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&amp;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&amp;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&amp;aid=1866458&amp;group_id=177891&amp;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