dye swap design
An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
MO_858
dye swap design
PERSON: Erik Segerdell
A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT?
cell harvester
cell harvester
PERSON: Erik Segerdell
PERSON:Bjoern Peters
A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application
cell permeabilization
OBI branch derived
Electroporation of HeLa cells to allow transfection with pUC19.
cell permeabilization
need to add output cell has_quality permeable
A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor.
vibration isolation table
vibration isolation table
United States Patent 6877711
PERSON:Bjoern Peters
handedness assay
http://en.wikipedia.org/wiki/Handedness
The Edinburgh handedness assay is a specific method of determing handedness
A handedness assay measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure.
handedness test
handedness assay
Helen Parkinson
tritiated thymidine
3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye.
tritiated thymidine
Geospiza
Geospiza
Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
Person:Jennifer Fostel
regulator
a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
regulator role
OBI
regulator role
T2 cell culture
IEDB
A human T-B lymphoblastoid hybrid cell line
T2 cell culture
IEDB
http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-1992&Template=cellBiology
ENU structure mapping assay
PMID:7002606 and PMID:2446263
single nucleotide resolution mapping assay using ENU probe
Person: Philippe Rocca-Serra
RNA ontology
ENU structure mapping assay
a single-nucleotide-resolution nucleic acid structure mapping assay which uses ENU as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure
fractional factorial design
A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run
Philippe Rocca-Serra
fractional factorial design
http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control
optical filter
John Quinn
http://en.wikipedia.org/wiki/Optical_filter
optical filter
An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
720 LP filter, 580/30 BP filter
OBI branch derived
artificially induced DNA repair
the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands
a protocol application to repair damaged DNA molecules
artificially induced DNA repair
PlanAndPlannedProcess Branch
RNA ontology group
chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent
PERSON:Philippe Rocca-Serra
PMID: 20171258. Comparative reactivity of mismatched and unpaired bases in relation to their type and surroundings. Chemical cleavage of DNA mismatches in mutation detection analysis.Yakubovskaya MG, Belyakova AA, Gasanova VK, Belitsky GA, Dolinnaya NG.
Biochimie. 2010 Feb 18.
chemical cleavage
chemical cleavage
Pleuronectidae
Pleuronectidae
granzyme B production
The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
granzyme B production
Ixoroideae
Ixoroideae
biological feature identification objective
Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
Jennifer Fostel
biological feature identification objective
service provider role
Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer.
is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person
service provider role
PERSON:Helen Parkinson
Ustilaginomycetes
Ustilaginomycetes
T cell receptor complex
A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains.
T cell receptor complex
A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared.
Philippe Rocca-Serra on behalf of MO
self vs self design
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
MO_490
self vs self design
The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia)
JY cell culture
IEDB
IEDB
JY cell culture
Anopheles
Anopheles
A specimen primarily composed of cells collected from a multicellular organism or a cell culture
cell specimen
cell specimen
MO_612 cell
PERSON: Chris Stoeckert, Jie Zheng
A contain function is a function to constrain a material entities location in space
Frank Gibson
Melanie Courtot
A syringe, a beaker
Bill Bug
contain function
contain function
Daniel Schober
An institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008
Internal Review Board
Person:Helen Parkinson
Animal protocol review board
OBI, CDISC
role of Institutional Review Board
the role of a organization that is realized by members reviewing study designs for their agreement with regulations
role of Institutional Review Board
Person:Jennifer Fostel
needle
OBI Instrument
needle
Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature.
Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
Philippe Rocca-Serra
a needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.
Enzyme-linked immunosorbent spot assay
ELISPOT assay
ELISPOT
IEDB
Determination of the frequency of cells producing IFN-gamma in response to viral peptides by placing effector cells on a anti IFN-gamma coated plate, and adding antigen presenting cells pulsed with a peptide. After washing, the bound IFN-gamma is detected with a secondary antibody linked to a dye that visualizes as one spot per cell.
ELISPOT assay
ELISPOT
IEDB
An assay in which the number of cells producing a material in a larger cell population are stained and counted. This is done by visualizing and counting the number of spots present on a surface via an antibody specific for the produced material. Each spot represents one cell producing the material of interest.
2/26/09: RESOLVE: we need to specify the produced substance that is desired to be detected. Analyte does not work, as this is not a concentration, and this is not present at the start of the assay.
Cebidae
Cebidae
sterilization function
sterilization function
a function to remove viable organisms from an input material
TRAIL production
TRAIL production
The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
replicate design
replicate design
MO_885
Philippe Rocca-Serra on behalf of MO
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
IEDB
T cell epitope recognition assay
An assay in which a positive measurement indicates TCR recognition of an epitope:MHC context. Inputs to the assay include: 1) the assay antigen which contains the epitope, 2) TCR molecules 3) restricting MHC molecules.
IEDB
T cell epitope assay
T cell epitope recognition assay
Geospiza scandens
Geospiza scandens
epitope specific interleukin-22 production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-22 production by T cells
Anopheles gambiae
Anopheles gambiae
monospecific T cell recognition of eluted MHC ligands
An assay in which the presence of a specific ligand in an elute is detected using the response of T cells that are known to be monospecific for that ligand as a readout
monospecific T cell recognition of eluted MHC ligands
PERSON:Bjoern Peters, Randi Vita
IEDB
Blinded medication
Person:Helen Parkinson
obsolete_blinded medication role
Inert pill shaped like aspirin tablet
Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance
115 patients received ipilimumab and blinded medication
Will be modelled using a blinding process and specified output blinded medication instead
Jennifer Fostel
A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
cell co-culturing
Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
PlanAndPlannedProcess Branch
OBI branch derived
cell co-culturing
2
analyte measurement objective
PERSON: Bjoern Peters
PPPB branch
The objective to measure the concentration of glucose in a blood sample
analyte measurement objective
is an assay objective to determine the presence or concentration of an analyte in the evaluant
metal vapor laser
A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer.
Gold vapor laser, Helium-cadmium metal-vapor laser
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
metal vapor laser
OBI branch derived
experimental disease induction
experimental disease induction
PlanAndPlannedProcess Branch
a protocol application to induce a specific disease in an organism
the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome.
cellular_component
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
cellular_component
Betaproteobacteria
Betaproteobacteria
accessed material role
the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism
is realized in a planned process where the bearer participates
AR: rent a DNA sequencer for a period of time. two realizations, payment for the service and also when the person who pays for the service uses it
accessed material role
agarose gel
Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
GROUP: OBI Biomaterial Branch
agarose gel
a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
PERSON: Philippe Rocca-Serra
Ectocarpaceae
Ectocarpaceae
antigen
antigen
IEDB
IEDB
is a material entity that has the antigen role
sub-investigator role
sub-investigator
sub-investigator role
Person: Jennifer Fostel
a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline
Geospiza magnirostris
Geospiza magnirostris
fluorescent reporter intensity
group:OBI
A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
person:Chris Stoeckert
fluorescent reporter intensity
chemokine (C-C motif) ligand 1 production
The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine (C-C motif) ligand 1 production
mixed argon-krypton gas laser
A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer.
John Quinn
argon-krypton laser in a cytometer
http://www.eio.com/repairfaq/sam/laserarg.htm
mixed argon-krypton gas laser
DNA sequence variation detection
DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule.
Philippe Rocca-Serra
OBI Biomaterial
DNA sequence variation detection
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
person:Jennifer Fostel
CDISC glossary
An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators.
electronic case report tabulation
electronic case report tabulation
John Quinn
http://www.dakousa.com/index/prod_search/prod_groups.htm?productareaid=16
MoFlo at TSRI Flow Cytometry Core Facility
MoFlo
A MoFlo is a flow_cytometer_sorter manufactured by Dako Cytomation. It features digital electronics, the option to include several lasers (solid state 488 nm, 635 nm, and a 351 nm diode laser), and has the filtering and collection capacity for up to 10 flouresecent parameters. The MoFlo is an instrument that can be used to both analyze quantitatively and collect cells in a flowing medium.
MoFlo
ambidextrous handedness
Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot.
ambidextrous handedness
oscilloscope
PERSON:Bjoern Peters
oscilloscope
A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis).
http://en.wikipedia.org/wiki/Oscilloscope
A cell line derived from human T cells.
Jurkat cell culture
IEDB
IEDB
Jurkat cell culture
http://www.biotech.ist.unige.it/cldb/cl5296.html
Ectocarpales
Ectocarpales
Acidaminococcaceae
Acidaminococcaceae
Aquificae
Aquificae
Pleuronectiformes
Pleuronectiformes
A processual entity that realizes a plan which is the concretization of a plan specification.
planned process
planned process
We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some
objectives is a planned process.
Bjoern Peters
'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)
Injecting mice with a vaccine in order to test its efficacy
branch derived
Amphiesmenoptera
Amphiesmenoptera
A specimen creation objective is to obtain a material entity for potential use as an input during an investigation
Bjoern Peters
Bjoern Peters
specimen creation objective
specimen creation objective
The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient.
positron emission tomography scanner
positron emission tomography scanner
http://en.wikipedia.org/wiki/Positron_emission_tomography
PERSON:Bjoern Peters
PET scanner
A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting
radionuclide (tracer), which is introduced into the body on a biologically active molecule.
Ehrlichia
Ehrlichia
Oryza
Oryza
Rickettsiales
Rickettsiales
subgraph degree calculation
PERSON: Richard Scheuermann
Richard Scheuermann
A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph.
subgraph degree calculation
Dechloromonas aromatica
Dechloromonas aromatica
stereo microscope
An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Optical_microscope#Stereo_microscope
stereo microscope
Dimethyl sulfate
Dimethyl sulfate
The dimethyl ester of sulfuric acid
A device that is used to heat microscope slides.
slide warmer
PERSON: Erik Segerdell
PERSON: Erik Segerdell
slide warmer
Fusobacterales
Fusobacterales
Funariaceae
Funariaceae
intramuscular injection
intramuscular injection
is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe
http://www.cytopeia.com/analyzer.htm
The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells.
inFlux Analyzer
inFlux Analyzer
John Quinn
Deinococci
Deinococci
PERSON: Jie Zheng
nuclear RNA extract
A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted.
UPenn Group
Isolation and purification of nuclear RNA from animal cells using Norgen Bioteck corp. cytoplasmic and nuclear RNA purification kit (http://www.norgenbiotek.com/display-product.php?ID=30)
PERSON: Chris Stoeckert
nuclear RNA extract
Bjoern Peters
creating a mixture of molecules in solution
PERSON: Helen Parkinson
is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations.
creating a mixture of molecules in solution
The production of PBS
Desulfuromonadales
Desulfuromonadales
SARS coronavirus
SARS coronavirus
Perciformes
Perciformes
Methanococcoides burtonii
Methanococcoides burtonii
Frank Gibson
http://en.wikipedia.org/wiki/Column_chromatography
chromatography column
Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms.
chromatography column
network subgraph quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network.
PERSON: Richard Scheuermann
Richard Scheuermann
network subgraph quality calculation
Ehrlichia canis
Ehrlichia canis
incubator
http://www.medterms.com/script/main/art.asp?articlekey=18426
Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells
Frank Gibson
incubator
a device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
Diethylpyrocarbonate
Diethylpyrocarbonate
The diethyl ester of dicarbonic acid
Funariales
Funariales
automatic tissue processor
A machine for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue.
automatic tissue processor
United States Patent 3762362
PERSON: Erik Segerdell
capillary electrophoresis instrument
An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass.
PERSON: Erik Segerdell
capillary electrophoresis instrument
http://en.wikipedia.org/wiki/Capillary_electrophoresis
Fusobacteriaceae
Fusobacteriaceae
PERSON:Bjoern Peters
micromanipulator
micromanipulator
http://en.wikipedia.org/wiki/Micromanipulator
A device that is used to physically interact with a sample under
a microscope, where a level of precision of movement is necessary that
cannot be achieved by the unaided human hand.
Platichthys flesus
Platichthys flesus
Melanie Courtot
The ImageStream is a multispectral_imaging_flow_cytometer manufactured by Amnis. Its has digital electronics, a single standard 488 nm solid state laser. In addition an optional 658 nm and your choice of either a 405 nm or 375 nm solid state laser can be added. Information is collected using cameras. The ImageStream system CCD camera produces six images of each cell, including darkfield, brightfield, and up to four fluorescent colors. Each image is used to calculate over 40 features, so a six-image assay results in ~250 morphometric and photometric features per cell. The ImageStream is a flow cytometer that takes pictures of the cells in flow.
It has both components, an Image cytometer and a flow cytometer.
It has both components, an Image cytometer and a flow cytometer.
Amnis ImageStream
John Quinn
http://www.amnis.com/
Amnis ImageStream
granulocyte macrophage colony-stimulating factor production
The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
granulocyte macrophage colony-stimulating factor production
Likelihood-ratio test
Likelihood-ratio test
Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models.
Tina Boussard
obsolete_study result
GROUP: OBI
Study result is an information content entity that is a specified data output of a study.
study result
unclassified Burkholderiales
unclassified Burkholderiales
Treponema
Treponema
Cytophaga
Cytophaga
Bryopsida
Bryopsida
molecular_function
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
molecular_function
Lactobacillus
Lactobacillus
PERSON: Erik Segerdell
perfusion station
perfusion station
A device or system in which perfusion units are integrated.
PERSON: Erik Segerdell
cloning plasmid
A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site.
Note: 'cloning vector role' is really a function. Should be dealt with globally
cloning plasmid
hepatocyte growth factor production
The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
hepatocyte growth factor production
helium neon ion laser
http://en.wikipedia.org/wiki/Laser#Gas_lasers
helium neon ion laser
John Quinn
A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm.
A helium neon laser can by used to irradiate cells in a flow cytometer.
Daniel Schober
a service provider role which is realized by a servicer provider organization performing access to some material
A person or organization who provides access to a DNA sequencer.
OBI
PERSON:Helen Parkinson
obsolete_material access provider role
material access provider role
obsolete during the San Diego workshop, March 2011
The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service.
Agrotis ipsilon
Agrotis ipsilon
Mus musculus
Mus musculus
helium cadmium ion laser
A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer.
John Quinn
KIMMON HeCd 325nm laser
helium cadmium ion laser
http://en.wikipedia.org/wiki/Laser#Gas_lasers
2010-01-31: Philippe Rocca-Serra: Need to add a restriction taking into account probe and transcript information
PMID: 18428227. Analysis of RNA by northern blot hybridization.
Brown T, Mackey K. Curr Protoc Hum Genet. 2001 Nov;Appendix 3:Appendix 3K.
Person: Philippe Rocca-Serra
northern blot
a northern blot analysis is an assay allowing monitoring presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing agarose gel, transfered by blotting procedure to a nitrocellulose or nylon membrane and immobilized by cross linking or baking to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager
northern blot analysis
northern blot analysis
hardware testing objective
Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner.
Jennifer Fostel
hardware testing objective
A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph.
quantitative subgraph degree calculation
PERSON: Richard Scheuermann
Richard Scheuermann
quantitative subgraph degree calculation
Anaplasmataceae
Anaplasmataceae
Treponema denticola
Treponema denticola
PERSON: Erik Segerdell
PERSON: Erik Segerdell
vacuum oven
vacuum oven
A device that heats materials in a vacuum.
top loading balance
A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass.
PERSON: Erik Segerdell
top loading balance
PERSON: Erik Segerdell
type I interferon production
The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
type I interferon production
Streptomycetaceae
Streptomycetaceae
rodent care
rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research.
keeping animal
PPPB branch
rodent care
PPPB branch
obsolete_left handedness
obsolete_left handedness
T cell mediated cytotoxicity
T cell mediated cytotoxicity
The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
Actinobacteria
Actinobacteria
N-methylisatoic anhydride
A 3,1-benzoxazin-1,4-dione having an N-methyl substituent.
N-methylisatoic anhydride
node shortest path identification
A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network.
PERSON: Richard Scheuermann
Richard Scheuermann
node shortest path identification
Guava_PCA-96
The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement.
http://www.guavatechnologies.com/main/products/PCA-96new.cfm
Guava Personal Cell Analysis-96
Guava Personal Cell Analysis-96
John Quinn
molecular feature identification objective
Jennifer Fostel
Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
molecular feature identification objective
rodent care protocol
A rodent care protocol is an animal protocol in which the animals being taken care of are rodents.
Bjoern Peters
Bjoern Peters
Keeping mice in the UCSD animals facility at 20 - 25 degrees celsius, in cages of 4 animals each and providing food twice daily.
rodent care protocol
hypothesis generating investigation
OBI branch derived
PlanAndPlannedProcess Branch
hypothesis generating investigation
is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
establishing a cancer cell line
Establishment of HeLa immortal cell line
Helen Parkinson
establishing a cancer cell line
is a planned process in which the objective is to generate a cell line from a natural population of cells which are already immortal
pattern matching objective
pattern matching objective
Tina Boussard
http://en.wikipedia.org/wiki/Pattern_matching
A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees.
A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned.
k-nearest neighbors
k-NN
PERSON: James Malone
k-nearest neighbors
James Malone
array manufacturer role
a manufacturer role which is played by the person or organization that manufactured the array
MO_695 array_manufacturer
PERSON: Chris Stoeckert, Jie Zheng
array manufacturer role
Halobacteria
Halobacteria
Mesobatrachia
Mesobatrachia
Xenopus [NCBITaxon:262014]
Xenopus [NCBITaxon:262014]
Fe-BABE
A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration.
Fe-BABE
Guava_PCA
Guava Personal Cell Analysis
A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement.
John Quinn
http://www.guavatechnologies.com/main/products/PCA-new.cfm
Guava Personal Cell Analysis
node out-degree calculation
A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node.
PERSON: Richard Scheuermann
Richard Scheuermann
node out-degree calculation
calorimetry instrument
A measurement device that is used to calculate the heat flow of a chemical reaction or physical change.
calorimeter
http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm
PERSON:Bjoern Peters
calorimeter
GROUP: Role branch
supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material.
supernatant role
supernatant role
OBI
Precipitation is the formation of a solid in a solution during a chemical reaction. When the reaction occurs, the solid formed is called the precipitate, and the liquid remaining above the solid is called the supernate. Wikipedia
hypothesis driven investigation
OBI branch derived
PlanAndPlannedProcess Branch
hypothesis driven investigation
is an investigation with the goal to test one or more hypothesis
PMID: 18946007.Pyrosequencing analysis of the oral microflora of healthy adults.
Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W. J Dent Res. 2008 Nov;87(11):1016-20.
454 Genome Sequence 20
is a DNA sequencer which is manufactured by 454 Life Science Corporation and enables pyrosequencing to be performed. It comprises both optics and fluidics subsystems, which are
controlled by a computer subsystem. The fluidics subsystem ensures accurate reagent dispensing. It consists of a reagents cassette (which holds the reagent containers), a sipper manifold, pumps, valves, and debubblers. The fluidics subsystem flows the sequencing reagents across the wells of the PicoTiterPlate device, and moves the spent reagents from the PicoTiterPlate device to the waste receptacle. The optics subsystem consists of a CCD camera and a camera controller. The camera captures the light emitted in the wells of the PicoTiterPlate device during each step of the sequencing cycle, and sends the digital images to the computer subsystem for processing. The computer controls the other Sequencer subsystems, and processes the digital images sent by the camera to extract the DNA sequence information.
454 Genome Sequence 20
GS 20
Philippe Rocca-Serra
Chlamydiae/Verrucomicrobia group
Chlamydiae/Verrucomicrobia group
interferon-beta production
The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interferon-beta production
Ryan Brinkman
peak matching
Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold
peak matching
PERSON: Ryan Brinkman
James Malone
Anaplasma phagocytophilum
Anaplasma phagocytophilum
PERSON: Erik Segerdell
A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required.
SPECT scanner
http://en.wikipedia.org/wiki/Single_photon_emission_computed_tomography
SPECT scanner
Lolium perenne
Lolium perenne
Anaplasma
Anaplasma
edge betweenness calculation
An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge.
PERSON: Richard Scheuermann
Richard Scheuermann
edge betweenness calculation
Physcomitrella patens
Physcomitrella patens
96-well neutralization assay
96-well neutralization assay
A serum neutralization of viral infectivity assay which done in a 96-well plate.
microneutralization assay
person: Bjoern Peters
person: Melanie Courtot
study intervention
GROUP: OBI
PERSON: Bjoern Peters
the part of the execution of an intervention design study which is varied between two or more subjects in the study
study intervention
reversible terminator sequencing
Solexa sequencing
PMID: 18987734
Accurate whole human genome sequencing using reversible terminator chemistry. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Nature. 2008 Nov 6;456(7218):53-9.
is a DNA sequencing which allows sequence identification by relying on use of DNA polymerase and reversible terminator. The methods requires immobilization of genomic DNA fragment onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on reversible terminator allow cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing.
Philippe Rocca-Serra
Solexa sequencing
adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009)
material combination objective
bp
PPPB branch
material combination objective
is an objective to obtain an output material that contains several input materials.
In biology, a host is an organism that harbors a virus or parasite, or a mutual or commensal symbiont, typically providing nourishment and shelter. http://en.wikipedia.org/wiki/Host_(biology) 30 March 09
host role
30 Mar09 submitted by vaccine community
30Mar09 virus reproducing inside a cell; bacteria causing a disease, host can be harmed or not. we want to avoid a cat sitting on my lap and an animal care technician; these are not examples or hosts; dental cares = on tooth, but part of outer layer of tooth, so covered by "within" in the definition
OBI
host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role
host role
GROUP: Role Branch
http://en.wikipedia.org/wiki/Host_(biology)
interferon-gamma production
The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.
interferon-gamma production
Chlamydiales
Chlamydiales
1,1-dihydroxy-3-ethoxy-2-butanone
1,1-dihydroxy-3-ethoxy-2-butanone
A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position.
Fungi/Metazoa group
Fungi/Metazoa group
Physcomitrella
Physcomitrella
clinical research coordinator role
clinical research coordinator
clinical research coordinator role
Person:Jennifer Fostel
a worker role comprised of handling the administrative duties of a trial or study.
DNA sequencing by ligation
DNA sequencing by ligation
PERSON: Philippe Rocca-Serra
PMID: 19546169. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding.
McKernan KJ, Peckham HE, Costa G, McLaughlin S, Tsung E, Fu Y,
Clouser C, Dunkan C, Ichikawa J, Lee C, Zhang Z, Sheridan A, Fu H, Ranade S, Dimilanta E, Sokolsky T, Zhang L, Hendrickson C, Li B, Kotler L, Stuart J, Malek J, Manning J, Antipova A, Perez D, Moore M, Hayashibara K, Lyons M, Beaudoin R, Coleman B, Laptewicz M, Sanicandro A, Rhodes M, De La Vega F, Gottimukkala RK, Hyland F, Reese M, Yang S, Bafna V, Bashir A, Macbride A, Aklan C, Kidd JM, Eichler EE, Blanchard AP. Genome Res. 2009 Jun 22.
is a DNA sequencing which relies on DNA ligase activity to perform chain extension during the sequencing reaction step.
material separation device
A device with a separation function realized in a planed process
flow cytometer
material separation device
nucleotide overhang cloning
nucleotide overhang cloning
Cloning vectors are commercially available and supplied in linearized form with 3' dT overhangs
Helen Parkinson
Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation
edge quality calculation
PERSON: Richard Scheuermann
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network.
edge quality calculation
Richard Scheuermann
water
An inorganic hydroxy compound that has formula H2O.
water
cytokine production
The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
cytokine production
Phanerochaete chrysosporium
Phanerochaete chrysosporium
Apini
Apini
Triticum turgidum subsp. dicoccoides
Triticum turgidum subsp. dicoccoides
commelinids
commelinids
N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide
A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents.
N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide
Lolium
Lolium
Heterobasidiomycetes
Heterobasidiomycetes
cytometric bead array assay of epitope specific interleukin-12 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-12 production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cytometric bead array assay of epitope specific interleukin-12 production by T cells
IL-12 release by cytometric bead array
Phanerochaete
Phanerochaete
Enterobacteriales
Enterobacteriales
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100
size exclusion column
A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size.
size exclusion column
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
Mutisieae
Mutisieae
Thermotoga
Thermotoga
liquid chromatography instrument
A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated
PERSON: Matthew Brush
PERSON: Matthew Brush
liquid chromatography instrument
Elisabetta Manduchi
A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling.
loess scale group transformation
Melanie Courtot
loess scale group transformation
OTHER: Editor's generalization based on MGED Ontology term
James Malone
PERSON:Daniel Schober
An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant.
GROUP:<http://msi-ontology.sourceforge.net>
organic acid column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01099
organic acid column
WEB:<http://www.scs.uiuc.edu/NMR/instruments/u400.php>
The predecessor series of the Varian UNITY INOVA spectrometer.
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400237
PERSON:Daniel Schober
Varian UNITY spectrometer
Varian UNITY spectrometer
volume
A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies.
volume
target of material addition
10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export.
A cell culture into which a mixture of peptides is being added.
IEDB
A material entity into which another is being added in a material combinatino process
target of material addition
Equidae
Equidae
Francisella tularensis subsp. novicida
Francisella tularensis subsp. novicida
Corynebacterium glutamicum
Corynebacterium glutamicum
Nicotianeae
Nicotianeae
culture of effector T cells
A cell culture including cells that have an effector T cell function
A culture of cytotoxic CD8+ T cells.
IEDB
culture of effector T cells
in vitro design
MO_347 in_vitro_design
Person: Chris Stoeckert, Jie Zheng
A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture.
in vitro design
WEB:<http://www.shsu.edu/~chm_tgc/publications/JPP/chasteen.htm>
PERSON:Daniel Schober
A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01087
fluorine-induced chemiluminescence detector
fluorine-induced chemiluminescence detector
Corticiaceae
Corticiaceae
epitope specific T cell activation
A process of T cell activation resulting from the recognition of a T cell epitope.
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific T cell activation
obscura group
obscura group
Melanie Courtot
loess group transformation
loess group transformation
Elisabetta Manduchi
A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs.
OTHER: Editor's generalization based on MGED Ontology term
James Malone
Philippe Rocca-Serra
a process by which an event or an entity is described before it actually happens or is being discovered and identified.
Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008 Oct 16;9(1):436. PMID: 18922190
prediction
Philippe Rocca-Serra
OBI
prediction
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific interleukin-10 production by T cells
IL-10 release
An assay that measures epitope specific interleukin-10 production by T cells
assay of epitope specific interleukin-10 production by T cells
IEDB (QTT)
Bruker autosampler
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400209
A Bruker autosampler is an autosampler made by Bruker.
Bruker autosampler
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
Chlamydiae (class)
Chlamydiae (class)
A mixture of peptides that is being added into a cell culture.
IEDB
material to be added
2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes
10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export
a material that is added to another one in a material combination process
material to be added
Euteleostomi
Euteleostomi
Equus
Equus
Chlamydiae
Chlamydiae
translation profiling assay
translation profiling assay
PERSON: James Malone
An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation.
EFO_0001033 translation profiling
epitope specific macrophage inflammatory protein-1 alpha production by T cells
epitope specific macrophage inflammatory protein-1 alpha production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope.
The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems.
high resolution probe with automatic tuning and matching
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400224
High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM
high resolution probe with automatic tuning and matching
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
An device that is used to determine the order of amino acids in protein sequences.
protein sequencer
PERSON: Erik Segerdell
PERSON: Erik Segerdell
protein sequencer
Aphyllophorales
Aphyllophorales
Heliantheae
Heliantheae
Bruker US 2 NMR magnet
An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion.
PERSON:Daniel Schober
Bruker US 2 NMR magnet
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400189
WEB:<http://www.bruker-biospin.com/nmr_magnets_950us2.html>
molecular concentration
molecular concentration
Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg.
the phosphate concentration should be 0.1M
This term represent a quality of molecular concentration. If there is need for some other sort of concentration - e.g. ratio of counts of cells, another term is needed.
OBI uses a standard unit for representing concentration qualities but this still needs to be decided on. A relation needs to be defined that relates the quality instance to the representation of its quantitative value in the chosen units. See http://en.wikipedia.org/wiki/Concentration
Measurements of concentration may be in any appropriate unit. Note that precise concentrations are virtually never known.
Finally, note that there is no such thing as a concentration of 0. A concentration is a *relational* quality and so can't exist unless both entities it inheres in exist. However one map make concentration measurements that turn out not to be about concentrations qualities, if it happens that the scattered molecular aggregate doesn't actually exist.
PERSON: Alan Ruttenberg
A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity.
Clostridia
Clostridia
Alcaligenaceae
Alcaligenaceae
Teleostomi
Teleostomi
A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors).
Elisabetta Manduchi
total intensity transformation paired
OTHER: Adjusted from MGED Ontology
total intensity transformation paired
This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays.
Philippe Rocca-Serra
EDTA methidiumpropylamide
A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe.
EDTA methidiumpropylamide
Francisella
Francisella
temperature control bath
Frank Gibson
temperature control bath
OBI Instrument branch
Alan Ruttenburg
VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C.
Daniel Schober
A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well.
ELISA of epitope specific interleukin-15 production by T cells
IL-15 release by ELISA
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An ELISA that measures epitope specific interleukin-15 production by T cells
ELISA of epitope specific interleukin-15 production by T cells
IEDB (QTT)
Thermotoga maritima
Thermotoga maritima
Capsiceae
Capsiceae
Bovinae
Bovinae
ELISPOT assay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An ELISPOT assay that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
ELISPOT assay of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
IEDB (QTT)
GM-CSF release by ELISPOT
Hymenomycetes
Hymenomycetes
protein expression profiling
a planned process which aims to provide information about protein expression and translation activity using protein extracts collected from a material entity using a range of techniques and instrument such as Mass spectrometers, Gel electrophoresis, Western Blots, Protein microarrays
protein expression profiling
OBI branch derived
Phlippe Rocca-Serra
Protein Expression Profiling During Chick Retinal Maturation: A Proteomics-based approach.
Finnegan S, Robson JL, Wylie M, Healy A, Stitt AW, Curry WJ.
Proteome Sci. 2008 Dec 10;6(1):34.PMID: 19077203
proteomic analysis
http://en.wikipedia.org/wiki/X-ray_generator
A device that is used to generate X-rays.
X-ray source
X-ray source
x-ray generator
PERSON: Erik Segerdell
PERSON:Daniel Schober
Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns.
guard column
guard column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01111
GROUP:<http://msi-ontology.sourceforge.net>
TCD, hot wire detector
PERSON:Daniel Schober
thermal conductivity detector
The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity).
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01084
WEB:<http://www.chromatography-online.org/Preparative/Apparatus/Detectors/rs27.html>
thermal conductivity detector
NMR sample tube
The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter.
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400132
GROUP:<http://msi-ontology.sourceforge.net>
NMR sample tube
delta/epsilon subdivisions
delta/epsilon subdivisions
A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice.
James Malone
Helen Parkinson
OTHER: Adjusted from MGED Ontology
Melanie Courtot
total intensity transformation single
This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)).
Philippe Rocca-Serra
Elisabetta Manduchi
total intensity transformation single
Clostridiales
Clostridiales
Perissodactyla
Perissodactyla
Francisella tularensis
Francisella tularensis
Tetraodon
Tetraodon
balance
A measuring instrument that is used to determine the weight or mass of an object.
PERSON: Erik Segerdell
balance
http://en.wikipedia.org/wiki/Weighing_scale
categorical measurement datum
nominal mesurement datum
Bjoern Peters
A measurement datum that is reported on a categorical scale
categorical measurement datum
Bjoern Peters
MO_1019 cell_component_comparison_design
cell component comparison design
cell component comparison design
A study design that compares samples from different cell components.
Person: Chris Stoeckert, Jie Zheng
Burkholderia cepacia complex
Burkholderia cepacia complex
Polytrichum
Polytrichum
ELISA of epitope specific lymphotoxin A production by T cells
IEDB (QTT)
ELISA of epitope specific lymphotoxin A production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An ELISA that measures epitope specific lymphotoxin A production by T cells
lymphotoxin A (TNFb) release by ELISA
a device that is able to chemically join two or more molecules.
molecular crosslinker
MO ?? cannot be found in MO
Trish Whetzel
molecular crosslinker
molecular crosslinker
Stratalinker
AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly.
mean centering
mean centering
Elisabetta Manduchi
mean centring
PERSON: Elisabetta Manduchi
A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input.
Philippe Rocca-Serra
This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be mean-centered.
Pediococcus
Pediococcus
Hypocreomycetidae
Hypocreomycetidae
Caprinae
Caprinae
Bruker Ultrastabilized NMR magnet
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400188
An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized.
Bruker Ultrastabilized NMR magnet
PERSON:Daniel Schober
WEB:<http://www.bruker-biospin.com/nmr_magnets_ultrastabilized.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F>
solvent mixer
GROUP:<http://msi-ontology.sourceforge.net>
A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry.
PERSON:Daniel Schober
solvent mixer
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01072
Peptococcaceae
Peptococcaceae
Filicopsida
Filicopsida
surface plasmon resonance instrument
A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Surface_plasmon_resonance
surface plasmon resonance instrument
SNP microarray
EFO_0002703 SNP array
Person: Helen Parkinson
a DNA microarray used to detect polymorphisms in DNA samples
SNP microarray
A cytometric bead array assay that measures epitope specific interleukin-5 production by T cells
cytometric bead array assay of epitope specific interleukin-5 production by T cells
IEDB (QTT)
cytometric bead array assay of epitope specific interleukin-5 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IL-5 release by cytometric bead array
Basidiomycota
Basidiomycota
training process
a process that achieves a training objective
e.g. a training course run by a vendor on their instrument, a training service on a assay by a core facility
training process
Polytrichaceae
Polytrichaceae
Ferroplasmaceae
Ferroplasmaceae
Thermoproteus
Thermoproteus
gadolinium molecular entities
gadolinium molecular entities
Vulpes vulpes
Vulpes vulpes
organization
PERSON: Philippe Rocca-Serra
GROUP: OBI
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:
1) there are organization_member_roles (president, treasurer, branch
editor), with individual persons as bearers
2) there are organization_roles (employer, owner, vendor, patent holder)
3) an organization has a charter / rules / bylaws, which specify what roles
there are, how they should be realized, and how to modify the
charter/rules/bylaws themselves.
It is debatable what the organization itself is (some kind of dependent
continuant or an aggregate of people). This also determines who/what the
bearer of organization_roles' are. My personal favorite is still to define
organization as a kind of 'legal entity', but thinking it through leads to
all kinds of questions that are clearly outside the scope of OBI.
Interestingly enough, it does not seem to matter much where we place
organization itself, as long as we can subclass it (University, Corporation,
Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,
W3C, University of Oklahoma), and have it play roles.
This leads to my proposal: We define organization through the statements 1 -
3 above, but without an 'is a' statement for now. We can leave it in its
current place in the is_a hierarchy (material entity) or move it up to
'continuant'. We leave further clarifications to BFO, and close this issue
for now.
PERSON: Bjoern Peters
PERSON: Alan Ruttenberg
PERSON: Susanna Sansone
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
organization
PERSON: Elisabetta Manduchi
This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles.
Elisabetta Manduchi
quantile transformation
quantile transformation
PERSON: Alan Ruttenberg
scattered molecular aggregate
A scattered molecular aggregate is a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates
scattered molecular aggregate
Collective
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
the sodium and chloride ions in a glass of salt water
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01238
A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins.
protein column
protein column
GROUP:<http://msi-ontology.sourceforge.net>
DNA transfection
PERSON:Kevin Clancy
DNA transfection
The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest
OBI branch derived
a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell
melanogaster subgroup
melanogaster subgroup
digital curation
Philippe Rocca-Serra
digital curation
wikipedia
Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
Orbiliaceae
Orbiliaceae
A detection of specific nucleic acids with complementary probes that measures epitope specific transforming growth factor-beta production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
detection of specific nucleic acids with complementary probes of epitope specific transforming growth factor-beta production by T cells
detection of specific nucleic acids with complementary probes of epitope specific transforming growth factor-beta production by T cells
TGFb release by RNA/DNA detection
denaturing high-performance liquid chromatography instrument
A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis.
doi:10.1385/1-59259-850-1:173
denaturing high-performance liquid chromatography instrument
PERSON: Erik Segerdell
Person: Chris Stoeckert, Jie Zheng
RNAi profiling by array design
Group: ArrayExpress production team
A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression.
RNAi profiling by array design
Thermoproteus tenax
Thermoproteus tenax
culture of antigen presenting cells
A culture of PBMCs. A culture of Hela cells.
IEDB
a cell culture including cells that have an antigen presentation function
culture of antigen presenting cells
Burkholderiaceae
Burkholderiaceae
Paxillaceae
Paxillaceae
connective tissue growth factor production
The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
connective tissue growth factor production
Polytrichales
Polytrichales
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01050
A pump system optimized for gradient chromatography.
gradient pump system
gradient pump system
WEB:<http://www.buchi.com/Gradient-Pump-System.531.0.html>
PERSON:Daniel Schober
Pediococcus pentosaceus
Pediococcus pentosaceus
Boletales
Boletales
Construction of pRSS1327 expression vector by molecular cloning of a 1327-bp cDNA, which includes sequences of the entire coding region for RSS, into pBluescript. Expression in Escherichia coli of a functional, full-length RSS was confirmed by immunoblot analysis and enzymatic activity.
vector mediated expression
vector mediated expression sis the generation of copies of biomaterial by in a cell_culture modified for this purpose by insertion of an expression vector
needs defined relationship to cell culture
OBI branch derived
vector mediated expression
PlanAndPlannedProcess Branch
software testing objective
Jennifer Fostel
Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software.
software testing objective
validation
Philippe Rocca-Serra
adapted from wordnet (wkipedia)
validation
PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16.
a planned process with objective to check that the accuracy or the quality of a claim or prediction satisfies some criteria and which is assessed by comparing with independent results
Aspergillus fumigatus
Aspergillus fumigatus
Corynebacterium
Corynebacterium
chromatography splitter
An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities.
chromatography splitter
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01041
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/EC-Dispersion/GC-Capillary-Columns/rs13.html>
Theropoda
Theropoda
innate behavior design
A study design in which the innate behavior of the organism is examined, e.g. path finding in bees.
Person: Chris Stoeckert, Jie Zheng
MO_355 innate_behavior_design
innate behavior design
agarose gel electrophoresis system
A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field.
PERSON: Erik Segerdell
agarose gel electrophoresis system
http://en.wikipedia.org/wiki/Agarose_gel_electrophoresis
Fusobacteria (class)
Fusobacteria (class)
Paxillus
Paxillus
chemokine production
The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
chemokine production
Batrachia
Batrachia
Sordariomycetidae
Sordariomycetidae
Vulpes
Vulpes
Philippe Rocca-Serra
electroporation
PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13.
electropermeabilization
electroporation
a process in which a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA
WEB:http://en.wikipedia.org/wiki/Electroporation
sponsor role
sponsor
Person: Jennifer Fostel
a responsible party role involved with any of the following activities: initiating, managing and funding a study
sponsor role
high temperature column
A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens.
PERSON:Daniel Schober
high temperature column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01233
GROUP:<http://msi-ontology.sourceforge.net>
a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material
pa_branch (Alan, Randi, Kevin, Jay, Bjoern)
recombinant vector cloning
recombinant vector cloning
OBI branch derived
molecular cloning
MO_997 linear_amplification
linear amplification
An example is the use of the T7 promoter for amplification by transcribing many RNA copies.
linear amplification
An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template.
PERSON: Chris Stoeckert, Jie Zheng
Glycine max
Glycine max
Mammalia
Mammalia
Ureaplasma
Ureaplasma
Methanothermobacter
Methanothermobacter
Panarthropoda
Panarthropoda
anion exchange column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01095
An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
anion exchange column
IEDB (QTT)
detection of specific nucleic acids with complementary probes of epitope specific interleukin-6 production by T cells
IL-6 release by RNA/DNA detection
detection of specific nucleic acids with complementary probes of epitope specific interleukin-6 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-6 production by T cells
Methylobacillus flagellatus
Methylobacillus flagellatus
Pasteurellales
Pasteurellales
antigen role
OBI
antigen role
Role Branch
Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response
An antigen is a substance that prompts the generation of antibodies and can cause an immune response. Wikipedia http://en.wikipedia.org/wiki/Antigen. In the strict sense, immunogens are those substances that elicit a response from the immune system, whereas antigens are defined as substances that bind to specific antibodies. Not all antigens produce an immunogenic response, but all immunogens are antigens
Helicobacteraceae
Helicobacteraceae
epitope specific type IV hypersensitivity by T cells
A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope.
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific type IV hypersensitivity by T cells
Philippe Rocca-Serra
wordnet.princeton.edu/perl/webwn
elution
PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13.
the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions)
elution
T cell help
PERSON: Randi Vita, Bjoern Peters
An assay that measures the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function
IEDB
assay of epitope specific T cell helper activity
assay of epitope specific T cell helper activity
Mucosa of nasopharynx
Mucosa of nasopharynx
Methylobacillus
Methylobacillus
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/HPLC/Refractive-Index/rs33.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01081
refractive index detector
refractive index detector
For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector.
fibroblast
A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped.
fibroblast
Campylobacteraceae
Campylobacteraceae
PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81
DNA Subtraction
a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library.
OBI-Branch
Philippe Rocca-Serra
DNA Subtraction
Salmonella enteritidis
Salmonella enteritidis
IEDB
T cell epitope protection experiment based on survival
host survival after challenge
An epitope protection experiment based on survival in which the evaluated responses are made by T cells
PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
T cell epitope protection experiment based on survival
Desulfovibrionales
Desulfovibrionales
genotyping by array design
MO_560 genotyping_design
Person: Chris Stoeckert, Jie Zheng
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology.
genotyping by array design
Deuterostomia
Deuterostomia
Bruker LC-NMR/MS platform
Bruker LC-NMR/MS platform
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400277
Includes the connection to a high-resolution TOF-LC-MS system.
A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.
group:OBI
person:Chris Stoeckert
standard error
standard error
mass spectrometry
PRIDE: PRIDE:0000027
Philippe Rocca-Serra
This is a measuring method consisting of turning elements in a sample into ions, isolating them according to the ratio between the mass and charge numbers and detecting it electrically.
mass spectrometry assay
mass spectrometry assay
Identification of Human Pituitary Growth Hormone Variants by Mass Spectrometry.
Kohler M, Thomas A, Püschel K, Schänzer W, Thevis M.
J Proteome Res. 2009 Jan 5. PMID: 19123788
Methanothermobacter thermautotrophicus
Methanothermobacter thermautotrophicus
Xanthomonadales
Xanthomonadales
Schizosaccharomyces
Schizosaccharomyces
IEDB (QTT)
A cytometric bead array assay that measures epitope specific transforming growth factor-beta production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
TGFb release by cytometric bead array
cytometric bead array assay of epitope specific transforming growth factor-beta production by T cells
cytometric bead array assay of epitope specific transforming growth factor-beta production by T cells
protein complex
A ribosome is a protein complex
Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or other small molecules.
protein complex
T cell response inhibition MHC binding assay
IEDB
IEDB
Incubating OT-1 cells together with their specific epitope SIINFEKL and its restricting MHC H-2 Kb and titrating in different amounts of the peptide SSSNFAKL and reading out proliferation to determine if SSSNFAKL binds H-2 Kb
T cell response inhibition MHC binding assay
An assay in which a T cell line known to respond to a certain MHC:epitope combination is incubated with the known epitope, another ligand to be evaluated and the MHC to determine if the evaluant can outcompete the known reactive epitope which indicates that the evaluant binds the MHC.
Sinorhizobium meliloti
Sinorhizobium meliloti
Philippe Rocca-Serra
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
nucleic acid hybridization
nucleic acid hybridization
a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity.
An assay that measures epitope specific interleukin-1 alpha production by T cells
assay of epitope specific interleukin-1 alpha production by T cells
assay of epitope specific interleukin-1 alpha production by T cells
IL-1a release
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
study design execution
a planned process that realizes the concretization of a study design
branch derived
injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design.
removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired.
study design execution
trial statistician role
trial statistician
trial statistician role
Person:Jennifer Fostel
a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated.
Mycetozoa
Mycetozoa
y-column connector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01237
A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
y-column connector
T cell recognition of HPLC fractionated MHC ligand eluate compared to synthetic ligand
An assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules.
T cell recognition of HPLC fractionated MHC ligand eluate compared to synthetic ligand
IEDB
PERSON: Bjoern Peters, Randi Vita
Schizosaccharomyces pombe
Schizosaccharomyces pombe
ex vivo design
A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment.
ex vivo design
MO_808 ex_vivo_design
Person: Chris Stoeckert, Jie Zheng
Lamiales
Lamiales
specific labeling
OBI branch derived
PlanAndPlannedProcess Branch
The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells
a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material
specific labeling
Mesorhizobium loti
Mesorhizobium loti
Salmonella
Salmonella
Ruminantia
Ruminantia
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400197
A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently.
AVANCE II spectrometer
WEB:<http://cermax.itqb.unl.pt/mambo/en/index.php?option=com_content&task=view&id=36&Itemid=93>
AVANCE II spectrometer
homogeneous polynomial transformation
A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree.
Elisabetta Manduchi
WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html
a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables.
homogeneous polynomial transformation
GROUP:<http://msi-ontology.sourceforge.net>
Bruker MATCH tube holder system
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400211
The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.\n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube.
Bruker MATCH tube holder system
Bruker Multiple Adjustable Tube Clamp Holder
Tina Boussard
anatomical entity
not super happy about liquids (blood, sperm), as they seem to be 'granular' somewhat, and not form a structure.
anatomical entity
Philippe Rocca-Serra
10/20/09: This class and all subclasses are currently problematic. They should all be imported from other OBO foundry ontologies. (FMA / CARO / UBERON). Currently two problems exist: There is no cross species anatomy that covers all the entities we need. Secondly: there is not good boundary between anatomical entities and smaller parts in FMA. Currently we will use anatomical entities as if they are valid across species.
Bjoern Peters
13-02-2009:
Biomaterial branch: change of label and definition following discussions at the OBI winter meeting 2009. It was felt that 'macroscopic part of multicellular organism' introduce an impractical delineation.
IMPORTANT NOTE: OBI 'anatomical entity' would essentially correspond to FMA 'material anatomical entity' rather than FMA 'physical anatomical entity'. OBI does not include 'immaterial anatomical entity' as it would clash with the parent class 'material entity'
DOCUMENTATION NOTE: OBI anatomical entity granularity level excludes cell and biological molecules.
Tissue, organ, system, sperm, blood or body location (arm).
An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'
MO
Biom call - January 2009 - Issues:
parasites are not macroscopic part or organism.
fetus is_a macroscopic part (but this is up for discussion)
cytometric bead array of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
cytometric bead array of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
GM-CSF release by cytometric bead array
A cytometric bead array assay that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
Pseudomonadaceae
Pseudomonadaceae
ELISA of epitope specific IP-10 production by T cells
IEDB (QTT)
ELISA of epitope specific IP-10 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IP-10 release by ELISA
An ELISA that measures epitope specific IP-10 production by T cells
pseudoobscura subgroup
pseudoobscura subgroup
assay of epitope specific interleukin-16 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific interleukin-16 production by T cells
IEDB (QTT)
An assay that measures epitope specific interleukin-16 production by T cells
IL-16 release
Bruker NMR Case sample changer
Bruker NMR Case sample changer
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400203
PERSON:Daniel Schober
WEB:<http://www.bruker-biospin.com/automation.html>
The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats.
Bruker SPE-NMR platform
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400278
A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra.
PERSON:Daniel Schober
Bruker SPE-NMR platform
Philippe Rocca-Serra
Elisabetta Manduchi
linlog transformation
A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm.
PMID: 16646782
linlog transformation
This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782.
Cetartiodactyla
Cetartiodactyla
radioactivity detection binding assay
PERSON:Bjoern
radioactivity detection binding assay
GROUP: OBI
An organism which contains cells or tissues with a different genotype
PERSON: Helen Parkinson
chimera
chimera
Cryptosporidiidae
Cryptosporidiidae
Xanthomonas axonopodis pv. citri
Xanthomonas axonopodis pv. citri
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01052
PERSON:Daniel Schober
A pump system optimized for nano flow chromatography.
nano pump system
nano pump system
GROUP:<http://msi-ontology.sourceforge.net>
Crocosphaera watsonii
Crocosphaera watsonii
T cell activation
T cell activation
The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
PERSON: Philippe Rocca-Serra
PERSON: Maura Gasparetto
blood serum specimen
WEB: http://en.wikipedia.org/wiki/Blood_plasma
A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
PERSON: Melanie Courtot
PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
blood serum specimen
auto injector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01058
A gas chromatography device that can auto-inject a small number of samples an inlet.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
auto injector
James Malone
variance stabilizing transformation
variance stabilizing transformation
A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper.
Elisabetta Manduchi
This can be used for expression microarray assay normalization and it is referred to as "variance stabilizing normalization", according to the procedure described e.g. in PMID 12169536.
PMID: 12169536
Melanie Courtot
variance stabilising transformation
Thermoanaerobacteriales
Thermoanaerobacteriales
Vibrionales
Vibrionales
Crocosphaera
Crocosphaera
James Malone
OTHER: Editor's generalization based on MGED Ontology term
Melanie Courtot
Philippe Rocca-Serra
loess global transformation
A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation.
Elisabetta Manduchi
loess global transformation
PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
plasma
blood plasma specimen
blood plasma specimen
PERSON: Melanie Courtot
PERSON: Maura Gasparetto
03/21/2010: BP, blood plasma is defined as the output of certain separation processes, so this is in the domain of OBI, not FMA.
WEB: http://en.wikipedia.org/wiki/Blood_plasma
PERSON: Philippe Rocca-Serra
a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended.
Nematoda
Nematoda
Varian NMR instrument
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400234
An NMR instrument that is manufactured by Varian.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
Varian NMR instrument
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400205
washing system/NMR tube washing system, XPS: device has function washing
NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material.
WEB:<http://www.used-line.com/c5983250s10028-Bruker_Biospin_NMR_Autoclean_Nuclear_Magnetic_Resonance_Organic_Solvents.htm>
Bruker AutoClean system
Bruker AutoClean system
is a planned process with specified input original document and specified output edited document
adapted from wikipedia
document editing
Philippe Rocca-Serra and OBI consortium
Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL.
Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
document editing
Dinosauria
Dinosauria
voltage clamp device
PERSON: Erik Segerdell
voltage clamp device
A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level.
http://en.wikipedia.org/wiki/Voltage_clamp
Candida dubliniensis
Candida dubliniensis
fluorescence
A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together.
fluorescence
Alteromonadales
Alteromonadales
luciferin
A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase.
luciferin
MO_84 OrganismStatus
specimen with pre- or post-mortem status
organizational term, used in description of specimen that is created from known pre- or post-mortem status
PERSON: Chris Stoeckert, Jie Zheng
specimen with pre- or post-mortem status
A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism.
Aquificaceae
Aquificaceae
Saurischia
Saurischia
Neosartorya fischeri
Neosartorya fischeri
volumetric flow rate unit
A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time .
volumetric flow rate unit
Moorella group
Moorella group
is a process in which following administration of a bolus a glucose in-vivo, glucose clearance from blood plasma is monitored over time by repeated glucose measurement in blood serum. the output of a process is a measure which can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance.
glucose tolerance test
Philippe Rocca-Serra
PMID: 19527607
Using the 100-g Oral Glucose Tolerance Test to Predict Fetal and Maternal Outcomes in Women with Gestational Diabetes Mellitus.
Lin CH, Wen SF, Wu YH, Huang MJ.
Chang Gung Med J. 2009 May-Jun;32(3):283-9.
NuGO OBI plan branch
glucose tolerance test
Neosartorya fischeri group
Neosartorya fischeri group
Gadiformes
Gadiformes
dissolved material entity
A material entity that has been going through a process of being put into solution
dissolved material entity
Person:Bjoern Peters
Salt molecules that have been mixed into water
Philippe Rocca-Serra
epitope specific interleukin-23 production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific interleukin-23 production by T cells
A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope.
PERSON: Philippe Rocca-Serra
Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic).
PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes.
phosphate buffered saline solution
WEB: http://en.wikipedia.org/wiki/Phosphate_buffered_saline
phosphate buffered saline solution
PERSON: Tina Boussard
PBS buffer
PERSON: Melanie Courtot
purification
purification
MO_406 purify
PERSON: Chris Stoeckert, Jie Zheng
A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest
Tylenchida
Tylenchida
Lactococcus lactis
Lactococcus lactis
T cell epitope treatment experiment
An epitope treatment experiment in which the evaluated response is made by T cells
IEDB
PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
T cell epitope treatment experiment
treatment assay, decreased disease symptoms
Thermoplasmata
Thermoplasmata
Ascomycota
Ascomycota
paired-end tag (PET) library
Philippe Rocca-Serra
paired-end library
mate-paired library
adapted from information provided by Solid web site
PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y.
is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs
paired-end library
Richard Scheuermann
PERSON: Richard Scheuermann
A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node.
node degree calculation
node degree calculation
Alexa Fluor 546
Alexa Fluor 546
An organic heteropentacyclic compound that has formula C44H45Cl3N4NaO14S3.
IEDB (QTT)
detection of specific nucleic acids with complementary probes of epitope specific interleukin-27 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-27 production by T cells
IL-27 release by RNA/DNA detection
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
detection of specific nucleic acids with complementary probes of epitope specific interleukin-27 production by T cells
Epstein Barr virus transformed B cell
PERSON: Susanna Sansone
Epstein Barr virus transformed B cell
PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8.
A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
GROUP: OBI Biomaterial Branch
Heteroderidae
Heteroderidae
An ion detector is a device that measures and records
the charge induced or current produced when an ion passes by or hits a
surface. In a scanning instrument the signal produced in the detector
during the course of the scan versus where the instrument is in the
scan (at what m/Q) will produce a mass spectrum, a record of ions as a
function of m/Q.
ion detector
http://en.wikipedia.org/wiki/Mass_spectrometry#Detector
ion detector
The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation
Frank Gibson
Thermococci
Thermococci
sampling time measurement datum
A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point.
MO_738 timepoint
Person: Chris Stoeckert
sampling time measurement datum
time point
Guava EasyCyte Mini
A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputting cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement.
http://www.guavatechnologies.com/main/products/easyCyteMini.cfm
Guava EasyCyte Mini
John Quinn
Group 2 species
Group 2 species
PERSON: Jie Zheng
Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)
polyA RNA extract
UPenn Group
PERSON: Chris Stoeckert
polyA RNA extract
A RNA extract that is the output of an extraction process in which RNA molecules with poly A tail at its 3’ end are purified.
Leishmania mexicana species complex
Leishmania mexicana species complex
Culicoidea
Culicoidea
quantitative node degree calculation
Richard Scheuermann
quantitative node degree calculation
PERSON: Richard Scheuermann
A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node.
Gadidae
Gadidae
Rhabditida
Rhabditida
Platichthys
Platichthys
Person:Bjoern Peters
edited document
The OBI manuscript is (much) edited imformation
A document which is the output of a document editing process
edited document
Philippe Rocca-Serra
An assay in which ligands are eluted from MHC molecules and identified by Edman degradation
Edman degradation of eluted MHC ligands
Edman degradation of eluted MHC ligands
PERSON: Bjoern Peters, Randi Vita
IEDB
phenotype
phenotype
A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species.
A Guava_EasyCyte_Plus System is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 4 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The EasyCyte plus accepts 96 well plates as well as tubes. The Guava_EasyCyte_Plus cytometer is a small portable cytometer particularly useful for field measurement.
http://www.guavatechnologies.com/main/products/easycyte-new.cfm
Guava EasyCyte Plus
John Quinn
Guava EasyCyte Plus
Leishmania major species complex
Leishmania major species complex
Saliceae
Saliceae
Mus
Mus
assay of epitope specific interleukin-18 production by T cells
IL-18 release
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific interleukin-18 production by T cells
IEDB (QTT)
An assay that measures epitope specific interleukin-18 production by T cells
Adjuvants are pharmacological or immunological agents that modify the effect of other agents (e.g., drugs, vaccines) while having few if any direct effects when given by themselves. http://en.wikipedia.org/wiki/Adjuvant
GROUP: Role branch
The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen.
immunologic adjuvant role
Vaccine Ontology, Wikipedia, OBI
11Feb09:Vaccine Ontology Definition: Adjuvant boosts immune response of a vaccine or antigen in the host.
the role 'adjuvant role' inheres in some 'material entity' and is realized by some 'immune response assay'.
immunologic adjuvant role
PERSON: Richard Scheuermann
A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node.
node in-degree calculation
Richard Scheuermann
node in-degree calculation
Deltaproteobacteria
Deltaproteobacteria
metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism
metabolite assay
Philippe Rocca-Serra
OBI
metabolite profiling
metabolite profiling
Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019
A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance
calibration substance role
calibration substance role
Jennifer Fostel
pH buffer used to calibrate a pH meter bears a calibration substance role
Saccharomycetaceae
Saccharomycetaceae
Parvoviridae
Parvoviridae
PMID: 18612301. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. Nat Biotechnol. 2008 Jul;26(7):779-85.
is an assay which aims at identifying methylated sites in genomic DNA and determining methylation pattern that affect gene transcription by relying on immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods.
Methylated DNA immunoprecipitation sequencing assay
adapted from wikipedia
Philippe Rocca-Serra
MeDIP-SEQ assay
MeDIP-SEQ assay
PERSON: Randi Vita; Bjoern Peters; Jason Greenbaum; Jorg Calis
fluoresence detection
IEDB
fluoresence detection
Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for.
an assay in which a materials fluorescence is determined
atmosphere
A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism.
MO_219 atmosphere
PERSON: Chris Stoeckert, Jie Zheng
atmosphere
Pinus [NCBITaxon:139271]
Pinus [NCBITaxon:139271]
guanyl-specific ribonuclease T1
A protein that is a translation product of the Aspergillus oryzae rntA gene or a 1:1 ortholog thereof.
guanyl-specific ribonuclease T1
A robotic device that is used to excise spots from gels.
PERSON: Erik Segerdell
spot cutter
spot cutter
PERSON: Erik Segerdell
Caenorhabditis briggsae
Caenorhabditis briggsae
Apocrita
Apocrita
intracellular cytokine staining assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
intracellular cytokine staining (ICS), cytokine release TNF
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An intracellular cytokine staining assay that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
TNF release by ICS
intracellular cytokine staining assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
Phaseoleae
Phaseoleae
http://en.wikipedia.org/wiki/Gas_laser
A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emission amplification. The gas is excited to emit light via an external light source or an electric current discharging through the gas.
Daniel Schober
helium-neon gas laser used to erradiate cells in a flow cytometer.
gas laser
John Quinn
gas laser
proton
Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u.
proton
Schizosaccharomycetaceae
Schizosaccharomycetaceae
A device that is used to apply microwave irradiation to chemical reactions.
microwave synthesis system
microwave synthesis system
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Microwave_chemistry
N-ethyl-N-nitrosourea
N-ethyl-N-nitrosourea
Caenorhabditis
Caenorhabditis
a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector
recombination enzyme based cloning
recombination enzyme based cloning
epitope specific perforin production by T cells
PERSON: Bjoern Peters, Randi Vita
Should be linked to a GO process, which will be requested by IEDB team. Along with granzyme B production, should be tied to T cell degranulation
The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope.
epitope specific perforin production by T cells
fluorescence detection binding assay
Bjoern
fluorescence detection binding assay
Rhizobium leguminosarum
Rhizobium leguminosarum
Gadus
Gadus
epitope specific monocyte chemotactic protein-1 production by T cells
IEDB (QTT)
epitope specific monocyte chemotactic protein-1 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope.
Saccharomycetes
Saccharomycetes
John Quinn
http://en.wikipedia.org/wiki/Flow_cytometer
FACS Calibur
A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.
flow cytometer
flow cytometer
Nostoc punctiforme
Nostoc punctiforme
http://en.wikipedia.org/wiki/Densitometer
A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface.
densitometer
densitometer
PERSON: Erik Segerdell
ion source
An ion source is a device that is part of a mass
spectrometer that ionizes the material under analysis. The ions are
then transported by magnetic or electric fields to the mass analyzer.
Techniques for ionization have been key to determining what types of
samples can be analyzed by mass spectrometry. Electron ionization and
chemical ionization are used for gases and vapors. In chemical
ionization sources, the material is ionized by chemical ion-molecule
reactions during collisions in the source. Two techniques often used
with liquid and solid biological samples include electrospray
ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser
desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp
(Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson
(Editor) (ISBN 0-941901-31-9))).
ion source
http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source
Frank Gibson
The ion source of a Voyager-DE‚Ñ¢ STR Biospectrometry Workstation
The peptide SIINFEKL binding to an empty murine H-2 Kb molecule to form a complex.
MHC protein complex binding to ligand
The process in which a ligand binds to an MHC molecule to form a stable complex
IEDB
6/13/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point.
PERSON: Bjoern Peters; Randi Vita
MHC protein complex binding to ligand
Diprotodontia
Diprotodontia
Gadus morhua
Gadus morhua
ABI 377 automated sequencer
is a DNA sequencer which is manufactured by Applied Biosystems corporation (formerly Perkin-Elmer). It allows automated chain termination DNA sequencing. It has part polyacrylamide gel electrophoresis system and a laser -based detection system to detect fluorescence intensity emitted by the dyes attached to the dideoxyterminator nucleotides or to the primers.
Applied Biosystems
Applied Biosystems
Philippe Rocca-Serra
Applied Biosystems
ABI 377 automated sequencer
Philippe Rocca-Serra
age
A time quality inhering in a bearer by virtue of how long the bearer has existed.
age
Cytophaga hutchinsonii
Cytophaga hutchinsonii
IP-10 release by RNA/DNA detection
IEDB (QTT)
detection of specific nucleic acids with complementary probes of epitope specific IP-10 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific IP-10 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
detection of specific nucleic acids with complementary probes of epitope specific IP-10 production by T cells
Entomoplasmatales
Entomoplasmatales
IEDB (QTT)
intracellular cytokine staining assay of epitope specific interleukin-22 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IL-22 release by ICS
An intracellular cytokine staining assay that measures epitope specific interleukin-22 production by T cells
intracellular cytokine staining assay of epitope specific interleukin-22 production by T cells
fluid pressure regulator
Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less frequently nitrogen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank.
Person: John Quinn
fluid pressure regulator
LSR2 fluid pressure regulator
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Saccharomycetales
Saccharomycetales
automatic staining machine
PERSON: Erik Segerdell
automatic staining machine
A device that is used to automatically stain tissue sections on slides or tissue specimens.
PERSON: Erik Segerdell
Caenorhabditis elegans
Caenorhabditis elegans
MO_374 dissect
A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures.
dissection
dissection
EFO_0003856 dissection
PERSON: Chris Stoeckert, Jie Zheng
Philippe Rocca-Serra
OBI plan and planned process branch
is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity
immunoprecipitation
PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8.
immunoprecipitation
pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material..
OBI
centrifuge pellet role
Definition of pellet :the material concentrated at the bottom of a centrifuge tube after centrifugation. http://www.everythingbio.com/glos/definition.php?word=pellet
GROUP: Role branch
centrifuge pellet role
number of lost events electronic
number of lost events electronic
74, 0, 14 events lost due to data acquisition electronic coincidence.
A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role.
person:Kevin Clancy
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
Glycine
Glycine
A cell culture analyte detection bioassay that measures epitope specific interleukin-3 production by T cells
IEDB (QTT)
cell culture analyte detection bioassay of epitope specific interleukin-3 production by T cells
IL-3 release by bioassay
cell culture analyte detection bioassay of epitope specific interleukin-3 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An assay that measures the production of perforin by T cells in response to the recognition of a T cell epitope
assay of epitope specific perforin release by T cells
PERSON: Bjoern Peters, Randi Vita
IEDB
assay of epitope specific perforin release by T cells
perforin release
pathologist role
Pathologist
pathologist role
Person:Jennifer Fostel
a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline
reference substance
Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
Person:Jennifer Fostel
reference substance role
a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference.
reference substance role
OBI
phenolsulfonphthalein
phenolsulfonphthalein
interleukin-14 production
The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-14 production
Elizabeth M. Goralczyk
Olga Tchuvatkina
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser.
John Quinn
light source
light source
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Clostridium sporogenes
Clostridium sporogenes
labeled specimen
A specimen that has been modified in order to be able to detect it in future experiments
OBI group
added during call 3/1/2010
labeled specimen
immunoglobulin complex, circulating
antibody
An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component.
immunoglobulin complex, circulating
contact to pathogen carrying biological vector
a process in which a vector carrying an infectious agent comes close enough to a potential host organism that a contact can result
contact to pathogen carrying biological vector
IEDB
IEDB
Melanie Courtot
spectrophotometer
spectrophotometer
Trish Whetzel
A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance.
MO
Helios Gamma Spectrophotometer
individual organism identifier
PERSON: Chris Stoeckert, Jie Zheng
MO_169 Individual
a symbol used to distinguish one individual organism from another.
individual organism identifier
confocal microscope
http://en.wikipedia.org/wiki/Confocal_microscopy
A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane.
confocal microscope
PERSON: Erik Segerdell
a device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125.
Daniel Schober
google
supernatant collection system harvesting frame
supernatant collection system harvesting frame
sample from organism
sample from organism
we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about.
5/29: This is a helper class for now
a material obtained from an organism in order to be a representative of the whole
Rhodospirillaceae
Rhodospirillaceae
MO
Piko(tm) 96-well Thermal Cycler
An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
thermal cycler
DNA_amplifier
Trish Whetzel
thermal cycler
Melanie Courtot
PCR_machine
thermocycler
Polymerase_Chain_Reaction_ machine
A laser is the most common way to irradiate a cell in a flow cytometer.
laser
light amplification by the stimulated emission of radiation
A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that contains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer.
John Quinn
laser
http://en.wikipedia.org/wiki/Laser
Daniel Schober
interleukin-15 production
The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-15 production
infectious agent
infectious agent
IEDB
IEDB
is a material entity bearing the disposition to infect an organism
Chlamydiaceae
Chlamydiaceae
dye swap quality control role
MO_524 dye_swap_quality_control
PERSON: Chris Stoeckert, Jie Zheng
a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes
dye swap quality control role
An image acquisition device that is responsive to an infrared emissive target within a given field of view.
infrared image acquisition device
infrared image acquisition device
PERSON: Erik Segerdell
United States Patent 4107530
Pterygota
Pterygota
obsolete_diethyl pyrocarbonate
Replaced by CHEBI_59051 Diethylpyrocarbonate
obsolete_diethyl pyrocarbonate
Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group.
Added duirng Mar 1, 2010 dev call
labeled RNA extract
labeled RNA extract
Group: OBI group
a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments.
Group: OBI group
interleukin-12 production
The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-12 production
long pass filter
750 LP filter
A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm.
long pass filter
John Quinn
http://en.wikipedia.org/wiki/high-pass_filter
small-animal image acquisition device
PERSON: Erik Segerdell
PERSON: Erik Segerdell
A device that is used to image small laboratory animals (e.g., rats and mice) in vivo.
small-animal image acquisition device
oligonucleotide synthesizer
An instrument used to chemically synthesize oligonucleotides.
Trish Whetzel
oligonucleotide synthesizer
Automated Multiplex Oligonucleotide Synthesizer
MO
MO_221 labeledExtract
Person: Jie Zheng
labeled nucleic acid extract
a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments.
labeled extract
labeled nucleic acid extract
cytological stain role
cytological stain role
cytological stain
a role of a stain that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization
Person:Helen Parkinson
Person:Jennifer Fostel
haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin
Elisabetta Manduchi
unit-variance scaling
unit-variance scaling
A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable.
Philippe Rocca-Serra
autoscaling
PMID:16762068
basophil
Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive.
basophil
Burkholderia mallei
Burkholderia mallei
Burkholderia pseudomallei
Burkholderia pseudomallei
statistical hypothesis test
James Malone
A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test.
PERSON: James Malone
statistical hypothesis test
lymphocyte
A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
lymphocyte
A specimen that has been frozen in order to store it.
Person:Alan Ruttenberg
frozen specimen
MO_610 frozen_sample
Frozen blood plasma
frozen specimen
surface plasmon resonance assay
PERSON:Bjoern Peters
surface plasmon resonance assay
IEDB
SPR assay
surface plasmon resonance
Running a Biacore instrument to measure the affinity, on and off rates of binding of a plate bound antibody to a antigen passing by in flow.
An assay that uses the detection of electromagnetic waves in a surface to
detect material entities adsorbed to the surface, which changes the local
index of refraction
Sphingomonadaceae
Sphingomonadaceae
interleukin-13 production
The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-13 production
logarithmic voltage amplifier
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
logarithmic voltage amplifier
HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH
A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportional to the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale.
Euteleostei
Euteleostei
environmental proximity to infectious agent
environmental proximity to infectious agent
IEDB
IEDB
Is a process in which an infectious agent comes close enough to a potential host organism in its habitat that a contact can result
PERSON: Erik Segerdell
incubator shaker
An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures).
PERSON: Erik Segerdell
incubator shaker
sonicator
Trish Whetzel
Sonicator 3000
sonicator
An instrument that converts a variable electrical current to mechanical vibration of a metallic probe. The instrument is used for the lysis of cells, the mixing of compounds or solutions, or to create emulsions.
MO
binding constant
A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process
PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum
The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants "IC50 = 12 nM" or "t 1/2 = 30 minutes".
binding constant
Neolepidoptera
Neolepidoptera
WEB:<http://homepages.onsnet.nu/%7Ealkema/html/whatisgc.html>
A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier.
PERSON:Daniel Schober
mass selective detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01198
mass spectrometry detector
mass selective detector
list-mode data file
One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people.
A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter.
list-mode data file
group:Flow Cytometry community
An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used.
person:Chris Stoeckert
A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data.
center value
PERSON: Monnie McGee
centre value
center value
PERSON: James Malone
Mycosphaerellaceae
Mycosphaerellaceae
jet_in_air_flow_chamber
A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermittent media other than air.
Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter
John Quinn
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
jet_in_air_flow_chamber
Bombyciformes
Bombyciformes
Aedes/Ochlerotatus group
Aedes/Ochlerotatus group
DNA polymerase complex
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
DNA polymerase complex
Heteroneura
Heteroneura
Bifidobacterium longum
Bifidobacterium longum
ArrayIt(r) Microarray Wash Station
microarray wash station
microarray wash station
MO_626 wash_station
a device that is used to wash Affymetrix-type arrays.
Trish Whetzel
Nocardiopsaceae
Nocardiopsaceae
cloning vector
A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site.
cloning vector
NTP-2000
Jennifer Fostel, Bjoern Peters
NTP-2000
a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents
cytometric bead array assay
multiplexed bead assay, CBA assay
Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture
PERSON:Bjoern Peters
cytometric bead array
An assay in which a series of beads coated with antibodies specific for different analytes and marked with discrete fluorescent labels are used to simultaneously capture and quantitate soluble analytes using flow cytometric analysis.
cytometric bead array assay
contract research organization role
contract research organization
contract research organization role
Person: Jennifer Fostel
a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution
A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
Frank Gibson
http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer
The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation
mass analyzer
PERSON: Daniel Schober
mass analyzer
hypothesis test objective
is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation
Person:Helen Parkinson
James Malone
WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing
statistical hypothesis test objective
statistical hypothesis test objective
ion laser
An ion laser is a gas laser which uses an ionized gas as its lasing medium.
http://en.wikipedia.org/wiki/Ion_laser
John Quinn
Daniel Schober
ion laser
2 Watt Lexel 88 Argon Ion laser
antigen processing and presentation
The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
antigen processing and presentation
Bjoern Peters
a information content entity created to indicate that information about something is not available to the person recording it.
record of missing knowledge
record of missing knowledge
This class should probably end up in IAO. It could be further breaken down to indicate different kinds of lack of knowledge, e.g. inability to determine something vs. no attempt made to determine something vs. no informatino available if it was even attempted to determine something. The design pattern should be generalizable. 'unknown sex' is the first example, and needed immediately.
A statement in a journal article indicating that the age of a patient at the onset of disease is not known. A statement indicating that the weight of a mouse was not measured.
network graph quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole.
PERSON: Richard Scheuermann
Richard Scheuermann
network graph quality calculation
Populus tremula x Populus alba
Populus tremula x Populus alba
Eimeriorina
Eimeriorina
Burkholderiales Genera incertae sedis
Burkholderiales Genera incertae sedis
Thermobifida
Thermobifida
single fragment library
Philippe Rocca-Serra
fragment library
is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs
single fragment library
exposure resulting in immune reactivity
a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity
IEDB
exposure resulting in immune reactivity
IEDB
Melanie Courtot
A LactoScope_C4 is a spectrophotometer with which the composition of milk and milk products is analysed via infrared technology. The LactoScope determines the amount of the constituents fat, protein, lactose and the total solids content with extreme accuracy.
LactoScope C4 Automatic Economical
http://www.aicompanies.com/DeltaCD/lacto_ftir_auto.htm
LactoScope C4
LactoScope C4
Josef Spidlen
subgraph modularity calculation
A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity.
PERSON: Richard Scheuermann
Richard Scheuermann
subgraph modularity calculation
Person: Jennifer Fostel
a reference participant role which is realized by making the reference to qualities at the start of the study or intervention
baseline participant role
baseline participant role
Subject at time = 0; subject before a stress test.
baseline participant
reduced dimension data set
PERSON: James Malone
PERSON: Monnie McGee
reduced dimension data set
A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set.
PERSON: James Malone
classified data set
PERSON: Monnie McGee
data set with assigned class labels
A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels.
classified data set
Euphyllophyta
Euphyllophyta
total RNA extraction
UPenn Group
Person: Chris Stoeckert
total RNA extraction
A RNA extraction process in which total cellular and organelle RNA are extracted.
Person: Jie Zheng
Acidithiobacillus
Acidithiobacillus
filtration
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
filtration
Philippe Rocca-Serra
OBI-Branch: adapted from wikipedia and wordnet
Yersinia
Yersinia
sodium chloride
An inorganic chloride salt that has formula ClNa.
sodium chloride
Borrelia burgdorferi group
Borrelia burgdorferi group
interleukin-16 production
The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-16 production
Student's t-test
WEB: http://en.wikipedia.org/wiki/T-test
Student's t-test
Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value.
James Malone
Model 777 Microarray Oven
vacuum dryer
Trish Whetzel
An instrument which removes liquid by the application of negative pressure, i.e. vacuum.
vacuum dryer
MO
intra subgraph connectivity calculation
A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph.
PERSON: Richard Scheuermann
Richard Scheuermann
intra subgraph connectivity calculation
role of independent data monitoring committee
independent data monitoring committee
role of independent data monitoring committee
Person: Jennifer Fostel
a trial monitor role charged recommending whether to continue, modify, or end the trial
krypton ion laser
Lexel 95L krypton laser
John Quinn
Daniel Schober
krypton ion laser
A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerful line), and 676 nm all at once. They have much lower gain than argon lasers however.
inductive reasoning
Bjoern Peters
inductive reasoning
wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning
Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer.
a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns.
western blot analysis
PMID: 6266278. "Western blotting": electrophoretic transfer of proteins from sodium dodecyl sulfate--polyacrylamide gels to unmodified nitrocellulose and radiographic detection with antibody and radioiodinated protein A. Anal Biochem. 1981 Apr;112(2):195-203
western blot analysis
a western blot analysis is an assay which allows detection of protein present in a extract resolved on polyacrylamide gel by electrophoresis, transferedd to a membrane made of nitrocellulose or polyvinylidene difluoride and immobilized using formaldehyde based cross linking. Specific proteins are probed using specific antibodies. detection is carried by staining with secondary antibody usually linked to biotin or to a reporter enzyme such as alkaline phosphatase or horseradish peroxidase. This means that several secondary antibodies will bind to one primary antibody and enhance the signal. Most commonly, a horseradish peroxidase-linked secondary is used to cleave a chemiluminescent agent, and the reaction product produces luminescence in proportion to the amount of protein. Detection can only be achieved by radio marking antibodies and using Phosphor imagers.
wikipedia
person: Philippe Rocca-Serra
protein immunoblotting
Francisellaceae
Francisellaceae
Rhizobium
Rhizobium
nucleic acid extraction using phenol chloroform
A material separation in which a desired component of an input material is separated from the remainder
extraction
extraction
Philippe Rocca-Serra
Person:Bjoern Peters
spike-in quality control role
MO_937 spike_quality_control
PERSON: Chris Stoeckert, Jie Zheng, Bjoern Peter
a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes
spike-in quality control role
Teleostei
Teleostei
deoxyribonucleic acids
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
deoxyribonucleic acids
Kevin Clancy, Bjoern Peters
restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector.
restriction enzyme based cloning
restriction enzyme based cloning
type IV hypersensitivity
An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation.
type IV hypersensitivity
A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created.
vortexer
VWR Genie 2
Melanie Courtot
Trish Whetzel
http://en.wikipedia.org/wiki/Vortex_mixer
vortex_mixer
vortexer
MO_437 gene_knock_in
a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a "targeted" insertion.
gene knock in
gene knock in
WEB: http://en.wikipedia.org/wiki/Gene_Knock-in
PERSON: Chris Stoeckert, Jie Zheng
carbon nanotube column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01107
Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well.
PERSON:Daniel Schober
WEB:<http://pubs.acs.org/cgi-bin/abstract.cgi/ancham/2005/77/i21/abs/ac050812j.html>
carbon nanotube column
Group: OBI group
wild type organism genotype information
proposed and discussed on San Diego OBI workshop, March 2011
a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms.
C57BL/6J wild type
wild type organism genotype information
Group: OBI group
Treponema pallidum
Treponema pallidum
Bilateria
Bilateria
Bordetella bronchiseptica
Bordetella bronchiseptica
dye role
A substance used to color materials www.answers.com/topic/dye 19feb09
Label role is a reagent role which inheres in a material entity and which is realized in the process of dyeing or imparting color to a target material
dye
Jennifer Fostel
dye role
portioning objective
The objective to obtain multiple aliquots of an enzyme preparation.
is the objective to separate material into multiple portions, each of which contains a similar composition of the input material.
portioning objective
PERSON: Frank Gibson
PERSON: Daniel Schober
PERSON: Melanie Courtot
Example: 'to blood pump' function_of 'heart'
function_of
GROUP:OBI:<http://obi.sourceforge.net>
A relation between a function F and an entity E. F function_of E iff: Q inheres_in E and Q is a function
PERSON: Chris Mungall
function_of
Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data.
consume data function
consume data function
electrical conductivity detector
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01239
The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area.
WEB:<http://www.chromatography-online.org/HPLC-Detectors/Electrical-Conductivity/rs83.html>
electrical conductivity detector
quaternary pump system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01047
A pump system that pump and mix up to four different solvents in parallel.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
quaternary pump system
interleukin-1 alpha production
The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-1 alpha production
IEDB (QTT)
assay of epitope specific interleukin-17 production by T cells
IL-17 release
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific interleukin-17 production by T cells
An assay that measures epitope specific interleukin-17 production by T cells
Bordetella
Bordetella
PERSON: Frank Gibson, Helen Parkinson
The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron
extracellular electrophysiology recording
An extracellular electrophysiology recording is process where the recording location of the electrode is extracellular and data
PERSON: Frank Gibson
extracellular electrophysiology recording
average value
PERSON: James Malone
PERSON: Monnie McGee
average value
A data item that is produced as the output of an averaging data transformation and represents the average value of the input data.
Cluster of the lymphocytes population.
person:Allyson
cluster
person:Chris Stoeckert
A data set which is a subset of data that are a similar to each other in some way.
group:OBI
cluster
NMR instrument
GROUP:<http://msi-ontology.sourceforge.net>
NMR instrument
An Instrument which is used to carry out a NMR analysis of some sample.
NMR instrument
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400059
PERSON:Daniel Schober
Sophophora
Sophophora
Acoelomata
Acoelomata
Asteroideae
Asteroideae
Bacteria
Solanoideae
Solanoideae
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A cytometric bead array assay that measures epitope specific interleukin-17 production by T cells
IL-17 release by cytometric bead array
cytometric bead array assay of epitope specific interleukin-17 production by T cells
IEDB (QTT)
cytometric bead array assay of epitope specific interleukin-17 production by T cells
PMID:16762068
Elisabetta Manduchi
A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable.
pareto scaling
Philippe Rocca-Serra
pareto scaling
WEB:http://www.uhhospitals.org/tabid/591/Default.aspx # A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation.
WEB:http://www.sceoc.com/glossaryofterms/ # a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students.
WEB:http://www.thebody.org/content/treat/art2612.html # a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site).
a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study.
Jennifer Fostel
In statistics and demography, a cohort is a group of subjects - most often humans from a given population - defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008
cohort role
cohort role
PERSON:Daniel Schober
Bruker UltraShield NMR magnet
Bruker UltraShield NMR magnet
An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design.
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400187
WEB:<http://www.bruker-biospin.com/nmr_magnets_us.html?&print=http%3A%2Fitsupportunit.com%2Fawstats%2Ficon%2Fnisum%2Fivuj%2F>
measure function
PERSON: Daniel Schober
PERSON:Frank Gibson
A glucometer measures blood glucose concentration, the glucometer has a measure function.
PERSON: Melanie Courtot
measure function
Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference.
PERSON: Helen Parkinson
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400193
GROUP:<http://msi-ontology.sourceforge.net>
Bruker solid magic angle spinning probe
PERSON:Daniel Schober
Bruker solid magic angle spinning probe
solid MAS probe
Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei.
Oryza sativa
Oryza sativa
Desulfitobacterium
Desulfitobacterium
A cytometric bead array assay that measures epitope specific interleukin-10 production by T cells
cytometric bead array assay of epitope specific interleukin-10 production by T cells
IL-10 release by cytometric bead array
IEDB (QTT)
cytometric bead array assay of epitope specific interleukin-10 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Canis
Canis
Bartonella quintana
Bartonella quintana
Helen Parkinson
Benjamini and Hochberg false discovery rate correction method
A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate
Statistical significance of the 8 most represented biological processes (GO level 4) among E7 6 month upregulated genes following analysis with DAVID software; Benjamini-Hochberg FDR (false discovery rate)
2011-03-31: [PRS].
specified input and output of dt which were missing
Benjamini and Hochberg false discovery rate correction method
Philippe Rocca-Serra
Helen Parkinson
www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf
PlanAndPlannedProcess Branch
OBI branch derived
Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules.
artificially induced nucleic acid hybridization
artificially induced nucleic acid hybridization
Label role is a role which inheres in a material entity and which is realized in a detection of label assay
label role
need to add a restriction that the material entity has the disposition / quality that permits it to be detected, and one way to say this (BP) is that the entity is such that an assay exists that detects the presence of the material entity
label role
Role Branch
label
Nucleotides synthesized with the incorporation of biotin were used to synthesize cDNA, which was then detected by adding fluorochrome-conjugated anti-biotin antibody. the fluorochrome bears label role, the antibody bears detector role, the biotin bears reporter role. may need to change the terms following discussion
OBI
we need to sort out probe, detector and reporter. See https://sourceforge.net/tracker/index.php?func=detail&aid=1866458&group_id=177891&atid=886178
WEB:<http://www.chromatography-online.org/HPLC/Basic-HPLC/Pump/Diaphragm/rs15.html>
piston-seal
piston-seal
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01116
PERSON:Daniel Schober
The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless.
binding complex 3D structure determination assay
Determination of KD value for an antibody binding a protein using a BIACORE assay.
binding characterization assay
A binding assay where the specified output characterizes numerically the disposition of two or more material entities to form a complex.
This class is probably not necessary, and we can instead use the more generic structure determination assay.
Trish Whetzel
A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature.
MO_497 hybridization station
hybridization station
Labnet Problot12
hybridization station
Thermoanaerobacter tengcongensis
Thermoanaerobacter tengcongensis
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
detection of specific nucleic acids with complementary probes of epitope specific interleukin-21 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-21 production by T cells
IL-21 release by RNA/DNA detection
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-21 production by T cells
IEDB (QTT)
P815 cell culture
A cell line derived from mouse mastocytoma.
P815 cell culture
IEDB
IEDB
http://www.biotech.ist.unige.it/cldb/cl5244.html
interleukin-10 production
The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-10 production
A material separation function is a function that decreases the resolution between two or more material entities.
OBI
Helen Parkinson
A stirrer has a material combination function
material combination function
material combination function
a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities
gradient separation
gradient separation
OBI branch derived
the use of a sucrose gradient to isolate mitochondria
PERSON:Kevin Clancy
GROUP:<http://msi-ontology.sourceforge.net>
Bruker NMR probe
An NMR probe that is manufactured by Bruker.
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400231
Bruker NMR probe
intracellular cytokine staining assay of epitope specific interleukin-5 production by T cells
IEDB (QTT)
intracellular cytokine staining assay of epitope specific interleukin-5 production by T cells
IL-5 release by ICS
An intracellular cytokine staining assay that measures epitope specific interleukin-5 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Sulfolobus
Sulfolobus
interleukin-11 production
The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-11 production
Beckman BioMek 2000
a device that is used for automated liquid transfer and handling.
liquid handler
MO_868 liquid_handler
liquid handler
liquid_handling_instrument
PERSON:Helen Parkinson
a service provider role which is realized by a servicer provider organization performing some training
obsolete during the San Diego workshop, March 2011
The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service.
OBI
obsolete_training service provider role
training service provider role
EBI provides training on databases and tools and has a training service provider role
binding assay
Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen.
The following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture.
An assay with the objective to characterize the disposition of two or more material entities to form a complex.
PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum
binding assay
group randomization
Philippe Rocca-Serra
adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
group randomization
A group assignment which relies on chance to assign materials to a group of materials in order to avoid bias in experimental set up.
PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.
is the objective to manufacture a material of a certain function (device)
PERSON: Frank Gibson
PERSON: Melanie Courtot
PERSON: Jennifer Fostel
PERSON: Philippe Rocca-Serra
manufacturing objective
GROUP: OBI PlanAndPlannedProcess Branch
PERSON: Bjoern Peters
manufacturing objective
OBI branch derived
The use of a protease to digest a protein into peptides
specific enzymatic cleavage
specific enzymatic cleavage
a protocol application to digest the fraction of input material that is susceptible to that enzyme
PERSON:Kevin Clancy
anion trap column
PERSON:Daniel Schober
An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins.
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01277
anion trap column
Ustilago maydis
Ustilago maydis
Lymnaeoidea
Lymnaeoidea
interleukin-1 beta production
The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-1 beta production
Poaceae
Poaceae
Sulfolobales
Sulfolobales
IEDB
splenocyte
A mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types.
IEDB
splenocyte
obsolete_ambidexterious handedness
obsolete_ambidexterious handedness
cell culture expansion
including grow of yeast and bacteria
a processual entity that results in the increase of cell numbers
cell culture expansion
MO_758 grow
PERSON: Chris Stoeckert, Jie Zheng
vaccine
vaccine
A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine.
PERSON: Philippe Rocca-Serra
This includes a single scientist making a processed material for personal use.
PERSON: Frank Gibson
manufacturing
Manufacturing implies reproducibility and responsibility AR
PERSON: Bjoern Peters
GROUP: OBI PlanAndPlannedProcess Branch
manufacturing
Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process
PERSON: Jennifer Fostel
PERSON: Melanie Courtot
A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01080
PERSON:Daniel Schober
fluorescene detector
WEB:<http://www.chromatography-online.org/HPLC-Detectors/Fluorescence/Single-Wavelength-Excitation/rs57.html>
fluorescene detector
OBI-Branch
a process by which a material entity status is modified and conferred a capability of reacting
(this sounds like a circular definition , hugh!)
Alan Ruttenberg 2010/11/22: After OBI call, this is too broad a term, and in any case would be in the scope of GO
activation
Philippe Rocca-Serra
PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63.
activation
Equus caballus
Equus caballus
interleukin-1 production
The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-1 production
Dictyostelium discoideum
Dictyostelium discoideum
Glass Array Hybridization Cassette
MO_563 hybridization_chamber
hybridization chamber
A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
hybridization chamber
Trish Whetzel
gene knock out
PERSON: Chris Stoeckert, Jie Zheng
MO_771 gene_knock_out
gene knock out
a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods.
vaccination
vaccination
Vaccination is: an 'administering substance in vivo' that involves in adding vaccine into a host (e.g., human, mouse) in vivo with the intend to invoke a protective immune response.
PERSON: Chris Stoeckert
PERSON: Jie Zheng
can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed
lyophilization storage
a storage process with input material entity and output freeze dried material for long time storage
lyophilization storage
tecmag EAGLE probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400248
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers.
tecmag EAGLE probe
artifact creation objective
PERSON: Frank Gibson
material transformation objective
PERSON: Jennifer Fostel
PERSON: Bjoern Peters
material transformation objective
GROUP: OBI PlanAndPlannedProcess Branch
The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS.
PERSON: Melanie Courtot
PERSON: Philippe Rocca-Serra
an objective specifiction that creates an specific output object from input materials.
Philippe Rocca-Serra
immobilization
immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum.
PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23.
OBI-Branch
immobilization
Poales
Poales
Glossata
Glossata
Canis familiaris
Canis familiaris
cellular developmental process
A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition.
cellular developmental process
OBI branch derived
DNA extraction
DNA extraction
PlanAndPlannedProcess Branch
A DNA extraction is a nucleic acid extraction where the desired output material is DNA.
spin column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01232
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits.
spin column
A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell.
disposition to be a product of antigen processing and presentation
disposition to be a product of antigen processing and presentation
IEDB
The disposition of the peptide AALKNLPLI to be created from the source protein long-chain-fatty-acid--CoA ligase 3 in murine macrophages through cleavage before residue 599 and after residue 607 by the proteasome and subsequent transport into the ER.
IEDB
Obsolete Class
Obsolete Class
Brassica juncea
Brassica juncea
Cryptococcus gattii
Cryptococcus gattii
Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection.
phage display library panning
phage display library panning
IEDB, http://en.wikipedia.org/wiki/Phage_display
Jason Greenbaum, Randi Vita, Bjoern Peters
Screening a libray of M13 phages displaying random peptide sequences for binding to the MHC molecule HLA-A*02:02 resulting in a subset of phages that encode peptides that bind.
PERSON:Kevin Clancy
OBI branch derived
selection by survival
selection by survival
the use of environmental conditions to select for the organism or cells that have a certain trait
The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected
Neisseria
Neisseria
Philippe Rocca-Serra
Elisabetta Manduchi
median centering
median centering
A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input.
median centring
PERSON: Elisabetta Manduchi
This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be median-centered.
Entomoplasmataceae
Entomoplasmataceae
interleukin-17F production
The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-17F production
mixed sex
A biological sex quality inhering in a population of multiple sexes.
mixed sex
Murinae
Murinae
mature NK T cell
A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response.
mature NK T cell
Cy5 dye
Cy5 dye
lowess global transformation
A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample.
MO_692 lowess_global_normalization
Person: Elisabetta Manduchi
lowess global transformation
intracellular cytokine staining assay of epitope specific interleukin-3 production by T cells
An intracellular cytokine staining assay that measures epitope specific interleukin-3 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IL-3 release by ICS
IEDB (QTT)
intracellular cytokine staining assay of epitope specific interleukin-3 production by T cells
A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
Elisabetta Manduchi
Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
differential expression analysis objective
PERSON: Elisabetta Manduchi
differential expression analysis objective
DNA cleavage, restriction analysis
restriction enzyme assay
DNA cleavage, restriction analysis
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
PERSON:Kevin Clancy
the use of enzymes to cut DNA molecules, the study of DNA through cleavage, mapping, and analysis of the fragments
Sulfolobus solfataricus
Sulfolobus solfataricus
Crustacea
Crustacea
interleukin-17A production
The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
interleukin-17A production
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01235
A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system.
transfer line
PERSON:Daniel Schober
WEB:<http://www.freepatentsonline.com/5702671.html>
transfer line
Clostridium acetobutylicum
Clostridium acetobutylicum
organism status comparison design
A study design that compares samples from live and dead organisms.
MO_841 organism_status_design
organism status comparison design
Person: Chris Stoeckert, Jie Zheng
technical replicate role
technical replicate
technical replicate role
technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay
Aliquots of a tissue subjected to parallel assays
Person: Jennifer Fostel
Gnathostomata
Gnathostomata
behavioral quality
An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation.
behavioral quality
Fusobacteria
Fusobacteria
dialysis
OBI branch derived
a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
dialysis
PERSON:Kevin Clancy
TGFb release by ICS
IEDB (QTT)
An intracellular cytokine staining assay that measures epitope specific transforming growth factor-beta production by T cells
intracellular cytokine staining assay of epitope specific transforming growth factor-beta production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
intracellular cytokine staining assay of epitope specific transforming growth factor-beta production by T cells
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400225
WEB:<http://www.bruker-biospin.com/probes_microimaging.html>
PERSON:Daniel Schober
Bruker micro imaging probe
Bruker micro imaging probe
For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples.
Alexa Fluor 532
Alexa Fluor 532
An organosulfonic acid that has formula C34H33N3O11S2.
MO_560 genotyping_design
A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques.
genotyping by high throughput sequencing design
genotyping by high throughput sequencing design
Person: Chris Stoeckert, Jie Zheng
Phasianinae
Phasianinae
A T cell epitope specific cytokine production assay that measures production of IL-IFNg by T cells utilizing the ELISPOT methodology.
IEDB
IEDB
IFNg release by ELISPOT
T cell epitope ELISPOT IFN-g assay
T cell epitope ELISPOT IFN-g assay
mass spectrometry of ligands eluted from secreted MHC
PERSON: Randi Vita, Bjoern Peters
mass spectrometry of ligands eluted from secreted MHC
An assay in which cells are utilized that express a form of MHC molecules that are secreted into the cell culture supernatant. The soluble MHC is harvested, ligands are eluted from the MHC molecules and individual ligands identified by mass spectrometry.
IEDB
Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process.
OBI
manufacturer role
GROUP: Role Branch
manufacturer role
With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role.
Person: Jennifer Fostel
a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment.
Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008
feed
feed role
OBI
feed role
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
MIP-1b release by ELISA
ELISA of epitope specific chemokine (C-C motif) ligand 4 production by T cells
ELISA of epitope specific chemokine (C-C motif) ligand 4 production by T cells
An ELISA that measures epitope specific chemokine (C-C motif) ligand 4 production by T cells
cell collecting
MO_982 harvest
A planned process that collects cells from culture.
PERSON: Chris Stoeckert, Jie Zheng
cell collecting
Neisseriaceae
Neisseriaceae
a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
OBI branch derived
PERSON:Kevin Clancy
Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.
electrophoresis
electrophoresis
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01234
custom made column
GROUP:<http://msi-ontology.sourceforge.net>
custom made column
A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group.
Brassica napus
Brassica napus
Cy3 dye
Cy3 dye
Coelurosauria
Coelurosauria
Simiiformes
Simiiformes
epitope specific tolerance induction by T cells
A process of tolerance induction by T cells resulting from the recognition of a T cell epitope.
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific tolerance induction by T cells
Sulfolobus acidocaldarius
Sulfolobus acidocaldarius
biomaterial purity
A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial.
biomaterial purity
simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure
http://en.wikipedia.org/wiki/Resampling_%28statistics%29
jackknifing
jackknifing method
Helen Parkinson
jackknifing method
Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method
Chloroflexales
Chloroflexales
PERSON:Daniel Schober
WEB:<http://composite.about.com/od/glossaries/l/bldef_g2419.htm>
gel permeation column
A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01103
gel permeation column
female
A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes.
female
MO_934 optimization_design
protocol optimization design
protocol optimization design
Person: Chris Stoeckert, Jie Zheng
A study design where different protocols or protocol parameters are compared aims to find an optimized protocol
clinical history
A series of statements representing health-relevant qualities of a patient and of a patient's family.
clinical history
cytometric bead array assay of epitope specific interferon-gamma production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A cytometric bead array assay that measures epitope specific interferon-gamma production by T cells
IFNg release by cytometric bead array
cytometric bead array assay of epitope specific interferon-gamma production by T cells
IEDB (QTT)
IL-17 release by RNA/DNA detection
IEDB (QTT)
detection of specific nucleic acids with complementary probes of epitope specific interleukin-17 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-17 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-17 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
enzymatic amplification
PERSON:Kevin Clancy
enzymatic amplification
OBI branch derived
the use of a polymerase chain reaction to amplify a fragment of DNA
the use of enzymes to increase the number of molecules of a biomaterial
concentration unit
A unit which represents a standard measurement of how much of a given substance there is mixed with another substance.
concentration unit
Neisseria meningitidis
Neisseria meningitidis
Pseudocoelomata
Pseudocoelomata
Rhabditidae
Rhabditidae
boostrapping
Helen Parkinson
boostrapping
Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient
Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points
Although widely accepted that high throughput biological data are typically highly noisy, the effects that this uncertainty has upon the conclusions we draw from these data are often overlooked. However, in order to assign any degree of confidence to our conclusions, we must quantify these effects. Bootstrap resampling is one method by which this may be achieved.
male
A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes.
male
Arabidopsis thaliana
Arabidopsis thaliana
Leishmania donovani species complex
Leishmania donovani species complex
Philippe Rocca-Serra
adapted from Wikipedia
NMR spectroscopy
Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202
Nuclear magnetic resonance spectroscopy
NMR spectroscopy
NMR spectroscopy is a process which exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures.
assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
TNF release
An assay that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
column chromatography detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01077
WEB:<http://www.chromatography-online.org/Principles/Basic-Chromatograph/Detector/rs56.html>
column chromatography detector
PERSON:Daniel Schober
There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles.
Clostridium
Clostridium
A study design that identifies forms and abundance of transcripts in the genome using microarray technology.
transcription profiling by array design
Person: Chris Stoeckert, Jie Zheng
MO_533 transcript_identification_design
transcription profiling by array design
cell proliferation
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
cell proliferation
cytokine production involved in immune response
The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels.
cytokine production involved in immune response
Muscomorpha
Muscomorpha
Leishmania infantum species complex
Leishmania infantum species complex
DNA transduction
OBI branch derived
a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism
PERSON:Kevin Clancy
The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein
DNA transduction
membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
membrane-bounded organelle
K-fold cross validation method
Person:Helen Parkinson
K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K − 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used
K-fold cross validation method
Tina Boussard
Bruker SampleJet system
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400208
Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.\n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement.
Bruker SampleJet system
PERSON:Daniel Schober
WEB:<http://www.bruker-biospin.com/automation.html>
Brassica
Brassica
ChIP-chip design
Person: Chris Stoeckert, Jie Zheng
A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays.
ChIP-chip design
MO_933 binding_site_identification_design
ChIP-on-chip design
MO_902 disease_state_design
Person: Chris Stoeckert, Jie Zheng
A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress.
disease state design
disease state design
epithelial cell
A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina.
epithelial cell
Arthropoda
Arthropoda
Chloroflexi (class)
Chloroflexi (class)
Nicotianoideae
Nicotianoideae
sodium phosphates
sodium phosphates
the use of trypsin to cleave pepsin into peptide fragments
protease cleavage
protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments).
enzymatic digestion
protease cleavage
OBI branch derived
PlanAndPlannedProcess Branch
the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme
PERSON: Bjoern Peters
original term: protein fragment split into synthetic polypeptide and fragment derived from protein
THE DEFINITION OF THIS SUGGESTS WE COVER THIS ALREADY IN PEPTIDE/POLYPETIDE. DO WE NEED THIS AND CAN WE DEAL WITH IT IN SOME OTHER WAY? JAMES
obsolete_fragment derived from protein
fragment derived from protein
A material entity which is derived from a protein
GROUP: IEDB
BP:03/21/2010:obsoleted as the class is no longer necessary, and we would otherwise need all kinds of 'fragment derived from' classes. Instead, use composite terms with the relationship 'derived from' some protein OR derived from some part_of protein.
PRS:22022008. result from protocol_application where input=protein and output=polypeptide or peptide (to capture: derives_from protein)
JEOL ECX NMR spectrometer
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400227
JEOL ECX NMR spectrometer
WEB:<http://www.jeol.com/PRODUCTS/AnalyticalInstruments/NuclearMagneticResonance/ECX/tabid/145/Default.aspx>
PERSON:Daniel Schober
The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world.
The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368
is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data
leave one out cross validation method
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178
Person:Helen Parkinson
leave one out cross validation method
organism
organism
13-02-2009:
OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.
This issue is outside the scope of OBI.
fungus
WEB: http://en.wikipedia.org/wiki/Organism
GROUP: OBI Biomaterial Branch
10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')
animal
virus
plant
A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
Neisseria gonorrhoeae
Neisseria gonorrhoeae
melanogaster group
melanogaster group
Mesorhizobium
Mesorhizobium
Promoter activity detection by reporter gene assay of epitope specific interleukin-2 production by T cells
IL-2 release by reporter gene assay
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Promoter activity detection by reporter gene assay of epitope specific interleukin-2 production by T cells
IEDB (QTT)
A Promoter activity detection by reporter gene assay that measures epitope specific interleukin-2 production by T cells
Mycobacterium tuberculosis complex
Mycobacterium tuberculosis complex
Plasmodium (Vinckeia)
Plasmodium (Vinckeia)
Lepidium
Lepidium
IEDB (QTT)
IL-15 release
assay of epitope specific interleukin-15 production by T cells
assay of epitope specific interleukin-15 production by T cells
An assay that measures epitope specific interleukin-15 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
bead
A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules.
DS: Probably better modeled as a role.
Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations.
OBI
bead
DNA sequencing
DNA sequencing
OBI Branch derived
Philippe Rocca-Serra
DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument.
Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858
enzymatic DNA replication
OBI branch derived
PERSON:Kevin Clancy
enzymatic DNA replication
the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial
the use of enzymes to duplicate DNA molecules
A primer in a PCR reaction. A probe on an Affymetrix chip.
complementary nucleotide probe role
PERSON:Bjoern Peters
A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence
complementary nucleotide probe role
Tremellomycetidae
Tremellomycetidae
eurosids II
eurosids II
epitope tolerance induction experiment
An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response
epitope tolerance induction experiment
tolerance induction
IEDB
IEDB
http://en.wikipedia.org/wiki/Scintillation_counter
scintillation counter
PERSON: Erik Segerdell
scintillation counter
A device that is used to measure ionizing radiation.
Pasteurella multocida
Pasteurella multocida
cytometric bead array assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells
A cytometric bead array assay that measures epitope specific macrophage inflammatory protein-1 alpha production by T cells
MIP-1a release by cytometric bead array
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
cytometric bead array assay of epitope specific macrophage inflammatory protein-1 alpha production by T cells
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
centrifugation
centrifugation
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
Philippe Rocca-Serra
recombinant vector
A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector.
recombinant vector
Richard Scheuermann
PERSON: Richard Scheuermann
subgraph in-degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph.
subgraph in-degree calculation
intracellular material detection by flow cytometry assay
An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer.
intracellular material detection by flow cytometry assay
intracellular staining
Rubrivivax
Rubrivivax
I think the statement is still about the instance of the biological sex quality of an organism. It is also about information available to the person making the statement.
a record indicating that the biological sex of an organism is not known.
Bjoern Peters
record of unknown sex
record of unknown sex
A database record indicating that the tissue sample in a microarray experiment came from an organism for which the biological sex is not known to the person who created the record.
Saccharomyces cerevisiae
Saccharomyces cerevisiae
A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures.
programmable array microscope
programmable array microscope
Verveer et al, Journal of Microscopy, vol. 189, pt. 3, pp. 192-8
PERSON: Erik Segerdell
mass spectrometry of MHC ligands eluted from whole cells
PERSON: Randi Vita, Bjoern Peters
IEDB
An assay in which ligands are eluted from MHC molecules expressed on the cell surface, and the specific ligands are identified by mass spectrometry.
mass spectrometry of MHC ligands eluted from whole cells
eurosids I
eurosids I
Ralstonia solanacearum
Ralstonia solanacearum
Strongyloides
Strongyloides
genetic characteristics information
MO_66 IndividualGeneticCharacteristics
Person: Chris Stoeckert, Jie Zheng
a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes.
genetic characteristics information
PERSON: Richard Scheuermann
subgraph out-degree calculation
subgraph out-degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph.
Richard Scheuermann
Philippe Rocca-Serra
staining
staining
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
Rubrivivax gelatinosus
Rubrivivax gelatinosus
restriction enzyme
Kevin Clancy, Bjoern Peters
restriction enzyme
an enzyme that has a specific target cleavage sites within nucleic acids
The enzyme EcoR1 cuts DNA at the canonical cleavage site CAATTG
Schizosaccharomycetes
Schizosaccharomycetes
cytoplasmic RNA extraction
A RNA extraction process in which the desired output material is RNA in the cytoplasm.
Person: Jie Zheng
UPenn Group
cytoplasmic RNA extraction
Person: Chris Stoeckert
A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared.
imprinting design
MO_914 imprinting_design
imprinting design
Person: Chris Stoeckert, Jie Zheng
Strongyloididae
Strongyloididae
Geobacter metallireducens
Geobacter metallireducens
Arabidopsis
Arabidopsis
WEB: http://en.wikipedia.org/wiki/Logarithm
log base
Elisabetta Manduchi
logarithm base
logarithmic base
log base
The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1.
washing
washing
OBI-Branch
PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4.
washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow.
Philippe Rocca-Serra
Brassicaceae
Brassicaceae
Aquifex aeolicus
Aquifex aeolicus
assay of epitope specific T cell activation
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
T cell activation
IEDB (QTT)
assay of epitope specific T cell activation
An assay that measures epitope specific T cell activation
Lachancea kluyveri
Lachancea kluyveri
IL-3 release
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An assay that measures epitope specific interleukin-3 production by T cells
assay of epitope specific interleukin-3 production by T cells
assay of epitope specific interleukin-3 production by T cells
Pseudomonas putida
Pseudomonas putida
Xanthomonas axonopodis
Xanthomonas axonopodis
a cell derived from a multicellular organism that has the potential to replicate indefinitely
PERSON: Bjoern Peters
a single Hela cell
immortal cell
immortal cell
GROUP: OBI Biomaterial Branch
DNA sequencing by synthesis
DNA sequencing by synthesis
PERSON: Philippe Rocca-Serra
PMID: 18263613. A new class of cleavable fluorescent nucleotides: synthesis and optimization as reversible terminators for DNA sequencing by synthesis. Turcatti G, Romieu A, Fedurco M, Tairi AP. Nucleic Acids Res. 2008 Mar;36(4):e25.
is a DNA sequencing which relies on DNA polymerase activity to perform chain extension during the sequencing reaction step.
Geobacter
Geobacter
An intracellular cytokine staining assay that measures epitope specific chemokine (C-C motif) ligand 4 production by T cells
MIP-1b release by ICS
IEDB (QTT)
intracellular cytokine staining assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells
intracellular cytokine staining assay of epitope specific chemokine (C-C motif) ligand 4 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Philippe Rocca-Serra
irradiation
irradiation
adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation)
irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves
PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370.
http://en.wikipedia.org/wiki/Cryofixation
PERSON: Erik Segerdell
cryofixation device
cryofixation device
A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy.
Antirrhinum
Antirrhinum
John Quinn
http://www.cytopeia.com/sorter.htm
Influx Cell Sorter
Influx Cell Sorter at TSRI Flow Cytometry Core Facility
A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. Filters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells.
Influx Cell Sorter
epitope specific granzyme B production by T cells
A process of granzyme B production by T cells resulting from the recognition of a T cell epitope.
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific granzyme B production by T cells
Eutheria
Eutheria
efficacy of T cell epitope intervention
efficacy of T cell epitope intervention experiment
An epitope intervention experiment in which the induced immune response is targeting a T cell epitope
IEDB
IEDB
efficacy of T cell epitope intervention experiment
regulation-assigned role
Approval letter
Person: Jennifer Fostel
Regulation-assigned role is a regulatory role defined by legislation or governmental orders
regulation-assigned role
Lactobacillus sakei
Lactobacillus sakei
Fringillidae
Fringillidae
MO_822 cell_cycle_design
cell cycle design
Person: Chris Stoeckert, Jie Zheng
A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells.
cell cycle design
Ureaplasma urealyticum
Ureaplasma urealyticum
A device that creates an appropriate environment for nucleic acid hybridization.
hybridization oven
PERSON: Erik Segerdell
PERSON: Erik Segerdell
hybridization oven
Fungi
Fungi
Antirrhinum majus
Antirrhinum majus
Plasmodium (Laverania)
Plasmodium (Laverania)
BP: 06/09/11: This needs to be coordinated with the broader treatment of 'purified materials' in general.
A mixture containing MHC molecules that was purified to remove non-MHC molecular entities.
Bjoern Peters
HLA A*0201 that was purified from cell lysate using an HLA class I specific antibody
purified MHC molecule preparation
purified MHC molecule preparation
feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation
This class is temporary and will be placed outside of data transformation ultimately (if it still remains at all after review)
mathematical feature
mathematical feature
James Malone
PERSON: James Malone
Percoidei
Percoidei
Rickettsia sibirica
Rickettsia sibirica
a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body.
regulatory role
OBI, CDISC
regulatory role
GROUP: Role branch
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
cryostat
cryostat
PERSON: Erik Segerdell
A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION
http://en.wikipedia.org/wiki/Cryostat
Saccharomyces bayanus
Saccharomyces bayanus
sodium citrate dihydrate
sodium citrate dihydrate
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-8 production by T cells
epitope specific interleukin-8 production by T cells
Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex.
disposition to be bound by an MHC protein complex
PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters
MHC ligand disposition
IEDB
disposition to be bound by an MHC protein complex
separation into different composition objective
The objective to obtain cells contained in a sample of blood.
We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives
is the objective to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities)
separation into different composition objective
Oryza sativa (indica cultivar-group)
Oryza sativa (indica cultivar-group)
material provider role
material supplier role
PERSON:Jennifer Fostel
Supplier role is a special kind of service, e.g. biobank
Jackson Labs is an organization which provide mice as experimental material
supplier
material supplier role
a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation.
damaged
A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired.
damaged
Yersinia pestis
Yersinia pestis
radioactive
A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity.
radioactive
microtome knife maker
microtome knife maker
PERSON: Erik Segerdell
PERSON: Erik Segerdell
A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy.
Saccharomyces
Saccharomyces
Homobasidiomycetes
Homobasidiomycetes
Point within the fluidic subsystem at which the laser intersects the stream, illuminating the cells where they emit their fluorescence and scatter the light. The laser irradiates the cell at the interrogation point.
John Quinn
interrogation_point
Interrogation point in BD FACS Calibur
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11
interrogation_point
Person: Chris Stoeckert, Jie Zheng
MO_726 injury_design
injury design
A study design in which the response of an organism(s) to injury or damage is studied.
injury design
Aquificales
Aquificales
Bordetella pertussis
Bordetella pertussis
Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site
pyrosequencing
Philippe Rocca-Serra
pyrosequencing
is a DNA sequencing which allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template.
ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin.
Pyrosequencing sheds light on DNA sequencing.
PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review.
Sauropsida
Sauropsida
Oryza sativa (japonica cultivar-group)
Oryza sativa (japonica cultivar-group)
Bacteroidetes
Bacteroidetes
whole organism preparation
putting a mouse in the blender. Not: putting a mouse on a scale
whole organism preparation
does this include injecting a dye to a patient to be able to visualize parts of his brain? If not, we should state that the components of the organism are substantially re-arranged.
A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained
Lactobacillus gasseri
Lactobacillus gasseri
B cell epitope specific immune intervention
An epitope specific immune intervention in which the induced response targets a B cell epitope
B cell epitope specific immune intervention
IEDB
Injecting a mouse with recombinant antibody targeting an anthrax epitope
PERSON: Randi Vita, Jason Greenbaum, Bjoern Peters
immunization
IEDB
Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope).
The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope.
immunization
IEDB
assay antigen role
assay antigen role
Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen. see OBI_1110120 below
IEDB
IEDB
Streptomycineae
Streptomycineae
Solanales
Solanales
amplified DNA
amplified DNA
Alan Ruttenberg
DNA that has been produced in an enzymatic amplification process
PERSON: Alan Ruttenberg
Amplied DNA created by PCR
GROUP: OBI
a material entity, organism or cell, that is the output of a genetic transformation process.
genetically modified material
genetically modified material
PERSON: Jie Zheng
PERSON: Erik Segerdell
http://www.biometra.de/
A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed.
capillary blotter
capillary blotter
A processed material which measures gamma radiation
Frank Gibson
gamma counter
A Geiger counter
gamma counter
http://en.wikipedia.org/wiki/Gamma_counter
Alicyclobacillaceae
Alicyclobacillaceae
Burkholderia fungorum
Burkholderia fungorum
liquid NMR probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400242
GROUP:<http://msi-ontology.sourceforge.net>
An NMR probe that is designed to hold a liquid sample.
liquid NMR probe
PERSON:Daniel Schober
This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc.
branch derived
The plan of researcher X to perform an experiment according to a protocol.
A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process.
plan
plan
AR, BP, JM, MC, PRS
blood harvesting
blood harvesting
A material separation where blood is taken from an organism.
IEDB
IEDB
Holacanthopterygii
Holacanthopterygii
MO_366 transfection
transfection
a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell
PERSON: Chris Stoeckert, Jie Zheng
transfection
http://medical-dictionary.thefreedictionary.com/angiograph
PERSON: Erik Segerdell
angiograph
angiograph
A device that records the patterns of pulse waves inside blood vessels.
Drosophilinae
Drosophilinae
data vector reduction objective
data vector reduction objective
PERSON: Richard H. Scheuermann
Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k.
James Malone
Richard H. Scheuermann
pH meter
pH meter
A device that is used to measure the pH (acidity or alkalinity) of a liquid.
http://en.wikipedia.org/wiki/PH_meter
PERSON: Erik Segerdell
A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure.
BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining.
CART
classification and regression trees
CART
James Malone
pathologic process
pathologic process
IEDB
IEDB
abnormal, harmful processes caused by or associated with a disease
Digenea
Digenea
primary cell culture
spleen cells put directly into culture
Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934
PERSON: Susanna Sansone
a primary cell culture is a cell culture where the cells derive from a fresh tissue source.
GROUP: OBI Biomaterial Branch
primary cell culture
Penaeoidea
Penaeoidea
allotransplantation
OBI branch derived
PlanAndPlannedProcess Branch
allotransplantation
is the transplantation of organs between members of the same species.
BEP clade
BEP clade
Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography).
GROUP:<http://msi-ontology.sourceforge.net>
flash pump system
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01048
PERSON:Daniel Schober
flash pump system
survival curve
PERSON:Melanie Courtot
survival curve
PERSON:James Malone
PERSON:Chris Stoeckert
A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time.
WEB: http://www.graphpad.com/www/book/survive.htm
Sphingobacteria
Sphingobacteria
Coffeeae
Coffeeae
Leishmania braziliensis
Leishmania braziliensis
8/19/09: Chris says that there may used to be a way of doing bisulfite sequencing comparing lengths of restriction fragments, which implies that it is possible to do without DNA sequencing.
adapted from Wikipedia
bisulfite sequencing
Philippe Rocca-Serra
is a DNA sequencing which allows to determine the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location.
bisulfite sequencing
PMID: 19581485. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Hodges E, Smith A, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang M, Ye K, Battacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks J.
Genome Res. 2009 Jul 6.
bioreactor
A device or system that supports a biologically active environment. ALAN SAYS NOT AN INSTRUMENT
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Bioreactor
bioreactor
chromosomal substitution
chromosomal substitution
MO_995 chromosomal_substitution
PERSON: Chris Stoeckert, Jie Zheng
A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'.
Jurkat cell line in RPMI w/ 10% FCS. PBMCs were purified from blood sample and put into tissue culture media.
Purification of recombinant human growth hormone from CHO cell culture supernatant by Gradiflow preparative electrophoresis technology.
Protein Expr Purif. 2003 Nov;32(1):126-34.
PMID: 14680949
GROUP: OBI Biomaterial Branch
PERSON: Bjoern Peters
cell culture
cell culture
a cell culture is a material entity consisting of a population of cells that is maintained in vitro
Helicobacter pylori
Helicobacter pylori
diluted
A concentration which relatively low.
diluted
Rhodocyclaceae
Rhodocyclaceae
nuclear RNA extraction
A RNA extraction process in which the desired output material is RNA in the nucleus.
Person: Chris Stoeckert
Person: Jie Zheng
UPenn Group
nuclear RNA extraction
notified body
notified body role
The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf
Notified Body (NB). A private institution charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive. This process, called Conformity Assessment, has EU-wide validity once completed by the NB.
OBI, CDISC
notified body role
Person: Jennifer Fostel
Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive
Varian UNITY INOVA spectrometer
Varian UNITY INOVA spectrometer
PERSON:Daniel Schober
The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips.
WEB:<http://www.varianinc.com/cgi-bin/nav?products/NMR/spectromet/inova/index&cid=HFIH>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400236
Populus euphratica
Populus euphratica
Corynebacterium glutamicum ATCC 13032
Corynebacterium glutamicum ATCC 13032
Trematoda
Trematoda
IEDB
T cell TCR:epitope:MHC binding assay
IEDB
epitope binding to TCR
Any assay that measures the binding of a TCR molecule to an epitope:MHC complex.
T cell TCR:epitope:MHC binding assay
A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity.
EAGLE-I
isolation function
stabilization function
stabilization function
3D structural organization datum
3D structural organization datum
A measurement datum that describes the structural orientation of a material entity in 3D space.
PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters
The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR.
antithrombin-III (AT-III) berichrome assay
1
An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard
WEB:http://www.clinchem.org/cgi/content/full/43/9/1783@2009/08/06
antithrombin-III (AT-III) berichrome assay
todo Reagents from Berichrom(r) Antithrombin III (A) and standard human plasma
IL-12 release by RNA/DNA detection
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-12 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-12 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-12 production by T cells
protein microarray
PERSON: Daniel Schober
A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions.
Daniel Schober
The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions.
protein microarray
dichroic mirror
John Quinn
dichroic mirror
A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
ViewLux Alexa 594 dichroic mirror
http://en.wikipedia.org/wiki/Dichroic_mirror
DNA sequencing service
is a DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized.
Eagle-i will supply better English definition
DNA sequencing service
Malpighiales
Malpighiales
Burkholderia thailandensis
Burkholderia thailandensis
clonal cell culture
GROUP: OBI Biomaterial Branch
PERSON: Susanna Sansone
a clonal cell culture is a cell culture in which all cells can be assumed to be identical, tracking back to a single ancestor cell.
cell cut
Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557
clonal cell culture
Bacillus
Bacillus
age since planting measurement datum
PERSON:Chris Stoeckert, Jie Zheng
An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing.
MO_495 planting
age since planting measurement datum
A current amplification function is an amplification function that increases the amplitude of a current.
current amplification function
EAGLE-I
current amplification function
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cytotoxic T cell degranulation
assay of epitope specific cytotoxic T cell degranulation
An assay that measures epitope specific cytotoxic T cell degranulation
assay of epitope specific cytotoxic T cell degranulation
Bifidobacterium
Bifidobacterium
material maintenance objective
PERSON: Bjoern Peters
is the objective to maintain some or all of the qualities of a material over time.
material maintenance objective
dichroic filter
http://en.wikipedia.org/wiki/Dichroic_filter
A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
John Quinn
dichroic filter
Cy3 Dichroic Filter
An assay in which a radioactive label is used to determine the interaction between an antigen and an antibody. This can be used to detect the presence of an antigen of interest or determine the specificity of an antibody.
radio immuno assay
PERSON: Bjoern Peters
To evaluate the specificity of antibody binding to
35S-labeled IA-2(256–760) in comparison with 35S-labeled IA-2IC
construct, the mutual inhibition activity of different concentrations of
unlabeled IA-2IC and/or IA-2(256–760) fragments were tested. The
unlabeled fragments were prepared by in vitro transcription and translation
as described above but replacing [35S]methionine with unlabeled methionine
in the amino acid mixture. Unlabeled recombinant IA-2(256–760) and/or
IA-2IC (0.5-, 1-, 2-, and 4-fold the amount of 35S-labeled protein) were
added to each tube and incubated overnight at 4°C with patient sera. The
following day, after incubation with radiolabeled 35S–IA-2(256–760) or
35S–IA-2IC proteins, samples were processed with the usual
radioimmunoprecipitation assay.
RIA
radio immuno assay
IEDB
immune epitope carrier role
IEDB
03/21/2010, BP: surveying the literature, this seems to be a messy term. Need to clarify what material entities can be carriers, and if only immunogenicity (not antigenicity) is effected by their presence.
immune epitope carrier role
A role inhering in a material entity that is covalently bound to an epitope in order to increase the epitopes immunogenicity.
IEDB
ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42."
A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation.
Elisabetta Manduchi
hyperlog transformation
Joseph Spliden
hyperlog transformation
This type of transformation is typically used in flow cytometry
http://flowcyt.sourceforge.net/gating/latest.pdf
Ryan Brinkman
Acidithiobacillus ferrooxidans
Acidithiobacillus ferrooxidans
Spirochaetales
Spirochaetales
Listeriaceae
Listeriaceae
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
blood taken from animal: animal continues in study, whereas blood has role specimen.
something taken from study subject, leaves the study and becomes the specimen.
a role borne by a material entity that is gained during a specimen creation process and that is realized by use of the specimen in an investigation
parasite example
- when parasite in people we study people, people are subjects and parasites are specimen
- when parasite extracted, they become subject in the following study
specimen can later be subject.
specimen role
OBI
liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient.
specimen role
GROUP: Role Branch
22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role.
PERSON: Susanna Sansone
HeLa cells
Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592
GROUP: OBI Biomaterial Branch
cell line culture
cell line culture
a cell line culture is a cell culture where the cells grown are from a cell line, long term culture of cells that are replicating continuously. The cell population is homogenous but not clonal
Edinburgh score
WEB:http://www.cse.yorku.ca/course_archive/2006-07/W/4441/EdinburghInventory.html
Person:Jessica Turner
Edinburgh score
PMID:5146491#Oldfield, R.C. (1971). The assessment and analysis of handedness: The Edinburgh inventory. Neuropsychologia, 9, 97-113
Person: Alan Ruttenberg
1
genetic transformation objective
Person: Jie Zheng
Person: Jie Zheng
a material transformation objective aims to create genetically modified organism or cell
genetic transformation objective
EFO_0002761 methylation profiling by high throughput sequencing
DNA methylation profiling by high throughput sequencing assay
An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology
DNA methylation profiling by high throughput sequencing assay
Group: ArrayExpress production team, James Malone, Helen Parkinson
MHC:ligand binding assay
IEDB
MHC:ligand binding assay
IEDB
an assay that measures the binding of a ligand to an MHC molecule
cell transfer function
A cell harvester has a cell transfer function.
EAGLE-I
cell transfer function
is a transfer function that displaces cells from one place to another
The presentation of a flashing light to a monkey during reward training
presentation of stimulus
Helen Parkinson, Jessica Turner, Dirk Derom
presentation of stimulus
Helen Parkinson, Jessica Turner, Dirk Derom
a planned process in which an organism is exposed to some stimulus with the intent to invoke an action
stimulation of organism
adjuvent role
IEDB
adjuvant role
IEDB
Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response.
adjuvant role
crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes.
x-ray crystallography
PERSON:Bjoern Peters
An assay which used the diffraction of X-ray beams to resolve the 3-dimensional structure of a material entity of interest in a crystal
X-ray crystallography assay
X-ray crystallography assay
PERSON: Melanie Courtot
real time reverse-transcription polymerase chain reaction assay
RRT-PCR
qRT-PCR
real time reverse-transcription polymerase chain reaction assay
PERSON: Bjoern Peters
RT-rt PCR
Is_a PCR real time preceded by a reverse transcription step (reverse transcription step = an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase)
Bjoern Peters
PERSON: Jennifer Fostel
the process of evaluating the data gathered in an investigation in the context of literature knowledge with the objective to generate more general conclusions or to identify what additional data is necessary to draw conclusions
PERSON: Bjoern Peters
interpreting data
Identifiying and removing outliers from data by eye. Examining data to and deriving a new hypothesis.
interpreting data
2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO
Person: Philippe Rocca-Serra
secondary structure of sequence macromolecule
A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure.
Secondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford.
secondary structure of sequence macromolecule
Wikipedia
electron microscope
electron microscope
A microscope that produces an image of an object by targeting it with an electron beam
Apis mellifera
Apis mellifera
lamiids
lamiids
IEDB
a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment
synthetic peptide
the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme
Bjoern Peters
changed from synthetic polypeptide to peptide, to get rid of the restriction of having more than 10 amino acids (required by Chebi).
synthetic peptide
Chromadorea
Chromadorea
pump function
EAGLE-I
a transfer unction where the transfer requires work to move the entity, often against a gradient.
pump function
induced mutation
MO_564 induced_mutation
PERSON: Chris Stoeckert, Jie Zheng
a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation.
induced mutation
MHC ligand processing and presentation assay
an assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them
MHC ligand processing and presentation assay
MHC ligand elution assay
IEDB
IEDB
A Spectrolyse Heparin (Xa) assay is intended for the quantitative determination of therapeutic Heparin in human plasma.
The principle inhibitor of Thrombin, Factor Xa and other coagulation serine proteases in plasma is Antithrombin III. The rate of inhibition, under normal conditions, is slow, but can be increased several thousand-fold by Heparin. This mechanism accounts for the anticoagulant effect of Heparin. Low Molecular Weight Therapeutic Heparin (LMWH) preparations appear to catalyze the reaction between Factor Xa and Antithrombin III more readily than the reaction between Thrombin and Antithrombin III while standard Heparin catalyzes both reactions equally. The Factor Xa inhibition test is the most useful test for assaying the widest variety of therapeutic Heparin preparations. In this method, when both Factor Xa and Antithrombin III are present in excess, the rate of Factor Xa inhibition is directly proportional to the Heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the Heparin concentration.
2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
spectrolyse heparin antifactor-Xa assay
WEB:http://www.kordia.nl/en/product/hemostasis/specialty_kits__reagens/598/spectrolyse_heparin_anti_xa@2009/08/06
PMID:19696660#Antifactor-Xa (anti-Xa) was determined using spectrolyse heparin (Xa) (Trinity Biotech plc, Bray, County Wicklow, Ireland).
spectrolyse heparin antifactor-Xa assay
Person:Alan Ruttenberg
An assay in which expression of a reporter gene is detected that was inserted under the control of a promoter of interest.
promoter activity detection by reporter gene assay
A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color.
promoter activity detection by reporter gene assay
reporter gene assay
PERSON:Bjoern Peters
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific transforming growth factor-beta production by T cells
A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope.
epitope specific transforming growth factor-beta production by T cells
IEDB (QTT)
disposition to infect an organism
disposition to infect an organism
IEDB
IEDB
Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease
phenol red in RPMI; pH=4 indicator dye (also carries reference role)
Person:Helen Parkinson
Person: Jennifer Fostel
pH indicator dye role
the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity
pH indicator dye role
pH indicator dye
bromophenol blue has a pH indicator dye role
Sarcopterygii
Sarcopterygii
PERSON: Bjoern Peters
PRS: 22-02-2008: while working on definition of cDNA library and looking at current example of usage, a screening library should be a defined class -> any material library which has input_role in a screening protocol application
change biomaterial to material in definition
screening library
a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process?
PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library]
screening library
GROUP: IEDB
Chlamydia
Chlamydia
organism feature identification objective
Jennifer Fostel
Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
organism feature identification objective
feature extraction objective
A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image.
feature extraction objective
James Malone
TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction
Elisabetta Manduchi
Hominidae
Hominidae
The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet
PERSON:Daniel Schober
needle assembly
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01065
needle assembly
OBI Instrument branch
OBI instrument branch
liquid chromatography mass spectrometry platform
A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI.
liquid chromatography mass spectrometry platform
injecting CFSE labeled target cells with and without loaded influenza peptide into a mouse, and comparing the recovery rate.
in vivo cell mediated cell killing assay
in vivo cell mediated cell killing assay
PERSON:Bjoern Peters
in vivo killing
An assay that measures the rate in which a target cell population is killed by effector cells within an organism
cross linking
cross linking can be used as a probe to link proteins together, to check protein protein interactions
A process in which bonds are created that link one polymer to another
http://en.wikipedia.org/wiki/Cross-link
cross linking
PERSON: Chris Stoeckert
device creation objective
OBI
PERSON: Helen Parkinson
an objective which aims to create a device with a specified function
device creation objective
age since egg laying measurement datum
PERSON:Chris Stoeckert, Jie Zheng
MO_767 egg laying
age since egg laying measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism.
gadolinium
A lanthanoid that has formula Gd.
gadolinium
nasopharyngeal aspirate specimen
A speciemn which derives from nasopharyngeal mucosa after
aspiration.
WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
PERSON: Melanie Courtot
type of sample used in the PCIRN influenza network
nasopharyngeal aspirate specimen
2011-03-31: [PRS].
specified input and output of dt which were missing
Westfall and Young family wise error rate correction
Westfall and Young family wise error rate correction
Helen Parkinson
Westfall and Young FWER correction
PRS: 2011-03-31: set specified input and specified output to the data transformation
Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing
euthanisia
life termination
death status type
difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing.
sacrifice
Terminal sacrifice of animals by cervical dislocation at the end of an investigation.
killing
Jennifer Fostel
killing
A protocol application in which an organism is intentionally put to death
CEBS, Biomaterial_branch
Philippe Rocca-Serra
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific transforming growth factor-beta production by T cells
TGFb release
IEDB (QTT)
assay of epitope specific transforming growth factor-beta production by T cells
An assay that measures epitope specific transforming growth factor-beta production by T cells
Saccharomyces pastorianus
Saccharomyces pastorianus
immune epitope assay
10/26/09, BP: Strictly speaking, the definition would exclude MHC ligand elution and binding assays. Need to either expand this definition in scope, or move out those subclasses.
IEDB
immune epitope assay
IEDB
immune epitope assay
is an assay that measures the binding of an epitope to an adaptive immune receptor or a immune response process resulting from such a binding event
Decapoda
Decapoda
Ryan Brinkman
Melanie Courtot
log-log curve fitting
James Malone
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446
log-log curve fitting
A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points.
Elisabetta Manduchi
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution.
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
person:Kevin Clancy
number of lost events computer
number of lost events computer
0, 125, 787 events lost due to computer busy.
A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role
cell mediated cell killing assay
An assay that measures the rate in which a target cell population is killed by effector cells.
PERSON:Bjoern Peters
cell mediated cell killing assay
The directed combination of a material entity with a specimen.
administration of material to specimen
Staining cells in a tissue slice with a dye.
Bjoern Peters
administration of material to specimen
Bjoern Peters
obsolete_platform
OBI Instrument branch
OBI Instrument branch
A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI.
platform
7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'.
Bjoern Peters
the process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment.
planning
planning
a process of creating or modifying a plan.
Bjoern Peters
PPPB branch
3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation
reverse transcription polymerase chain reaction
reverse transcribed polymerase chain reaction
reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity.
Philippe Rocca-Serra
Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group.
Span PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW.
Eur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094
RT-PCR
reverse transcribed polymerase chain reaction
Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog
A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time.
spike train datum
needs more work to see exactly what the data set looks like - HP
Jessica Turner, NIF
Helen Parkinson, Alan Ruttenberg
spike train datum
spike train measurement
freezing storage
A process in which a material entity has it's temperature lowered to below the freezing point in order to bring it to a state in which it can be maintained at this lower temperature in order to preserve some of its qualities
Person: Alan Ruttenberg
Freezing a pellet for later assay
freezing storage
MO_481 frozen_storage
OBI
2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance"
The prothrombin time is an assay most commonly measured using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant by binding the calcium in a sample. The blood is mixed, then centrifuged to separate blood cells from plasma. In newborns, whole blood is used. The plasma is analyzed by a biomedical scientist on an automated instrument at 37 degrees C, which takes a sample of the plasma. An excess of calcium is added (thereby reversing the effects of citrate), which enables the blood to clot again. For an accurate measurement the proportion of blood to citrate needs to be fixed; many laboratories will not perform the assay if the tube is underfilled and contains a relatively high concentration of citrate. If the tube is underfilled or overfilled with blood, the standardized dilution of 1 part anticoagulant to 9 parts whole blood is no longer valid. For the prothrombin time test the appropriate sample is the blue top tube, or sodium citrate tube, which is a liquid anticoagulant. Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically. Some laboratories use a mechanical measurement, which eliminates interferences from lipemic and icteric samples. The prothrombin ratio is the prothrombin time for a patient, divided by the result for control plasma.
2009/10/18 Alan Ruttenberg. This assay was added during the fucoidan use case exercise but still needs to be fleshed out. Only the AT-III assay has more carefully specified inputs and outputs
PMID:19696660#The prothrombin time (PT) was quantitatively determined using RecombiPlasTin (Instrumentation Laboratory Company, Lexington, Massachusetts, USA).
WEB:http://en.wikipedia.org/wiki/Prothrombin_time@2009/10/06
prothrombin time assay
Person:Alan Ruttenberg
prothrombin time assay
terbium
A lanthanoid that has formula Tb.
terbium
polynomial transformation
polynomial transformation
A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
Elisabetta Manduchi
a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1
variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables
WEB: http://mathworld.wolfram.com/Polynomial.html
Person:Bjoern Peters
2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178
Different routes and means of administration should go as children underneath this
A process by which a substance is intentionally given to an organism
Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells
administering substance in vivo
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
1
IEDB
Bjoern Peters
administering substance in vivo
Heterodera glycines
Heterodera glycines
Dermis
Dense irregular connective tissue which consists of a papillary layer and a reticular layer.
Dermis
Lachancea
Lachancea
Dictyosteliida
Dictyosteliida
multispectral imaging flow cytometer
multispectral imaging flow cytometer
A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations.
http://www.amnis.com/
Melanie Courtot
MIFC
FWER adjusted p-value
adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate)
http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html
A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests
FWER adjusted p-value
PERS:Philippe Rocca-Serra
Dendrobranchiata
Dendrobranchiata
B cell epitope recognition assay
B cell epitope recognition assay
is an assay that measures the binding of an epitope to an antibody or B cell receptor, or an immune response process resulting from such a binding event
IEDB
IEDB
Saccharomyces paradoxus
Saccharomyces paradoxus
box-cox transformation
box-cox transformation
ARTICLE: Box, G. E. P. and Cox, D.R. (1964), "An analysis of transformations", Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246.
A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246.
Ryan Brinkman
fluorescein
A xanthene dye that has formula C20H12O5.
fluorescein
acrylamide
An acrylamide that has formula C3H5NO.
acrylamide
Aspergillus niger
Aspergillus niger
intravenous injection
intravenous injection
is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe
PERSON: Melanie Courtot
flow cytometry assay
FACS
Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody.
PERSON:Randi Vita, Bjoern Peters
flow cytometry assay
An assay that uses a flow cytometer to detect fluorescence in individual particles that flow by a laser in solution.
Rasborinae
Rasborinae
Bjoern Peters
human subject enrollment
As with group assignment, should the specified output here be an organism which bears a role
IEDB
The enrollment of humans for an investigation based on some eligibility criteria
human subject enrollment
enlisting familiy members of HIV patients into a study
WEB: http://en.wikipedia.org/wiki/Logarithm
logarithmic transformation
logarithmic transformation
Elisabetta Manduchi
A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm.
PERSON:Chris Stoeckert, Jie Zheng
MO_745 hatching
age since hatching measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg.
age since hatching measurement datum
Denaturing DNA in alcohol
http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29
Is a process in which the tertiary or secondary structure of a polymer is disrupted
denaturing
denaturing
Hominoidea
Hominoidea
Malacostraca
Malacostraca
epitope specific interleukin-27 production by T cells
IEDB (QTT)
A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-27 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Daniel Schober
An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays.
microarray
A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position.
PERSON: Chris Stoeckert
microarray
Bacillales
Bacillales
A gas generator that generates nitrogen gas.
nitrogen generator
PERSON:Daniel Schober
nitrogen generator
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01034
PERSON: Chris Stoeckert
PERSON: Jie Zheng
Group: UPenn Group
RNA extract
an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen.
RNA extract
Joseph Spliden
Elisabetta Manduchi
biexponential transformation
biexponential transformation
Ryan Brinkman
A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation.
This type of transformation is typically used in flow cytometry.
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
WEB: http://en.wikipedia.org/wiki/Exponential_function
Elisabetta Manduchi
exponential transformation
exponential transformation
An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function.
WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function
Rickettsia rickettsii
Rickettsia rickettsii
CD4-positive, alpha-beta T cell
A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor.
CD4-positive, alpha-beta T cell
Coprinopsis
Coprinopsis
A sequencing centre has a service provision objective
OBI
Helen Parkinson
An objective which is fulfilled by the provision of some service e.g. a training service
service provision objective
service provision objective
collecting specimen from organism
PERSON:Bjoern Peters
IEDB
collecting specimen from organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient
a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation
A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of
exudate and epithelial debris for microbiological or cellular examination.
nasal swab specimen
WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
PERSON: Melanie Courtot
nasal swab specimen
type of sample used in the PCIRN influenza network
An assay that measures the duration of temporal interval of a process that is part of the life of the bearer, where the initial time point of the measured process is the beginning of some transitional state of the bearer such as birth or when planted.
OBI group
PERSON: Alan Ruttenberg
This assay measures time not developmental stage. we recognize that development takes different time periods under different conditions such as media / temperature. For example, age measurement assay of fly age, the output likes 28 days but not mid-life of age at room temperature.
age measurement assay
age measurement assay
Cercopithecoidea
Cercopithecoidea
informing investigator of subject study arm
09/28/2009 Alan Ruttenberg. This and the class informing-subject-of-study-arm are defined in order to solve the question of how to represent single and double blind experiments. To represent the aspect of double blinding pertaining to investigators, we say that the study execution doesn't include any processes of this sort
A process in which an investigator is made aware of which study arm that a patient is participating in, for example whether they are receiving a placebo or a treatment with an investigational compound.
Person:Alan Ruttenberg
informing investigator of subject study arm
Any assay that measures the production of a cytokine by T cells resulting from the recognition of a T cell epitope.
T cell epitope specific cytokine production assay
cytokine release
IEDB
IEDB
T cell epitope specific cytokine production assay
An assay that measures epitope specific helper T cell enhancement of T cell mediated immune response
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
T cell help for T cell response
assay of epitope specific helper T cell enhancement of T cell mediated immune response
assay of epitope specific helper T cell enhancement of T cell mediated immune response
Eucarida
Eucarida
Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03
A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
PERSON: Frank Gibson
Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115
DNA microarray
DNA Chip
DNA microarray
PERSON: Daniel Schober
DNA-array
CD8-positive, alpha-beta T cell
A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor.
CD8-positive, alpha-beta T cell
PERSON: Jennifer Fostel
PERSON: Philippe Rocca-Serra
03/21/2010: BP, obsoleting this term, as it is duplicated by 'material sample'. Use that instead term instead, which now also has 'sample population' as an alternative label.
recruited population
sample population
GROUP: OBI Biomaterial Branch
A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers.
Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458
obsolete_sample population
GROUP:<http://msi-ontology.sourceforge.net>
autosampler
autosampler
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400002
An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. \n alt The autosampler is an automatic sample changer device.
software optimization objective
Jennifer Fostel
Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software.
software optimization objective
The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement.
nitrogen phosphorous detector
nitrogen phosphorous detector
WEB:<http://www.chromatography-online.org/topics/nitrogen/phosphorus/detector.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01089
PERSON:Daniel Schober
Rickettsia prowazekii
Rickettsia prowazekii
Pongo pygmaeus
Pongo pygmaeus
Lepidoptera
Lepidoptera
Entomobryoidea
Entomobryoidea
IL-3 release by ELISA
ELISA of epitope specific interleukin-3 production by T cells
ELISA of epitope specific interleukin-3 production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
An ELISA that measures epitope specific interleukin-3 production by T cells
campanulids
campanulids
grading of tumor
Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues. Values can be described by terms from NCI Thesaurus.
tumor grading
tumor grading
OBI branch derived; submitted by MO
Penaeus monodon
Penaeus monodon
chip spotting device
chip spotting device
United States Patent 7416705
PERSON: Erik Segerdell
A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray.
Cyprininae
Cyprininae
PERSON:Bjoern Peters
D-MEM
Dulbecco's modified Eagle medium
A cell culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins.
Logical definition should contain all components listed in textual definition at some point.
Dulbecco's modified Eagle medium
DMEM
A data transformation is a process which produces output data from input data
James Malone
Helen Parkinson
Philippe Rocca-Serra
Melanie Courtot
Branch editors
The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
data processing
data analysis
Richard Scheuermann
Ryan Brinkman
data transformation
Tina Hernandez-Boussard
Elisabetta Manduchi
data transformation
Thermotogales
Thermotogales
Rickettsia conorii
Rickettsia conorii
WEB:<http://www.buchi.com/Isocratic-Pump-System.253.0.html>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01049
isocratic pump system
A pump system optimized for isocratic chromatography.
isocratic pump system
PERSON:Daniel Schober
person:Chris Stoeckert
ratio of collected to emitted light
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
10%
ratio of collected to emitted light
person:Kevin Clancy
A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role
non-negative matrix factorization
non-negative matrix factorization
Non-negative matrix factorization is used in text mining where document-term matrix is constructed with the weights of various terms (typically weighted word frequency information) from a set of documents. This matrix is factored into a term-feature and a feature-document matrix.
Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero.
http://en.wikipedia.org/wiki/Non-negative_matrix_factorization
tris
A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC.
tris
ELISA of epitope specific interleukin-1 alpha production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
An ELISA that measures epitope specific interleukin-1 alpha production by T cells
ELISA of epitope specific interleukin-1 alpha production by T cells
IL-1a release by ELISA
Glires
Glires
power pack
PSU
sep:00093
Frank Gibson
PERSON: Daniel Schober
power supply unit
A AC/DC transformer that generates the reqired power for an electrophoresis apparatus
power supply
electrical power supply
power supply
Daniel Schober
A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time.
a protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition.
OBI branch derived
PlanAndPlannedProcess Branch
clinical diagnosis
performing a clinical assessment
performing a clinical assessment
Rubrobacter xylanophilus
Rubrobacter xylanophilus
animal euthanization
Melissa Haendel
animal euthanization
animal sacrifice
may later be refined with more specific list of organisms
Helen Parkinson and Melissa Haendel
Rats were euthanized with CO2
A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject
http://www.biotech.ist.unige.it/cldb/cl3075.html
IEDB
L cell culture
A cell line derived from mouse fibroblasts.
L cell culture
IEDB
digital camera
http://en.wikipedia.org/wiki/Digital_camera
digital camera
An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor.
PERSON: Erik Segerdell
soft independent modeling of class analogy analysis
Tina Hernandez-Boussard
SIMCA
WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies
Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes.
soft independent modeling of class analogy analysis
Rickettsia
Rickettsia
James Malone
Ryan Brinkman
The above definition refers to the 'fully specified' logit-log model. The reduced form of this, when it is assumed that y_0=0, is named 'partially specified' logit-log model.
logit-log curve fitting
logit-log curve fitting
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively.
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448
Elisabetta Manduchi
Melanie Courtot
A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points.
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400279
Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process.
Bruker Capillary LC-NMR platform
Bruker Capillary LC-NMR platform
PERSON:Daniel Schober
WEB:<http://www.bruker-biospin.com/hyphenation_caplcnmr.html>
Noctuidae
Noctuidae
Pseudomonas
Pseudomonas
A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample.
Kevin Lister
OBI
fluorometer
Allyson Lister
fluorometer
laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300
Chlorophyceae
Chlorophyceae
Eukaryota
biotin
A biotin that has formula C10H16N2O3S.
biotin
Euarchontoglires
Euarchontoglires
nucleic acid template role
a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009
nucleic acid template role
a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy.
nucleic acid
A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid.
nucleic acid
Penaeidae
Penaeidae
renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms
IEDB
is process in which a material substance is added to a cell culture
adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient
adding substance to cell culture
Bjoern Peters
adding substance to cell culture
Pasteuria nishizawae
Pasteuria nishizawae
Right now this may be incomplete. Should also cover e.g. sound, light as well.
growth environment
OBI group
The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth.
growth environment
PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters
PERSON:Daniel Schober
A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven.
gas chromatography oven
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01039
gas chromatography oven
OBI Instrument branch
OBI Instrument branch
microarray platform
microarray platform
A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI.
Ovis aries
Ovis aries
WEB: http://www.statsoft.com/textbook/stdiscan.html
discriminant function analysis
discriminant function analysis
Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
Tina Hernandez-Boussard
Elisabetta Manduchi
Melanie Courtot
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448
James Malone
Ryan Brinkman
logistic-log curve fitting
A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n).
logistic-log curve fitting
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve.
Lactobacillales
Lactobacillales
Chlamydia trachomatis
Chlamydia trachomatis
Sus scrofa
Sus scrofa
Bombycidae
Bombycidae
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
ELISA of epitope specific interleukin-8 production by T cells
IL-8 release by ELISA
ELISA of epitope specific interleukin-8 production by T cells
An ELISA that measures epitope specific interleukin-8 production by T cells
IEDB (QTT)
Arthropleona
Arthropleona
human antithrombin-III protein
2009/09/28 Alan Ruttenberg. Fucoidan-use-case
Schizophora
Schizophora
Pseudomonas aeruginosa
Pseudomonas aeruginosa
Trichocomaceae
Trichocomaceae
Gammaproteobacteria
Gammaproteobacteria
polypeptide
polypeptide sequence
A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation.
polypeptide
Streptosporangineae
Streptosporangineae
Laurasiatheria
Laurasiatheria
ribonucleic acids
Naturally occurring polyribonucleotides.
ribonucleic acids
Thermoplasma
Thermoplasma
F minus mating type
A bacterial mating type indicating the absence of F plasmid in a bacterial cell.
F minus mating type
Suidae
Suidae
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
epitope specific interleukin-9 production by T cells
A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-9 production by T cells
wild type allele information
MO_605 genotype
Person: Chris Stoeckert, Jie Zheng
an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism.
discussed on San Diego OBI workshop, March 2011
wild type allele information
PERSON:Daniel Schober
capillary column
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01066
A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm.
capillary column
fluid flow rate
A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time.
A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time.
fluid flow rate
tolerance induction
A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it.
tolerance induction
Bartonella koehlerae
Bartonella koehlerae
Thermoplasma acidophilum
Thermoplasma acidophilum
The extraction of RNA from an input material that specifically isolates viral RNA
viral RNA extraction
viral RNA extraction
Person:Bjoern Peters
The AccuPrepTM Viral RNA Extraction Kit is designed for the rapid and convenient extraction of viral RNA from cell-free samples as serum, plasma, CSF, urine, etc - http://www.biokits.com/moreinfos.html?id=2703
magnoliids
magnoliids
Sauria
Sauria
F mating type
A bacterial mating type indicating the presence of F plasmid in a bacterial cell.
F mating type
Sus
Sus
Oenococcus
Oenococcus
An assay that measures epitope specific interferon-gamma production by T cells
assay of epitope specific interferon-gamma production by T cells
assay of epitope specific interferon-gamma production by T cells
IEDB (QTT)
IFNg release
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
Macaca fuscata
Macaca fuscata
sample inlet
The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head.
WEB:<http://en.wikipedia.org/wiki/Gas_chromatography#Inlets>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01044
PERSON:Daniel Schober
sample inlet
PCR product
We are using PCR and not the written out words, as this is the most common used.
PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA.
PCR product
is double stranded DNA that is the specified output of a polymerase chain reaction
GROUP: OBI BIomaterial Branch
GROUP: OBI BIomaterial Branch
h plus
A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus.
h plus
Ciona intestinalis
Ciona intestinalis
John Quinn
CytoSence
A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites.
CytoSence
http://www.cytobuoy.com/
Ephydroidea
Ephydroidea
A cell culture analyte detection bioassay that measures epitope specific interleukin-6 production by T cells
IL-6 release by bioassay
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cell culture analyte detection bioassay of epitope specific interleukin-6 production by T cells
IEDB (QTT)
cell culture analyte detection bioassay of epitope specific interleukin-6 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-10 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-10 production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
detection of specific nucleic acids with complementary probes of epitope specific interleukin-10 production by T cells
IL-10 release by RNA/DNA detection
primer role
(cell and molecular biology) A short strand of RNA that is synthesized along single-stranded DNA during replication, initiating DNA polymerase-catalyzed synthesis of the complementary strand. http://www.answers.com/topic/rna-primer
a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation.
primer role
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400204
NMR tube washing system
PERSON:Daniel Schober
GROUP:<http://msi-ontology.sourceforge.net>
An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling.
NMR tube washing system
Macaca fascicularis
Macaca fascicularis
Ciona
Ciona
h minus
A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus.
h minus
Spleen
Spleen
CytoSub
CytoSub
http://www.cytobuoy.com/
A CytoSub is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSub is the submersible version equipped with a high pressure sample inlet loop and a high pressure housing to allow underwater operation down to 200 m, lowered on a cable or mounted on a flooded underwater vehicle.
John Quinn
TNF release by cyotmetric bead array
IEDB (QTT)
cytometric bead array assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cytometric bead array assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
A cytometric bead array assay that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
Aspergillus clavatus
Aspergillus clavatus
IEDB (QTT)
A cytometric bead array assay that measures epitope specific RANTES production by T cells
cytometric bead array assay of epitope specific RANTES production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cytometric bead array assay of epitope specific RANTES production by T cells
RANTES/CCL5 release by cytometric bead array
Frank Gibson
gel dryer
sep:00094
A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels
gel dryer
A component of an NMR instrument that controls the activities of the other components.
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400015
PERSON:Daniel Schober
NMR console
GROUP:<http://msi-ontology.sourceforge.net>
NMR console
core eudicotyledons
core eudicotyledons
Solanaceae
Solanaceae
Cionidae
Cionidae
Person: Chris Stoeckert, Jie Zheng
A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
cellular process design
cellular process design
MO_810 cellular_process_design
sort function
Daniel Schober
Frank Gibson
Melanie Courtot
A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
sort function
Aspergillus
Aspergillus
ion exchange column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01105
An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation.
GROUP:<http://msi-ontology.sourceforge.net>
ion exchange column
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400210
WEB:<http://www.bruker-biospin.com/automation.html>
Bruker B-ACS system
Bruker B-ACS system
PERSON:Daniel Schober
The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit.
cell type comparison design
Person: Chris Stoeckert, Jie Zheng
cell type comparison design
MO_764 cell_type_comparison_design
A study design that compares cells of different type, for example different cell lines.
Canidae
Canidae
Phlebobranchia
Phlebobranchia
Eumetazoa
Eumetazoa
Vibrionaceae
Vibrionaceae
Antirrhineae
Antirrhineae
Leishmania [NCBITaxon:38568]
Leishmania [NCBITaxon:38568]
ruthenium
An iron group element that has formula Ru.
ruthenium
Group: ArrayExpress production team
A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation.
Person: Chris Stoeckert, Jie Zheng
translation profiling design
translation profiling design
IEDB (QTT)
A process of RANTES production by T cells resulting from the recognition of a T cell epitope.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific RANTES production by T cells
epitope specific RANTES production by T cells
PERSON:Daniel Schober
rapid resolution column
A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution.
rapid resolution column
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01102
GROUP:<http://msi-ontology.sourceforge.net>
PACCAD clade
PACCAD clade
Euryarchaeota
Euryarchaeota
Methanomicrobia
Methanomicrobia
Geospiza difficilis
Geospiza difficilis
macromolecule
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
macromolecule
polymer
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific interleukin-23 production by T cells
IL-23 release
An assay that measures epitope specific interleukin-23 production by T cells
IEDB (QTT)
assay of epitope specific interleukin-23 production by T cells
An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
environment control function
Daniel Schober
Melanie Courtot
Frank Gibson
Bill Bug
environment control function
Aves
Aves
GROUP:<http://msi-ontology.sourceforge.net>
Designed to perform capillary LC with injection of sample volumes ranging from nL to L.
liquid chromatography autosampler
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01061
liquid chromatography autosampler
PERSON:Daniel Schober
Homo
Homo
Acalyptratae
Acalyptratae
Haloferax
Haloferax
Geobacteraceae
Geobacteraceae
cell cycle
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
cell cycle
genetic alteration information
Group: OBI group
Group: OBI group
a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc.
genetic alteration information
proposed and discussed on San Diego OBI workshop, March 2011
an organism that is the output of a genetic transformation process
OBI Biomaterial
PERSON: Philippe Rocca-Serra
genetically modified organism
A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis.
Nat Protoc. 2008;3(10):1550-8. PMID: 18802436
genetically modified organism
Daniel Schober
Bill Bug
display function
A display function is a function to present information by translating that information through some lookup process into visual form.
display function
Melanie Courtot
Frank Gibson
Macaca mulatta
Macaca mulatta
vacuum degasser
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01053
WEB:<http://www.chromatography-online.org/topics/vacuum.html>
PERSON:Daniel Schober
A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily.
vacuum degasser
Homo sapiens
human being
Homo sapiens
Ascidiacea
Ascidiacea
hermaphrodite
A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual.
hermaphrodite
PERSON: Helen Parkinson
organ section
A liver slice used in a perfusion experiment.
Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
PERSON: Philippe Rocca-Serra
GROUP: CEBS
GROUP: OBI Biomaterial Branch
A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)
organ section
Person: Anna Farne
transcription profiling by RT-PCR assay
transcription profiling by RT-PCR assay
An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR)
EFO_0002943: transcription profiling by RT-PCR
Lotus
Lotus
topologically preserved clustered data set
A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived.
James Malone
PERSON: James Malone
the output data set generated from a self-organizing map.
topologically preserved clustered data set
Cyan
A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine fluorescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of individual cells.
http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm
Cyan
John Quinn
Rhodospirillales
Rhodospirillales
Eurypterygii
Eurypterygii
Hypocrea jecorina
Hypocrea jecorina
Thiotrichales
Thiotrichales
Liriodendron
Liriodendron
Urochordata
Urochordata
Asterales
Asterales
principal investigator role
principal investigator
principal investigator role
Person: Jennifer Fostel
a responsible party role played by a person responsible for the overall conduct of a study
Actinopterygii
Actinopterygii
GROUP: IEDB
bronchial alveolar lavage
solution containing lung derived T cells, eosinophils, and TNFa.
PERSON: Bjoern Peters
bronchial alveolar lavage
Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
BAL
MA transformation
Elisabetta Manduchi
An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation.
MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2.
MA transformation
Philippe Rocca-Serra
PERSON: Elisabetta Manduchi
A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
epitope specific chemokine (C-C motif) ligand 4 production by T cells
epitope specific chemokine (C-C motif) ligand 4 production by T cells
Borrelia burgdorferi
Borrelia burgdorferi
nucleic acid restriction enzyme digest
A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site
Kevin Clancy, Bjoern Peters
nucleic acid restriction enzyme digest
http://www.partec.de/products/cyflow-ml.html
A CyFlow_ML is a flow_cytometer_analyser manufactured by Partec. It is a digital machine which uses 4 light sources: triple laser configurations including new powerful 200mW@488nm blue solid state laser + 100W UV lamp for highest resolution DNA analysis, and can collect 16 optical parameters: FSC1, FSC2, SSC, FL1-FL13. Ultracompact high end desktop multilaser Flow Cytometer for all applications in cell analysis and absolute counting.
CYFlow ML
John Quinn
CYFlow ML
Drosophiliti
Drosophiliti
Strigeidida
Strigeidida
Leishmania mexicana
Leishmania mexicana
Ctenosquamata
Ctenosquamata
Pseudomonadales
Pseudomonadales
Bacteroidetes/Chlorobi group
Bacteroidetes/Chlorobi group
Chordata
Chordata
responsible party role
responsible party role
Person: Jennifer Fostel
responsible party
he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
OBI
cation exchange column
A cation exchange column is a chromatography column that is used in cation exchange chromatography.
cation exchange column
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01096
PERSON:Daniel Schober
Schistosoma japonicum
Schistosoma japonicum
Borrelia
Borrelia
exponential base
The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1).
WEB: http://en.wikipedia.org/wiki/Exponential_function
exponential base
Elisabetta Manduchi
Schistosoma
Schistosoma
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Part of the fluidics subsystem. The collection tube is a vessel for capturing cells of interest that have been identified by a sorter. The collection tube is the end location of sorted cells.
LSR2 collection tube
John Quinn
cell sorter collection tube
cell sorter collection tube
pseudomallei group
pseudomallei group
Acanthomorpha
Acanthomorpha
A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts.
person:Chris Stoeckert
Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
measured expression level
measured expression level
OBI Data Transformation branch
Pecora
Pecora
direct detection NMR probe
PERSON:Daniel Schober
An NMR probe designed to allow the direct detection of acquisition nuclei.
GROUP:<http://msi-ontology.sourceforge.net>
direct detection NMR probe
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400280
material sample role
7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off.
A material sample role is a specimen role borne by a material entity that is the output of a material sampling process.
a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
material sample role
cytometric bead array assay of epitope specific interleukin-6 production by T cells
IL-6 release by cytometric bead array
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cytometric bead array assay of epitope specific interleukin-6 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-6 production by T cells
Spirochaetaceae
Spirochaetaceae
Philippe Rocca-Serra
MC, 20100316: Replaced by Chebi polymer and usage polymerization also fixed.
obsolete_polymer
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
TERM: CHEBI:33839
James Malone
obsolete_polymer
Schistosoma mansoni
Schistosoma mansoni
polynomial degree
The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
polynomial degree
Nectriaceae
Nectriaceae
Actinomycetaceae
Actinomycetaceae
Euacanthomorpha
Euacanthomorpha
number of variables
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space.
number of variables
Euglenozoa
Euglenozoa
alpha mating type (yeast)
A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids.
alpha mating type (yeast)
Schizosaccharomycetales
Schizosaccharomycetales
biological vector role
OBI and Wikipedia
Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector)
biological vector role
Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280
GROUP: Role Branch
a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission.
1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
Haplorrhini
Haplorrhini
Thermococcales
Thermococcales
A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research.
CyFlow Space
CyFlow Space at TSRI Flow Cytometry Core Facility
http://www.partec.de/products/cyflowspace.html
John Quinn
CyFlow Space
agglomerative hierarchical clustering
agglomerative hierarchical clustering
An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining.
Elisabetta Manduchi
James Malone
PERSON: Elisabetta Manduchi
bottom-up hierarchical clustering
Pichia pastoris
Pichia pastoris
Passeriformes
Passeriformes
Novosphingobium
Novosphingobium
wikipedia http://en.wikipedia.org/wiki/Documenting
obsolete_documenting
IAO_0000572
Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database.
Bjoern Peters
6/11/9: Edited at workshop. Should go into IAO. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape
obsolete_documenting
Rubiaceae
Rubiaceae
Clostridium thermocellum
Clostridium thermocellum
ChIP-chip by tiling array assay
Group: ArrayExpress production team
An assay where chromatin immunoprecipitation (ChIP) is used in combination with tiling microarray technology
ChIP-chip by tiling array assay
EFO_0002762 ChIP-chip by tiling array
treatment
treatment
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
Muridae
Muridae
Apinae
Apinae
Leishmania donovani
Leishmania donovani
John Quinn, Melanie Courtot
CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations
CytoBuoy
http://www.cytobuoy.com/
CytoBuoy
A CytoBuoy is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters.
material sample
OBI: workshop
A material entity that has the material sample role
sample population
material sample
blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general.
Sparus
Sparus
divisive hierarchical clustering
Elisabetta Manduchi
divisive hierarchical clustering
James Malone
top-down hierarchical clustering
PERSON: Elisabetta Manduchi
A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain.
immune response assay
an assay with the objective to determine information about an immune response
immune response assay
histological sample preparation
OBI branch derived
PERSON:Bjoern Peters
histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
histological sample preparation
Thermoplasma volcanium
Thermoplasma volcanium
ChIP-chip by tiling array design
Group: ArrayExpress production team
Person: Chris Stoeckert, Jie Zheng
A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays.
ChIP-chip by tiling array design
A study design that examines the relationship between the size of the administered dose and the extent of the response.
dose response design
dose response design
Person: Chris Stoeckert, Jie Zheng
MO_485 dose_response_design
Leishmania major
Leishmania major
http://www.partec.de/products/cyflow.html
CyFlow SL
CyFlow SL
John Quinn
a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels.
Alteromonadaceae
Alteromonadaceae
Sparus aurata
Sparus aurata
Psathyrellaceae
Psathyrellaceae
James Malone
PERSON: Ryan Brinkman
PERSON: Richard Scheuermann
Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets.
data partitioning
data partitioning
PERSON: Melanie Courtot
material sampling process
A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity
material sampling process
transplantation
a protocol application to replace an organ or tissue of an organism
OBI branch derived
transplantation
PlanAndPlannedProcess Branch
TNFa release
An assay that measures epitope specific tumor necrosis factor production by T cells
assay of epitope specific tumor necrosis factor production by T cells
assay of epitope specific tumor necrosis factor production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
a mating type (yeast)
A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating.
a mating type (yeast)
Gibberella zeae
Gibberella zeae
A CyFlow_Sl3 is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37 , highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser, other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for real time data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing. The CyFlow SL3 is a compact and dedicated portable Flow Cytometer for accurate and affordable cell analysis and true volumetric absolute counting in HIV Monitoring and AIDS patient follow-up by precise and direct CD4 and CD4% measurement.
John Quinn
CyFlow SL3
http://www.partec.de/products/cyflowsl3.html
CyFlow SL3
T cell epitope specific killing assay
Any assay that measures the killing of an antigen presenting cell (APC) by a T cell that occurs in response to TCR on that T cell binding an epitope:MHC complex on that APC.
IEDB
T cell epitope specific killing assay
cytotoxicity
IEDB
Thermococcaceae
Thermococcaceae
Citrus clementina
Citrus clementina
Gentianales
Gentianales
PERSON:Chris Stoeckert, Jie Zheng
An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth.
age since germination measurement datum
Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance.
age since germination measurement datum
MO_590 germination
Takifugu rubripes
Takifugu rubripes
ELISA microplate reader
A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA).
ELISA microplate reader
PERSON: Erik Segerdell
PERSON: Erik Segerdell
IEDB
The function inhering in a T cell that is realized in an immune response that results from the T cell receptor binding to the MHC:epitope complex.
effector T cell function
IEDB
effector T cell function
waiting
OBI branch derived
PERSON:Alan Ruttenberg
not actively doing anything to a material for a duration of time.
waiting
PERSON: Susanna Sansone
collection (of entities of organismal origin)
a collection is a bfo:aggregate object, that is a set of material object of the same kind
2009-11-04, MC: Entity of organismal origin has been deprecated a while ago. We still have collection (of entities of organismal origin). I am not sure we could replace with collection of material entity without altering the meaning (i.e. deprecating the class). In addition, if we do deprecate that class, should we just assert the children under material entity?
set, group, ensemble
03/17/2010: obsoleted (on call), and replaced by 'material entity' and/or specimen. No need for the 'collection' part of this class any more after merging bfo:aggregate object into material entity, and by dealing with 'specimen' rather than with entities of organismal origin.
added during 22-02-2008 biomaterial call to distinguish library and population
PERSON: Philippe Rocca-Serra
obsolete_collection (of entities of organismal origin)
PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings]
Bjoern Peters
cell line immortalization
OBI
cell line immortalization
Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs
is the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro. Has specified output cell line
For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01068
column compartment
GROUP:<http://msi-ontology.sourceforge.net>
column compartment
PERSON:Daniel Schober
A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule
5/22 Need to explore if there are GO / other classes exist that capture this. We need it now for cloning experiments
Kevin Clancy, Bjoern Peters
replaced by imported PRO: DNA ligase
DNA ligase
obsolete_DNA ligase
ligase
Pseudomonas fluorescens
Pseudomonas fluorescens
Agrobacterium tumefaciens
Agrobacterium tumefaciens
Thiomonas sp. 3As
Thiomonas sp. 3As
Streptophytina
Streptophytina
validation by reverse transcription PCR design
validation by reverse transcription PCR design
PERSON: Chris Stoeckert, Jie Zheng
a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results
MO_986 reverse_transcription_PCR_quality_control
APC
a function inhering in a cell that expresses MHC molecules which is realized in the process of antigen processing and presentation of antigen derived parts by MHC molecules on the cell surface.
antigen presentation function
antigen presentation function
IEDB
IEDB
A measurement device that detects biological, chemical or physical events of samples in microtiter plates.
microplate reader
PERSON: Erik Segerdell
microplate reader
http://en.wikipedia.org/wiki/Plate_reader
capillary pump system
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01051
capillary pump system
A pump system optimized for capillary chromatography.
survival assessment
Need to point out more specifically that survival / death is measured.
survival assessment
Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time
UPenn Group
Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.)
PERSON: Jie Zheng
cytoplasmic RNA extract
A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted.
cytoplasmic RNA extract
PERSON: Chris Stoeckert
physical document
GROUP: OBI
PERSON: Bjoern Peters
A physical document is an object serving as a record of information by means of symbolic marks.
a book is a physical document
physical document
Agrobacterium
Agrobacterium
gadodiamide
A gadolinium coordination entity that has formula C16H26GdN5O8.
gadodiamide
high performance liquid chromatography instrument
A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column.
PERSON: Erik Segerdell
high performance liquid chromatography instrument
http://en.wikipedia.org/wiki/High_performance_liquid_chromatography
Xylella
Xylella
MO_876 eclosion
An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon.
age since eclosion measurement datum
PERSON:Chris Stoeckert, Jie Zheng
age since eclosion measurement datum
Neurospora crassa
Neurospora crassa
IEDB
immunogen role
IEDB
any entity capable of eliciting an immune response when introduced to components of the immune system
immunogen role
lead(0)
An elemental lead that has formula Pb.
lead(0)
epitope specific IL-18 release by T cells
epitope specific IL-18 release by T cells
IEDB
IEDB
A biological process where T cells produce IL-18 resulting from the recognition of a T cell epitope.
CD8 receptor
A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor.
CD8
CD8 receptor
This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009.
WEB: http://en.wikipedia.org/wiki/CD8
pool of specimens
PERSON: Jennifer Fostel
check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
pool of specimens
GROUP: CEBS
A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
Kaplan Meier
PERSON: James Malone
Kaplan Meier
http://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator
a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored)
PERSON: Tina Boussard
RNA-directed DNA polymerase activity
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
RNA-directed DNA polymerase activity
Rhizobiales
Rhizobiales
evaporative light scattering detector
WEB:<http://www.chromatography-online.org/HPLC-Detectors/Evaporative-Light-Scattering/rs73.html>
PERSON:Daniel Schober
The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01082
evaporative light scattering detector
http://en.wikipedia.org/wiki/Microtiter_plate
Melanie Courtot
microtiter plate
A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
microplate
microtiter plate
A microtiter_plate is a flat plate with multiple wells used as small test tubes.
protocol
protocol
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice.
a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process.
PlanAndPlannedProcess Branch
Bryophyta
Bryophyta
processed material
Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples
Is a material entity that is created or changed during material processing.
PERSON: Alan Ruttenberg
processed material
DNA synthesizer
An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides.
DNA synthesizer
PERSON: Erik Segerdell
http://www.globalspec.com/LearnMore/Labware_Scientific_Instruments/Clinical_Research_Labware/DNA_Synthesizers
Xylella fastidiosa
Xylella fastidiosa
Neurospora
Neurospora
age since sowing measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination.
age since sowing measurement datum
MO_748 sowing
PERSON:Chris Stoeckert, Jie Zheng
column cartridger
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01054
GROUP:<http://msi-ontology.sourceforge.net>
A chromatography device where the column cartridge is inserted into and stabilised.
column cartridger
PERSON:Daniel Schober
03/21/2010: This sense of 'host' is used not only in infectious diseases but also allergy, cancer, transplantation, etc. which is why it is needed separately from the 'host of infectious agent' meaning, which will be imported from IDO.
host of immune response role
is a role borne by an organism. It is realized by the organism during an immunization or an immune response taking place inside or on the surface of the organism, and in which the responding or stimulated immune system is part of the host.
IEDB
IEDB
host of immune response role
random primed DNA labeling
PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13.
Person: Bjoern Peters
Person: Chris Stoeckert
need to add Klenow subunit of DNA polymerase I under material entity
a labeling in which random primers are used to uniformly label input DNA
PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR.
Methods Mol Biol. 1996;58:27-9.
Person: Philippe Rocca-Serra
random primed DNA labeling
IEDB
T cell epitope specific proliferation assay
Any assay that measures the proliferation of a T cell that occurs in response to TCR on that T cell binding an epitope:MHC complex.
T cell proliferation
T cell epitope specific proliferation assay
IEDB
epitope specific IL-1b release by T cells
epitope specific IL-1b release by T cells
IEDB
A biological process where T cells produce IL-1b resulting from the recognition of a T cell epitope.
IEDB
OBI, CDISC
role of regulator of consumables and medical devices
FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html
Person: Jennifer Fostel
role of regulator of consumables and medical devices
a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices
drug regulatoy authority
multiple testing procedure
multiple testing correction method
Monnie McGee
A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.
multiple testing correction method
Agrotis segetum
Agrotis segetum
a process in which cells with a single nucleus are isolated from a blood sample
PERSON: bjoern peters
isolation of PBMCs
cells are extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, with monocytes and lymphocytes forming a buffy coat under a layer of plasma. This buffy coat contains the PBMCs.
isolation of PBMCs
wiki http://en.wikipedia.org/wiki/PBMC
normalization data transformation
James Malone
A normalization data transformation is a data transformation that has objective normalization.
PERSON: James Malone
normalization data transformation
GROUP: ArrayExpress production team
Person: Chris Stoeckert, Jie Zheng
DNA methylation profiling by array design
A study design in which the methylation state of DNA is determined and is compared between samples using array technology.
DNA methylation profiling by array design
PERSON:Chris Stoeckert, Jie Zheng
MO_783 coitus
An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction.
age since coitus measurement datum
age since coitus measurement datum
double-stranded RNA-specific adenosine deaminase
A protein that is a translation product of the ADAR gene or a 1:1 ortholog thereof.
double-stranded RNA-specific adenosine deaminase
vascular endothelial growth factor production
The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
vascular endothelial growth factor production
A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device.
PERSON: Erik Segerdell
http://en.wikipedia.org/wiki/Nipkow_disk
spinning-disk confocal microscope
spinning-disk confocal microscope
Streptococcus suis
Streptococcus suis
Neoteleostei
Neoteleostei
Mycosphaerella graminicola
Mycosphaerella graminicola
animal feeding
branch derived
In an investigation, this will typically be part of an animal care process
Bjoern Peters
animal feeding
giving crickets to a snake.
animal feeding is a process in which animals are provided with food
Agrotis
Agrotis
Coxiella
Coxiella
mass spectrometer
mass spectrometer
LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific
Frank Gibson
http://en.wikipedia.org/wiki/Mass_spectrometry
A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum
http://www.bdbiosciences.com/features/products/display_product.php?keyID=42
FACSvantage
FACSvantage
John Quinn
FACSvantage at TSRI Flow Cytometry Core Facility
The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parameters and side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells.
Apoidea
Apoidea
Bjoern Peters
pre-mortem specimen
MO_705 premortem
a specimen that was taken from a live organism
pre-mortem specimen
material obtained through a liver biopsy from a human patient
Heterodera
Heterodera
IEDB (QTT)
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-22 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-22 production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interleukin-22 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IL-22 release by RNA/DNA detection
Mesoplasma florum
Mesoplasma florum
validation by real time PCR design
validation by real time PCR design
MO_434 real_time_PCR_quality_control
a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results
PERSON: Chris Stoeckert, Jie Zheng
PET synthesizer
PET synthesizer
A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
Rhodobacterales
Rhodobacterales
Liriodendron tulipifera
Liriodendron tulipifera
Rickettsiaceae
Rickettsiaceae
Frank Gibson
a device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.
chromatography device
chromatography device
chromatography instrument
http://en.wikipedia.org/wiki/Chromatography
WEB: http://www.virology.ws/2009/05/28/influenza-microneutralization-assay/
person: Bjoern Peters
influenza neutralization assay
serum neutralization of viral infectivity assay
person: Melanie Courtot
serum neutralization of viral infectivity assay
A quantitative assay where different
dilutions of serum are mixed with virus and used to infect cells. At
the lower dilutions, antibodies will block infection, but at higher
dilutions, there will be too few antibodies to have an effect. The
simple process of dilution provides a way to compare the virus-
neutralizing abilities of different sera. The neutralization titer is
expressed as the reciprocal of the highest dilution at which virus
infection is blocked.
John Quinn
FACSAria
FACSAria
FACSAria at TSRI Flow Cytometry Core Facility
A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 fluorescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters.
http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/SJ-0003-00Aria.pdf
chromium-51
A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.
chromium-51
Sanger sequencing
dye terminator sequencing
chain termination sequencing
PMID: 271968. DNA sequencing with chain-terminating inhibitors.
Sanger F, Nicklen S, Coulson AR. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7.
Philippe Rocca-Serra
is a DNA sequencing which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position
adapted from wikipedia
chain termination sequencing
Medicago truncatula
Medicago truncatula
Rubrobacterineae
Rubrobacterineae
Insecta
Insecta
flow cell
Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
Biofilm Flow Cell
flow cell
flow_cell
Person:John Quinn
epitope specific IL-4 release by T cells
IEDB
A biological process where T cells produce IL-4 resulting from the recognition of a T cell epitope.
epitope specific IL-4 release by T cells
IEDB
A cytometer is an instrument for counting and measuring cells.
cytometer
cytometer
Melanie Courtot
http://medical.merriam-webster.com/medical/cytometer
Streptococcus mutans
Streptococcus mutans
Rattus
Rattus
Bombyx mori
Bombyx mori
Viridiplantae
Viridiplantae
Caulobacterales
Caulobacterales
Tetraodontidae
Tetraodontidae
Rhodocyclales
Rhodocyclales
note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet.
life of bearer doesn't imply organism
this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature
age as a quality is dubious; we plan to revisit
stages in development are currently handled with controlled vocabulary, such as 2-somite stage
age measurement datum
age measurement datum
A time measurement datum that is the result of measurement of age of an organism
PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng
MO_178 Age
PERSON: Erik Segerdell
A device that moves charged particles through a medium by using an electric field induced by electrodes.
electrophoresis system
electrophoresis system
http://en.wikipedia.org/wiki/Category:Electrophoresis
Neoptera
Neoptera
DNA sequencing of a sample by a core lab which returns data to the consumer
protocol service provider role
PERSON:Helen Parkinson
a service provider role which is realized by a servicer provider organization performing a protocol execution
obsolete during the San Diego workshop, March 2011
The reason is that we decided to pursue a different modeling approach for services keeping just the 'service consumer' and 'service provider' roles and differentiate just at the level of planned process offered a s service.
obsolete_protocol service provider role
Otocephala
Otocephala
specimen
Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation.
GROUP: OBI Biomaterial Branch
PERSON: James Malone
PERSON: Philippe Rocca-Serra
specimen
A material entity that has the specimen role.
Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen.
AB SOLiD System
PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57.
Applied Biosystems
is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation
AB SOLiD System
Philippe Rocca-Serra
Strongyloides ratti
Strongyloides ratti
viral hemagglutination inhibition assay
viral hemeagglutination inhibition assay
person: Melanie Courtot
a highly sensitive procedure for the measurement of soluble antigens in biologic specimens; the amount of hemagglutination reflects the amount of free antibody present after reaction with the specimen and thus varies inversely with amount of antigen in the specimen.
person: BJoern Peters
HAI
viral hemagglutination inhibition assay
WEB: http://www.virology.ws/2009/05/27/influenza-hemagglutination-inhibition-assay/
MO_701 fertilization
Definition of fertilization comes from GO.
An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote.
age since fertilization measurement datum
PERSON:Chris Stoeckert, Jie Zheng
age since fertilization measurement datum
FC 500
http://www.beckmancoulter.com/products/instrument/flowcytometry/fc500series.asp
FC 500
A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 fluorescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications.
John Quinn
Takifugu
Takifugu
Bombyx
Bombyx
Sphingomonadales
Sphingomonadales
Burkholderia cepacia
Burkholderia cepacia
two-photon laser/detector
A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons.
http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy
PERSON: Erik Segerdell
two-photon laser/detector
Coxiella burnetii
Coxiella burnetii
An assay in which a specified input material is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes.
Primer based PCR assay, Norther blot, Southern Blot, RNAse protection assay
detection of specific nucleic acids with complementary probes
RNA/DNA detection
detection of specific nucleic acids with complementary probes
is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length.
true single molecule sequencing
Philippe Rocca-Serra
Helicos sequencing
PMID: 18388294. Single-molecule DNA sequencing of a viral genome.
Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9.
adapted from wikipedia
Helicos sequencing
peritoneum
peritoneum
BP: should be imported in the future, but I need it now to demonstrate how to define intraperitoneal injection
is the serous membrane that forms the lining of the abdominal cavity
Bacilli
Bacilli
Bartonellaceae
Bartonellaceae
computed tomography scanner
CT scanner
An image acquisition device that generates a
three-dimensional image of the inside of an object from a large series of
two-dimensional X-ray images taken around a single axis of rotation.
X-ray computed tomography scanner
computed tomography scanner
PERSON:Bjoern Peters
http://en.wikipedia.org/wiki/X-ray_computed_tomography
Bacillaceae
Bacillaceae
Alexa Fluor 555
A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate.
Alexa Fluor 555
Leuconostoc
Leuconostoc
Stage II breast cancer, The timepoint of recovery from a disease
PERSON: Bjoern peters
disease stage
disease stage
a part of an occurrence of a disease process which is associated with position in the normal progression of the disease
Bacillus cereus
Bacillus cereus
loess group transformation two-channel
A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
Elisabetta Manduchi
OTHER: Editor's generalization based on MGED Ontology term
loess group transformation two-channel
genotyping by array assay
Group: ArrayExpress production team
An assay in which an array is used to detect polymorphisms in DNA samples
EFO_0002767: genotyping by array
genotyping by array assay
cell killing
Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
cell killing
image cytometer
http://web.mit.edu/solab/Research/ImageCytometry.html
Melanie Courtot
image cytometer
An image_cytometer is an instrument for image-based study or measurement of cells.
The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining.
hydrogen generator
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01035
A gas generator that generates hydrogen gas.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
hydrogen generator
PERSON: Tina Boussard
PERSON: James Malone
longitudinal data analysis
longitudinal data analysis
Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time.
longitudinal data analysis
correlation analysis
bioassay
IEDB curation of Pubmed 12445737:
CTLL-2 cells were grown in the presence of hybridoma supernatants and monitoring growth by a 3H-thymidine incorporation (cell proliferation) assay in order to detect IL-2 in the hybridoma supernatant.'
PERSON:Bjoern Peters
cell culture analyte detection bioassay
An assay in which a reporter cell line is cultured which is affected in its growth characteristics by the presence of a specific analyte. Monitoring the cell line growth is used to detect the analyte in an input material (the evaluant).
cell culture analyte detection bioassay
age since birth measurement datum
An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother.
MO_710 birth
PERSON:Chris Stoeckert, Jie Zheng
age since birth measurement datum
Orbiliomycetes
Orbiliomycetes
IEDB
epitope specific IL-12 release by T cells
epitope specific IL-12 release by T cells
IEDB
A biological process where T cells produce IL-12 resulting from the recognition of a T cell epitope.
molecular entity
Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well
molecular entity
Apis
Apis
a specimen that is output of a process that cell culture inoculated into agar for long term storage.
agar stab specimen
agar stab specimen
PERSON: Chris Stoeckert
MO_971 agar_stab
PERSON: Jie Zheng
alpha-beta T cell
A T cell that expresses an alpha-beta T cell receptor complex.
alpha-beta T cell
A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
loess group transformation one-channel
loess group transformation one-channel
Elisabetta Manduchi
A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
OTHER: Editor's generalization based on MGED Ontology term
Streptococcus gordonii
Streptococcus gordonii
Populus tremula
Populus tremula
epitope specific interleukin-16 production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope.
epitope specific interleukin-16 production by T cells
Pyrococcus
Pyrococcus
place holder for sequence ontology term
Information about a sequence region
sequence feature annotation
Bjoern Peters
Bjoern Peters
sequence feature annotation
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400192
high resolution magic angle spin probe
high resolution magic angle spin probe
high resolution MAS, hr-MAS
PERSON:Daniel Schober
Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used.
GROUP:<http://msi-ontology.sourceforge.net>
Citrus aurantiifolia
Citrus aurantiifolia
Kaplan meier data transformation
http://en.wikipedia.org/wiki/Survival_analysis
survival analysis objective
A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables
survival analysis
PERSON: Tina Boussard
survival analysis objective
PERSON: James Malone
Helicobacter
Helicobacter
viral hemeagglutination assay
person: Bjoern Peters
WEB: http://en.wikipedia.org/wiki/Hemagglutination_assay
person: Melanie Courtot
The viral hemagglutination assay (HA) is a quantification of viruses by hemagglutination.
viral hemagglutination assay
viral hemagglutination assay
HI
HA
dose
A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses.
An organism has been injected 1ml of vaccine
dose
transcription profiling design
A study design that identifies forms and abundance of transcripts in the genome.
MO_533 transcript_identification_design
Person: Chris Stoeckert, Jie Zheng
transcription profiling design
plasma cell
A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin.
plasma cell
Orbiliales
Orbiliales
Aquificae (class)
Aquificae (class)
WEB: http://mathworld.wolfram.com/Cosine.html
cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc.
A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html.
Philippe Rocca-Serra
cosine transformation
Elisabetta Manduchi
cosine transformation
cell
Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
cell
Magnoliophyta
Magnoliophyta
IEDB (QTT)
chemokine (C-C motif) ligand 1 (TCA-3) release
assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
assay of epitope specific chemokine (C-C motif) ligand 1 production by T cells
An assay that measures epitope specific chemokine (C-C motif) ligand 1 production by T cells
Bjoern Peters
MO_416 postmortem
a specimen that was taken from a dead organism
the spleen taken from a dead mouse
post mortem specimen
post mortem specimen
network analysis
Richard Scheuermann
network topology analysis
PERSON: Richard Scheuermann
A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network.
network analysis
intranasal mucosal administration
PERSON: Melanie Courtot
The administration of a substance into the intranasal mucosis of an organism
intranasal mucosal administration
Bartonella
Bartonella
isolation of adherent cells
a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells.
isolation of adherent cells
sine transformation
sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc.
sine transformation
A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html.
WEB: http://mathworld.wolfram.com/Sine.html
Elisabetta Manduchi
single-nucleotide-resolution nucleic acid structure mapping assay
2010-01-31: Philippe Rocca-Serra: OBI needs to review 'structure assay' as currently defined. Need to get feedback from Kevin Clancy.
Person: Philippe Rocca-Serra
single-nucleotide-resolution nucleic acid structure mapping assay
RNAO
is an assay which aims to provide information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity.
detection of specific nucleic acids with complementary probes of epitope specific interleukin-2 production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interleukin-2 production by T cells
IL-2 release by RNA/DNA detection
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
detection of specific nucleic acids with complementary probes of epitope specific interleukin-2 production by T cells
B cell receptor complex
An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins.
B cell receptor complex
PERSON: James Malone
sequence analysis objective
sequence analysis objective
A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
James Malone
in vitro cell mediated cell killing assay
An assay that measures the rate in which a target cell population is killed by effector cells in a cell culture.
in vitro cell mediated cell killing assay
PERSON:Bjoern Peters
Sordariaceae
Sordariaceae
Amphibia
Amphibia
glass column
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01101
A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations.
GROUP:<http://msi-ontology.sourceforge.net>
glass column
assay of epitope specific type IV hypersensitivity by T cells
An assay that measures epitope specific type IV hypersensitivity by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
assay of epitope specific type IV hypersensitivity by T cells
type IV hypersensitivity (DTH)
loess global transformation two-channel
A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
Elisabetta Manduchi
Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
OTHER: Editor's generalization based on MGED Ontology term
loess global transformation two-channel
Gastropoda
Gastropoda
Oenococcus oeni
Oenococcus oeni
Methanosarcinales
Methanosarcinales
obsolete_DNA sequencing training service
03/22/2010:workshop: there is a user requirement that not in all cases of the training the trainee gains the skills.
A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments
DNA sequencing training service
spread calculation data transformation
EDITOR
A spread calculation is a data transformation that has objective spread calculation.
James Malone
spread calculation data transformation
liquid chromatography column
A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix.
GROUP:<http://msi-ontology.sourceforge.net>
liquid chromatography column
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01227
GROUP:<http://msi-ontology.sourceforge.net>
A series of older Bruker NMR magnets, now out of production.
Bruker AC series NMR instrument
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400241
Bruker AC series NMR instrument
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400243
solid NMR probe
PERSON:Daniel Schober
An NMR probe that is designed to hold a solid sample.
solid NMR probe
GROUP:<http://msi-ontology.sourceforge.net>
Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water.
BP
branch derived
adding a material entity into a target
adding a material entity into a target
Class was renamed from 'administering substance', as this is commonly used only for additions into organisms.
is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'.
Bacillus anthracis
Bacillus anthracis
FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument
pump valve switch
OBI
OBI Instrument branch
A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow.
pump valve switch
Thermoplasmatales
Thermoplasmatales
Group: OBI group
labeled DNA extract
labeled DNA extract
a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments.
Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group.
Added duirng Mar 1, 2010 dev call
Group: OBI group
detector lamp
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01119
A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed.
PERSON:Daniel Schober
WEB:<http://www.chromatography-online.org/HPLC/UV-Detectors/Fixed-Wavelength/rs23.html>
detector lamp
IEDB
epitope specific IL-17 release by T cells
epitope specific IL-17 release by T cells
IEDB
A biological process where T cells produce IL-17 resulting from the recognition of a T cell epitope.
Chlorophyta
Chlorophyta
Sordaria macrospora
Sordaria macrospora
cell culture analyte detection bioassay of epitope specific transforming growth factor-beta production by T cells
cell culture analyte detection bioassay of epitope specific transforming growth factor-beta production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A cell culture analyte detection bioassay that measures epitope specific transforming growth factor-beta production by T cells
TGFb release by bioassay
IEDB (QTT)
Mollusca
Mollusca
Thermoanaerobacteriaceae
Thermoanaerobacteriaceae
Caudate nucleus
Caudate nucleus
Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species.
column connector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01236
PERSON:Daniel Schober
column connector
A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness.
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01070
column frit
A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density).
WEB:<http://www.chromatography-online.org/topics/radial/columns.html>
PERSON:Daniel Schober
column frit
growth condition intervention design
PERSON: Bjoern Peters
MO_588 growth_condition_design
growth condition intervention design
A study design in which the independent variable is the environmental condition in which the specimen is growing
drug role
drug role
OBI, CDISC
http://www.answers.com/topic/drug
1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication.
2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act.
drug
Role Branch
a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism
Any device used in a gas chromatography experiment.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01030
gas chromatography equipment
gas chromatography equipment
PERSON:Daniel Schober
GROUP:<http://msi-ontology.sourceforge.net>
Glucose in blood (measured in an assay to determine the concentration of glucose).
analyte role
GROUP: Role Branch
Analyte role is a role borne by a molecular entity and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role
qualities such as weight, color are not assayed but measured, so they do not fall into this category.
interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role
pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested.
analyte role
OBI
This type of transformation is typically used in flow cytometry
split-scale transformation
Joseph Spliden
Ryan Brinkman
A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t.
split-scale transformation
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
Elisabetta Manduchi
Photobacterium profundum
Photobacterium profundum
Sordaria
Sordaria
Chlamydomonadales
Chlamydomonadales
T cell
A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex.
T cell
cloacal specimen
A specimen obtained by inserting a swab deeply into the vent of the cloaca of
an organism and vigorously swabbing the wall. The swab should be deeply
stained with fecal material and is then placed in transport medium.
WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf
type of sample used in the PCIRN influenza network
cloacal specimen
PERSON: Melanie Courtot
transcription profiling by high throughput sequencing
RNA-seq assay
An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance
RNA-seq assay
EFO_0002770 transcription profiling by high throughput sequencing
PERSON: James Malone
Streptococcus
Streptococcus
Leuconostoc mesenteroides
Leuconostoc mesenteroides
Lepidium sativum
Lepidium sativum
OTHER: Editor's generalization based on MGED Ontology term
loess global transformation one-channel
Elisabetta Manduchi
loess global transformation one-channel
Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
syringe filter
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01122
A small membrane filter of defined pore size, that filters samples from a syringe.
GROUP:<http://msi-ontology.sourceforge.net>
PERSON:Daniel Schober
syringe filter
Apidae
Apidae
is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
xenotransplantation
OBI branch derived
xenotransplantation
PlanAndPlannedProcess Branch
The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis
performing a diagnosis
performing a diagnosis
Diagnosing that a patient has pneumonia based on information on measurements of temperature, sound of breathing, and patient complaining about a headache.
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400239
Varian GEMINI spectrometer
Varian GEMINI spectrometer
An older Varian Broadband NMR spectrometer.
PERSON:Daniel Schober
PCR instrument
03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent.
A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
PCR instrument
An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01219
open tubular column
WEB:<http:www.iupac.org/publications/pac/1993/pdf/6504x0819.pdf>
open tubular column
PERSON:Daniel Schober
IEDB
epitope specific IL-13 release by T cells
A biological process where T cells produce IL-13 resulting from the recognition of a T cell epitope.
epitope specific IL-13 release by T cells
IEDB
induced hemagglutination
person: Melanie Courtot
WEB: http://medical-dictionary.thefreedictionary.com/hemagglutination
person: Bjoern Peters
MC, 20100217: This term was originally submitted to GO, see discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=2947975&group_id=36855&atid=440764. After discussion it was agreed that this isn't a natural in vivo process and therefore out of scope for GO.
Dev call Nov 22, 2010: To reflect this, the term's label has been updated to 'induced hemagglutination'.
The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances
hemeagglutination
induced hemagglutination
IEDB
IEDB
restricting MHC role
restricting MHC role
The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell.
An ELISPOT assay that measures epitope specific tumor necrosis factor superfamily cytokine production by T cells
IEDB (QTT)
TNF release by ELISPOT
ELISPOT assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
ELISPOT assay of epitope specific tumor necrosis factor superfamily cytokine production by T cells
Hexapoda
Hexapoda
Staphylococcus aureus subsp. aureus MSSA476
Staphylococcus aureus subsp. aureus MSSA476
Streptococcaceae
Streptococcaceae
IEDB (QTT)
cytometric bead array assay of epitope specific interleukin-13 production by T cells
IL-13 release by cytometric bead array
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cytometric bead array assay of epitope specific interleukin-13 production by T cells
A cytometric bead array assay that measures epitope specific interleukin-13 production by T cells
Bruker SampleRail system
This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back.
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400207
Bruker SampleRail system
WEB:<http://www.bruker-biospin.com/automation.html>
loess scale group transformation two-channel
A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar.
Elisabetta Manduchi
Loess scale group normalization applied to data from a two-channel expression microarray assay.
OTHER: Adjusted from MGED Ontology
loess scale group transformation two-channel
mass spectrometry analysis
A data transformation which has the objective of spectrum analysis.
mass spectrometry analysis
general scalar measurement datum
1
4/10/2011 BP: It is unclear to me why we need this, and don't just use the scalar measurement datum.
general scalar measurement datum
manual injection system
manual injection system
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01064
The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe.
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01069
chart recorder
chart recorder
GROUP:<http://msi-ontology.sourceforge.net>
The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration.
PERSON:Daniel Schober
IEDB
donor
IEDB
donor role
donor
A T cell line from a PPD(+) donor.
A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro.
The planned process of providing material entities
to be used in an investigation.
supplying
Jennifer Fostel
Jackson Labs supplies mouse strains.
Jennifer Fostel
supplying
cell culture analyte detection bioassay of epitope specific interleukin-5 production by T cells
IL-5 release by bioassay
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
A cell culture analyte detection bioassay that measures epitope specific interleukin-5 production by T cells
cell culture analyte detection bioassay of epitope specific interleukin-5 production by T cells
OTHER: Editor's adjustment based on MGED Ontology term
loess scale group transformation one-channel
loess scale group transformation one-channel
Elisabetta Manduchi
Loess scale group normalization applied to data from two one-channel expression microarray assays.
A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar.
continuous wave NMR instrument
continuous wave NMR instrument
PERSON:Daniel Schober
WEB:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400283
Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned).
electrophoresis box
CHEF gel box, slab gel box, capillary electrophoresis
electrophoresis unit
sep:00095
gel tank
Person:Kevin Clancy
gel tank
a device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules.
Person:Frank Gibson
protein binding site identification design
A study design that investigates protein binding sites on nucleic acids.
MO_933 binding_site_identification_design
Person: Chris Stoeckert, Jie Zheng
protein binding site identification design
Firmicutes
Firmicutes
Protacanthopterygii
Protacanthopterygii
Thermoproteaceae
Thermoproteaceae
Bovidae
Bovidae
Ryan Brinkman
This type of transformation is typically used in flow cytometry.
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
Joseph Spliden
logical transformation
A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation.
Elisabetta Manduchi
logical transformation
Flexibacteraceae
Flexibacteraceae
In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation.
fourier transformation NMR instrument
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400284
GROUP:<http://teaching.shu.ac.uk/hwb/chemistry/tutorials/molspec/nmr3.htm>
fourier transformation NMR instrument
mitosporic Orbiliaceae
mitosporic Orbiliaceae
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
detection of specific nucleic acids with complementary probes of epitope specific interferon-beta production by T cells
IFNb release by RNA/DNA detection
A detection of specific nucleic acids with complementary probes that measures epitope specific interferon-beta production by T cells
detection of specific nucleic acids with complementary probes of epitope specific interferon-beta production by T cells
putamen
Nucleus of brain which lies ventral to the caudate nucleus and internal capsule and medial to the external capsule. The putamen and caudate nucleus together form the dorsal striatum. It is also one of the structures that comprises the basal ganglia. Through various pathways, the putamen is connected to the substantia nigra and globus pallidus. The main function of the putamen is to regulate movements and influence various types of learning. It employs dopamine to perform its functions. The putamen also plays a role in degenerative neurological disorders, such as Parkinson's disease.
putamen
deoxyribonuclease-1
A protein that is a translation product of the DNASE1 gene or a 1:1 ortholog thereof.
deoxyribonuclease-1
Moss Superclass V
Moss Superclass V
Coniferophyta
Coniferophyta
Lymph node
Lymph node
Thermoproteales
Thermoproteales
Tetraodon nigroviridis
Tetraodon nigroviridis
JEOL NMR instrument
JEOL NMR instrument
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400226
An NMR instrument that is manufactured by JEOL.
GROUP:<http://msi-ontology.sourceforge.net>
T cell proliferation
T cell proliferation
The expansion of a T cell population by cell division. Follows T cell activation.
gadoteridol
gadoteridol
Monacrosporium
Monacrosporium
transcription profiling by tiling array design
A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals.
transcription profiling by tiling array design
MO_507 tiling_path_design
Person: Chris Stoeckert, Jie Zheng
Gerbera hybrid cultivar
Gerbera hybrid cultivar
Caulobacter vibrioides
Caulobacter vibrioides
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400212
GROUP:<http://msi-ontology.sourceforge.net>
NMR sample holder
PERSON:Daniel Schober
NMR sample holder
An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample.
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
detection of specific nucleic acids with complementary probes of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific granulocyte macrophage colony-stimulating factor production by T cells
GM-CSF release by RNA/DNA detection
detection of specific nucleic acids with complementary probes of epitope specific granulocyte macrophage colony-stimulating factor production by T cells
Coniferales
Coniferales
gadodiamide hydrate
gadodiamide hydrate
PERSON:Daniel Schober
chromatography consumable
A chromatography consumable is a consumable that is used in a chromatography experiment.
chromatography consumable
GROUP:<http://msi-ontology.sourceforge.net>
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115
sex comparison design
MO_575 sex_design
sex comparison design
A study design that assays differences associated with an organism's sex, gender or mating type.
Person: Chris Stoeckert, Jie Zheng
Kluyveromyces waltii
Kluyveromyces waltii
Burkholderia
Burkholderia
A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting.
post-transcriptional modification design
post-transcriptional modification design
post transcription modification design?
or more clear RNAi design / antibody targeting design?
need to check the use cases
Person: Chris Stoeckert, Jie Zheng
MO_392 cellular_modification_design
Phasianidae
Phasianidae
PERSON:Daniel Schober
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01262
chromatography instrument
chromatography instrument
GROUP:<http://msi-ontology.sourceforge.net>
Any instrument that is used to carry out a chromatography experiment.
inter-rater reliability objective
inter-rater reliability objective
A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability.
Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation.
Person:Helen Parkinson
a data transformation objective of determining the concordance or agreement between human judges.
http://en.wikipedia.org/wiki/Inter-rater_reliability
Person:Alan Ruttenberg
inter-rater agreement
Thermotogaceae
Thermotogaceae
normal phase column
A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column.
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01097
PERSON:Daniel Schober
GROUP:<http://msi-ontology.sourceforge.net>
normal phase column
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
epitope specific interferon-beta production by T cells
A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope.
epitope specific interferon-beta production by T cells
Craniata
Craniata
epitope specific tumor necrosis factor superfamily cytokine production by T cells
A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope.
epitope specific tumor necrosis factor superfamily cytokine production by T cells
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
5'-adenylyl sulfate
5'-adenylyl sulfate
An acyl sulfate that has formula C10H14N5O10PS.
generalized family wise error rate correction method
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
Monnie McGee
gFWER correction
generalized family wise error rate correction method
A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer.
Thermotogae (class)
Thermotogae (class)
Sinorhizobium
Sinorhizobium
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400249
APOLLO console
APOLLO console
WEB:<http://www.tecmag.com/apollo.htm>
The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application.
PERSON:Daniel Schober
podzol
Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics.
podzol
allele information
discussed on San Diego OBI workshop, March 2011
allele information
a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition.
MO_58 Allele
Person: Chris Stoeckert, Jie Zheng
genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information
epitope specific helper T cell enhancement of T cell mediated immune response
A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope.
IEDB (QTT)
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
epitope specific helper T cell enhancement of T cell mediated immune response
Rutaceae
Rutaceae
Leishmania
Leishmania
BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features.
http://msi-ontology.sourceforge.net/ontology/NMR.owl#msi_400223
HR Probe
PERSON:Daniel Schober
GROUP:<http://msi-ontology.sourceforge.net>
Bruker high resolution probe
Bruker high resolution probe
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
An intracellular staining assay that measures epitope specific granzyme B production by T cells
granzyme B release by intracellular staining
intracellular material detection of epitope specific granzyme B production by T cells
intracellular material detection of epitope specific granzyme B production by T cells
Pichia
Pichia
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
A cytometric bead array assay that measures epitope specific tumor necrosis factor production by T cells
cytometric bead array assay of epitope specific tumor necrosis factor production by T cells
TNFa release by cytometric bead array
cytometric bead array assay of epitope specific tumor necrosis factor production by T cells
IEDB (QTT)
Adeno-associated virus - 2
Adeno-associated virus - 2
Dependovirus
Dependovirus
hydroxyl
A reactive oxygen specy that has formula HO.
hydroxyl
chromatography detector
chromatography detector
http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01012
A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range.
WEB:<http://www.chromatography-online.org/GC-Detectors/Classification/rs1.html>
PERSON:Daniel Schober
MO_953 organism_part_comparison_design
A study design that compares tissues, regions, organs within or between organisms
organism part comparison design
Person: Chris Stoeckert, Jie Zheng
organism part comparison design
IL-17 release by ELISPOT
IEDB (QTT)
An ELISPOT assay that measures epitope specific interleukin-17 production by T cells
ELISPOT assay of epitope specific interleukin-17 production by T cells
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
ELISPOT assay of epitope specific interleukin-17 production by T cells
2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
PERSON: Chris Stoeckert
independent variable specification
independent variable specification
PERSON: Bjoern Peters
PERSON: Alan Ruttenberg
Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled
WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables
2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled.
PERSON: Chris Stoeckert
dependent variable specification
PERSON: Alan Ruttenberg
dependent variable specification
PERSON: Bjoern Peters
dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies.
false discovery rate correction method
false discovery rate correction method
The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. .
2011-03-31: [PRS].
creating a defined class by specifying the necessary output of dt
allows correct classification of FDR dt
FDR correction method
Philippe Rocca-Serra
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate
Monnie McGee
Isolation and characterization of an immortalized oral keratinocyte cell line of mouse origin.
Arch Oral Biol. 2008 Nov;53(11):1091-100. Epub 2008 Aug 21. PMID: 1872191
GROUP: OBI Biomaterial Branch
immortalized cell line culture
immortalized cell line culture
An immortalized cell line is a cell line that is able to replicate indefinitely as a result of an in vitro cell line immortalization process
GROUP: OBI Biomaterial Branch
immortalized cell line
Actinopteri
Actinopteri
RNA extraction/purification instrument
A device that is used to isolate and collect RNA for subsequent molecular analysis.
PERSON: Erik Segerdell
PERSON: Erik Segerdell
RNA extraction/purification instrument
Biomphalaria
Biomphalaria
Caniformia
Caniformia
Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid.
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
differential pressure gauge
differential pressure gauge
LSR2 differential pressure gauge
Brain
Brain
Segment of neuraxis that has as its parts gray matter and white matter that surround the cerebral ventricular system; Examples: There is only one brain.
predicted data item
BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted.
Philippe Rocca-Serra; Bjoern Peters
predicted data item
A data item that was generated on the basis of a calculation or logical reasoning
a reference participant role realized by equivalent treatment of participants
A member of a dose-time group; a patient in a given arm of a trial
biological replicate role
biological replicate role
biological replicate
OBI
Person:Jennifer Fostel
Rhizobium/Agrobacterium group
Rhizobium/Agrobacterium group
A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses.
proportion of expected false positives correction method
Monnie McGee
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21
PEFP correction method
proportion of expected false positives correction method
Elopocephala
Elopocephala
Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
sequence feature identification objective
sequence feature identification objective
Jennifer Fostel
Rattus norvegicus
Rattus norvegicus
DNA extract
The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas.
Person: Jie Zheng
DNA extract
Group: UPenn group
Actinomycetales
Actinomycetales
Feliformia
Feliformia
John Quinn
diode laser
diode laser
Daniel Schober
A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer.
FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc.
Planorbidae
Planorbidae
Andropogoneae
Andropogoneae
Buchnera
Buchnera
Salmonella enterica
Salmonella enterica
quantile number of false positives correction method
QNFP
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed'
quantile number of false positives correction method
Monnie McGee
Medicago sativa
Medicago sativa
Person:Philippe Rocca-Serra
mean-centered data
a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value
mean-centered data
Person:Helen Parkinson
Clupeocephala
Clupeocephala
worker role
OBI
worker
a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
Person:Jennifer Fostel
"executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study
worker role
Trypanosomatidae
Trypanosomatidae
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
John Quinn
Rhodamine 101 dye laser used to irradiate cells in a flow cytometer.
dye laser
Daniel Schober
dye laser
A dye laser is a laser in which the lasing medium is a fluorescent dye, usually dissolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emission amplification.
Pooideae
Pooideae
TPPFP correction method
A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1.
Monnie McGee
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20
tail probability for the proportion of false positives correction method
tail probability for the proportion of false positives correction method
Sinorhizobium/Ensifer group
Sinorhizobium/Ensifer group
detection of specific nucleic acids with complementary probes of epitope specific interferon-gamma production by T cells
IFNg release by RNA/DNA detection
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
IEDB (QTT)
detection of specific nucleic acids with complementary probes of epitope specific interferon-gamma production by T cells
A detection of specific nucleic acids with complementary probes that measures epitope specific interferon-gamma production by T cells
Panagrolaimoidea
Panagrolaimoidea
Equus subg. Equus
Equus subg. Equus
OBI branch derived
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
intervention design
intervention design
Philppe Rocca-Serra
An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
GROUP: OBI Biomaterial Branch
cell line cell
cell line cell
A material entity that represents generations of a primary culture.
PERSON: Susanna Sansone
cellular process
Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level.
cellular process
Photobacterium
Photobacterium
Otophysi
Otophysi
Kinetoplastida
Kinetoplastida
Loteae
Loteae
Panicoideae
Panicoideae
Biomphalaria glabrata
Biomphalaria glabrata
Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
person:Chris Stoeckert
group:OBI
gene list
gene list
A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
Cypriniphysi
Cypriniphysi
Medicago
Medicago
data normalization objective
PERSON: Helen Parkinson
Helen Parkinson
PERSON: James Malone
data normalization objective
PERSON: Elisabetta Manduchi
A normalization objective is a data transformation objective where the aim is to remove
systematic sources of variation to put the data on equal footing in order
to create a common base for comparisons.
Elisabetta Manduchi
James Malone
Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
spotted fever group
spotted fever group
FACS Calibur
The FACS Calibur is one of the most popular cytometers in use for research.
"http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11"
"FACS Calibur at TFL, BCCRC, Vancouver"
John Quinn
FACS Calibur
Festuca brevipila
Festuca brevipila
Methanobacteriaceae
Methanobacteriaceae
rate unit
A unit which represents a standard measurement occurrence of a process per unit time.
rate unit
Bernoulli trial
OBI branch derived
Bernoulli trial
is an assay where the output data is a datum with one of two values denoted success and failure.
PlanAndPlannedProcess Branch
Populus tomentosa
Populus tomentosa
biological_process
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
biological_process
Azotobacter vinelandii
Azotobacter vinelandii
PERSON: James Malone
A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself
Type I error correction
James Malone
correction objective
PERSON: Melanie Courtot
correction objective
Primates
Primates
Trypanozoon
Trypanozoon
Basommatophora
Basommatophora
Ehrhartoideae
Ehrhartoideae
FACS Canto
FACS Canto
A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 fluorescent parameters. The FACS_Canto is an analyser usually used in clinical applications.
http://www.bdbiosciences.com/pdfs/brochures/23-8742-00.pdf
John Quinn
Methanobacteriales
Methanobacteriales
Moorella thermoacetica
Moorella thermoacetica
cell differentiation design
MO_892 development_or_differentiation_design
A study design that assays events associated with cell development or differentiation.
Person: Chris Stoeckert, Jie Zheng
cell differentiation design
Crenarchaeota
Crenarchaeota
xenograft
xenograft
WEB: http://en.wikipedia.org/wiki/Xenograft
xenotransplant
A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species.
PERSON: Melanie Courtot
Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world
PERSON: Philippe Rocca-Serra
type III interferon production
The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type III interferons are members of the interferon-lambda gene family.
type III interferon production
Azotobacter group
Azotobacter group
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21
quantile proportion of false positives correction method
quantile proportion of false positives correction method
Monnie McGee
QPFP correction method
A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate).
Archaea
Taeniopygia
Taeniopygia
peptide
Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid.
peptide
A FACS_Canto2 is a flow_cytometer_analyser manufactured by BD. It features digital electronics, two solid state lasers at 488 and 633 nm with the option for a third 405 nm laser, and filters and collectors for measuring up to 8 fluorescent paramters with either the 2 or 3 laser option. The FACS_Canto2 is an analyser usually used in clinical applications.
FACS Canto2
FACS Canto2
http://www.bdbiosciences.com/cgi-bin/literature/view?part_num=23-8786-01
John Quinn
Trifolieae
Trifolieae
Funariidae
Funariidae
GROUP: Penn Group
an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results
assay validation objective
PERSON: Chris Stoeckert, Jie Zheng
assay validation objective
500, 200, 0
number of particles in subset
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
number of particles in subset
person:Kevin Clancy
Azotobacter
Azotobacter
Streptomyces
Streptomyces
data transformation objective
A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
James Malone
PERSON: James Malone
data transformation objective
normalize objective
Sylvia communis
Sylvia communis
Person: Jennifer Fostel
impartial witness. A person, who is independent of the trial, who cannot be unfairly influenced by people involved with the trial, who attends the informed consent process if the subject or the subject's legally acceptable representative cannot read, and who
role of impartial witness
Person: Helen Parkinson
role of impartial witness
impartial witness
a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial
According to GCP , an impartial witness should be present for an
illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html
digoxigenin
A 12beta-hydroxy steroid that has formula C23H34O5.
digoxigenin
Taeniopygia guttata
Taeniopygia guttata
Vicieae
Vicieae
http://www.brc.ubc.ca/brc/facs.html
FACS Scan
A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three fluorescent parameters The FACS_Scan is usually used for research applications.
FACS Scan
John Quinn
Kluyveromyces
Kluyveromyces
obsoleted_utilizes_device
obsoleted_utilizes_device
Alan Ruttenberg
Relationship between protocol application and an intrument in which it participates
see example_of_usage for is_device_for
is_concretized_as
Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
PERSON: Alan Ruttenberg
PERSON: Barry Smith
is_concretized_as
example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the
function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity'
denotes a function and not a process). We leave open the possibility of defining
in future the sub-relations directly_realizes (as bewteen a function and it's
functioning) and indirectly_realizes.
involves_execution_of
executes
Relation between a process and a function, where the unfolding of the
process requires the execution of the function. Class level: P realizes F iff:
given any p that instantiates P, there exists some f, t such that f instantiates
F at t and p *realizes* f. Here, *realizes* is the primitive
instance level relation [GOC:cjm]
PERSON: Chris Mungal
realizes
realizes
is_realization_of
has_function_part
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Larry Hunter
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
has_specified_input
PERSON: Bjoern Peters
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
has_specified_input
PERSON: Melanie Coutot
8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works.
objective_achieved_by
This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process.
definition needs clean up to indicate directionality
objective_achieved_by
bearer_of
is grain of
is grain of
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
PERSON: Alan Ruttenberg
obsoleted_is_specified_information_output_of
A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation.
Editor
PERSON: James Malone
is replaced by has_specified_output_of
is_specified_information_output_of
towards
A relation between a relational quality and an independent continuant, subproperty of inheres that distinguishes the main bearers of a relational quality from additional dependents.
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
towards
bound_to
bound_to
achieves_planned_objective
A cell sorting process achieves the objective specification 'material separation objective'
BP, AR, PPPB branch
PPPB branch derived
This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process.
achieves_planned_objective
PERSON:Bjoern Peters
IEDB
process is result of
The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR
is a relationship between a process and a preceding occurrent that directly caused the later one to occur
process is result of
has category label
has category label
obsoleted_utilizes_reagent
obsoleted_utilizes_reagent
Alan Ruttenberg
Relationship between a protocol application and a substance that has role reagent that participates in the protocol application
see example_of_usage for is_reagent_in
is_proxy_for
is_proxy_for
A relation between continuant instances c1 and c2 where within a protocol
application, measurement of c1 is related to a what would be the
measurement of c2.
A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.
Alan Ruttenberg
position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples:
A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality.
Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
level of radioactivity is_proxy_for level of toxicity
executed_during
is_realized_by
is_realized_as
is_realized_by
Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]
GROUP:OBI:<http://obi.sourceforge.net>
has_realization
PERSON: Chris Mungall
has_manufacturer
is_manufactured_by
Alan Ruttenberg
is_manufactured_by
Liju Fan
c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
has_make
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
role_of
A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
role_of
obsoleted_is_specified_information_intput_of
Is the inverse relation of has_specfied_input_information
is replaced by is_specified_intput_of
obsoleted_is_specified_information_intput_of
PERSON:Bjoern Peters
is_specified_input_of
A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of.
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
is_specified_input_of
Alan Ruttenberg
obsoleted_is_device_for
obsoleted_is_device_for
Alan Ruttenberg
Relationship between a device and a protocol application in which it participates
some LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
obsoleted_has_specified_output_information
PERSON: Frank Gibson
obsoleted_has_specified_output_information
A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data.
PERSON: Alan Ruttenberg
obsolete_results_from
2009/11/23: BP, dev call:o bsoleted as discussed in tracker https://sourceforge.net/tracker/?func=detail&aid=2899860&group_id=177891&atid=886178
. Should be replaced by instead creating defined classes for materials, which are specified output of the process that conveys the
obsolete_results_from
quality_of
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
A relation between a quality Q and an entity E. Q quality_of E iff: Q inheres_in E and Q is a quality
quality_of
has_specified_output
PERSON: Melanie Courtot
PERSON: Bjoern Peters
PERSON: Alan Ruttenberg
PERSON: Larry Hunter
has_specified_output
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
has grain
PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349
has grain
the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car.
Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form
PERSON: Alan Ruttenberg
PERSON: Frank Gibson
PERSON: Alan Rutternberg
has_supplier
PERSON: Melanie Courtot
A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
PERSON: Cristian Cocos
has_supplier
is_described_by
is_described_by
obsoleted_has_specified_input_information
PERSON: Frank Gibson
consumes data
has specified input information
A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data.
PERSON:Alan Ruttenberg
Relating a legal person to an organization in the case where the legal person has a role as member of the organization
Person:Helen Parkinson
2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population
is member of organization
Person:Helen Parkinson
is member of organization
Person:Alan Ruttenberg
Person:Alan Ruttenberg
is_concretization_of
Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
PERSON: Alan Ruttenburg
PERSON: Barry Smith
is_concretization_of
is_specified_output_of
PERSON:Bjoern Peters
is_specified_output_of
A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of.
Alan Ruttenberg
obsoleted_is_reagent_in
obsoleted_is_reagent_in
Alan Ruttenberg
Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole
some Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
has_function
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
has_function
Relation between an independent continuant and a function.
heart has_function to-pump-blood
supplies
A relation between an organisation or person and a material entity who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner.
GROUP: Relations branch
supplies
has_role
PERSON:Chris Mungal
has_role
GROUP:OBI:<http://obi.sourceforge.net>
A relation between a continuant C and a role R. The reciprocal relation of role_of.
has_quality
PERSON: Chris Mungall
has_quality
GROUP:OBI:<http://obi.sourceforge.net>
A relation between an entity and a quality. For types: E has_quality Q iff:
for any eEt, exists qQt such that q inheres_in e at t.
For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm]
has_feature_value
has_feature_value
James Malone
has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values.
Luminex
A supplier of flow cytometry analyzers
Karin Breuer
Luminex
WEB:http://www.luminexcorp.com/@2011/04/11
pH
A dimensionless concentration notation which denotes the acidity of a solution in terms of activity of hydrogen ions (H+).
pH
GenePattern module SVM
GenePattern module SVM
GenePattern module SVM is a GenePattern software module which is used to run a support vector machine data transformation.
James Malone
Ryan Brinkman
GenePattern SVM
GenePattern SVM
James Malone
Invitrogen
A supplier of flow cytometry analyzers
Invitrogen
Karin Breuer
WEB:http://www.invitrogen.com/@2011/04/11
GenePattern module CARTXValidation
GenePattern module CARTXValidation
GenePattern module CARTXValidation is a GenePattern software module which uses a CART decision tree induction with a leave one out cross validation data transformations.
GenePattern LOOCV
GenePattern LOOCV
GenePattern CART
GenePattern CART
James Malone
Agilent
Agilent
Philippe Rocca-Serra
GenePattern module KMeansClustering
GenePattern module KMeansClustering
GenePattern module KMeansClustering is a GenePattern software module which is used to perform a k Means clustering data transformation.
James Malone
PERSON: James Malone
GenePattern k-means clustering
GenePattern k-means clustering
James Malone
Millipore
A supplier of flow cytometry analyzers
Karin Breuer
Millipore
WEB:http://www.guavatechnologies.com/@2011/04/11
GenePattern module KNNXValidation
GenePattern module KNNXValidation
GenePattern module KNNXValidation is a GenePattern software module which uses a k-nearest neighbours clustering with a leave one out cross validation data transformations.
James Malone
PERSON: James Malone
GenePattern module PeakMatch
GenePattern module PeakMatch
GenePattern peak matching
GenePattern peak matching
James Malone
Ryan Brinkman
GenePattern module KNN
GenePattern module KNN
GenePattern module KNN is a GenePattern software module which perform a k-nearest neighbors data transformation.
James Malone
GenePattern k-nearest neighbors
GenePattern k-nearest neighbors
James Malone
GenePattern module HierarchicalClustering
GenePattern module HierarchicalClustering
GenePattern module HierarchicalClustering is a GenePattern software module which is used to perform a hierarchical clustering data transformation.
James Malone
PERSON: James Malone
GenePattern hierarchical clustering
GenePattern hierarchical clustering
James Malone
Bruker Corporation
Bruker Corporation
Philippe Rocca-Serra
Dako Cytomation
A supplier of flow cytometry analyzers
Dako Cytomation
Karin Breuer
WEB:http://www.dakousa.com/@2011/04/11
Bruker Daltonics
Bruker Daltonics
Philippe Rocca-Serra
cubic centimeter
cc
A volume unit which is equal to one millionth of a cubic meter or 10^[-9] m^[3], or to 1 ml.
cubic centimeter
milliliter
ml
A volume unit which is equal to one thousandth of a liter or 10^[-3] L, or to 1 cubic centimeter.
milliliter
liter
L
A volume unit which is equal to one thousandth of a cubic meter or 10^[-3] m^[3], or to 1 decimeter.
liter
GenePattern module PCA
GenePattern module PCA
GenePattern module PCA is a GenePattern software module which is used to perform a principal components analysis dimensionality reduction data transformation.
James Malone
PERSON: James Malone
GenePattern PCA
GenePattern PCA
Cytopeia
A supplier of flow cytometry analyzers
Cytopeia
Karin Breuer
WEB:http://www.cytopeia.com/@2011/04/11
volume percentage
% v/v
percent vol per vol
A dimensionless concentration unit which denotes the volume of the solute in mL per 100 mL of the resulting solution.
volume percentage
GenePattern module HeatMapViewer
A GenePattern software module which is used to generate a heatmap view of data.
GenePattern module HeatMapViewer
James Malone
GenePattern HeatMapViewer data visualization
GenePattern HeatMapViewer data visualization
James Malone
The GenePattern process of generating Heat Maps from clustered data.
mass percentage
% w/w
percent weight pr weight
A dimensionless concentration unit which denotes the mass of a substance in a mixture as a percentage of the mass of the entire mixture.
mass percentage
mass volume percentage
% w/v
percent vol per vol
A dimensionless concentration unit which denotes the mass of the substance in a mixture as a percentage of the volume of the entire mixture.
mass volume percentage
obsolete_the manufacturer role of Waters
obsolete_the manufacturer role of Waters
GenePattern module HierarchicalClusteringViewer
A GenePattern software module which is used to generate a view of data that has been hierarchically clustered.
GenePattern module HierarchicalClusteringViewer
James Malone
GenePattern HierarchicalClusteringViewer data visualization
GenePattern HierarchicalClusteringViewer data visualization
James Malone
The GenePattern process of generating hierarchical clustering visualization from clustered data.
CytoBuoy
A supplier of flow cytometry analyzers
CytoBuoy
Karin Breuer
WEB:http://www.cytobuoy.com/@2011/04/11
obsolete_manufacturer role of Bruker Corporation
obsolete_manufacturer role of Bruker Corporation
Exbio Antibodies
A supplier of flow cytometry analyzers
Exbio Antibodies
Karin Breuer
WEB:http://www.exbio.cz/@2011/04/11
Becton Dickinson (BD Biosciences)
A supplier of flow cytometry analyzers
Becton Dickinson (BD Biosciences)
Karin Breuer
WEB:http://www.bdbiosciences.com/@2011/04/11
gram per liter
g per L
g/L
A mass unit density which is equal to mass of an object in grams divided by the volume in liters.
gram per liter
Apogee Flow Systems
A supplier of flow cytometry analyzers
Apogee Flow Systems
Karin Breuer
WEB:http://www.apogeeflow.com/@2011/04/11
milligram per milliliter
mg per ml
mg/ml
A mass unit density which is equal to mass of an object in milligrams divided by the volume in milliliters.
milligram per milliliter
micromole
umol
A substance unit equal to a millionth of a mol or 10^[-6] mol.
micromole
hour
h
hr
A time unit which is equal to 3600 seconds or 60 minutes.
hour
day
A time unit which is equal to 24 hours.
day
minute
min
A time unit which is equal to 60 seconds.
minute
year
A time unit which is equal to 12 months which is science is taken to be equal to 365.25 days.
year
week
A time unit which is equal to 7 days.
week
month
A time unit which is approximately equal to the length of time of one of cycle of the moon's phases which is science is taken to be equal to 30 days.
month
Exalpha Biological
A supplier of flow cytometry analyzers
Exalpha Biological
Karin Breuer
WEB:http://www.exalpha.com/@2011/04/11
nanomole
nmol
A substance unit equal to one thousandth of one millionth of a mole or 10^[-9] mol.
nanomole
example of usage
editor preferred term
picomole
pmol
A substance unit equal to 10^[-12] mol.
picomole
Affymetrix
Affymetrix
Affymetrix supplied microarray
An organization which supplies technology, tools and protocols for use in high throughput applications
obsolete_the supplier role of Affymetrix
obsolete_the supplier role of Affymetrix
OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file.
OWL
OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)
person:Jennifer Fostel
web-page:http://www.w3.org/2004/OWL/
OWL
milliliter per liter
ml per L
ml/l
A volume per unit volume unit which is equal to one millionth of a liter of solute in one liter of solution.
milliliter per liter
gram per deciliter
g/dl
A mass density unit which is equal to mass of an object in grams divided by the volume in deciliters.
gram per deciliter
nanomolar
nM
A unit of molarity which is equal to one thousandth of one millionth of a molar or 10^[-9] M.
nanomolar
micromolar
uM
A unit of molarity which is equal to one millionth of a molar or 10^[-6] M.
micromolar
millimolar
mM
A unit of molarity which is equal to one thousandth of a molar or 10^[-3] M.
millimolar
molar
M
A unit of concentration which expresses a concentration of 1 mole of solute per liter of solution (mol/L).
molar
term editor
definition
editor note
RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document
person:Jennifer Fostel
XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
XML
web-page:http://www.w3.org/XML/
XML
ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)
ACS
web-page:http://www.isac-net.org/content/view/607/150/
person:Jennifer Fostel
d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
ACS
person:Jennifer Fostel
web-page:http://www.gnu.org/software/tar/manual/
tar
Example.tar file.
tar
tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
U.S. Food and Drug Administration
FDA
U.S. Food and Drug Administration
obsolete_manufacturer role of applied biosystems
obsolete_manufacturer role of applied biosystems
zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)
MagicDraw MDZIP archive, Java JAR file.
person:Jennifer Fostel
zip
web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/
zip
A FOAF file, a SKOS file, an OWL file.
RDF
RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)
RDF
web-page:http://www.w3.org/RDF/
person:Jennifer Fostel
compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment
web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf
Compensation-ML
Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)
person:Jennifer Fostel
Compensation-ML
d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
web-page:http://www.fcspress.com/
FCS
FCS
FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
person:Jennifer Fostel
Bentley Instruments
A supplier of flow cytometry analyzers
Bentley Instruments
Karin Breuer
WEB:http://bentleyinstruments.com/@2011/04/11
picomolar
pM
A unit of molarity which is equal to 10^[-12] M.
picomolar
Miltenyi Biotec
A supplier of flow cytometry analyzers
Karin Breuer
Miltenyi Biotec
WEB:http://www.miltenyibiotec.com/@2011/04/11
Thermo
Philippe Rocca-Serra
Thermo
Waters
Philippe Rocca-Serra
Waters
BIO-RAD
BIO-RAD
Philippe Rocca-Serra
web-page:http://www.flowcyt.org/gating/
Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
foogate.xml, Gating-ML file describing gates used in a GvHD experiment.
Gating-ML
person:Jennifer Fostel
Gating-ML
AES Chemunex
A supplier of flow cytometry analyzers
AES Chemunex
Karin Breuer
WEB:http://www.aeschemunex.com/@2011/04/11
Ambion
Ambion
Philippe Rocca-Serra
Transformation-ML file describing parameter transformations used in a GvHD experiment.
Transformation-ML
web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf
person:Jennifer Fostel
Transformation-ML
Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)
kilogram
kg
A mass unit which is equal to the mass of the International Prototype Kilogram kept by the BIPM at Svres, France.
kilogram
meter
m
A length unit which is equal to the length of the path traveled by light in vacuum during a time interval of 1/299 792 458 of a second.
meter
colony forming unit per volume
A concentration unit which a measure of viable bacterial numbers in a given volume.
colony forming unit per volume
FGED alternative term
An alternative term used by the Functional Genomics Data (FGED) Society.
PERSON: Chris Stoeckert, Jie Zheng
Penn Group
alternative term
IEDB alternative term
An alternative term used by the IEDB.
IEDB
PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters
cubic decimeter
A volume unit which is equal to one thousand of a cubic meter or 10^[-3] m^[3], or to 1 L.
cubic decimeter
microliter
ul
A volume unit which is equal to one millionth of a liter or 10^[-6] L.
microliter
nanoliter
nl
A volume unit which is equal to one thousandth of one millionth of a liter or 10^[-9] L.
nanoliter
picoliter
pl
A volume unit which is equal to 10^[-12] L.
picoliter
hertz
A frequency unit which is equal to 1 complete cycle of a recurring phenomenon in 1 second.
hertz
gram
g
A mass unit which is equal to one thousandth of a kilogram or 10^[-3] kg.
gram
picogram
pg
A mass unit which is equal to 10^[-12] g.
picogram
nanogram
ng
A mass unit which is equal to one thousandth of one millionth of a gram or 10^[-9] g.
nanogram
microgram
ug
A mass unit which is equal to one millionth of a gram or 10^[-6] g.
microgram
milligram
mg
A mass unit which is equal to one thousandth of a gram or 10^[-3] g.
milligram
degree celsius
C
degree C
A temperature unit which is equal to one Kelvin degree. However, they have their zeros at different points. The Centigrade scale has its zero at 273.15 K.
degree celsius
second
s
sec
A time unit which is equal to the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the caesium 133 atom.
second
centimeter
cm
A length unit which is equal to one hundredth of a meter or 10^[-2] m.
centimeter
micrometer
um
A length unit which is equal to one millionth of a meter or 10^[-6] m.
micrometer
millimeter
mm
A length unit which is equal to one thousandth of a meter or 10^[-3] m.
millimeter
angstrom
A length unit which is equal to 10 [-10] m.
angstrom
nanometer
nm
A length unit which is equal to one thousandth of one millionth of a meter or 10^[-9] m.
nanometer
obsolete_the manufacturer role of Thermo
obsolete_the manufacturer role of Thermo
obsolete_the manufacturer role of Roche
obsolete_the manufacturer role of Roche
obsolete_the manufacturer role of Li-Cor
obsolete_the manufacturer role of Li-Cor
imported from
eBioscience
A supplier of flow cytometry analyzers
Karin Breuer
WEB:http://www.ebioscience.com/@2011/04/11
eBioscience
microliters per minute
A volumetric flow rate unit which is equal to one microliter volume through a given surface in one minute.
microliters per minute
microgram per liter
ng/ml
ug/L
A mass unit density which is equal to mass of an object in micrograms divided by the volume in liters.
microgram per liter
obsolete_the manufacturer role of Agilent
obsolete_the manufacturer role of Agilent
obsolete_manufacturer role of Bruker Daltonics
obsolete_manufacturer role of Bruker Daltonics
Advanced Instruments Inc. (AI Companies)
A supplier of flow cytometry analyzers
Advanced Instruments Inc. (AI Companies)
Karin Breuer
WEB:http://www.aicompanies.com/@2011/04/11
Beckman Coulter
A supplier of flow cytometry analyzers
Beckman Coulter
Karin Breuer
WEB:http://www.beckmancoulter.com/@2011/04/11
obsolete_the manufacturer role of Helicos
obsolete_the manufacturer role of Helicos
obsolete_the manufacturer role of Illumina
obsolete_the manufacturer role of Illumina
obsolete_the regulator role of the FDA
obsolete_the regulator role of the FDA
obsolete_the manufacturer role of BIO-RAD
obsolete_the manufacturer role of BIO-RAD
obsolete_the manufacturer role of Ambion
obsolete_the manufacturer role of Ambion
Antigenix
A supplier of flow cytometry analyzers
Antigenix
Karin Breuer
WEB:http://www.antigenix.com/@2011/04/11
Partec
A supplier of flow cytometry analyzers
Karin Breuer
Partec
WEB:http://www.partec.de/@2011/04/11
count per nanomolar second
A rate unit which is equal to one over one nanomolar second.
count per nanomolar second
count per molar second
A rate unit which is equal to one over one molar second.
count per molar second