2011-07-20 2011-07-20 This file is based on checkout of our SVN repository revision $Revision: 3272 $ en Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester Alan Ruttenberg Allyson Lister An ontology for the annotation of biomedical and functional genomics experiments. Barry Smith Bill Bug Bjoern Peters Carlo Torniai Chris Mungall Chris Stoeckert Chris Taylor Cristian Cocos Daniel Rubin Daniel Schober Dawn Field Dirk Derom Elisabetta Manduchi Eric Deutsch Frank Gibson Gilberto Fragoso Helen C. Causton Helen Parkinson Holger Stenzhorn James Malone Jay Greenbaum Jeffrey Grethe Jennifer Fostel Jessica Turner Jie Zheng Joe White John Westbrook Kevin Clancy Larisa Soldatova Lawrence Hunter Liju Fan Luisa Montecchi Matthew Pocock Melanie Courtot Melissa Haendel Mervi Heiskanen Monnie McGee Norman Morrison OWL-DL Ontology for Biomedical Investigation Philip Lord Philippe Rocca-Serra Pierre Grenon Richard Bruskiewich Richard Scheuermann Robert Stevens Ryan R. Brinkman Stefan Wiemann Susanna-Assunta Sansone Tanya Gray 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. Tina Hernandez-Boussard Trish Whetzel Yongqun He free, no license required. derives_from Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant. ro_bfo_bridge relationship OBO_REL:0000015 derived_from derived_from Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'. PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'. PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 derived_into OBO_REL:0000016 relationship ro_bfo_bridge Description An account of the content of the resource. Description may include but is not limited to: an abstract, table of contents, reference to a graphical representation of content or a free-text account of the content. has_participant Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. OBO_REL:0000019 ro_bfo_bridge relationship P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 definition GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. GROUP:OBI:<http://purl.obfoundry.org/obo/obi> PERSON:Daniel Schober editor note Contributor An entity responsible for making contributions to the content of the resource. Examples of a Contributor include a person, an organisation, or a service. Typically, the name of a Contributor should be used to indicate the entity. has curation status OBI_0000281 PERSON:Alan Ruttenberg PERSON:Bill Bug PERSON:Melanie Courtot has curation status definition source Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 function_of A relation between a function F and an entity E. F function_of E iff: Q inheres_in E and Q is a function Example: 'to blood pump' function_of 'heart' GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall function_of term editor 20110707, MC: label update to term editor and definition modified accordingly. See http://code.google.com/p/information-artifact-ontology/issues/detail?id=115. GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people PERSON:Daniel Schober term editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober alternative term preceded_by An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. ro_bfo_bridge OBO_REL:0000017 relationship P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 editor preferred term GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) editor preferred term example of usage A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Daniel Schober example Creator An entity primarily responsible for making the content of the resource. Examples of a Creator include a person, an organisation, or a service. Typically, the name of a Creator should be used to indicate the entity. quality_of A relation between a quality Q and an entity E. Q quality_of E iff: Q inheres_in E and Q is a quality GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall quality_of Subject and Keywords The topic of the content of the resource. Typically, a Subject will be expressed as keywords, key phrases or classification codes that describe a topic of the resource. Recommended best practice is to select a value from a controlled vocabulary or formal classification scheme. precedes OBO_REL:0000018 relationship ro_bfo_bridge IEDB alternative term An alternative term used by the IEDB. IEDB PERSON:Randi Vita, Jason Greenbaum, Bjoern Peters imported from For external terms/classes, the ontology from which the term was imported GROUP:OBI:<http://purl.obolibrary.org/obo/obi> PERSON:Alan Ruttenberg PERSON:Melanie Courtot imported from located_in Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus relationship OBO_REL:0000008 ro_bfo_bridge C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.) PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.) PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 Date A date associated with an event in the life cycle of the resource. Typically, Date will be associated with the creation or availability of the resource. Recommended best practice for encoding the date value is defined in a profile of ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format. Format The physical or digital manifestation of the resource. Typically, Format may include the media-type or dimensions of the resource. Format may be used to determine the software, hardware or other equipment needed to display or operate the resource. Examples of dimensions include size and duration. Recommended best practice is to select a value from a controlled vocabulary (for example, the list of Internet Media Types [MIME] defining computer media formats). participates_in relationship OBO_REL:0000020 ro_bfo_bridge Title Typically, a Title will be a name by which the resource is formally known. A name given to the resource. Rights Management Typically, a Rights element will contain a rights management statement for the resource, or reference a service providing such information. Rights information often encompasses Intellectual Property Rights (IPR), Copyright, and various Property Rights. If the Rights element is absent, no assumptions can be made about the status of these and other rights with respect to the resource. Information about rights held in and over the resource. has measurement unit label is about 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. Smith, Ceusters, Ruttenberg, 2000 years of philosophy This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. person:Alan Ruttenberg denotes 2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive. g denotes r =def r is a portion of reality there is some c that is a concretization of g every c that is a concretization of g specifically denotes r A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance "Alan" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between "Alan" and the person that is being named. Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan denotes is a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically person:Alan Ruttenberg is quality measurement of 8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later Alan Ruttenberg From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important] This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. -- From the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009] unit of measure is a quality, e.g. the length of a ruler. [We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label] [Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory] a represents b means either a denotes b or a describes describe: a describes b means a is about b and a allows an inference of at least one quality of b We have had a long discussion about denotes versus describes. From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully. a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality. From the second meeting on IAO: An attempt at defining assay using Barry's "reliability" wording assay: process and has_input some material entity and has_output some information content entity and which is such that instances of this process type reliably generate outputs that describes the input. This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail. Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details. m is a quality measurement of q at t when q is a quality there is a measurement process p that has specified output m, a measurement datum, that is about q is duration of Person:Alan Ruttenberg relates a process to a time-measurement-datum that represents the duration of the process has time stamp Alan Ruttenberg relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken has measurement datum Alan Ruttenberg relates a time stamped measurement datum to the measurement datum that was measured has_specified_input 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. PERSON: Alan Ruttenberg see is_input_of example_of_usage is_concretization_of Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. PERSON: Alan Ruttenburg PERSON: Barry Smith is_concretization_of a relationship between a generically dependent continuant and at least one specifically dependent continuant upon which it existentially depends is_concretized_as Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter. PERSON: Alan Ruttenberg PERSON: Barry Smith is_concretized_as a relationship between a generically dependent continuant and at least one specifically dependent continuant upon which it existentially depends has_quality A relation between an entity and a quality. For types: E has_quality Q iff: for any eEt, exists qQt such that q inheres_in e at t. For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm] GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall has_quality has_specified_output PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg is_realized_by GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm] executed_during has_realization is_realized_as is_realized_by is_manufactured_by Alan Ruttenberg Liju Fan c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. has_make has_manufacturer http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) is_manufactured_by has_function GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall Relation between an independent continuant and a function. has_function heart has_function to-pump-blood realizes GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungal Relation between a process and a function, where the unfolding of the process requires the execution of the function. Class level: P realizes F iff: given any p that instantiates P, there exists some f, t such that f instantiates F at t and p *realizes* f. Here, *realizes* is the primitive instance level relation [GOC:cjm] example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity' denotes a function and not a process). We leave open the possibility of defining in future the sub-relations directly_realizes (as bewteen a function and it's functioning) and indirectly_realizes. executes has_function_part involves_execution_of is_realization_of realizes is_specified_output_of PERSON:Bjoern Peters is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg is_proxy_for is_proxy_for A relation between continuant instances c1 and c2 where within a protocol application, measurement of c1 is related to a what would be the measurement of c2. A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be. Alan Ruttenberg position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples: A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality. Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay level of radioactivity is_proxy_for level of toxicity has_role A relation between a continuant C and a role R. The reciprocal relation of role_of. GROUP:OBI:<http://obi.sourceforge.net> PERSON:Chris Mungal has_role achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' BP, AR, PPPB branch PPPB branch derived This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. achieves_planned_objective has grain PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349 has grain the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car. Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form PERSON: Alan Ruttenberg objective_achieved_by This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. definition needs clean up to indicate directionality objective_achieved_by has category label has category label process is result of IEDB PERSON:Bjoern Peters The production of IFN-gamma by effector T cells is a process result of T cell stimulation through the TCR is a relationship between a process and a preceding occurrent that directly caused the later one to occur process is result of bound_to bound_to bearer_of function_of A relation between a function F and an entity E. F function_of E iff: Q inheres_in E and Q is a function Example: 'to blood pump' function_of 'heart' GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall function_of inheres in This clarifies that only specifically dependent continuants inhere in (specifically) one independent continuant over all time. For GDCs, there in implicitly inherence to all the independent continuants in which the concretizations inhere. Should add a 'cardinality 1' restriction to the definition of specifically dependent continuant. This relation belongs in BFO/RO, and will be in BFO 2 quality_of A relation between a quality Q and an entity E. Q quality_of E iff: Q inheres_in E and Q is a quality GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall quality_of role_of A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall role_of towards A relation between a relational quality and an independent continuant, subproperty of inheres that distinguishes the main bearers of a relational quality from additional dependents. GROUP:OBI:<http://obi.sourceforge.net> PERSON: Chris Mungall towards adjacent_to Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum OBO_REL:0000012 relationship C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 derived_into OBO_REL:0000016 relationship ro_bfo_bridge derives_from Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant. ro_bfo_bridge relationship OBO_REL:0000015 Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'. PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 derived_from Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'. PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 derived_from has_part relationship OBO_REL:0000003 has_participant Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. OBO_REL:0000019 ro_bfo_bridge relationship P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 located_in Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus relationship OBO_REL:0000008 ro_bfo_bridge C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.) PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.) PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 part_of Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. relationship OBO_REL:0000002 There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 participates_in relationship OBO_REL:0000020 ro_bfo_bridge preceded_by An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. ro_bfo_bridge OBO_REL:0000017 relationship P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 precedes OBO_REL:0000018 relationship ro_bfo_bridge has measurement value has_feature_value has_feature_value James Malone has_feature_value datatype property is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values. geographical location A reference to a place on the Earth, by its name or by its geographical location. measurement unit label 2009-03-16: provenance: a term measurement unit was proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and Cristian Cocos, and subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definition of this, different, term. 2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. Examples of measurement unit labels are liters, inches, weight per volume. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." Answers the question, why did you do this experiment? OBI Plan and Planned Process/Roles Branch OBI_0000217 PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. objective specification purpose of a study; support of hypothesis, discovery of new information action specification Alan Ruttenberg OBI Plan and Planned Process branch Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take label A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label GROUP: IAO http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n label software GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot Software is a plan specification composed of a series of instructions that can be interpreted by or directly executed by a processing unit. see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 software journal article Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. OBI_0000159 a report that is published in a journal group:OBI journal article person:Alan Ruttenberg person:Chris Stoeckert model number A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. Person: Alan Ruttenberg manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers model number data item 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. Data items include counts of things, analyte concentrations, and statistical summaries. JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. data data item symbol 20091104, MC: this needs work and will most probably change PERSON: Jonathan Rees a smallish, word-like datum... symbol information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. OBI_0000142 PERSON: Chris Stoeckert an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity information content entity information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. scalar measurement datum 1 1 10 feet. 3 ml. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form PERSON: Alan Ruttenberg PERSON: Melanie Courtot Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. directive information entity 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO An information content entity whose concretizations indicate to their bearer how to realize them in a process. PERSON: Alan Ruttenberg PERSON: Bjoern Peters Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan dot plot A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions. Dot plot of SSC-H and FSC-H. OBI_0000123 dot plot group:OBI person:Allyson Lister person:Chris Stoeckert graph A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way. OBI_0000240 PERSON: Lawrence Hunter graph group:OBI person:Alan Ruttenberg person:Allyson Lister algorithm A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. OBI_0000270 PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. Philippe Rocca-Serra PlanAndPlannedProcess Branch adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm curation status specification Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 PERSON:Bill Bug The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value. curation status specification density plot A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel. Density plot of SSC-H and FSC-H. OBI_0000179 density plot group:Flow Cytometry community person:Allyson Lister person:Chris Stoeckert report 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on something that has completed." Should it be restricted to those things that are completed? For example, a progress report is (usually) about something that definitely has *not* been completed, or may include (only) projections. I think the definition would not suffer if the whole sentence is deleted. 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. GROUP: OBI OBI_0000099 PERSON: Alan Ruttenberg PERSON: Melanie Courtot PERSON:Chris Stoeckert a document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record) disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification report data set 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). OBI_0000042 data set group:OBI person:Allyson Lister person:Chris Stoeckert image An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface. OBI_0000030 group:OBI image person:Alan Ruttenberg person:Allyson person:Chris Stoeckert data about an ontology part Person:Alan Ruttenberg data about an ontology part is a data item about a part of an ontology, for example a term plan specification 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. Alan Ruttenberg Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved OBI Plan and Planned Process branch OBI_0000344 PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. a directive information entity that when concretized it is realized in a process in which the bearer tries to achieve the objectives, in part by taking the actions specified. Plan specifications includes parts such as objective specification, action specifications and conditional specifications. plan specification measurement datum 2/2/2009 is_specified_output of some assay? A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. OBI_0000305 group:OBI measurement datum person:Chris Stoeckert version number A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. GROUP: IAO Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version version number serial number A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots. GROUP: IAO Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-) serial number lot number A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots. GROUP: IAO batch number lot number setting datum 2/3/2009 Feedback from OBI This should be a "setting specification". There is a question of whether it is information about a realizable or not. Pro other specification are about realizables. Cons sometimes specifies a quality which is not a realizable. A settings datum is a datum that denotes some configuration of an instrument. Alan grouped these in placeholder for the moment. Name by analogy to measurement datum. conclusion textual entity 2009/09/28 Alan Ruttenberg. Fucoidan-use-case 2009/10/23 Alan Ruttenberg: We need to work on the definition still A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. Person:Alan Ruttenberg conclusion textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. GROUP:OBI PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot histogram heatmap A heatmap is a report graph which is a graphical representation of data where the values taken by a variable(s) are shown as colors in a two-dimensional map. GROUP:OBI PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot heatmap dendrogram A dendrogram is a report graph which is a tree diagram frequently used to illustrate the arrangement of the clusters produced by a clustering algorithm. Dendrograms are often used in computational biology to illustrate the clustering of genes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram scatter plot A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis. Comparison of gene expression values in two samples can be displayed in a scatter plot PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot scattergraph textual entity A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. PERSON: Lawrence Hunter Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities text textual entity table A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions PERSON: Lawrence Hunter table | T F --+----- T | T F F | F F figure An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. Any picture, diagram or table PERSON: Lawrence Hunter figure diagram A figure that expresses one or more propositions A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. PERSON: Lawrence Hunter diagram document A collection of information content entities intended to be understood together as a whole A journal article, patent application, laboratory notebook, or a book PERSON: Lawrence Hunter document publication A document that has been accepted by a publisher A journal article or book PERSON: Lawrence Hunter publication length measurement datum A scalar measurement datum that is the result of measurement of length quality Alan Ruttenberg mass measurement datum 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A scalar measurement datum that is the result of measurement of mass quality Person:Alan Ruttenberg hypothesis textual entity 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A textual entity that expresses an assertion that is intended to be tested. Person:Alan Ruttenberg hypothesis textual entity that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660 time measurement datum 2009/09/28 Alan Ruttenberg. Fucoidan-use-case A scalar measurement datum that is the result of measuring a temporal interval Person:Alan Ruttenberg postal address A textual entity that is used as directive to deliver something to a person, or organization 2010-05-24 Alan Ruttenberg. Use label for the string representation. See issue http://code.google.com/p/information-artifact-ontology/issues/detail?id=59 documenting 6/11/9: Edited at OBI workshop. 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 Bjoern Peters Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. a planned process in which a document is created or added to by including the specified input in it. wikipedia http://en.wikipedia.org/wiki/Documenting time stamped measurement datum time sampled measurement data set A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time. Alan Ruttenberg experimental time series pmid:20604925 - time-lapse live cell microscopy planned process '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.) Bjoern Peters Injecting mice with a vaccine in order to test its efficacy 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. branch derived planned process A processual entity that realizes a plan which is the concretization of a plan specification. planned process 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 material supplier role Jackson Labs is an organization which provide mice as experimental material Supplier role is a special kind of service, e.g. biobank material provider role material supplier role supplier PERSON:Jennifer Fostel a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. classified data set PERSON: James Malone PERSON: Monnie McGee classified data set 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. reference substance role reference substance reference substance role 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 OBI Person:Jennifer Fostel a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference. cytological stain role Person:Helen Parkinson 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 cytological stain cytological stain role haemotoxylin is a general purpose nuclear stain extracted from the wood of the logwood tree WEB: http://en.wikipedia.org/wiki/Haematoxylin Person:Jennifer Fostel supernatant role GROUP: Role branch 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 supernatant role 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. 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. Frank Gibson chromatography column http://en.wikipedia.org/wiki/Column_chromatography drug role drug http://www.answers.com/topic/drug 1. A substance used in the diagnosis, treatment, or prevention of a disease or as a component of a medication. 2. Such a substance as recognized or defined by the U.S. Food, Drug, and Cosmetic Act. OBI, CDISC Role Branch a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism drug role waiting OBI branch derived PERSON:Alan Ruttenberg not actively doing anything to a material for a duration of time. waiting processed material Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples Is a material entity that is created or changed during material processing. PERSON: Alan Ruttenberg processed material chromatography device Frank Gibson a device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated. chromatography device chromatography instrument http://en.wikipedia.org/wiki/Chromatography microarray platform OBI Instrument branch OBI Instrument branch A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI. microarray platform 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 positive 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 "100%" response positive reference substance positive reference substance role MMS mutagen Person: Jennifer Fostel 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 a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). investigation evaluant role GROUP: Role Branch OBI 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) When a specimen of blood is assayed for glucose concentration, the blood has the 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 evaluant role examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected") assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. any method A planned process with the objective to produce information about some evaluant OBI branch derived PlanAndPlannedProcess Branch assay measuring scientific observation quantitative confidence value group:OBI A data item which is used to indicate the degree of uncertainty about a measurement. person:Chris Stoeckert quantitative confidence value sample preparation for assay A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI. OBI branch derived PlanAndPlannedProcess Branch sample preparation for assay study diagnosis textual entity Jennifer Fostel diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. diagnosis textual entity 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. culture medium culture medium role A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008 OBI Person: Jennifer Fostel reagent role reagent reagent role www.answers.com/topic/reagent; November 2008 Buffer, dye, a catalyst, a solvating agent. GROUP: Role Branch a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances 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 patient role patient patient role GROUP:Role Branch OBI, CDISC a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 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 material processing A cell lysis, production of a cloning vector, creating a buffer. PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material processing A planned process which results in physical changes in a specified input material OBI branch derived PERSON: Bjoern Peters material transformation 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 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. GROUP: Role Branch study subject role measured expression level OBI Data Transformation branch 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. Examples are quantified data from an expression microarray experiment, PCR measurements, etc. measured expression level person:Chris Stoeckert responsible party role responsible party responsible party role OBI Person: Jennifer Fostel 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 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 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 transplantation OBI branch derived PlanAndPlannedProcess Branch a protocol application to replace an organ or tissue of an organism transplantation biological vector role Feb 20, 2009. The material transmitted can be genetic information (as in cloning vector) or a pathogen (as in a disease vector) GROUP: Role Branch OBI and Wikipedia 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. biological vector role 1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria. 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 specimen role 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. GROUP: Role Branch 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. 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 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 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. 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. sequence feature identification objective Jennifer Fostel Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide. sequence feature identification objective intervention design An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays. OBI branch derived PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study. Philppe Rocca-Serra intervention design worker role "executes the study plan" includes the suppliers and manufacturers of reagents and other materials used in the study worker worker role OBI Person:Jennifer Fostel Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline gene list group:OBI A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis. gene list person:Chris Stoeckert 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 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 incubator Frank Gibson 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 a device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled http://www.medterms.com/script/main/art.asp?articlekey=18426 incubator label role OBI label Label role is a role which inheres in a material entity and which is realized in a detection of label assay 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 Role Branch 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 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 baseline participant role a reference participant role which is realized by making the reference to qualities at the start of the study or intervention baseline participant baseline participant role Person: Jennifer Fostel Subject at time = 0; subject before a stress test. filter paper Frank Gibson a device manufacture with the intent to provide a porous unsized paper used for filtering. filter paper sep:00107 cell co-culturing 2 A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one. Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay OBI branch derived PlanAndPlannedProcess Branch cell co-culturing 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 radiolabel role Jennifer Fostel radiolabel radiolabel role radiolabel role is a role which inheres in a material entity which is realized by the process of radioactivity detection cDNA library 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. PERSON: Luisa Montecchi PERSON: Philippe Rocca-Serra PMID:6110205. collection of cDNA derived from mouse splenocytes. cDNA library 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 autotransplantation OBI branch derived PlanAndPlannedProcess Branch autotransplantation is the transplantation of tissue from one part of \nthe body to another in the same individual. ) parameter threshold Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt 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 person:Kevin Clancy study group role The group of randomized participants that are assigned to a treatment arm of the trial study group population study group role 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 p-value 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). WEB: http://en.wikipedia.org/wiki/P-value 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. PERSON:Chris Stoeckert p-value population PERSON: Philippe Rocca-Serra 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. 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 population 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 biological replicate role a reference participant role realized by equivalent treatment of participants biological replicate biological replicate role A member of a dose-time group; a patient in a given arm of a trial OBI Person:Jennifer Fostel radioactivity detection An assay in which a material's radioactivity is measured. Measurment of the radioactivity of a supernatant, as in chromium_release_assay. OBI branch derived PlanAndPlannedProcess Branch radioactivity detection investigation agent role 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 investigator GROUP: Role Branch 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 The person perform microarray experiments and submit microarray results (including raw data, processed data) with experiment description to ArrayExpress. nutrient role nutrient nutrient role GROUP: Role branch 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 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. methodology testing objective 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 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 negative reference substance role Person: Jennifer Fostel Saline solution 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 reference subject role reference participant reference subject role Jennifer Fostel OBI Saline treated rat; one of three identically-treated subjects 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 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 enzymatic cleavage OBI branch derived PlanAndPlannedProcess Branch 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 enzymatic cleavage enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme hardware optimization objective Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware. Jennifer Fostel hardware optimization objective standard error group:OBI 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. person:Chris Stoeckert standard error antigen role 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 OBI antigen role Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response Role 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 organization GROUP: OBI PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone 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. 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. 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. organization feed role 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. feed feed role OBI Person: Jennifer Fostel 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 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 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 cluster group:OBI A data set which is a subset of data that are a similar to each other in some way. Cluster of the lymphocytes population. cluster person:Allyson person:Chris Stoeckert cohort role 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). 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. cohort role 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 Jennifer Fostel 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. artificially induced nucleic acid hybridization 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. OBI branch derived PlanAndPlannedProcess Branch artificially induced nucleic acid hybridization 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 DNA extraction A DNA extraction is a nucleic acid extraction where the desired output material is DNA. DNA extraction OBI branch derived PlanAndPlannedProcess Branch plan The plan of researcher X to perform an experiment according to a protocol. 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. A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. AR, BP, JM, MC, PRS branch derived plan 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 protocol OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice. PlanAndPlannedProcess Branch a protocol is a plan specification which has sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the process. protocol adding a material entity into a target BP Class was renamed from 'administering substance', as this is commonly used only for additions into organisms. Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water. adding a material entity into a target branch derived is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'. analyte role GROUP: Role Branch Glucose in blood (measured in an assay to determine the concentration of glucose). OBI analyte role interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested. qualities such as weight, color are not assayed but measured, so they do not fall into this category. Analyte role is a role borne by a molecular entity and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role disease stage PERSON: Bjoern peters disease stage Stage II breast cancer, The timepoint of recovery from a disease a part of an occurrence of a disease process which is associated with position in the normal progression of the disease intraperitoneal injection BP intraperitoneal injection 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 precipitate GROUP: OBI Biomaterial Branch PERSON: Philippe Rocca-Serra 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 a precipitate is a material entity which is output of a precipitation process precipitate precipited material 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 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 eluate OBI Bionaterial PERSON: Philippe Rocca-Serra Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263 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 eluate eluted material need to add restriction to indicate: has_part some (material entity has_role mobile phase) need to add mobile phase as role material to be added role OBI 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 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 peritoneum peritoneum BP: should be imported in the future, but I need it now to demonstrate how to define intraperitoneal injection is the serous membrane that forms the lining of the abdominal cavity planning 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 Bjoern Peters PPPB branch planning the process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. a process of creating or modifying a plan. histological sample preparation OBI branch derived PERSON:Bjoern Peters histological sample preparation histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay metabolite profiling OBI Philippe Rocca-Serra metabolite assay 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 metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism light emission function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A light emission function is an excitation function to excite a material to a specific excitation state that it emits light. light emission function contain function A syringe, a beaker Bill Bug Daniel Schober Frank Gibson Melanie Courtot A contain function is a function to constrain a material entities location in space contain function heat function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A heat function is a function that increases the internal kinetic energy of a material heat function material separation function Bill Bug Daniel Schober Frank Gibson Melanie Courtot 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. material separation function excitation function Bill Bug Daniel Schober Frank Gibson Melanie Courtot 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 synthesizing function 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. Bill Bug Daniel Schober Frank Gibson Melanie Courtot synthesizing function perturb function Bill Bug Daniel Schober Frank Gibson Melanie Courtot 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 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 mechanical function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force). http://en.wikipedia.org/wiki/Mechanical_work mechanical function transfer function Bill Bug Daniel Schober Frank Gibson Melanie Courtot A transfer function is a function to displace a material from one location to another. transfer function electricity supply function Daniel Schober Frank Gibson Melanie Courtot the function of supplying current during a neuroscience experiment. 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. electricity supply function power supply cool function Daniel Schober Frank Gibson Melanie Courtot 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. cool function energy supply function 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 information processor function Frank Gibson An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process. data processor function information processor function image acquisition function Frank Gibson An image acquisition function is a function to acquire an image of a material image acquisition function 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 solid support function Daniel Schober Frank Gibson Melanie Courtot Taped, glued, pinned, dried or molecularly bonded to a solid support solid support function 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 environment control function Bill Bug Daniel Schober Frank Gibson Melanie Courtot 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 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 PCR product GROUP: OBI BIomaterial Branch GROUP: OBI BIomaterial Branch PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA. PCR product We are using PCR and not the written out words, as this is the most common used. is double stranded DNA that is the specified output of a polymerase chain reaction 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 The extraction of RNA from an input material that specifically isolates viral RNA viral RNA extraction nucleic acid template role a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009 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 template role recombinant plasmid GROUP: OBI Biomaterial Branch PERSON: Bjoern Peters PERSON: Kevin Clancy PERSON: Melanie Courtot a plasmid in which extraneous DNA has been inserted. recombinant plasmid cloning vector role PERSON: Helen Parkinson cloning vector role pBluescript plays the role of a cloning vector 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. cell cycle synchronization Bjoern Peters and Nicole Washington 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. a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle polymerase chain reaction OBI Plan adapted from wikipedai polymerase chain reaction Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413 PCR 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. 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" GROUP: Role branch OBII and Wikipedia cloning insert role 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. measuring glucose concentration in blood serum An assay that determines the concentration of glucose molecules in a blood serum sample Person:Bjoern Peters measuring glucose concentration in blood serum reverse transcriptase group:OBI person:Melanie Courtot enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase activity) reverse transcriptase syringe OBI Instrument adapted from Wikipedia Philippe Rocca-Serra syringe 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 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 extract GROUP: OBI Biomatrial Branch PERSON: Philippe Rocca-Serra 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 an extract is a material entity which results from an extraction process extract extracted material transcription profiling assay OBI Philippe Rocca-Serra transcription profiling assay 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 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 averaging objective Elisabetta Manduchi PERSON: 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. An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. James Malone averaging objective injection OBI Biomaterial Philippe Rocca-Serra injection 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 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. enzyme GROUP:OBI 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. person: Melanie Courtot (protein or rna) or has_part (protein or rna) and has_function some GO:0003824 (catalytic activity) enzyme intraperitoneal administration Person:Bjoern Peters 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 The administration of a substance into the peritoneum of an organism intraperitoneal administration plasmid group:OBI person:Melanie Courtot plasmid plasmid = DNA and has_quality circular and has_function (is_realized_as some gene expression) GO:0010467 injection into organ section A process in which an input substance is injected into a organ section. Person:Bjoern Peters Staining a specimen of human lung tissue with hematoxylin and eosin in order as a preparative step in histology injection into organ section DNA sequence feature detection An assay with the objective to determine a sequence feature of DNA DNA sequence feature detection OBI Person:Bjoern Peters Philippe Rocca-Serra genotyping using an Affymetrix chip should be a defined class where interpretation of data generated by assay qualifies a DNA sequence 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 genotyping assay OBI Biomaterial Philippe Rocca-Serra 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 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. genotype profiling, SNP genotyping 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 DNA sequence variation detection DNA sequence variation detection OBI Biomaterial Philippe Rocca-Serra Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641 DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule. assay objective PPPB branch PPPB branch assay objective the objective to determine the weight of a mouse. is the specification of an objective to determine a specified type of information about an evaluated entity (independent continuant bearing evaluant role) analyte assay PERSON:Bjoern Peters PERSON:Helen Parkinson PERSON:Philippe Rocca-Serra PERSON:Alan Ruttenberg GROUP:OBI Planned process branch PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg analyte assay 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. 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. 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 target of material addition role 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. GROUP: Role Branch OBI peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application. target of material addition role target of material addition role is a role realized by an entity into which a material is added in a material addition process 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. measure function A glucometer measures blood glucose concentration, the glucometer has a measure function. PERSON: Daniel Schober PERSON: Helen Parkinson PERSON: Melanie Courtot PERSON:Frank Gibson 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. measure function consume data function PERSON: Daniel Schober PERSON: Frank Gibson PERSON: Melanie Courtot 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 material transformation objective GROUP: OBI PlanAndPlannedProcess Branch PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. material transformation objective an objective specifiction that creates an specific output object from input materials. artifact creation objective manufacturing GROUP: OBI PlanAndPlannedProcess Branch Manufacturing implies reproducibility and responsibility AR PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra 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 This includes a single scientist making a processed material for personal use. manufacturing objective GROUP: OBI PlanAndPlannedProcess Branch PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra manufacturing objective is the objective to manufacture a material of a certain function (device) 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 isolation of cell population Person: Bjoern Peters a process in which a population of cells with certain characteristics is isolated from a larger population isolation of cell population removing CD4+ cells from PBMCs using magnetic beads. copy number variation profiling CNV analysis Philippe Rocca-Serra 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 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. isolation of adherent cells a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells. isolation of adherent cells isolation of PBMCs PERSON: bjoern peters a process in which cells with a single nucleus are isolated from a blood sample cells are extracted from whole blood using ficoll, a hydrophilic polysaccharide that separates layers of blood, with monocytes and lymphocytes forming a buffy coat under a layer of plasma. This buffy coat contains the PBMCs. isolation of PBMCs wiki http://en.wikipedia.org/wiki/PBMC reverse transcribed polymerase chain reaction 3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation 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 Philippe Rocca-Serra RT-PCR 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. reverse transcribed polymerase chain reaction reverse transcription polymerase chain reaction manufacturer role GROUP: Role Branch Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. OBI 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. manufacturer role scattered molecular aggregate scattered molecular aggregate the sodium and chloride ions in a glass of salt water 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 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 PERSON: Alan Ruttenberg molecular concentration 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. Discussion in Karslruhe, Oct 2008, with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. PERSON: Alan Ruttenberg 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. molecular concentration the phosphate concentration should be 0.1M 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 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 proteomic analysis DNA sequencing DNA sequencing 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 OBI Branch derived Philippe Rocca-Serra DNA methylation profiling assay DNA methylation profiling assay 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 OBI branch derived Philippe Rocca-Serra 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. material separation objective PPPB branch PPPB branch The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood. is an objective to transform a material entity into spatially separated components. material separation objective clustered data set A clustered data set is the output of a K means clustering data transformation PERSON: James Malone PERSON: Monnie McGee clustered data set data set with assigned discovered class labels 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. 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. differential expression analysis data transformation A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of James Malone Melanie Courtot Monnie McGee WEB: differential expression analysis data transformation urine specimen 4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. 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 a portion of urine collected from an organism are we happy calling collection of urine a material separation? urine specimen material combination Mixing two fluids. Adding salt into water. Injecting a mouse with PBS. bp bp created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes. is a material processing with the objective to combine two or more material entities as input into a single material entity as output. material combination fuzzy clustering objective PERSON: James Malone PERSON: Ryan Brinkman 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. James Malone fuzzy clustering objective 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 blood specimen Bjoern Peters Bjoern Peters a material entity derived from a portion of blood collected from an organism blood drawn from a human for glucose assay blood specimen 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. data representational model 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. GROUP: OBI Melanie Courtot data representational model data structure data structure specification gene regulatory graph model phylogenetic tree protein interaction network 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 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. 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). 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. PERSON: James Malone class prediction data transformation 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 error correction data transformation EDITORS 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. James Malone error correction data transformation sample from organism 5/29: This is a helper class for now a material obtained from an organism in order to be a representative of the whole 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. 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 center value PERSON: James Malone PERSON: Monnie McGee center value centre value A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data. statistical hypothesis test objective Person:Helen Parkinson WEB: http://en.wikipedia.org/wiki/Statistical_hypothesis_testing 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 James Malone statistical hypothesis test objective 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. 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 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. whole organism preparation 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 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. putting a mouse in the blender. Not: putting a mouse on a scale whole organism preparation 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 specimen creation objective A specimen creation objective is to obtain a material entity for potential use as an input during an investigation Bjoern Peters Bjoern Peters The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. specimen creation objective creating a mixture of molecules in solution Bjoern Peters PERSON: Helen Parkinson The production of PBS creating a mixture of molecules in solution is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations. material combination objective PPPB branch bp is an objective to obtain an output material that contains several input materials. material combination 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 454 Genome Sequence 20 454 Genome Sequence 20 GS 20 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. Philippe Rocca-Serra 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. immunoprecipitation OBI plan and planned process branch PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8. Philippe Rocca-Serra immunoprecipitation is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity ABI 377 automated sequencer ABI 377 automated sequencer Applied Biosystems Philippe Rocca-Serra 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. MeDIP-SEQ assay MeDIP-SEQ assay Methylated DNA immunoprecipitation sequencing assay 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. Philippe Rocca-Serra adapted from wikipedia 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. animal feeding Bjoern Peters In an investigation, this will typically be part of an animal care process animal feeding animal feeding is a process in which animals are provided with food branch derived giving crickets to a snake. chain termination sequencing PMID: 271968. DNA sequencing with chain-terminating inhibitors. Sanger F, Nicklen S, Coulson AR. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463-7. Philippe Rocca-Serra Sanger sequencing adapted from wikipedia chain termination sequencing dye terminator sequencing is a DNA sequencing which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position AB SOLiD System AB SOLiD System Applied Biosystems PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR. Methods. 2009 Jul;48(3):249-57. Philippe Rocca-Serra is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation Helicos sequencing Helicos sequencing PMID: 18388294. Single-molecule DNA sequencing of a viral genome. Harris TD, Buzby PR, Babcock H, Beer E, Bowers J, Braslavsky I, Causey M, Colonell J, Dimeo J, Efcavitch JW, Giladi E, Gill J, Healy J, Jarosz M, Lapen D, Moulton K, Quake SR, Steinmann K, Thayer E, Tyurina A, Ward R, Weiss H, Xie Z. Science. 2008 Apr 4;320(5872):106-9. Philippe Rocca-Serra adapted from wikipedia is a DNA sequencing which allows sequence identification of billions of DNA molecules immobilized to a surface by using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not requires amplification step and is typically able to produce reads of 25 base pair length. true single molecule sequencing survival assessment Need to point out more specifically that survival / death is measured. Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time survival assessment 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. James Malone PERSON: Ryan Brinkman Ryan Brinkman SVM support vector machine self-organizing map 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. James Malone PERSON: Ryan Brinkman Ryan Brinkman SOM self-organizing map 454 Genome Sequencer FLX 454 GS FLX 454 Genome Sequencer FLX 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. Philippe Rocca-Serra 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 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. Illumina Genome Analyzer II Illumina Corporation Illumina Genome Analyzer II PMID: 19336255. RNA-Seq-quantitative measurement of expression through massively parallel RNA-sequencing. Wilhelm BT, Landry JR.Methods. 2009 Jul;48(3):249-57. Philippe Rocca-Serra 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 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. James Malone decision tree induction objective 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. Philippe Rocca-Serra SOLiD sequencing adapted from Wikipedia and Applied Biosystems web site 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 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 laboratory animal care a process that realizes an animal care protocol that specifies how animals are kept and maintained laboratory animal care Li-Cor 4300 DNA Analysis System Li-Cor 4300 DNA Analysis System OBI and Li-Cor Philippe Rocca-Serra is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing library preparation 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. Philippe Rocca-Serra 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 library preparation pathogen challenge A pathogen challenge is the administration of a live pathogenic organism to a host pathogen challenge 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. graph of vertices 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. Bjoern Peters Chris Stoeckert For example, if the nodes are cities, then the edges may have numerical values that correspond to the distances between the cities. James Malone WEB: http://mitpress.mit.edu/books/FLAOH/cbnhtml/glossary-G.html graph of vertices 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 ChIP-seq assay ChIP-seq assay 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 adapted from Wikipedia 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. chromatin immunoprecipitation sequencing assay HeliScope Single Molecule Sequencer 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 pathogen role GROUP: Role Branch OBI 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 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 vaccine preparation OBI The production of B. pertussis vaccine. vaccine preparation vaccine preparation is a planned process with specified output a vaccine glucose tolerance test NuGO OBI plan branch 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. Philippe Rocca-Serra glucose tolerance test 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. paired-end library 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. Philippe Rocca-Serra adapted from information provided by Solid web site is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs mate-paired library paired-end library paired-end tag (PET) library 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. 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. Philippe Rocca-Serra Solexa sequencing adapted from Wikipedia and Illumina / Solexa web site (SS_DNAsequencing.pdf document available on july 2009) 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. reversible terminator sequencing 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 GROUP: Role Branch 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 OBI host role 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 http://en.wikipedia.org/wiki/Host_(biology) peak matching James Malone PERSON: Ryan Brinkman 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 Ryan Brinkman peak matching k-nearest neighbors k-NN 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. James Malone PERSON: James Malone k-nearest neighbors rodent care PPPB branch PPPB branch keeping animal 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. pyrosequencing Philippe Rocca-Serra Pyrosequencing sheds light on DNA sequencing. PMID: 1115661. Ronaghi M. Genome Res. 2001 Jan;11(1):3-11. Review. Wikipedia (http://en.wikipedia.org/wiki/Pyrosequencing) and Roche 454 life science web site 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 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 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. 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 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 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 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 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 material sampling process A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity material sampling process material sample A material entity that has the material sample role OBI: workshop 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. material sample sample population bisulfite sequencing 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. 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. Philippe Rocca-Serra adapted from Wikipedia bisulfite sequencing 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. CART classification and regression trees 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 James Malone independent variable specification PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables independent variable specification 2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled dependent variable specification PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert WEB: http://en.wikipedia.org/wiki/Dependent_and_independent_variables dependent variable specification 2/2/2009 In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled. dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies. controlled variable specification PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert WEB: http://en.wikipedia.org/wiki/Control_variable 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 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. 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. Oliver He adapted from wikipedia http://en.wikipedia.org/wiki/Survival_rate survival rate 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 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 http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation 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 transcription factor binding site PLace_holder for sequence ontology term SO:0000235 transcription factor binding site purification objective BP PERSON:Bjoern Peters 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 isolation objective purification objective the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides. cross linking A process in which bonds are created that link one polymer to another PERSON: Chris Stoeckert cross linking cross linking can be used as a probe to link proteins together, to check protein protein interactions http://en.wikipedia.org/wiki/Cross-link spike train datum A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time. Helen Parkinson, Alan Ruttenberg Jessica Turner, NIF Measurement of temporal regularity of spike train responses in auditory nerve fibers of the green treefrog needs more work to see exactly what the data set looks like - HP spike train datum spike train measurement denaturing Denaturing DNA in alcohol Is a process in which the tertiary or secondary structure of a polymer is disrupted denaturing http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 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 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 presentation of stimulus Helen Parkinson, Jessica Turner, Dirk Derom Helen Parkinson, Jessica Turner, Dirk Derom The presentation of a flashing light to a monkey during reward training a planned process in which an organism is exposed to some stimulus with the intent to invoke an action presentation of stimulus stimulation of organism amplified DNA Alan Ruttenberg Amplied DNA created by PCR DNA that has been produced in an enzymatic amplification process PERSON: Alan Ruttenberg amplified DNA informed consent process 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. Person:Alan Ruttenberg 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. http://clinicaltrials.gov/ct2/info/glossary#informed informed consent process 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 to be treated with active ingredient role 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 PERSON: Helen Parkinson Person:Alan Ruttenberg Role of a patient in a group treated with an active substance in a clinical trial to be treated with active ingredient role 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. GROUP: OBI Philly workshop WEB:http://en.wikipedia.org/wiki/calibration calibration the process of using pH buffer adjust a pH meter 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 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 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 DNA residue methylation DNA residue methylation a quality of a DNA residue that has a methyl group attached to it measurement device A ruler, a microarray scanner, a Geiger counter. GROUP:OBI Philly workshop OBI a processed material created to have the function to measure measurement device 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 manufacturer A person or organization that has a manufacturer role manufacturer 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 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 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 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 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 test substance role 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 Group:OBI Person:Alan Ruttenberg fucoidan bears a test substance role in a study to test safety taking a certain dosage of it orally test substance role polyA RNA extraction A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA. Person: Chris Stoeckert Person: Jie Zheng UPenn Group polyA RNA extraction organellar RNA extraction A RNA extraction process in which the desired output material is RNA in the organelle(s). Person: Chris Stoeckert Person: Jie Zheng UPenn Group organellar RNA extraction record of missing knowledge 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. Bjoern Peters 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 information content entity created to indicate that information about something is not available to the person recording it. record of missing knowledge total RNA extraction A RNA extraction process in which total cellular and organelle RNA are extracted. Person: Chris Stoeckert Person: Jie Zheng UPenn Group total RNA extraction complementary nucleotide probe role A primer in a PCR reaction. A probe on an Affymetrix chip. 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 PERSON:Bjoern Peters complementary nucleotide probe role 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. Bjoern Peters 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. record of unknown sex cytoplasmic RNA extraction A RNA extraction process in which the desired output material is RNA in the cytoplasm. Person: Chris Stoeckert Person: Jie Zheng UPenn Group cytoplasmic RNA extraction 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. Likelihood-ratio test Tina Boussard 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. 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 PERSON: Jie Zheng UPenn Group nuclear RNA extract 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 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. Tina Boussard http://en.wikipedia.org/wiki/Pattern_matching pattern matching objective 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. PERSON: Chris Stoeckert 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.) UPenn Group polyA RNA extract single-nucleotide-resolution nucleic acid structure mapping assay 2010-01-31: Philippe Rocca-Serra: OBI needs to review 'structure assay' as currently defined. Need to get feedback from Kevin Clancy. Person: Philippe Rocca-Serra RNAO is an assay which aims to provide information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity. single-nucleotide-resolution nucleic acid structure mapping assay pre-mortem specimen Bjoern Peters a specimen that was taken from a live organism material obtained through a liver biopsy from a human patient pre-mortem specimen MO_705 premortem detection of specific nucleic acids with complementary probes An assay in which a specified input material is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes. Primer based PCR assay, Norther blot, Southern Blot, RNAse protection assay RNA/DNA detection detection of specific nucleic acids with complementary probes cytoplasmic RNA extract A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted. Cytoplasmic RNA extraction from mammalian tissues to create cDNA library (Carninci P, Nakamura M, Sato K, Hayashizaki Y, Brownstein MJ. Cytoplasmic RNA extraction from fresh and frozen mammalian tissues. Biotechniques. 2002;33:306–309.) PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group cytoplasmic RNA extract cell line immortalization Bjoern Peters OBI Production of a cell line for the purposes of experimentation e.g. EBV transformation of PBMs cell line immortalization is the planned process of experimentally creating a cell line which is capable of dividing indefinitely in vitro. Has specified output cell line random primed DNA labeling PMID: 6312838. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Feinberg AP, Vogelstein B. Anal Biochem. 1983 Jul 1;132(1):6-13. PMID: 8713846. Random primed 32P-labeling of DNA. Smith DR. Methods Mol Biol. 1996;58:27-9. Person: Bjoern Peters Person: Chris Stoeckert Person: Philippe Rocca-Serra a labeling in which random primers are used to uniformly label input DNA need to add Klenow subunit of DNA polymerase I under material entity random primed DNA labeling RNA extract Group: UPenn Group PERSON: Chris Stoeckert PERSON: Jie Zheng RNA extract an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen. secondary structure of sequence macromolecule 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 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. Person: Philippe Rocca-Serra Wikipedia secondary structure of sequence macromolecule 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 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. Note that cell proliferation assays can often be a part of another assay. For example, to detect an analyte with a cell culture bioassay. PERSON:Bjoern Peters cell proliferation assay 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. Q-PCR WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction kinetic polymerase chain reaction person: Bjoern Peters person: Melanie Courtot qPCR quantitative real time polymerase chain reaction real time polymerase chain reaction assay protein extract 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 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, protein extract total RNA extract A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. Extraction of total RNA from cells with Qiagen mini RNeasy kit. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group total RNA extract organellar RNA extract 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. Extraction of organellar RNA from plant cells using organellar RNA binding protein. PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group organellar RNA extract post mortem specimen Bjoern Peters a specimen that was taken from a dead organism post mortem specimen the spleen taken from a dead mouse MO_416 postmortem sequence feature annotation Bjoern Peters Bjoern Peters Information about a sequence region place holder for sequence ontology term sequence feature annotation supplying Jackson Labs supplies mouse strains. Jennifer Fostel Jennifer Fostel The planned process of providing material entities to be used in an investigation. supplying labeled DNA extract Group: OBI group Group: OBI group 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 a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments. labeled DNA extract cloacal specimen A specimen obtained by inserting a swab deeply into the vent of the cloaca of an organism and vigorously swabbing the wall. The swab should be deeply stained with fecal material and is then placed in transport medium. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf cloacal specimen type of sample used in the PCIRN influenza network real time reverse-transcription polymerase chain reaction assay 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) PERSON: Bjoern Peters PERSON: Melanie Courtot RRT-PCR RT-rt PCR qRT-PCR real time reverse-transcription polymerase chain reaction assay 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. An assay in which expression of a reporter gene is detected that was inserted under the control of a promoter of interest. PERSON:Bjoern Peters promoter activity detection by reporter gene assay reporter gene assay nasopharyngeal aspirate specimen A speciemn which derives from nasopharyngeal mucosa after aspiration. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasopharyngeal aspirate specimen type of sample used in the PCIRN influenza network freezing storage 2010/3/3 Alan Ruttenberg: There is a question of whether we should have a separate objective to "prepare for maintenance" 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 Freezing a pellet for later assay OBI Person: Alan Ruttenberg freezing storage MO_481 frozen_storage nasal swab specimen 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. PERSON: Melanie Courtot WEB: http://www.wpro.who.int/NR/rdonlyres/EFD2B9A7-2265-4AD0-BC98-97937B4FA83C/0/manualonanimalaidiagnosisandsurveillance.pdf nasal swab specimen type of sample used in the PCIRN influenza network Dulbecco's modified Eagle medium A cell culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins. D-MEM DMEM Dulbecco's modified Eagle medium Logical definition should contain all components listed in textual definition at some point. PERSON:Bjoern Peters animal euthanization 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 Helen Parkinson and Melissa Haendel Melissa Haendel Rats were euthanized with CO2 animal euthanization animal sacrifice may later be refined with more specific list of organisms cytometric bead array assay 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. PERSON:Bjoern Peters Using a Luminex machine to detect IFN-gamma and IL-10 in the supernatant of a cell culture cytometric bead array cytometric bead array assay multiplexed bead assay, CBA assay labeled RNA extract Group: OBI group Group: OBI group 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 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. labeled RNA extract frozen specimen A specimen that has been frozen in order to store it. Frozen blood plasma MO_610 frozen_sample Person:Alan Ruttenberg frozen specimen 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 infectious agent infectious agent IEDB IEDB is a material entity bearing the disposition to infect an organism lyophilization storage PERSON: Chris Stoeckert PERSON: Jie Zheng a storage process with input material entity and output freeze dried material for long time storage can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed lyophilization storage material combination function A material separation function is a function that decreases the resolution between two or more material entities. A stirrer has a material combination function Helen Parkinson OBI material combination function study intervention GROUP: OBI PERSON: Bjoern Peters study intervention the part of the execution of an intervention design study which is varied between two or more subjects in the study material separation device A device with a separation function realized in a planed process flow cytometer material separation device 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 categorical measurement datum A measurement datum that is reported on a categorical scale Bjoern Peters Bjoern Peters categorical measurement datum nominal mesurement datum 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 service consumer role A biologist who uses a sequencing services fulfills the role of a service consumer OBI Person:Helen Parkinson a role which inheres in a person who uses a service service consumer role 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 chemical cleavage 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. RNA ontology group chemical cleavage 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 sterilization function a function to remove viable organisms from an input material sterilization function service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. PERSON:Helen Parkinson 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 accessed material role 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 is realized in a planned process where the bearer participates the role of the DNA sequencer to which someone gets access to a period of time, e.g. by payment, or other mechanism paraffin specimen MO_990 paraffin_sample PERSON: Chris Stoeckert PERSON: Jie Zheng a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin liver tissue embedded in paraffin paraffin specimen 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. an intervention design in which the treatment is the administration of a compound compound treatment design oral administration PERSON: Melanie Courtot The administration of a substance into the mouth of an organism oral administration processed specimen A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters processed specimen subcutaneous injection PERSON: Melanie Courtot 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 subcutaneous injection training objective A training objective is fulfilled by e.f. a bioconductor tutorial which instructs the user in the use of a package An training objective which is fulfilled by the provision of some training Helen Parkinson OBI training objective categorical label 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. A label that is part of a categorical datum and that indicates the category of that datum Bjoern Peters Bjoern Peters 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. categorical label lyophilized specimen MO_589 freeze_dried_sample PERSON: Chris Stoeckert PERSON: Jie Zheng a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage. freezing dried DNA lyophilized specimen in live organism assay An assay in which a measurement is made by observing entities located in an organism. Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells. PERSON:Bjoern Peters in live organism assay in vivo assay 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 device A device is a processed material which is designed to perform some function or functions A voltmeter is a measurement device which is intended to perform some measure function. OBI Vancouver workshop 2010 PERSON: Helen Parkinson device food should not classify as a device - counter example for using manufacturer and not device. macroscopic only 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. instrument would include reagents 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 scalar score from composite inputs questionaire score scalar score from composite inputs fresh specimen MO_730 fresh_sample PERSON: Chris Stoeckert PERSON: Jie Zheng a liver freshly removed from a rat a specimen that is output of a specimen creation process used for an investigation without storage. fresh specimen sequence data A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement. GROUP: OBI Person:Chris Stoeckert example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search. sequence data paraffin storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage need to specify paraffin or wax is one of specified input of the process paraffin storage agar stab specimen MO_971 agar_stab PERSON: Chris Stoeckert PERSON: Jie Zheng a specimen that is output of a process that cell culture inoculated into agar for long term storage. agar stab specimen dose A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses. An organism has been injected 1ml of vaccine dose growth condition intervention design A study design in which the independent variable is the environmental condition in which the specimen is growing MO_588 growth_condition_design PERSON: Bjoern Peters growth condition intervention design general scalar measurement datum 1 4/10/2011 BP: It is unclear to me why we need this, and don't just use the scalar measurement datum. general scalar measurement datum PCR instrument 03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent. A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. PCR instrument DNA sequencing service DNA sequencing service Eagle-i will supply better English definition 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. administration of material to specimen Bjoern Peters Bjoern Peters Staining cells in a tissue slice with a dye. The directed combination of a material entity with a specimen. administration of material to specimen growth environment OBI group PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters Right now this may be incomplete. Should also cover e.g. sound, light as well. 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 agar stab storage PERSON: Chris Stoeckert PERSON: Jie Zheng UPenn Group a storage process with input cell culture and agar and output agar stab for long time storage agar stab storage need to specify that agar is one of input for this process image acquisition A planned process that captures an image of an object. PERSON: Jie Zheng Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel image acquisition 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 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 nucleic acid extract 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 feature extraction A planed process with objective of obtaining quantified values from an image. MO_928: feature_extraction PERSON: Jie Zheng feature extraction array image acquisition An image acquisition process that generate an image from the array. MO_929: image_acquisition PERSON: Jie Zheng array image acquisition light emission device A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics) OBI Person:Helen Parkinson a device which has a function to emit light. light emission device perturbation device A homogenizer is a perturbation device. A perturbation device is a device which is designed to perform a perturb function Helen Parkinson OBI Vancouver workshop 2010 PERSON: Helen Parkinson perturbation device environmental control device A growth chamber is an environmental control device. An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity. Helen Parkinson OBI environmental control device 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 RNA extraction/purification instrument A device that is used to isolate and collect RNA for subsequent molecular analysis. PERSON: Erik Segerdell PERSON: Erik Segerdell RNA extraction/purification instrument DNA extract DNA extract Group: UPenn group Person: Jie Zheng The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. 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 hybridization oven A device that creates an appropriate environment for nucleic acid hybridization. PERSON: Erik Segerdell PERSON: Erik Segerdell hybridization oven incubator shaker An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures). PERSON: Erik Segerdell PERSON: Erik Segerdell incubator shaker 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) nucleic acid sequencer An device that is used to determine the order of nucleotides in nucleic acid sequences. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid sequencer bead array reader A device that is used to acquire and image bead array data. PERSON: Erik Segerdell PERSON: Erik Segerdell bead array reader 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 nucleic acid extraction/purification instrument A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis. PERSON: Erik Segerdell PERSON: Erik Segerdell nucleic acid extraction/purification instrument 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 cell harvester A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT? PERSON: Erik Segerdell PERSON: Erik Segerdell cell harvester microdissection instrument A device that is used for the dissection of tissues under magnification. PERSON: Erik Segerdell http://medical-dictionary.thefreedictionary.com/microdissection microdissection instrument individual organism identifier PERSON: Chris Stoeckert, Jie Zheng MO_169 Individual a symbol used to distinguish one individual organism from another. individual organism identifier 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 labeled nucleic acid extract MO_221 labeledExtract Person: Jie Zheng 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 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 cell culture expansion MO_758 grow PERSON: Chris Stoeckert, Jie Zheng a processual entity that results in the increase of cell numbers cell culture expansion including grow of yeast and bacteria gene knock out MO_771 gene_knock_out PERSON: Chris Stoeckert, Jie Zheng 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. gene knock out gene knock in PERSON: Chris Stoeckert, Jie Zheng MO_437 gene_knock_in WEB: http://en.wikipedia.org/wiki/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 chromosomal substitution 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'. MO_995 chromosomal_substitution PERSON: Chris Stoeckert, Jie Zheng chromosomal substitution genetically modified material GROUP: OBI PERSON: Jie Zheng a material entity, organism or cell, that is the output of a genetic transformation process. genetically modified material transfection MO_366 transfection transfection PERSON: Chris Stoeckert, Jie Zheng a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell genetic transformation objective Person: Jie Zheng Person: Jie Zheng a material transformation objective aims to create genetically modified organism or cell genetic transformation objective 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 age since planting measurement datum 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 PERSON:Chris Stoeckert, Jie Zheng age since planting measurement datum 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. MO_745 hatching PERSON:Chris Stoeckert, Jie Zheng age since hatching measurement datum age measurement assay 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 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. MO_767 egg laying PERSON:Chris Stoeckert, Jie Zheng age since egg laying measurement datum assay validation objective GROUP: Penn Group PERSON: Chris Stoeckert, Jie Zheng an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results assay validation objective age since germination measurement datum An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth. Definition of germination comes from GO. However, the term is deprecated from GO now because it is a grouping term without biological significance. MO_590 germination PERSON:Chris Stoeckert, Jie Zheng age since germination measurement datum validation by reverse transcription PCR design MO_986 reverse_transcription_PCR_quality_control PERSON: Chris Stoeckert, Jie Zheng a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results validation by reverse transcription PCR design age since eclosion measurement datum An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon. MO_876 eclosion PERSON:Chris Stoeckert, Jie Zheng age since eclosion measurement datum age since sowing measurement datum An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination. MO_748 sowing PERSON:Chris Stoeckert, Jie Zheng age since sowing measurement datum age since coitus measurement datum An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction. MO_783 coitus PERSON:Chris Stoeckert, Jie Zheng age since coitus measurement datum validation by real time PCR design MO_434 real_time_PCR_quality_control PERSON: Chris Stoeckert, Jie Zheng a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results validation by real time PCR design age measurement datum A time measurement datum that is the result of measurement of age of an organism MO_178 Age PERSON: Alan Ruttenberg, Chris Stoeckert, Jie Zheng note that we are currently defining subtypes of age measurement datum that specify when the age is relative to, e.g. planting, as we don't have adequate temporal predicates yet. life of bearer doesn't imply organism this assay measures time not developmental stage. we recognize that development can take different time periods under different conditions such as media / temperature age as a quality is dubious; we plan to revisit stages in development are currently handled with controlled vocabulary, such as 2-somite stage age measurement datum age since fertilization measurement datum An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. Definition of fertilization comes from GO. MO_701 fertilization PERSON:Chris Stoeckert, Jie Zheng age since fertilization measurement datum age since birth measurement datum An age measurement datum that is the result of the measurement of the age of an organism since birth, the process of emergence and separation of offspring from the mother. MO_710 birth PERSON:Chris Stoeckert, Jie Zheng age since birth measurement datum reverse transcription polymerase chain reaction assay GROUP: Penn Group PERSON: Chris Stoeckert, Jie Zheng 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. reverse transcription polymerase chain reaction assay half life datum (t 1/2) Bjoern Peters Bjoern Peters The time it takes for 50% of a class of stochastic processes to occur. half life datum (t 1/2) t 1/2 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 service A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer. Carlo; Matt OBI workshop San Diego 2011 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 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 RNA sequencing BP 12/21:Created based on a request from Melanie Bjoern Peters Bjoern Peters RNA sequencing RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact 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 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 selectively maintained organism An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Jie Zheng, Chris Stoeckert MO_9 StrainOrLine, MO_71 Ecotype, MO_124 Cultivar cultivar ecotype strain selectively maintained organism 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 operator variation design Person: Chris Stoeckert, Jie Zheng A study design that assesses the operator performance and relation to data consistency and quality. MO_519 operator_variation_design operator variation design comparative genome hybridization by array design Person: Chris Stoeckert, Jie Zheng A study design that detects genomic copy number variations using microarray technology. MO_856 comparative_genome_hybridization_design comparative genome hybridization by array design in vivo design Person: Chris Stoeckert, Jie Zheng A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model. MO_454 in_vivo_design in vivo design genotyping by high throughput sequencing 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 high througput sequencing techniques. genotyping by high throughput sequencing design innate behavior design Person: Chris Stoeckert, Jie Zheng A study design in which the innate behavior of the organism is examined, e.g. path finding in bees. MO_355 innate_behavior_design innate behavior design SNP microarray EFO_0002703 SNP array Person: Helen Parkinson a DNA microarray used to detect polymorphisms in DNA samples SNP microarray cell component comparison design A study design that compares samples from different cell components. Person: Chris Stoeckert, Jie Zheng MO_1019 cell_component_comparison_design cell component comparison design ex vivo design Person: Chris Stoeckert, Jie Zheng 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. MO_808 ex_vivo_design ex vivo design normalization testing design Person: Chris Stoeckert, Jie Zheng A study design that tests different normalization procedures. MO_729 normalization_testing_design normalization testing design ChIP-chip by SNP array assay Group: ArrayExpress production team An assay where chromatin immunoprecipitation (ChIP) is used in combination with SNP microarray technology ChIP-chip by SNP array assay EFO_0002764 ChIP-chip by SNP array genetic population background information Group: OBI group Group: OBI group a genetic characteristics information which is a part of genotype information that identifies the population of organisms genetic population background information genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information proposed and discussed on San Diego OBI workshop, March 2011 environmental history design MO_698 environmental_history_design Person: Chris Stoeckert, Jie Zheng 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 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 transcription profiling by tiling array assay Person: James Malone An assay in which the transcriptome of a biological sample is analysed using a tiling path array. EFO_0002769 transcription profiling by tiling array transcription profiling by tiling array assay transcription profiling by high thoughput sequencing design Person: Chris Stoeckert, Jie Zheng 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 Group: ArrayExpress production team transcription profiling by high thoughput sequencing design genotyping by high throughput sequencing assay Person: James Malone 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 ChIP-chip assay ChIP-on-chip assay Person: James Malone WEB: http://en.wikipedia.org/wiki/ChIP-on-chip 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. ChIP-chip assay array platform variation design Person: Chris Stoeckert, Jie Zheng A study design in which the array platform is compared, e.g. Agilent versus Affymetrix. MO_899 array_platform_variation_design array platform variation 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. ChIP-seq design Person: Chris Stoeckert, Jie Zheng translational bias design Person: Chris Stoeckert, Jie Zheng A study design that characterizes the association of transcripts and translation machinery. MO_939 translational_bias_design translational bias design FWER adjusted p-value FWER adjusted p-value 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 PERS:Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Familywise_error_rate) http://ugrad.stat.ubc.ca/R/library/LPE/html/mt.rawp2adjp.html DNA methylation profiling by high throughput sequencing assay EFO_0002761 methylation profiling by high throughput sequencing Group: ArrayExpress production team, James Malone, Helen Parkinson 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 RNA-seq assay An assay in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and or to quantitate transcript abundance EFO_0002770 transcription profiling by high throughput sequencing PERSON: James Malone RNA-seq assay transcription profiling by high throughput sequencing genotyping by array assay Group: ArrayExpress production team An assay in which an array is used to detect polymorphisms in DNA samples EFO_0002767: genotyping by array genotyping by array assay DNA methylation profiling by array design Person: Chris Stoeckert, Jie Zheng A study design in which the methylation state of DNA is determined and is compared between samples using array technology. DNA methylation profiling by array design GROUP: ArrayExpress production team translation profiling assay 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 PERSON: James Malone translation profiling assay 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. MO_347 in_vitro_design in vitro design RNAi profiling by array design Person: Chris Stoeckert, Jie Zheng 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. Group: ArrayExpress production team RNAi profiling by array design transcription profiling by array design MO_533 transcript_identification_design Person: Chris Stoeckert, Jie Zheng A study design that identifies forms and abundance of transcripts in the genome using microarray technology. transcription profiling by array design 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. MO_902 disease_state_design disease state design wild type organism genotype information C57BL/6J wild type Group: OBI group Group: OBI group 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. proposed and discussed on San Diego OBI workshop, March 2011 wild type organism genotype information RNAi profiling by array assay 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 PERSON: James Malone RNAi profiling by array assay genotype information 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 Group: OBI group Group: OBI group 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. discussed on San Diego OBI workshop, March 2011 genotype information RNA stability design Person: Chris Stoeckert, Jie Zheng A study design that examines the stability and/or decay of RNA transcripts. MO_553 RNA_stability_design RNA stability design 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 species comparison design A study design that assays differences between distinct species. Person: Chris Stoeckert, Jie Zheng MO_675 species_design species comparison design transcription profiling by RT-PCR design Person: Chris Stoeckert, Jie Zheng A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR). Group: ArrayExpress production team transcription profiling by RT-PCR design proteomic profiling by array assay Person: James Malone An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology EFO_0002765 proteomic profiling by array proteomic profiling by array assay 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 organism development design Person: Chris Stoeckert, Jie Zheng A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state. MO_892 development_or_differentiation_design organism development design family history design Person: Chris Stoeckert, Jie Zheng A study design in which the family history such as traits, characteristics, susceptibility to disease is studied. MO_544 family_history_design family history design 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 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 microRNA profiling by array assay An assay in which a microRNA array is used to analyse the microRNA component of the transcriptome. EFO_0000753 microRNA profiling by array PERSON: James Malone microRNA profiling by array assay quality control testing design Person: Chris Stoeckert, Jie Zheng A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance. MO_981 quality_control_testing_design quality control testing design clinical history design 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 allele information MO_58 Allele Person: Chris Stoeckert, Jie Zheng a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition. allele information discussed on San Diego OBI workshop, March 2011 genotype information 'C57BL/6J Hnf1a+/-' in this case, Hnf1a+/- is the allele information post-transcriptional modification design Person: Chris Stoeckert, Jie Zheng A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting. MO_392 cellular_modification_design post transcription modification design? or more clear RNAi design / antibody targeting design? need to check the use cases post-transcriptional modification design 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 Person: Anna Farne transcription profiling by RT-PCR assay 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 cellular process design 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. MO_810 cellular_process_design cellular process design 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 injury design Person: Chris Stoeckert, Jie Zheng A study design in which the response of an organism(s) to injury or damage is studied. MO_726 injury_design injury design organism status comparison design Person: Chris Stoeckert, Jie Zheng A study design that compares samples from live and dead organisms. MO_841 organism_status_design organism status comparison design 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 comparative genomic hybridization by array assay 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. EFO_0000749: comparative genomic hybridization by array Person: James Malone array CGH comparative genomic hybridization by array assay stimulus or stress design Person: Chris Stoeckert, Jie Zheng 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. MO_568 stimulus_or_stress_design stimulus or stress design 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 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 MO_934 optimization_design protocol optimization design ChIP-chip design ChIP-on-chip design 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 Person: Chris Stoeckert, Jie Zheng 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 imprinting design Person: Chris Stoeckert, Jie Zheng 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. MO_914 imprinting_design imprinting 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. MO_822 cell_cycle_design cell cycle design translation profiling design Person: Chris Stoeckert, Jie Zheng 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. Group: ArrayExpress production team translation profiling design cell type comparison design Person: Chris Stoeckert, Jie Zheng A study design that compares cells of different type, for example different cell lines. MO_764 cell_type_comparison_design cell type comparison design ChIP-chip by tiling array design Group: ArrayExpress production team Person: Chris Stoeckert, Jie Zheng A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays. ChIP-chip by tiling array design dose response design Person: Chris Stoeckert, Jie Zheng A study design that examines the relationship between the size of the administered dose and the extent of the response. MO_485 dose_response_design dose response design 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 organism part comparison design A study design that compares tissues, regions, organs within or between organisms Person: Chris Stoeckert, Jie Zheng MO_953 organism_part_comparison_design organism part comparison design protein binding site identification design A study design that investigates protein binding sites on nucleic acids. MO_933 binding_site_identification_design Person: Chris Stoeckert, Jie Zheng protein binding site identification design sex comparison design A study design that assays differences associated with an organism's sex, gender or mating type. Person: Chris Stoeckert, Jie Zheng MO_575 sex_design sex comparison design transcription profiling by tiling array design MO_507 tiling_path_design Person: Chris Stoeckert, Jie Zheng A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals. transcription profiling by tiling array design cell differentiation design Person: Chris Stoeckert, Jie Zheng A study design that assays events associated with cell development or differentiation. MO_892 development_or_differentiation_design cell differentiation design transcription profiling design A study design that identifies forms and abundance of transcripts in the genome. MO_533 transcript_identification_design Person: Chris Stoeckert, Jie Zheng transcription profiling design operon identification design Person: Chris Stoeckert, Jie Zheng A study design that identifies locations and members of operons in a genome. MO_772 operon_identification_design operon identification design DNA methylation profiling by high throughput sequencing design 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 all pairs design Person: Chris Stoeckert, Jie Zheng A study design in which all specimens are compared to every other specimen. MO_565 all_pairs all pairs design proteomic profiling by array design Person: Chris Stoeckert, Jie Zheng A study design in which proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology Group: ArrayExpress production team proteomic profiling by array design 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)" q-value 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. Adapted from several sources, including http://.en/wikipedia.org/wiki/False_discovery_rate http://svitsrv25.epfl.ch/R-doc/library/qvalue.html FDR adjusted p-value PERS:Philippe Rocca-Serra 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. MO_560 genotyping_design genotyping 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 individual genetic characteristics comparison design pathogenicity design Person: Chris Stoeckert, Jie Zheng 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. MO_807 pathogenicity_design pathogenicity design genetic modification design Person: Chris Stoeckert, Jie Zheng 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. MO_447 genetic_modification_design genetic modification design transcription profiling by array assay An assay in which the transcriptome of a biological sample is analysed using array technology. Person: James Malone EFO_0002768: transcription profiling by array transcription profiling by array assay strain comparison design Person: Chris Stoeckert, Jie Zheng A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. MO_462 strain_or_line_design strain comparison design cell specimen A specimen primarily composed of cells collected from a multicellular organism or a cell culture MO_612 cell PERSON: Chris Stoeckert, Jie Zheng cell specimen 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 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 lowess transformation 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. MO_720 lowess_normalization Person: Elisabetta Manduchi lowess transformation tissue specimen 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 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 cell collecting A planned process that collects cells from culture. MO_982 harvest PERSON: Chris Stoeckert, Jie Zheng cell collecting linear amplification An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template. An example is the use of the T7 promoter for amplification by transcribing many RNA copies. MO_997 linear_amplification PERSON: Chris Stoeckert, Jie Zheng linear amplification 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 dissection A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures. EFO_0003856 dissection MO_374 dissect PERSON: Chris Stoeckert, Jie Zheng dissection purification 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 MO_406 purify PERSON: Chris Stoeckert, Jie Zheng purification 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. MO_84 OrganismStatus PERSON: Chris Stoeckert, Jie Zheng organizational term, used in description of specimen that is created from known pre- or post-mortem status specimen with pre- or post-mortem status 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 Epstein Barr virus transformed B cell GROUP: OBI Biomaterial Branch PERSON: Susanna Sansone A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity 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. chimera An organism which contains cells or tissues with a different genotype GROUP: OBI PERSON: Helen Parkinson chimera anatomical entity 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. Biom call - January 2009 - Issues: parasites are not macroscopic part or organism. fetus is_a macroscopic part (but this is up for discussion) Bjoern Peters Philippe Rocca-Serra anatomical entity 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. 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 Tina Boussard Tissue, organ, system, sperm, blood or body location (arm). not super happy about liquids (blood, sperm), as they seem to be 'granular' somewhat, and not form a structure. blood plasma specimen PERSON: Philippe Rocca-Serra 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. PERSON: Maura Gasparetto PERSON: Melanie Courtot 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. WEB: http://en.wikipedia.org/wiki/Blood_plasma a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended. blood plasma specimen plasma blood serum specimen PERSON: Philippe Rocca-Serra A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors. PERSON: Maura Gasparetto 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. WEB: http://en.wikipedia.org/wiki/Blood_plasma blood serum specimen organism 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') 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. GROUP: OBI Biomaterial Branch 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. WEB: http://en.wikipedia.org/wiki/Organism animal fungus organism plant virus immortal cell GROUP: OBI Biomaterial Branch PERSON: Bjoern Peters a cell derived from a multicellular organism that has the potential to replicate indefinitely a single Hela cell immortal cell specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra A material entity that has the specimen role. GROUP: OBI Biomaterial Branch specimen cell line cell PERSON: Susanna Sansone A material entity that represents generations of a primary culture. GROUP: OBI Biomaterial Branch cell line cell immortalized cell line culture GROUP: OBI Biomaterial Branch immortalized cell line immortalized cell line culture An immortalized cell line is a cell line that is able to replicate indefinitely as a result of an in vitro cell line immortalization process GROUP: OBI Biomaterial Branch Isolation and characterization of an immortalized oral keratinocyte cell line of mouse origin. Arch Oral Biol. 2008 Nov;53(11):1091-100. Epub 2008 Aug 21. PMID: 1872191 xenograft PERSON: Philippe Rocca-Serra A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species. Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world PERSON: Melanie Courtot WEB: http://en.wikipedia.org/wiki/Xenograft xenograft xenotransplant cell culture GROUP: OBI Biomaterial Branch 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 PERSON: Bjoern Peters a cell culture is a material entity consisting of a population of cells that is maintained in vitro cell culture primary cell culture GROUP: OBI Biomaterial Branch PERSON: Susanna Sansone a primary cell culture is a cell culture where the cells derive from a fresh tissue source. 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 cell line culture GROUP: OBI Biomaterial Branch 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 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 cell line culture 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 screening library GROUP: IEDB PERSON: Bjoern Peters 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] 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 a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process? screening library synthetic peptide Bjoern Peters 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 changed from synthetic polypeptide to peptide, to get rid of the restriction of having more than 10 amino acids (required by Chebi). synthetic peptide the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme organ section GROUP: OBI Biomaterial Branch PERSON: Philippe Rocca-Serra 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 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) GROUP: CEBS PERSON: Helen Parkinson organ section bronchial alveolar lavage BAL GROUP: IEDB 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. PERSON: Bjoern Peters bronchial alveolar lavage solution containing lung derived T cells, eosinophils, and TNFa. data transformation Philippe Rocca-Serra 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. A data transformation is a process which produces output data from input data Branch editors Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing data transformation 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). ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 Elisabetta Manduchi James Malone Melanie Courtot Ryan Brinkman 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. logistic-log curve fitting logit-log curve fitting 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. ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448 Elisabetta Manduchi James Malone Melanie Courtot 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. 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. logit-log curve fitting 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. ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446 Elisabetta Manduchi James Malone Melanie Courtot Ryan Brinkman Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. log-log curve fitting feature extraction objective Elisabetta Manduchi 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. James Malone TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction feature extraction objective biexponential transformation 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. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf biexponential transformation box-cox transformation 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. 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 box-cox transformation hyperlog transformation 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. ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42." Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry http://flowcyt.sourceforge.net/gating/latest.pdf hyperlog transformation loess scale group transformation one-channel A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar. Elisabetta Manduchi Loess scale group normalization applied to data from two one-channel expression microarray assays. OTHER: Editor's adjustment based on MGED Ontology term loess scale group transformation one-channel logical transformation A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf logical transformation loess scale group transformation two-channel A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar. Elisabetta Manduchi Loess scale group normalization applied to data from a two-channel expression microarray assay. OTHER: Adjusted from MGED Ontology loess scale group transformation two-channel loess global transformation one-channel A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. Elisabetta Manduchi Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. OTHER: Editor's generalization based on MGED Ontology term loess global transformation one-channel split-scale transformation A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry WEB: http://flowcyt.sourceforge.net/gating/latest.pdf split-scale transformation loess global transformation two-channel A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay. Elisabetta Manduchi Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases. OTHER: Editor's generalization based on MGED Ontology term loess global transformation two-channel sine transformation A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/Sine.html sine transformation sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc. cosine transformation Philippe Rocca-Serra A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html. Elisabetta Manduchi WEB: http://mathworld.wolfram.com/Cosine.html cosine transformation cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc. loess group transformation one-channel A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess group transformation one-channel loess group transformation two-channel A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay. Elisabetta Manduchi OTHER: Editor's generalization based on MGED Ontology term loess group transformation two-channel 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 linlog transformation Philippe Rocca-Serra 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. Elisabetta Manduchi PMID: 16646782 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. linlog 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 James Malone Melanie Courtot PMID: 12169536 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. variance stabilising transformation variance stabilizing transformation loess global transformation Philippe Rocca-Serra 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 James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess global transformation loess group transformation Philippe Rocca-Serra 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. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess group transformation loess scale group transformation 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. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess scale group transformation total intensity transformation single Philippe Rocca-Serra 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. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot OTHER: Adjusted from MGED Ontology 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)). total intensity transformation single total intensity transformation paired Philippe Rocca-Serra 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 OTHER: Adjusted from MGED Ontology 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. total intensity transformation paired quantile transformation 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 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. quantile transformation mean centering Philippe Rocca-Serra 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. Elisabetta Manduchi 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 mean-centered. mean centering mean centring median centering Philippe Rocca-Serra 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. Elisabetta Manduchi 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. median centering median centring differential expression analysis objective 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. 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 Elisabetta Manduchi PERSON: Elisabetta Manduchi differential expression analysis objective K-fold cross validation method 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 Person:Helen Parkinson Tina Boussard K-fold cross validation method 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 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 jackknifing method Helen Parkinson Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method http://en.wikipedia.org/wiki/Resampling_%28statistics%29 jackknifing method simple weighting procedure is suggested for combining information over alleles and loci, and sample variances may be estimated by a jackknife procedure jackknifing boostrapping 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. Bootstrapping is a data transformation process which estimates the precision of sampling statistics by drawing randomly with replacement from a set of data points Helen Parkinson 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 boostrapping 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 Helen Parkinson Helen Parkinson 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 pareto scaling 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. Elisabetta Manduchi PMID:16762068 Philippe Rocca-Serra pareto scaling modular decomposition 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. Tina Hernandez-Boussard editor modular decomposition k-means clustering Elisabetta Manduchi 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). James Malone WEB: http://en.wikipedia.org/wiki/K-means k-means clustering hierarchical clustering 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). James Malone WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering hierarchical clustering average linkage hierarchical clustering 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. Elisabetta Manduchi PERSON: Elisabetta Manduchi average linkage hierarchical clustering 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 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 Benjamini and Yekutieli false discovery rate correction method A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate Helen Parkinson Helen Parkinson The expression set was compared univariately between the stroke patients and controls, gene list was generated using False Discovery Rate correction (Benjamini and Yekutieli) 2011-03-31: [PRS]. specified input and output of dt which were missing Benjamini and Yekutieli false discovery rate correction method Philippe Rocca-Serra dimensionality reduction Philippe Rocca-Serra data projection 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. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot dimensionality reduction principal components analysis dimensionality reduction Philippe Rocca-Serra 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. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot pca data reduction principal components analysis dimensionality reduction probabilistic algorithm A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data. James Malone PERSON: James Malone probabilistic algorithm 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 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 dye swap merge 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. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi PERSON: James Malone dye swap merge moving average Philippe Rocca-Serra 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. Elisabetta Manduchi Helen Parkinson PERSON: Elisabetta Manduchi PERSON: Helen Parkinson The moving average is often used to handle data from tiling arrays. moving average 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. Elisabetta Manduchi Helen Parkinson PERSON: Helen Parkinson PERSON:Elisabetta Manduchi Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data. replicate analysis data imputation ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60. 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. Monnie McGee data imputation Holm-Bonferroni family-wise error rate correction method Person:Helen Parkinson WEB: http://en.wikipedia.org/wiki/Holm%E2%80%93Bonferroni_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 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 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 Philippe Rocca-Serra 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. Tina Hernandez-Boussard edge weighting editor loess transformation Philippe Rocca-Serra 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. Elisabetta Manduchi James Malone Melanie Courtot OTHER: Editor's generalization based on MGED Ontology term loess transformation curve fitting data transformation 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 James Malone Melanie Courtot WEB: http://en.wikipedia.org/wiki/Curve_fitting curve fitting data transformation family wise error rate correction method 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 Monnie McGee 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FWER dt FWER correction Philippe Rocca-Serra family wise error rate correction method submatrix extraction 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.) Elisabetta Manduchi James Malone Melanie Courtot 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. 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. submatrix extraction row submatrix extraction 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. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone 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 column submatrix extraction 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. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone 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 samples out, the resulting data set corresponds to a column submatrix of the original set. column submatrix extraction descriptive statistical calculation objective 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. Elisabetta Manduchi James Malone Melanie Courtot Monnie McGee PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Monnie McGee descriptive statistical calculation objective mean calculation Philippe Rocca-Serra 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 Monnie McGee PERSON: James Malone PERSON: Monnie McGee mean calculation network analysis network topology analysis A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network. PERSON: Richard Scheuermann Richard Scheuermann network analysis sequence analysis objective James Malone PERSON: James Malone A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns. sequence analysis objective longitudinal data analysis PERSON: James Malone PERSON: Tina Boussard correlation analysis longitudinal data analysis Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time. longitudinal data analysis survival analysis objective A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables Kaplan meier data transformation PERSON: James Malone PERSON: Tina Boussard http://en.wikipedia.org/wiki/Survival_analysis survival analysis survival analysis objective spread calculation data transformation EDITOR A spread calculation is a data transformation that has objective spread calculation. James Malone spread calculation data transformation Kaplan Meier PERSON: James Malone PERSON: Tina Boussard a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored) http://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator Kaplan Meier multiple testing correction method A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate Monnie McGee PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10. multiple testing correction method multiple testing procedure inter-rater reliability objective A study was conducted to determine the inter-rater reliability of common clinical examination procedures proposed to identify patients with lumbar segmental instability. Examples include joint-probability of agreement, Cohen's kappa and the related Fleiss' kappa, inter-rater correlation, concordance correlation coefficient and intra-class correlation. Person:Alan Ruttenberg Person:Helen Parkinson a data transformation objective of determining the concordance or agreement between human judges. http://en.wikipedia.org/wiki/Inter-rater_reliability inter-rater agreement inter-rater reliability objective Westfall and Young family wise error rate correction Helen Parkinson Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing 2011-03-31: [PRS]. specified input and output of dt which were missing PRS: 2011-03-31: set specified input and specified output to the data transformation Westfall and Young FWER correction Westfall and Young family wise error rate correction 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 WEB: http://mathworld.wolfram.com/Polynomial.html 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 polynomial transformation logarithmic transformation 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. Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Logarithm logarithmic 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. Elisabetta Manduchi WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function WEB: http://en.wikipedia.org/wiki/Exponential_function exponential transformation non-negative matrix factorization 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. 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. http://en.wikipedia.org/wiki/Non-negative_matrix_factorization non-negative matrix factorization soft independent modeling of class analogy analysis soft independent modeling of class analogy analysis SIMCA 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. Tina Hernandez-Boussard WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies 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 WEB: http://www.statsoft.com/textbook/stdiscan.html discriminant function analysis canonical variate analysis CVA Tina Hernandez-Boussard WEB: http://en.wikipedia.org/wiki/Canonical_analysis 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. linear discriminant functional analysis 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 Tina Hernandez-Boussard linear discriminant functional analysis 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 regression analysis method multiple linear regression analysis Tina Hernandez-Boussard WEB:http://en.wikipedia.org/wiki/Linear_regression multiple linear regression analysis 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. principal component regression 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. Tina Hernandez-Boussard WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html principal component regression 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 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 WEB: http://www.statsoft.com/textbook/stdiscan.html discriminant analysis 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 eh transformation 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. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf eh transformation b transformation 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. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf b transformation s transformation 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. Elisabetta Manduchi Joseph Spliden Ryan Brinkman This type of transformation is typically used in flow cytometry. WEB: http://flowcyt.sourceforge.net/gating/latest.pdf s transformation data visualization Generation of a heatmap from a microarray dataset data encoding as image data visualization An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard Tina Boussard visualization 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 PERSON: Elisabetta Manduchi similarity calculation 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 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 loess fitting Philippe Rocca-Serra 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). 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 mode calculation 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. James Malone Monnie McGee PERSON: James Malone PERSON: Monnie McGee mode calculation quantile calculation 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. Monnie McGee WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html quantile calculation median calculation 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 Monnie McGee PERSON: James Malone PERSON: Monnie McGee median calculation variance calculation 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. Monnie McGee PERSON: Monnie McGee variance 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. Monnie McGee PERSON: Monnie McGee standard deviation calculation interquartile-range calculation Monnie McGee PERSON: Monnie McGee 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. interquartile-range calculation skewness calculation 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 Monnie McGee WEB: http://www.riskglossary.com/link/skewness.htm skewness calculation kurtosis calculation 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 Monnie McGee WEB: http://davidmlane.com/hyperstat/A53638.html kurtosis calculation data combination data pooling 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 data combination editor 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. PERSON: Richard Scheuermann Richard Scheuermann network graph construction 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 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 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. PERSON: Richard Scheuermann Richard Scheuermann node quality calculation node degree calculation 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. PERSON: Richard Scheuermann Richard Scheuermann node degree calculation quantitative node degree calculation 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. PERSON: Richard Scheuermann Richard Scheuermann quantitative node degree calculation node in-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 into an individual object node. PERSON: Richard Scheuermann Richard Scheuermann node in-degree calculation 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 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 edge 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 edge relationships in the network. PERSON: Richard Scheuermann Richard Scheuermann edge quality calculation 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 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 subgraph 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 of an individual subgraph. PERSON: Richard Scheuermann Richard Scheuermann subgraph degree calculation quantitative subgraph degree calculation 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. PERSON: Richard Scheuermann Richard Scheuermann quantitative subgraph degree calculation mathematical feature PERSON: James Malone mathematical feature James Malone This class is temporary and will be placed outside of data transformation ultimately (if it still remains at all after review) feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation log base Elisabetta Manduchi 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. WEB: http://en.wikipedia.org/wiki/Logarithm log base logarithm base logarithmic base 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. PERSON: Richard Scheuermann Richard Scheuermann subgraph in-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. PERSON: Richard Scheuermann Richard Scheuermann subgraph out-degree calculation 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 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 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 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. Elisabetta Manduchi PMID:16762068 Philippe Rocca-Serra autoscaling unit-variance scaling MA transformation 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. Elisabetta Manduchi MA 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. PERSON: Elisabetta Manduchi Philippe Rocca-Serra exponential base Elisabetta Manduchi 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 polynomial degree Elisabetta Manduchi PERSON: Elisabetta Manduchi 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. polynomial degree 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 agglomerative hierarchical clustering Elisabetta Manduchi bottom-up 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. James Malone PERSON: Elisabetta Manduchi agglomerative hierarchical clustering divisive hierarchical clustering Elisabetta Manduchi top-down hierarchical clustering 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. James Malone PERSON: Elisabetta Manduchi divisive hierarchical clustering data partitioning Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets. James Malone PERSON: Melanie Courtot PERSON: Richard Scheuermann PERSON: Ryan Brinkman data partitioning data vector reduction objective James Malone 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. PERSON: Richard H. Scheuermann Richard H. Scheuermann data vector reduction objective generalized family wise error rate correction method A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer. Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 Monnie McGee gFWER correction generalized family wise error rate correction method quantile number of false positives correction method A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed' Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19 Monnie McGee QNFP quantile number of false positives correction method tail probability for the proportion of false positives correction method A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1. Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20 Monnie McGee TPPFP correction method tail probability for the proportion of false positives correction method false discovery rate correction method Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 and http://www.wikidoc.org/index.php/False_discovery_rate Monnie McGee The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. . 2011-03-31: [PRS]. creating a defined class by specifying the necessary output of dt allows correct classification of FDR dt FDR correction method Philippe Rocca-Serra false discovery rate correction method proportion of expected false positives correction method A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses. Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 Monnie McGee PEFP correction method proportion of expected false positives correction method quantile proportion of false positives correction method A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate). Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21 Monnie McGee QPFP correction method quantile proportion of false positives correction method data transformation objective A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed. James Malone PERSON: James Malone data transformation objective normalize objective data normalization objective Elisabetta Manduchi Helen Parkinson PERSON: Elisabetta Manduchi PERSON: Helen Parkinson A normalization objective is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. James Malone PERSON: James Malone Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238. data normalization objective correction objective PERSON: James Malone PERSON: Melanie Courtot A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself James Malone Type I error correction correction objective normalization data transformation James Malone A normalization data transformation is a data transformation that has objective normalization. PERSON: James Malone normalization data transformation averaging data transformation James Malone An averaging data transformation is a data transformation that has objective averaging. PERSON: James Malone averaging data transformation partitioning data transformation James Malone A partitioning data transformation is a data transformation that has objective partitioning. PERSON: James Malone partitioning data transformation partitioning objective Elisabetta Manduchi PERSON: Elisabetta Manduchi A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. 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. James Malone partitioning objective background correction objective 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. James Malone background correction objective curve fitting objective Elisabetta Manduchi PERSON: Elisabetta Manduchi 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. James Malone curve fitting objective class discovery data transformation James Malone clustering data transformation unsupervised classification data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. PERSON: James Malone class discovery data transformation Fisher's exact test Fisher's exact test 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. James Malone WEB:http://mathworld.wolfram.com/FishersExactTest.html center calculation objective PERSON: James Malone A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. 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 class discovery objective PERSON: Elisabetta Manduchi PERSON: James Malone clustering 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. James Malone class discovery objective discriminant analysis objective unsupervised classification objective class prediction objective PERSON: Elisabetta Manduchi PERSON: James Malone 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 class prediction objective supervised classification objective spread calculation objective Person:Helen Parkinson Spread calculation can be achieved by use of a standard deviation, which measures distance from the mean 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 Awaiting English definition from Monnie McGee James Malone spread calculation objective 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 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 scaling objective Person:Helen Parkinson Scaling gene expression data for cross platform analysis http://www.springerprotocols.com/Abstract/doi/10.1007/978-1-59745-454-4_13 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 Awaiting English definition from Monnie McGee James Malone scaling objective 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 scaling data transformation A scaling data transformation is a data transformation that has objective scaling. James Malone PERSON: James Malone scaling data transformation 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 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 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 merging objective 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. James Malone combining objective merging of columns from two different data sets clustered data visualization 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 gene list visualization 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. James Malone gene list visualization classified data visualization 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 background corrected data visualization 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. James Malone Monnie McGee background corrected data visualization survival analysis data transformation A data transformation which has the objective of performing survival analysis. James Malone PERSON: James Malone survival analysis data transformation proportional hazards model estimation Cox model Cox proportional hazards model PERSON: James Malone PERSON: Tina Boussard Proportional hazards model is a data transformation model to estimate the effects of different covariates influencing the times-to-failure of a system. WEB: http://en.wikipedia.org/wiki/Cox_proportional_hazards_model proportional hazards model estimation 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 chi square test PERSON: James Malone PERSON: Tina Boussard 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. chi square test 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 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 observation design OBI branch derived PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study. Philippe Rocca-Serra observation design observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists. pool of specimens GROUP: CEBS PERSON: Jennifer Fostel A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish. check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish pool of specimens chemical solution GROUP: OBI Biomaterial Branch PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra 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. 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. chemical solution liquid chemical solution solvent role Philippe Rocca-Serra adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation) solvent role PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors. 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 solute role Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Solute) solute role 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 is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution liver GROUP: OBI Biomaterial Branch 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. 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 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. denatured polymer PERSON: Alan Ruttenberg denatured polymer http://en.wikipedia.org/wiki/Denaturation_%28biochemistry%29 Is a polymer which has lost secondary or tertiary structure decapitated organism Philippe Rocca-Serra decapitated organism OBI Biomaterial 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 validated information OBI PMID: 20084519: "..Three of four interactions were validated via functional magnetic resonance imaging (fMRI) in an independent sample of healthy controls;..." Person:Philippe Rocca-Serra validated information 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. curated information 2009-11-10 Bjoern Peters. Need to check if this was intended. overlap with 'edited information', and has the same logical restrictions. 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 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. OBI PMID: 17344875: A curated compendium of phosphorylation motifs.Nat Biotechnol. 2007 Mar;25(3):285-6. Person:Bjoern Peters Person:Philippe Rocca-Serra curated information randomized group participant role A person enrolled in a randomized clinical trial bears a randomized group participant role Person:Helen Parkinson Philippe Rocca-Serra a role that borne by an organism and realized by some group randomization process randomized group participant role genetically modified organism 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 OBI Biomaterial an organism that is the output of a genetic transformation process predicted data item BP 12/21: Edited the incomplete definition from Philippe. It is still unclear to me if this should be a data item at all, or an information content entity. This will be important, because if we exclude predictions from data items, we will run into issues that we willl have to duplicate things like 'weight datum' etc. all of which can be predicted. Philippe Rocca-Serra; Bjoern Peters predicted data item A data item that was generated on the basis of a calculation or logical reasoning mean-centered data Person:Helen Parkinson Person:Philippe Rocca-Serra a data item which has been processed by a mean centering data transformation where each output value is produced by subtracting the mean from the inout value mean-centered data dissolved material entity A material entity that has been going through a process of being put into solution Person:Bjoern Peters Philippe Rocca-Serra Salt molecules that have been mixed into water dissolved material entity extraction A material separation in which a desired component of an input material is separated from the remainder Person:Bjoern Peters Philippe Rocca-Serra extraction nucleic acid extraction using phenol chloroform filtration OBI-Branch: adapted from wikipedia and wordnet Philippe Rocca-Serra filtration PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4. filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device centrifugation Philippe Rocca-Serra adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm 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. 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 staining Philippe Rocca-Serra adapted from Wikipedia: http://en.wikipedia.org/wiki/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. 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. washing OBI-Branch Philippe Rocca-Serra washing 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. irradiation Philippe Rocca-Serra adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation) irradiation 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. 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 polymerization OBI-Branch Philippe Rocca-Serra polymerization 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. PRS:22102008: need to import catalyst from CHEBI 35223 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 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 enzymatic ligation OBI-Branch Philippe Rocca-Serra 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 PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202. storage 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 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. Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis] cell lysis 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. 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. electrocution OBI branch Philippe Rocca-Serra electrocution PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376. electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process. cervical dislocation OBI branch Philippe Rocca-Serra 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 PRS:21102008: Input must be restricted to Vertebrates (requires import from NCBI tax) 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 asphyxiation OBI branch Philippe Rocca-Serra asphyxiation 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- 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. intentional overdosing 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 is a process by which an excess dose of a chemical compound is given with the intent of causing death lethal injection 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..) 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. activation 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 OBI-Branch Philippe Rocca-Serra activation 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. a process by which a material entity status is modified and conferred a capability of reacting (this sounds like a circular definition , hugh!) immobilization OBI-Branch Philippe Rocca-Serra immobilization PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23. 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. nucleic acid hybridization Philippe Rocca-Serra adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization] nucleic acid hybridization PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27. 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. elution Philippe Rocca-Serra elution wordnet.princeton.edu/perl/webwn 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) DNA Subtraction OBI-Branch Philippe Rocca-Serra DNA Subtraction 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 a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library. prediction OBI Philippe Rocca-Serra prediction Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008 Oct 16;9(1):436. PMID: 18922190 a process by which an event or an entity is described before it actually happens or is being discovered and identified. 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 electroporation Philippe Rocca-Serra WEB:http://en.wikipedia.org/wiki/Electroporation electropermeabilization electroporation PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13. 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 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. 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. FACS Calibur, Luminex 100 John Quinn flow cytometer analyzer http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm 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. Cyan John Quinn http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm flow cell flow cell flow_cell Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell. Biofilm Flow Cell Person:John Quinn http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm light source 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. Elizabeth M. Goralczyk John Quinn Olga Tchuvatkina Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253 light source optical filter 720 LP filter, 580/30 BP 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. John Quinn http://en.wikipedia.org/wiki/Optical_filter optical filter photodetector 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 John Quinn http://einstein.stanford.edu/content/glossary/glossary.html photodetector 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 DNA sequencer MO 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 GenePix 4200A, GenePix4000B Trish Whetzel array scanner arrayer BioRobotics Microgrid II TAS, Affymetrix GMS 417 MO_697 arrayer Trish Whetzel a device which deposits biological material onto a substrate in a defined pattern. arrayer centrifuge A device with a rapidly rotating container that applies centrifugal force to its contents Person: Jennifer Fostel Melanie Courtot Trish Whetzel centrifuge http://en.wikipedia.org/wiki/Centrifuge computer A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions. Apple PowerBook, Dell OptiPlex Melanie Courtot Trish Whetzel computer http://en.wikipedia.org/wiki/Computer 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. Glass Array Hybridization Cassette MO_563 hybridization_chamber Trish Whetzel hybridization chamber hybridization station A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature. Labnet Problot12 MO_497 hybridization station Trish Whetzel hybridization station thermal cycler An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. DNA_amplifier MO Melanie Courtot PCR_machine Piko(tm) 96-well Thermal Cycler Polymerase_Chain_Reaction_ machine Trish Whetzel thermal cycler thermocycler microarray wash station ArrayIt(r) Microarray Wash Station MO_626 wash_station Trish Whetzel a device that is used to wash Affymetrix-type arrays. microarray wash station temperature control bath Alan Ruttenburg Daniel Schober Frank Gibson OBI Instrument branch 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. 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. temperature control bath power supply Frank Gibson sep:00093 A AC/DC transformer that generates the reqired power for an electrophoresis apparatus 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. Daniel Schober PERSON: Daniel Schober PSU electrical power supply power pack power supply power supply unit microarray 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. PERSON: Chris Stoeckert 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. Daniel Schober microarray DNA microarray PERSON: Frank Gibson 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. DNA Chip DNA microarray DNA-array 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 PERSON: Daniel Schober 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 microtome PERSON: Daniel Schober PERSON: Phillippe Rocca-Serra 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. 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 animal cage OBI biomaterial branch PERSON: Phillippe Rocca-Serra PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice. a processed material which has the function to define a bounded habitat which is amenable to keeping animals. animal cage laboratory cage study design 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. 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. 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 study design clinical study design Clinical Research Glossary Version 4.0 CDICS glossary group 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] PlanAndPlannedProcess Branch The definition needs to be extended to other things than simply patients clinical study design 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 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 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 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. 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 parallel group design 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. Philippe Rocca-Serra http://www.holah.karoo.net/experimentaldesigns.htm independent measure design parallel group design 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 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 loop design A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design MO_912 PMID: 12933549 Philippe Rocca-Serra on behalf of MO loop design reference design A reference experiment design type is where all samples are compared to a common reference. MO_699 PMID: 12933549 Philippe Rocca-Serra on behalf of MO reference design 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 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 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 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) 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 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 dye swap design An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip MO_858 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. Philippe Rocca-Serra on behalf of MO dye swap design replicate design 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. MO_885 Philippe Rocca-Serra on behalf of MO replicate design self vs self design A study design that investigates variance and error estimates in the experimental system, and is where the same extract is compared. MO_490 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. Philippe Rocca-Serra on behalf of MO self vs self design 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 adding substance to cell culture renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms Bjoern Peters IEDB 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 is process in which a material substance is added to a cell culture tumor grading 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. OBI branch derived; submitted by MO grading of tumor tumor grading collecting specimen from organism IEDB PERSON:Bjoern Peters a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation 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 killing Philippe Rocca-Serra A protocol application in which an organism is intentionally put to death CEBS, Biomaterial_branch Jennifer Fostel Terminal sacrifice of animals by cervical dislocation at the end of an investigation. 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. euthanisia killing life termination sacrifice administering substance in vivo 1 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178 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 Person:Bjoern Peters Bjoern Peters Different routes and means of administration should go as children underneath this IEDB administering substance in vivo injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally 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. acquisition Bjoern Peters IEDB acquisition the process of obtaining a continuant from a source. 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 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 environmental material collection Bjoern Peters, Alan Ruttenberg IEDB 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. data acquisition data collection Bjoern Peters Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC OBI branch derived 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. data acquisition material component separation Bjoern Peters IEDB 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 material component separation group assignment cohort assignment study 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 OBI Plan Philippe Rocca-Serra group assignment group assignment is a process which has an organism as specified input and during which a role is assigned pooling specimens 2 pooling specimens OBI branch derived PlanAndPlannedProcess Branch 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 physical combination of several instances of like material sample pooling detection of label 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 OBI branch derived PERSON:Bjoern Peters detection of label the detection of the amount of a label which is a proxy for the detection of the labeled biomaterial material portioning OBI branch derived PERSON:Bjoern Peters a material processing in which the input substance is partitioned into a number of portions that are similar in composition. aliquoting apportioning material portioning pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock non-specific labeling OBI branch derived PlanAndPlannedProcess Branch 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 histology histopathology OBI branch derived PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney 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 cell fixation OBI branch derived PERSON:Bjoern Peters a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time cell fixation 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 should include capturing what qualities are being preserved excision Alan Ruttenberg, Kevin Clancy Cutting out the portion of a gel which contains a DNA fragment excision the use physical means to remove a portion of a substance from the rest www.crohnsresource.com/glossary.jsp (via google define:resection) maintaining cell culture OBI branch derived PlanAndPlannedProcess Branch 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 a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing maintaining cell culture artificially induced cell membrane lysis ---\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. OBI branch derived PlanAndPlannedProcess Branch a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate artificially induced cell membrane lysis 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. artificially induced reverse transcription 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. OBI branch derived PERSON:Kevin Clancy The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA 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 a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA) artificially induced reverse transcription 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. This does not apply to the case where the cells are lysed a protocol which results in the separation of supernatant material from a cell culture isolation of cell culture supernatant experimental disease induction OBI branch derived PlanAndPlannedProcess Branch a protocol application to induce a specific disease in an organism experimental disease induction the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome. cell permeabilization A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application Electroporation of HeLa cells to allow transfection with pUC19. OBI branch derived PERSON:Bjoern Peters cell permeabilization need to add output cell has_quality permeable precipitation OBI branch derived PERSON:Kevin Clancy The use of ethanol to precipitate DNA molecules from a solution containing DNA 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) precipitation establishing cell culture 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. OBI branch derived PlanAndPlannedProcess Branch 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 cell culture splitting OBI branch derived PlanAndPlannedProcess Branch 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. 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 cell culture splitting labeling OBI branch derived PERSON:Kevin Clancy 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+. labeling the addition of a labeling reagent to an input biomaterial in order to detect the labeled material in the future artificially induced methylation A planned process of adding methyl groups to polymers OBI branch derived PERSON:Kevin Clancy artificially induced methylation the use of enzymes to add methyl groups to DNA molecules synthesis synthesis OBI branch derived PERSON:Kevin Clancy This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription making cDNA from nucleotides using RNA as a template synthesize the construction of a biomaterial from simpler biomaterials concentrate Evaporation of the solution containing DNA to increase the concentration of the DNA molecules OBI branch derived 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 genetic transformation OBI branch derived PERSON:Kevin Clancy The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35 genetic modification genetic transformation the introduction. alteration or integration of genetic material into a cell or organism lavage A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid OBI branch derived PlanAndPlannedProcess Branch This is not washing, in which case the material of interest is not the resulting fluid lavage the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present 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. OBI branch derived PERSON:Kevin Clancy The use of gas chromatography in order to identify the presence of pesticides in a sample of eggs chromatography 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 sequencing assay OBI branch derived PlanAndPlannedProcess Branch The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template has_output should be sequence of input; we don't have sequence well defined yet sequencing assay the use of a chemical or biochemical means to infer the sequence of a biomaterial vector mediated amplification vector mediated amplification E coli expressing the gene for M avium p35 were cultured in order to produce p35. OBI branch derived PERSON:Kevin Clancy The process of creating a copy of some biological entity in cell culture DNA polymerase amplification Philippe Rocca-Serra DNA polymerase amplification DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input OBI branch derived PERSON:Kevin Clancy The use of taq polymerase to amplify a DNA fragment during a PCR. gradient separation OBI branch derived PERSON:Kevin Clancy 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 the use of a sucrose gradient to isolate mitochondria dialysis OBI branch derived PERSON:Kevin Clancy a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition dialysis the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage protease cleavage OBI branch derived PlanAndPlannedProcess Branch enzymatic digestion protease cleavage protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments). the use of trypsin to cleave pepsin into peptide fragments enzymatic amplification OBI branch derived PERSON:Kevin Clancy enzymatic amplification 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 DNA transduction DNA transduction OBI branch derived PERSON:Kevin Clancy The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism DNA transfection DNA transfection OBI branch derived PERSON:Kevin Clancy The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell recombinant vector cloning molecular cloning OBI branch derived 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 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 RNA extraction A RNA extraction is a nucleic acid extraction where the desired output material is RNA OBI branch derived PlanAndPlannedProcess Branch RNA extraction nucleic acid extraction OBI branch derived 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. PlanAndPlannedProcess Branch a material separation to recover the nucleic acid fraction of an input material nucleic acid extraction phage display library PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra 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] WEB: http://www.immuneepitope.org/home.do 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. display library phage display library cell lysate 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 lysed material GROUP: PSI PERSON: Susanna Sansone 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 a cell lysate is a material entity which is output of a cell lysis process cell lysate lysate transgenic organism PERSON: Philippe Rocca-Serra GROUP:IEDB 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 PERSON: Bjoern Peters PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it transgenic organism whole mount tissue PERSON: Philippe Rocca-Serra 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 GROUP: OBI PERSON: Helen Parkinson whole mount sample whole mount tissue epitope epitope IEDB IEDB a material entity bearing the epitope role occurrence of disease occurrence of disease An occurrence of disease is a process involving pathologic changes within an organism IEDB IEDB 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. 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 occurrence of infectious disease occurrence of infectious disease IEDB IEDB Is an occurrence of a disease caused by an infection disposition to cause an allergic reaction allergenic disposition disposition to cause an allergic reaction 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. allergic reaction allergic reaction IEDB IEDB an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen) 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. Immunization in vivo Immunization in vivo IEDB IEDB Process of administering an object playing the role of immunogen to a living organism adaptive immune effector function adaptive immune effector function 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. IEDB IEDB infection infection IEDB IEDB the detrimental process in which an infectious agent colonizes or replicates in a host environment adaptive immune receptor adaptive immune receptor IEDB IEDB is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes. immunogen immunogen IEDB IEDB a material entity bearing the immunogen role 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 host of immune response 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. 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. host of immune response An organism in which an immune response process occurs. IEDB IEDB 293-T cell culture 293-T cell culture 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 IEDB http://www.biotech.ist.unige.it/cldb/cl5008.html C1R cell culture A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL)). C1R cell culture IEDB IEDB 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 EL-4 cell culture A cell line derived from mouse (C57BL/6N) lymphoma cells. EL-4 cell culture IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl1160.html HeLa cell culture A cell line derived from human cervical cancer cells. HeLa cell culture IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl1597.html JAWS II cell culture A cell line derived from mouse dendritic cells. JAWS II cell culture IEDB IEDB http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-11904&Template=cellBiology antigen antigen IEDB IEDB is a material entity that has the antigen role Jurkat cell culture A cell line derived from human T cells. Jurkat cell culture IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl5296.html JY cell culture JY cell culture The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia) IEDB IEDB T cell epitope recognition assay T cell epitope recognition assay T cell epitope 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 IEDB RMA cell culture 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 IEDB IEDB T2 cell culture A human T-B lymphoblastoid hybrid cell line T2 cell culture IEDB IEDB http://www.atcc.org/ATCCAdvancedCatalogSearch/ProductDetails/tabid/452/Default.aspx?ATCCNum=CRL-1992&Template=cellBiology infectious disease infectious disease IEDB IEDB is a disease caused by an infectious agent 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. lymph node cell IEDB IEDB 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 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 disposition to be bound by an adaptive immune receptor disposition to be bound by an adaptive immune receptor epitope disposition IEDB IEDB Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor. organ harvesting organ harvesting IEDB IEDB The process of removing an organ from its source organism CD3+ T cell culture A T cell population characterized by expressing the CD3 molecule on its surface. CD3+ T cell culture IEDB IEDB CD3- T cell culture A T cell population characterized by not expressing the CD3 molecule on its surface. CD3- T cell culture IEDB IEDB allergy allergy IEDB 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 CD4- T cell culture A T cell population characterized by not expressing the CD4 molecule on its surface. CD4- T cell culture IEDB IEDB CD8- T cell culture A T cell population characterized by not expressing the CD8 molecule on its surface. CD8- T cell culture IEDB IEDB CD4-/CD8- T cell culture A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface. CD4-/CD8- T cell culture IEDB IEDB cancer cancer A disease characterized by abnormal and uncontrolled cell division IEDB IEDB autoimmune disease autoimmune disease IEDB IEDB Is a disease characterized by an immune response of an organism against parts of itself disease disease IEDB IEDB placeholder to be imported from disease ontology MHC:epitope complex binding to TCR MHC:epitope complex binding to TCR IEDB IEDB 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. immunogen role immunogen role IEDB IEDB any entity capable of eliciting an immune response when introduced to components of the immune system host of immune response role 03/21/2010: This sense of 'host' is used not only in infectious diseases but also allergy, cancer, transplantation, etc. which is why it is needed separately from the 'host of infectious agent' meaning, which will be imported from IDO. host of immune response role IEDB IEDB is a role borne by an organism. It is realized by the organism during an immunization or an immune response taking place inside or on the surface of the organism, and in which the responding or stimulated immune system is part of the host. effector T cell function effector T cell function IEDB IEDB The function inhering in a T cell that is realized in an immune response that results from the T cell receptor binding to the MHC:epitope complex. antigen presentation function antigen presentation function APC IEDB IEDB a function inhering in a cell that expresses MHC molecules which is realized in the process of antigen processing and presentation of antigen derived parts by MHC molecules on the cell surface. restricting MHC role restricting MHC role IEDB IEDB The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell. donor A T cell line from a PPD(+) donor. donor donor role A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro. IEDB IEDB 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 immunization Infection with influenza (the immunogen) leading to B cells producing antibodies (the effector function) against surface regions of the HA protein (the epitope). immunization IEDB IEDB 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. blood harvesting blood harvesting A material separation where blood is taken from an organism. IEDB IEDB L cell culture A cell line derived from mouse fibroblasts. L cell culture IEDB IEDB http://www.biotech.ist.unige.it/cldb/cl3075.html 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 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 material to be added 10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export 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 A mixture of peptides that is being added into a cell culture. IEDB a material that is added to another one in a material combination process material to be added 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. A material entity into which another is being added in a material combinatino process IEDB target of material addition 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 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. splenocyte IEDB 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 pathologic process pathologic process IEDB IEDB abnormal, harmful processes caused by or associated with a disease 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. immune epitope assay immune epitope assay IEDB IEDB 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 CD8 receptor A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor. CD8 CD8 receptor This term does not belong in ONTIE. It should be imported from PRO, but there seems to be no appropriate term as of 08/17/2009. WEB: http://en.wikipedia.org/wiki/CD8 clinical history A series of statements representing health-relevant qualities of a patient and of a patient's family. clinical history 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. treatment treatment A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder 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 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 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 DNA ligase Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule ligase A protein that is a translation product of the ligA gene or a 1:1 ortholog thereof. DNA ligase 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. 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. portion of tissue Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships. portion of tissue 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 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 water An inorganic hydroxy compound that has formula H2O. water biotin A biotin that has formula C10H16N2O3S. biotin peptide Amide derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid. peptide 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 hydrogensulfite A sulfur oxoanion that has formula HO3S. hydrogensulfite glucose glucose molecular entity Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well molecular entity 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 ribonucleic acids Naturally occurring polyribonucleotides. ribonucleic acids amino acids Carboxylic acids containing one or more amino groups. amino acids 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 Cy3 dye Cy3 dye Cy5 dye Cy5 dye double-stranded DNA double-stranded DNA Alexa Fluor 532 Alexa Fluor 532 An organosulfonic acid that has formula C34H33N3O11S2. Alexa Fluor 546 Alexa Fluor 546 An organic heteropentacyclic compound that has formula C44H45Cl3N4NaO14S3. Alexa Fluor 555 A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate. Alexa Fluor 555 cell Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .." cell 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 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 T cell A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. T cell 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 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 erythrocyte A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen. erythrocyte 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 B cell A lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity. B cell 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 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 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 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 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 plasma cell A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin. plasma cell alpha-beta T cell A T cell that expresses an alpha-beta T cell receptor complex. alpha-beta T cell 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 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 mononuclear cell A leukocyte with a single non-segmented nucleus in the mature form. mononuclear cell 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 podzol Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics. podzol 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. Mouth Mouth Lymph node Lymph node 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 Brain Brain Segment of neuraxis that has as its parts gray matter and white matter that surround the cerebral ventricular system; Examples: There is only one brain. Mucosa of oropharynx Mucosa of oropharynx Mucosa of nasopharynx Mucosa of nasopharynx Dermis Dense irregular connective tissue which consists of a papillary layer and a reticular layer. Dermis Hypodermis Hypodermis Spleen Spleen 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 Portion of blood Body substance which consists of plasma and blood cells Portion of blood 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 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 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 RNA-directed DNA polymerase activity Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time. RNA-directed DNA polymerase activity 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 immune response Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat. immune response 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 biological_process Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. biological_process cell proliferation The multiplication or reproduction of cells, resulting in the expansion of a cell population. cell proliferation cellular process Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level. cellular process 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 B cell receptor complex An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins. B cell receptor complex 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 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 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 DNA polymerase complex A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA. DNA polymerase complex 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 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 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 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 Insulin resistance Insulin resistance `Increased resistance` (PATO:0001650) towards `insulin` (PRO:000009054). Cricetinae Cricetinae Phodopus Phodopus Phodopus sungorus Phodopus sungorus Muridae Muridae Mus Mus Mus musculus Mus musculus Rattus Rattus Rattus norvegicus Rattus norvegicus Viruses Viruses Asteroideae Asteroideae Heliantheae Heliantheae Mutisieae Mutisieae Obtectomera Obtectomera Rhodobacter Rhodobacter canis group canis group phagocytophilum group phagocytophilum group Rhodobacter sphaeroides Rhodobacter sphaeroides mitosporic Filobasidiales mitosporic Filobasidiales Thlaspi caerulescens Thlaspi caerulescens Cryptococcus [NCBITaxon:107441] Cryptococcus [NCBITaxon:107441] Parvoviridae Parvoviridae Dependovirus Dependovirus Adeno-associated virus - 2 Adeno-associated virus - 2 Rhodospirillum Rhodospirillum Rhodospirillum rubrum Rhodospirillum rubrum Chloroflexaceae Chloroflexaceae Nectriaceae Nectriaceae Chloroflexus Chloroflexus Chloroflexus aurantiacus Chloroflexus aurantiacus Coronaviridae Coronaviridae Coronavirus Coronavirus Penaeoidea Penaeoidea pseudomallei group pseudomallei group Cyanobacteria Cyanobacteria Chroococcales Chroococcales Synechococcus Synechococcus Polytrichopsida Polytrichopsida Populus tremula Populus tremula Synechocystis Synechocystis spotted fever group spotted fever group typhus group typhus group Synechocystis sp. Synechocystis sp. Saccharomyces kudriavzevii Saccharomyces kudriavzevii Saccharomyces mikatae Saccharomyces mikatae Funariidae Funariidae Synechocystis sp. PCC 6803 Synechocystis sp. PCC 6803 Oscillatoriales Oscillatoriales Nostocales Nostocales Nostocaceae Nostocaceae Anabaena Anabaena Anabaena variabilis Anabaena variabilis Teleostomi Teleostomi Euteleostomi Euteleostomi Nostoc Nostoc Sphingobacteria Sphingobacteria mitosporic Saccharomycetales mitosporic Saccharomycetales Populus tomentosa Populus tomentosa Brucellaceae Brucellaceae Sulfolobaceae Sulfolobaceae Deinococcales Deinococcales Coxiellaceae Coxiellaceae Legionellales Legionellales Burkholderiaceae Burkholderiaceae unclassified Burkholderiales unclassified Burkholderiales Thermoanaerobacter tengcongensis Thermoanaerobacter tengcongensis Chromadorea Chromadorea Bombyciformes Bombyciformes Acidithiobacillus Acidithiobacillus Trichodesmium Trichodesmium Trichodesmium erythraeum Trichodesmium erythraeum Paracoccidioides brasiliensis Paracoccidioides brasiliensis Proteobacteria Proteobacteria Neoteleostei Neoteleostei Eurypterygii Eurypterygii Ctenosquamata Ctenosquamata Acanthomorpha Acanthomorpha Euacanthomorpha Euacanthomorpha Holacanthopterygii Holacanthopterygii Gammaproteobacteria Gammaproteobacteria Firmicutes Firmicutes Leuconostoc Leuconostoc Leuconostoc mesenteroides Leuconostoc mesenteroides Oenococcus oeni Oenococcus oeni Pediococcus Pediococcus Pediococcus pentosaceus Pediococcus pentosaceus Staphylococcus Staphylococcus Staphylococcus aureus Staphylococcus aureus Polytrichum juniperinum Polytrichum juniperinum Deinococcus-Thermus Deinococcus-Thermus Deinococcus Deinococcus Deinococcus radiodurans Deinococcus radiodurans Euacanthopterygii Euacanthopterygii Streptococcaceae Streptococcaceae Streptococcus Streptococcus Streptococcus gordonii Streptococcus gordonii Streptococcus suis Streptococcus suis Streptococcus mutans Streptococcus mutans Streptococcus agalactiae Streptococcus agalactiae Streptophytina Streptophytina Streptococcus pneumoniae Streptococcus pneumoniae Magnetospirillum Magnetospirillum Streptococcus pyogenes Streptococcus pyogenes Thlaspi Thlaspi Burkholderia mallei Burkholderia mallei Penaeus Penaeus Coffea Coffea Coffea arabica Coffea arabica Burkholderia fungorum Burkholderia fungorum Enterococcus Enterococcus Enterococcus faecalis Enterococcus faecalis Enterococcus faecium Enterococcus faecium Gerbera Gerbera Xanthomonadales Xanthomonadales Pseudomonadaceae Pseudomonadaceae Alteromonadales Alteromonadales Vibrionales Vibrionales Pasteurellales Pasteurellales Lactococcus Lactococcus Lactococcus lactis Lactococcus lactis Spirochaetales Spirochaetales Pseudomonas aeruginosa group Pseudomonas aeruginosa group Pseudomonas fluorescens group Pseudomonas fluorescens group Pseudomonas putida group Pseudomonas putida group Spirochaetaceae Spirochaetaceae Borrelia Borrelia Pteridaceae Pteridaceae Bacillales Bacillales Bacillus Bacillus Borrelia burgdorferi Borrelia burgdorferi Bacillus anthracis Bacillus anthracis Pinus [NCBITaxon:139271] Pinus [NCBITaxon:139271] Bacillus cereus Bacillus cereus Bacillus subtilis Bacillus subtilis Mycetozoa Mycetozoa Methanothermobacter Methanothermobacter Methanothermobacter thermautotrophicus Methanothermobacter thermautotrophicus Ehrhartoideae Ehrhartoideae Pooideae Pooideae Panicoideae Panicoideae PACCAD clade PACCAD clade Oryzeae Oryzeae Poeae Poeae Triticeae Triticeae Andropogoneae Andropogoneae Saccharomycotina Saccharomycotina Pezizomycotina Pezizomycotina Dothideomycetes et Chaetothyriomycetes incertae sedis Dothideomycetes et Chaetothyriomycetes incertae sedis Eurotiomycetes Eurotiomycetes Sordariomycetes Sordariomycetes Sordariomycetes incertae sedis Sordariomycetes incertae sedis Schizosaccharomycetes Schizosaccharomycetes Magnaporthe Magnaporthe Magnaporthe grisea Magnaporthe grisea Clostridium Clostridium Clostridium acetobutylicum Clostridium acetobutylicum Clostridium botulinum Clostridium botulinum Clostridium sporogenes Clostridium sporogenes Clostridium thermocellum Clostridium thermocellum Moorella thermoacetica Moorella thermoacetica Tremellomycetidae Tremellomycetidae Homobasidiomycetes Homobasidiomycetes Caulobacter vibrioides Caulobacter vibrioides Plantaginaceae Plantaginaceae Group 2 species Group 2 species Treponema Treponema Lactobacillus Lactobacillus Treponema denticola Treponema denticola Citrus aurantiifolia Citrus aurantiifolia Lactobacillus gasseri Lactobacillus gasseri Lactobacillus sakei Lactobacillus sakei Treponema pallidum Treponema pallidum Lactobacillus salivarius Lactobacillus salivarius Listeria Listeria Phaseoleae Phaseoleae Trifolieae Trifolieae Vicieae Vicieae Loteae Loteae Listeria monocytogenes Listeria monocytogenes Listeria innocua Listeria innocua Corynebacteriaceae Corynebacteriaceae Actinomyces Actinomyces Actinomyces naeslundii Actinomyces naeslundii Novosphingobium Novosphingobium Heterobasidiomycetes Heterobasidiomycetes Bifidobacterium Bifidobacterium Ixoroideae Ixoroideae Coffeeae Coffeeae Corynebacterium Corynebacterium Rosoideae Rosoideae Corynebacterium glutamicum Corynebacterium glutamicum Passeroidea Passeroidea Thermoanaerobacter Thermoanaerobacter Actinobacteria (class) Actinobacteria (class) Mycobacteriaceae Mycobacteriaceae Mycobacterium Mycobacterium Mycobacterium leprae Mycobacterium leprae Mycobacterium tuberculosis Mycobacterium tuberculosis Gerbera hybrid cultivar Gerbera hybrid cultivar Deinococcaceae Deinococcaceae Enterogona Enterogona Thermoprotei Thermoprotei Methanobacteria Methanobacteria Halobacteria Halobacteria Thermoplasmata Thermoplasmata Thermococci Thermococci Archaeoglobi Archaeoglobi Psathyrellaceae Psathyrellaceae Coprinopsis Coprinopsis Drosophiliti Drosophiliti Entomoplasmatales Entomoplasmatales Actinopteri Actinopteri Elopocephala Elopocephala Clupeocephala Clupeocephala Otophysi Otophysi Cypriniphysi Cypriniphysi Otocephala Otocephala Clostridia Clostridia Clostridiales Clostridiales Peptococcaceae Peptococcaceae Thermoanaerobacteriaceae Thermoanaerobacteriaceae Bacillaceae Bacillaceae Listeriaceae Listeriaceae Alicyclobacillaceae Alicyclobacillaceae Lactobacillales Lactobacillales Neognathi Neognathi Salmonoidei Salmonoidei Anurophorinae Anurophorinae Cryptopygus Cryptopygus Cryptopygus antarcticus Cryptopygus antarcticus Aquificae (class) Aquificae (class) Magnetospirillum magnetotacticum Magnetospirillum magnetotacticum Streptomyces Streptomyces Thermotogae (class) Thermotogae (class) Thermotogaceae Thermotogaceae Deinococci Deinococci Orbiliomycetes Orbiliomycetes Orbiliales Orbiliales Zinnia Zinnia Streptomyces coelicolor Streptomyces coelicolor Lepidium Lepidium Campylobacter Campylobacter Desulfovibrionaceae Desulfovibrionaceae Pleuronichthys Pleuronichthys Pleuronichthys verticalis Pleuronichthys verticalis Corynebacterium glutamicum ATCC 13032 Corynebacterium glutamicum ATCC 13032 Campylobacter jejuni Campylobacter jejuni Pancrustacea Pancrustacea Mandibulata Mandibulata Bacteria Sphingobacteriales Sphingobacteriales Aquificae Aquificae Chloroflexi Chloroflexi Thermotogae Thermotogae Actinobacteria Actinobacteria Thermobifida fusca Thermobifida fusca Fusobacteria (class) Fusobacteria (class) Fusobacterales Fusobacterales Fusobacteriaceae Fusobacteriaceae Spirochaetes Spirochaetes Spirochaetes (class) Spirochaetes (class) Actinomycetales Actinomycetales Chlamydiae Chlamydiae Chlamydiae (class) Chlamydiae (class) Rhodospirillales Rhodospirillales Rhodobacterales Rhodobacterales Sphingomonadales Sphingomonadales Caulobacterales Caulobacterales Herminiimonas arsenicoxydans Herminiimonas arsenicoxydans Actinomycetaceae Actinomycetaceae Streptomycetaceae Streptomycetaceae Methylophilales Methylophilales Neisseriales Neisseriales Rhodocyclales Rhodocyclales Homo/Pan/Gorilla group Homo/Pan/Gorilla group Mycoplasmatales Mycoplasmatales Pasteuria nishizawae Pasteuria nishizawae Helicobacter Helicobacter Mycoplasmataceae Mycoplasmataceae Mycoplasma Mycoplasma Mycoplasma genitalium Mycoplasma genitalium Helicobacter pylori Helicobacter pylori Streptococcus mutans UA159 Streptococcus mutans UA159 Mycoplasma pneumoniae Mycoplasma pneumoniae Mycoplasma pulmonis Mycoplasma pulmonis Ureaplasma Ureaplasma Ureaplasma urealyticum Ureaplasma urealyticum Desulfovibrionales Desulfovibrionales Geobacteraceae Geobacteraceae Campylobacterales Campylobacterales Mesoplasma florum Mesoplasma florum Archaea Methanobacteriales Methanobacteriales Methanobacteriaceae Methanobacteriaceae Sylvia communis Sylvia communis Lymnaeoidea Lymnaeoidea Antirrhineae Antirrhineae Bifidobacterium longum Bifidobacterium longum Mutisioideae Mutisioideae Methanosarcinaceae Methanosarcinaceae Methanosarcina Methanosarcina Methanosarcina barkeri Methanosarcina barkeri Methanosarcina mazei Methanosarcina mazei Methanococcoides Methanococcoides Hypocreomycetidae Hypocreomycetidae Sordariomycetidae Sordariomycetidae Archaeoglobales Archaeoglobales Archaeoglobaceae Archaeoglobaceae Archaeoglobus Archaeoglobus Archaeoglobus fulgidus Archaeoglobus fulgidus Halobacteriales Halobacteriales Halobacteriaceae Halobacteriaceae Halobacterium Halobacterium Halobacterium salinarum Halobacterium salinarum Halobacterium sp. Halobacterium sp. Burkholderiales Genera incertae sedis Burkholderiales Genera incertae sedis Haloferax volcanii Haloferax volcanii Methanomicrobia Methanomicrobia Acidithiobacillales Acidithiobacillales Acidithiobacillaceae Acidithiobacillaceae Haloferax Haloferax Thermococcales Thermococcales Thermococcaceae Thermococcaceae Pyrococcus Pyrococcus Thermoproteales Thermoproteales Thermoproteaceae Thermoproteaceae Thermoproteus Thermoproteus Thermoproteus tenax Thermoproteus tenax Rhizobium/Agrobacterium group Rhizobium/Agrobacterium group Sinorhizobium/Ensifer group Sinorhizobium/Ensifer group Paxilineae Paxilineae SARS coronavirus SARS coronavirus Sulfolobales Sulfolobales Sulfolobus Sulfolobus Sulfolobus acidocaldarius Sulfolobus acidocaldarius Sulfolobus solfataricus Sulfolobus solfataricus Thermoplasmatales Thermoplasmatales Thermoplasma Thermoplasma Thermoplasma acidophilum Thermoplasma acidophilum Rubus Rubus magnoliids magnoliids Thermotoga Thermotoga Thermotoga maritima Thermotoga maritima Brucella Brucella Brucella abortus Brucella abortus Rutaceae Rutaceae Xylella Xylella Xylella fastidiosa Xylella fastidiosa Saliceae Saliceae Moniliformopses Moniliformopses Thermotogales Thermotogales Rubiaceae Rubiaceae Rubrobacterineae Rubrobacterineae Dechloromonas aromatica Dechloromonas aromatica Francisella Francisella Xenopus [NCBITaxon:262014] Xenopus [NCBITaxon:262014] Francisella tularensis Francisella tularensis Crocosphaera Crocosphaera Crocosphaera watsonii Crocosphaera watsonii Francisella tularensis subsp. novicida Francisella tularensis subsp. novicida Rickettsia sibirica subgroup Rickettsia sibirica subgroup Citrus Citrus Citrus sinensis Citrus sinensis Aquifex Aquifex Nostoc punctiforme Nostoc punctiforme Saccharomyces paradoxus Saccharomyces paradoxus Saccharomyces pastorianus Saccharomyces pastorianus Eukaryota Bovinae Bovinae Coregonus Coregonus Rubrivivax Rubrivivax Rubrivivax gelatinosus Rubrivivax gelatinosus Ralstonia syzygii Ralstonia syzygii Sinorhizobium Sinorhizobium Alphaproteobacteria Alphaproteobacteria Betaproteobacteria Betaproteobacteria Deltaproteobacteria Deltaproteobacteria Geobacter Geobacter Geobacter metallireducens Geobacter metallireducens Staphylococcus aureus subsp. aureus MSSA476 Staphylococcus aureus subsp. aureus MSSA476 Burkholderia pseudomallei Burkholderia pseudomallei Trichocomaceae Trichocomaceae Pseudomonas Pseudomonas Pseudomonas aeruginosa Pseudomonas aeruginosa Phaeophyceae Phaeophyceae Ectocarpales Ectocarpales Ectocarpaceae Ectocarpaceae Ectocarpus Ectocarpus Ectocarpus siliculosus Ectocarpus siliculosus Crenarchaeota Crenarchaeota Euryarchaeota Euryarchaeota Salmonella enterica Salmonella enterica Burkholderia cepacia Burkholderia cepacia ssDNA viruses ssDNA viruses Cryptococcus gattii Cryptococcus gattii Methanococcoides burtonii Methanococcoides burtonii Pseudomonas fluorescens Pseudomonas fluorescens Veillonella Veillonella Veillonella parvula Veillonella parvula Epsilonproteobacteria Epsilonproteobacteria Ceratopteris Ceratopteris Ceratopteris thalictroides Ceratopteris thalictroides Vitis vinifera Vitis vinifera Hypocrea Hypocrea Collembola Collembola Lachancea Lachancea Pseudomonas putida Pseudomonas putida Mesobatrachia Mesobatrachia Pipoidea Pipoidea Herminiimonas Herminiimonas Chlorophyta Chlorophyta Chlamydomonadales Chlamydomonadales Ralstonia solanacearum Ralstonia solanacearum Chlamydomonadaceae Chlamydomonadaceae Chlamydomonas Chlamydomonas Chlamydomonas reinhardtii Chlamydomonas reinhardtii Cyprinoidea Cyprinoidea Pleuronectoidei Pleuronectoidei Tetraodontiformes Tetraodontiformes Tetraodontoidei Tetraodontoidei Tetraodontidae Tetraodontidae Takifugu Takifugu Takifugu rubripes Takifugu rubripes Schistosomatoidea Schistosomatoidea Schistosomatidae Schistosomatidae Laurasiatheria Laurasiatheria Euarchontoglires Euarchontoglires Glires Glires Simiiformes Simiiformes Cercopithecoidea Cercopithecoidea Hominoidea Hominoidea Chlorophyceae Chlorophyceae Saccharophagus Saccharophagus Embryophyta Embryophyta Bifidobacteriaceae Bifidobacteriaceae Mollicutes Mollicutes Acidaminococcaceae Acidaminococcaceae Clostridiaceae Clostridiaceae Rhodobacteraceae Rhodobacteraceae Burkholderia Burkholderia Methylophilaceae Methylophilaceae Thiomonas Thiomonas Xanthomonadaceae Xanthomonadaceae Synechococcus elongatus Synechococcus elongatus Chloroflexi (class) Chloroflexi (class) Chloroflexales Chloroflexales Fusobacteria Fusobacteria Aquificales Aquificales Bryophyta Bryophyta Polytrichales Polytrichales Polytrichaceae Polytrichaceae Polytrichum Polytrichum Bryopsida Bryopsida Funariales Funariales Funariaceae Funariaceae Physcomitrella Physcomitrella Physcomitrella patens Physcomitrella patens Buchnera Buchnera Rubus idaeus Rubus idaeus Sophophora Sophophora melanogaster group melanogaster group melanogaster subgroup melanogaster subgroup obscura group obscura group pseudoobscura subgroup pseudoobscura subgroup Lycopodiophyta Lycopodiophyta Isoetopsida Isoetopsida Selaginellales Selaginellales Teleostei Teleostei Euteleostei Euteleostei Selaginellaceae Selaginellaceae Acanthopterygii Acanthopterygii Selaginella Selaginella Percomorpha Percomorpha Tetradontoidea Tetradontoidea Paracanthopterygii Paracanthopterygii Ostariophysi Ostariophysi Tetrapoda Tetrapoda Amniota Amniota Theria Theria Sauria Sauria Filicophyta Filicophyta Filicales Filicales Ralstonia pickettii Ralstonia pickettii Filicopsida Filicopsida Bartonella grahamii Bartonella grahamii Dictyosteliida Dictyosteliida Viridiplantae Viridiplantae Coniferophyta Coniferophyta Lepidium sativum Lepidium sativum Coniferales Coniferales Fungi/Metazoa group Fungi/Metazoa group Eremothecium gossypii Eremothecium gossypii Eremothecium Eremothecium Aspergillus terreus Aspergillus terreus Pinaceae Pinaceae Onygenales Onygenales Metazoa Metazoa Bilateria Bilateria Acoelomata Acoelomata Pseudocoelomata Pseudocoelomata Picea Picea Tylenchina Tylenchina Tylenchoidea Tylenchoidea Heteroderinae Heteroderinae Picea glauca Picea glauca Coelomata Coelomata Protostomia Protostomia Neoptera Neoptera Pinus Pinus Endopterygota Endopterygota Pinus radiata Pinus radiata Deuterostomia Deuterostomia Sciurognathi Sciurognathi Carnivora Carnivora Alveolata Alveolata stramenopiles stramenopiles Euglenozoa Euglenozoa Cricetidae Cricetidae Muroidea Muroidea Xanthomonas Xanthomonas Felinae Felinae Xanthomonas campestris Xanthomonas campestris Streptomyces avermitilis Streptomyces avermitilis Entomoplasmataceae Entomoplasmataceae Lactobacillaceae Lactobacillaceae Magnoliophyta Magnoliophyta Rickettsieae Rickettsieae Xanthomonas campestris pv. campestris Xanthomonas campestris pv. campestris Magnoliales Magnoliales Magnoliaceae Magnoliaceae Francisellaceae Francisellaceae Liriodendron Liriodendron Liriodendron tulipifera Liriodendron tulipifera Zinnia elegans Zinnia elegans Lotus japonicus Lotus japonicus Schizosaccharomycetales Schizosaccharomycetales mitosporic Trichocomaceae mitosporic Trichocomaceae mitosporic Onygenales mitosporic Onygenales Strongyloides ratti Strongyloides ratti Heterodera Heterodera Apoidea Apoidea Cannabaceae Cannabaceae Cannabis Cannabis Cannabis sativa Cannabis sativa Fagales Fagales Betula Betula Betula pendula Betula pendula Cryptosporidiidae Cryptosporidiidae Azotobacter group Azotobacter group Betulaceae Betulaceae Azotobacter Azotobacter ssRNA positive-strand viruses, no DNA stage ssRNA positive-strand viruses, no DNA stage Azotobacter vinelandii Azotobacter vinelandii Streptophyta Streptophyta Suina Suina Pecora Pecora Equus subg. Equus Equus subg. Equus Rhizobiales Rhizobiales Agrobacterium Agrobacterium Rickettsia sibirica Rickettsia sibirica Agrobacterium tumefaciens Agrobacterium tumefaciens BEP clade BEP clade Vitaceae Vitaceae Vitis Vitis Isotomidae Isotomidae Sylviidae Sylviidae Malpighiales Malpighiales Neosartorya Neosartorya Neosartorya fischeri Neosartorya fischeri Desulfitobacterium Desulfitobacterium Salicaceae Salicaceae Populus Populus Populus trichocarpa Populus trichocarpa Populus trichocarpa x Populus deltoides Populus trichocarpa x Populus deltoides Populus deltoides Populus deltoides Brassicales Brassicales Brassicaceae Brassicaceae Arabidopsis Arabidopsis Arabidopsis thaliana Arabidopsis thaliana Brassica Brassica Brassica juncea Brassica juncea Brassica napus Brassica napus Brassica rapa Brassica rapa Rosales Rosales Rosaceae Rosaceae Aedes/Ochlerotatus group Aedes/Ochlerotatus group Ditrysia Ditrysia Bombycoidea Bombycoidea Noctuoidea Noctuoidea Estrildidae Estrildidae Viannia Viannia Leishmania braziliensis species complex Leishmania braziliensis species complex Haplorrhini Haplorrhini Rhizobium Rhizobium Feliformia Feliformia Caniformia Caniformia Fabaceae Fabaceae Mesorhizobium loti Mesorhizobium loti Papilionoideae Papilionoideae Sinorhizobium meliloti Sinorhizobium meliloti Bartonella henselae Bartonella henselae Rhizobium leguminosarum Rhizobium leguminosarum Glycine Glycine Glycine max Glycine max Leishmania [NCBITaxon:38568] Leishmania [NCBITaxon:38568] Leishmania infantum species complex Leishmania infantum species complex Leishmania donovani species complex Leishmania donovani species complex Leishmania major species complex Leishmania major species complex Leishmania mexicana species complex Leishmania mexicana species complex Diprotodontia Diprotodontia Lotus Lotus Medicago Medicago Medicago sativa Medicago sativa Medicago truncatula Medicago truncatula Poales Poales Pisum Pisum Pisum sativum Pisum sativum Paracoccidioides Paracoccidioides Trifolium Trifolium Trifolium repens Trifolium repens Murinae Murinae Cyprininae Cyprininae Rasborinae Rasborinae Trypanozoon Trypanozoon Oryza sativa (indica cultivar-group) Oryza sativa (indica cultivar-group) Oryza sativa (japonica cultivar-group) Oryza sativa (japonica cultivar-group) Linaceae Linaceae Linum Linum Linum usitatissimum Linum usitatissimum Thraupini Thraupini Parvovirinae Parvovirinae Estrildinae Estrildinae Vitales Vitales Methylobacillus Methylobacillus Moss Superclass V Moss Superclass V Methylobacillus flagellatus Methylobacillus flagellatus Gentianales Gentianales Mammalia Mammalia Solanales Solanales Solanaceae Solanaceae Capsicum Capsicum Capsicum annuum Capsicum annuum Solanum lycopersicum Solanum lycopersicum Nicotiana Nicotiana Nicotiana benthamiana Nicotiana benthamiana Neosartorya fennelliae Neosartorya fennelliae Solanum Solanum Solanum tuberosum Solanum tuberosum Glossata Glossata Neolepidoptera Neolepidoptera Heteroneura Heteroneura Mycosphaerella Mycosphaerella Rhodospirillaceae Rhodospirillaceae Sphingomonadaceae Sphingomonadaceae Lamiales Lamiales Antirrhinum Antirrhinum Antirrhinum majus Antirrhinum majus Neopterygii Neopterygii Batrachia Batrachia Protacanthopterygii Protacanthopterygii Plasmodium (Vinckeia) Plasmodium (Vinckeia) Plasmodium (Laverania) Plasmodium (Laverania) Culicoidea Culicoidea Sapindales Sapindales Asterales Asterales Asteraceae Asteraceae Rubrobacter Rubrobacter Aconoidasida Aconoidasida Eimeriorina Eimeriorina Candida dubliniensis Candida dubliniensis Solanoideae Solanoideae Nicotianoideae Nicotianoideae Nicotianeae Nicotianeae Capsiceae Capsiceae Solaneae Solaneae Thiomonas sp. 3As Thiomonas sp. 3As Moorella group Moorella group Trichoderma reesei QM6a Trichoderma reesei QM6a Sylvia Sylvia Dinosauria Dinosauria Saurischia Saurischia Theropoda Theropoda Coelurosauria Coelurosauria Muscomorpha Muscomorpha Schizophora Schizophora Acalyptratae Acalyptratae Ephydroidea Ephydroidea Culicimorpha Culicimorpha Anophelinae Anophelinae Culicinae Culicinae Drosophilinae Drosophilinae Cyanothece Cyanothece Cyanothece sp. ATCC 51142 Cyanothece sp. ATCC 51142 Moorella Moorella Liliopsida Liliopsida Cellia Cellia Pyretophorus Pyretophorus gambiae species complex gambiae species complex Dictyostelium discoideum Dictyostelium discoideum Poaceae Poaceae Hordeum Hordeum Hordeum vulgare Hordeum vulgare Lolium Lolium Lolium perenne Lolium perenne Oryza Oryza Oryza sativa Oryza sativa Triticum Triticum Triticum aestivum Triticum aestivum Triticum turgidum subsp. durum Triticum turgidum subsp. durum Triticum turgidum Triticum turgidum Zea Zea Zea mays Zea mays Festuca Festuca Festuca arundinacea Festuca arundinacea Staphylococcus aureus subsp. aureus Staphylococcus aureus subsp. aureus Mesoplasma Mesoplasma Oenococcus Oenococcus Thermoplasmataceae Thermoplasmataceae Moraxellaceae Moraxellaceae Drosophilini Drosophilini Drosophilina Drosophilina Acinetobacter Acinetobacter Acinetobacter baumannii Acinetobacter baumannii Orbiliaceae Orbiliaceae Tetraodon Tetraodon commelinids commelinids Fungi Fungi Schizotrypanum Schizotrypanum Agrotis Agrotis Agrotis segetum Agrotis segetum Neisseriaceae Neisseriaceae Neisseria Neisseria Neisseria gonorrhoeae Neisseria gonorrhoeae Neisseria meningitidis Neisseria meningitidis Ralstonia Ralstonia Geospiza Geospiza Geospiza conirostris Geospiza conirostris Geospiza fortis Geospiza fortis Geospiza magnirostris Geospiza magnirostris Geospiza scandens Geospiza scandens Ascomycota Ascomycota Saccharomycetes Saccharomycetes Saccharomycetales Saccharomycetales Saccharomycetaceae Saccharomycetaceae Novosphingobium aromaticivorans Novosphingobium aromaticivorans Schizosaccharomycetaceae Schizosaccharomycetaceae Schizosaccharomyces Schizosaccharomyces Schizosaccharomyces pombe Schizosaccharomyces pombe Kluyveromyces Kluyveromyces Kluyveromyces waltii Kluyveromyces waltii Pichia Pichia Pichia pastoris Pichia pastoris Lycopersicon Lycopersicon Saccharomyces Saccharomyces Saccharomyces bayanus Saccharomyces bayanus Rubrobacter xylanophilus Rubrobacter xylanophilus Saccharomyces cerevisiae Saccharomyces cerevisiae Desulfitobacterium hafniense Desulfitobacterium hafniense Lachancea kluyveri Lachancea kluyveri Thermoplasma volcanium Thermoplasma volcanium Eurotiales Eurotiales Aspergillus Aspergillus Insecta Insecta Aspergillus clavatus Aspergillus clavatus Alcaligenaceae Alcaligenaceae Aspergillus niger Aspergillus niger Aspergillus fumigatus Aspergillus fumigatus Heterodera glycines Heterodera glycines Hypocreales Hypocreales Gibberella Gibberella Hypocreaceae Hypocreaceae Chlamydiae/Verrucomicrobia group Chlamydiae/Verrucomicrobia group Chlamydiales Chlamydiales Sordariales Sordariales Neurospora Neurospora Neurospora crassa Neurospora crassa Hypocrea jecorina Hypocrea jecorina Sordaria Sordaria Sordaria macrospora Sordaria macrospora Sordariaceae Sordariaceae Ciona savignyi Ciona savignyi Bordetella Bordetella Bordetella bronchiseptica Bordetella bronchiseptica Bordetella pertussis Bordetella pertussis Basidiomycota Basidiomycota Festuca rubra Festuca rubra Ustilaginomycetes Ustilaginomycetes Ustilaginales Ustilaginales Ustilaginaceae Ustilaginaceae Ustilago Ustilago Ustilago maydis Ustilago maydis Leymus Leymus Hymenomycetes Hymenomycetes Aphyllophorales Aphyllophorales Corticiaceae Corticiaceae Phanerochaete Phanerochaete Phanerochaete chrysosporium Phanerochaete chrysosporium Agaricales Agaricales Xanthomonas axonopodis Xanthomonas axonopodis Coprinopsis cinerea Coprinopsis cinerea Stegomyia Stegomyia Culicini Culicini Paxillaceae Paxillaceae Paxillus Paxillus Pyrococcus horikoshii Pyrococcus horikoshii mitosporic Orbiliaceae mitosporic Orbiliaceae Monacrosporium Monacrosporium Zymomonas Zymomonas Zymomonas mobilis Zymomonas mobilis Enterobacteriaceae Enterobacteriaceae Mycosphaerella graminicola Mycosphaerella graminicola Candida Candida Candida albicans Candida albicans Candida glabrata Candida glabrata Pinus resinosa Pinus resinosa Gibberella zeae Gibberella zeae Panagrolaimoidea Panagrolaimoidea Rhabditoidea Rhabditoidea Peloderinae Peloderinae Escherichia Escherichia Escherichia coli Escherichia coli Agrotis ipsilon Agrotis ipsilon Kinetoplastida Kinetoplastida Trypanosomatidae Trypanosomatidae Leishmania Leishmania Leishmania braziliensis Leishmania braziliensis Leishmania donovani Leishmania donovani Leishmania major Leishmania major Leishmania mexicana Leishmania mexicana Leishmania infantum Leishmania infantum Trypanosoma Trypanosoma Trypanosoma brucei Trypanosoma brucei Trypanosoma cruzi Trypanosoma cruzi Dictyostelium Dictyostelium Apicomplexa Apicomplexa Coccidia Coccidia Burkholderia thailandensis Burkholderia thailandensis Coniferopsida Coniferopsida Tracheophyta Tracheophyta Spermatophyta Spermatophyta Cryptosporidium Cryptosporidium Cryptosporidium parvum Cryptosporidium parvum Haemosporida Haemosporida Plasmodium Plasmodium Plasmodium berghei Plasmodium berghei Plasmodium falciparum Plasmodium falciparum Salmonella Salmonella Salmonella enteritidis Salmonella enteritidis Taeniopygia Taeniopygia Taeniopygia guttata Taeniopygia guttata Coregonus clupeaformis Coregonus clupeaformis Salmonella typhi Salmonella typhi Salmonella typhimurium Salmonella typhimurium Eumetazoa Eumetazoa Neosartorya fischeri group Neosartorya fischeri group Platyhelminthes Platyhelminthes Trematoda Trematoda Digenea Digenea Strigeidida Strigeidida Schistosoma Schistosoma Schistosoma japonicum Schistosoma japonicum Schistosoma mansoni Schistosoma mansoni Emberizinae Emberizinae Nematoda Nematoda Rhabditida Rhabditida Caenorhabditis Caenorhabditis Caenorhabditis briggsae Caenorhabditis briggsae Caenorhabditis elegans Caenorhabditis elegans Rhabditidae Rhabditidae Strongyloididae Strongyloididae Strongyloides Strongyloides Spirurida Spirurida Brugia Brugia Brugia malayi Brugia malayi Yersinia Yersinia Ustilaginomycetidae Ustilaginomycetidae Filarioidea Filarioidea Onchocercidae Onchocercidae Tylenchida Tylenchida Heteroderidae Heteroderidae Yersinia pestis Yersinia pestis Aquifex aeolicus Aquifex aeolicus Vibrionaceae Vibrionaceae Mollusca Mollusca Gastropoda Gastropoda Buchnera sp. Buchnera sp. Borrelia burgdorferi group Borrelia burgdorferi group Aquificaceae Aquificaceae Pulmonata Pulmonata Basommatophora Basommatophora Planorbidae Planorbidae Biomphalaria Biomphalaria Biomphalaria glabrata Biomphalaria glabrata Photobacterium Photobacterium Vibrio Vibrio Arthropoda Arthropoda Crustacea Crustacea Vibrio cholerae Vibrio cholerae Malacostraca Malacostraca Eucarida Eucarida Decapoda Decapoda Dendrobranchiata Dendrobranchiata Penaeidae Penaeidae Penaeus monodon Penaeus monodon Mesorhizobium Mesorhizobium Thermoanaerobacteriales Thermoanaerobacteriales Bacteroidetes/Chlorobi group Bacteroidetes/Chlorobi group delta/epsilon subdivisions delta/epsilon subdivisions Boletales Boletales Phyllobacteriaceae Phyllobacteriaceae Desulfuromonadales Desulfuromonadales Hexapoda Hexapoda Lepidoptera Lepidoptera Bombycidae Bombycidae Bombyx Bombyx Bombyx mori Bombyx mori Apinae Apinae Noctuidae Noctuidae Paxillus involutus Paxillus involutus Pasteurellaceae Pasteurellaceae eudicotyledons eudicotyledons asterids asterids rosids rosids Actinobacillus Actinobacillus Diptera Diptera Nematocera Nematocera Actinobacillus pleuropneumoniae Actinobacillus pleuropneumoniae Culicidae Culicidae Aedes Aedes Aedes aegypti Aedes aegypti Anopheles Anopheles Anopheles gambiae Anopheles gambiae Fabales Fabales Brachycera Brachycera Eumalacostraca Eumalacostraca Drosophilidae Drosophilidae Drosophila Drosophila Drosophila erecta Drosophila erecta Drosophila mauritiana Drosophila mauritiana Drosophila melanogaster Drosophila melanogaster Thiotrichales Thiotrichales Pseudomonadales Pseudomonadales Alteromonadaceae Alteromonadaceae Helicobacteraceae Helicobacteraceae Campylobacteraceae Campylobacteraceae Drosophila orena Drosophila orena Drosophila pseudoobscura Drosophila pseudoobscura Drosophila sechellia Drosophila sechellia Haemophilus Haemophilus Drosophila simulans Drosophila simulans Drosophila teissieri Drosophila teissieri Drosophila yakuba Drosophila yakuba Haemophilus influenzae Haemophilus influenzae Dechloromonas Dechloromonas Hymenoptera Hymenoptera Apocrita Apocrita Photobacterium profundum Photobacterium profundum Aculeata Aculeata Monacrosporium haptotylum Monacrosporium haptotylum Pasteurella Pasteurella Apidae Apidae Apis Apis Apis mellifera Apis mellifera Pasteurella multocida Pasteurella multocida Pterygota Pterygota Ferroplasma Ferroplasma Caulobacter Caulobacter Oxalobacteraceae Oxalobacteraceae Populus euphratica Populus euphratica Eucoccidiorida Eucoccidiorida Rhodocyclaceae Rhodocyclaceae Rickettsiales Rickettsiales Anaplasma Anaplasma Nidovirales Nidovirales Caulobacteraceae Caulobacteraceae Chordata Chordata Urochordata Urochordata Ascidiacea Ascidiacea Phlebobranchia Phlebobranchia Cionidae Cionidae Ciona Ciona Ciona intestinalis Ciona intestinalis Bartonellaceae Bartonellaceae Stolidobranchia Stolidobranchia Pyuridae Pyuridae Bartonella Bartonella Herdmania Herdmania Herdmania momus Herdmania momus Vertebrata Vertebrata Rickettsiaceae Rickettsiaceae Coxiella Coxiella Mycobacterium tuberculosis complex Mycobacterium tuberculosis complex Coxiella burnetii Coxiella burnetii Gnathostomata Gnathostomata Rickettsia Rickettsia Rickettsia conorii Rickettsia conorii Rickettsia prowazekii Rickettsia prowazekii Rickettsia rickettsii Rickettsia rickettsii Euphyllophyta Euphyllophyta Actinopterygii Actinopterygii Cypriniformes Cypriniformes Cyprinidae Cyprinidae Danio Danio Danio rerio Danio rerio Cyprinus Cyprinus Cyprinus carpio Cyprinus carpio Arthropleona Arthropleona Entomobryoidea Entomobryoidea Ellipura Ellipura Salmoniformes Salmoniformes Salmonidae Salmonidae Oncorhynchus Oncorhynchus Oncorhynchus mykiss Oncorhynchus mykiss Salmo Salmo Bartonella quintana Bartonella quintana Salmo salar Salmo salar Salmo trutta Salmo trutta Gadiformes Gadiformes Gadidae Gadidae Gadus Gadus Gadus morhua Gadus morhua Burkholderiales Burkholderiales Populus tremula x Populus alba Populus tremula x Populus alba Chlamydiaceae Chlamydiaceae Chlamydia Chlamydia Magnaporthaceae Magnaporthaceae Perciformes Perciformes Percoidei Percoidei Chlamydia trachomatis Chlamydia trachomatis Sparidae Sparidae Sparus Sparus Sparus aurata Sparus aurata Leuconostocaceae Leuconostocaceae Enterococcaceae Enterococcaceae Rhizobiaceae Rhizobiaceae Pleuronectiformes Pleuronectiformes Pleuronectidae Pleuronectidae Platichthys Platichthys Platichthys flesus Platichthys flesus Sarcopterygii Sarcopterygii Amphibia Amphibia Apini Apini Anura Anura Pipidae Pipidae Xenopus Xenopus Xenopus laevis Xenopus laevis Chlamydophila Chlamydophila Chlamydophila pneumoniae Chlamydophila pneumoniae Xenopodinae Xenopodinae Silurana Silurana Xenopus tropicalis Xenopus tropicalis Nocardiopsaceae Nocardiopsaceae Thermobifida Thermobifida Sauropsida Sauropsida Fusobacterium Fusobacterium Archosauria Archosauria Rubrobacteridae Rubrobacteridae Rubrobacterales Rubrobacterales Rubrobacteraceae Rubrobacteraceae Actinobacteridae Actinobacteridae Bifidobacteriales Bifidobacteriales Actinomycineae Actinomycineae Corynebacterineae Corynebacterineae Streptomycineae Streptomycineae Streptosporangineae Streptosporangineae Fusobacterium nucleatum Fusobacterium nucleatum Dicondylia Dicondylia Amphiesmenoptera Amphiesmenoptera Citrus clementina Citrus clementina Triticum turgidum subsp. dicoccoides Triticum turgidum subsp. dicoccoides Paxillus filamentosus Paxillus filamentosus Pasteuria Pasteuria Leymus cinereus Leymus cinereus Leymus triticoides Leymus triticoides Saccharophagus degradans Saccharophagus degradans Bacillus cereus group Bacillus cereus group Bacillus halodurans Bacillus halodurans Geospiza difficilis Geospiza difficilis Desulfovibrio Desulfovibrio Desulfovibrio desulfuricans Desulfovibrio desulfuricans Aves Aves Burkholderia cepacia complex Burkholderia cepacia complex Neognathae Neognathae Panarthropoda Panarthropoda Flexibacteraceae Flexibacteraceae Craniata Craniata Galliformes Galliformes Phasianidae Phasianidae Ferroplasmaceae Ferroplasmaceae Gallus Gallus Gallus gallus Gallus gallus Phasianinae Phasianinae Filobasidiales Filobasidiales Staphylococcaceae Staphylococcaceae Bacilli Bacilli Passeriformes Passeriformes Fringillidae Fringillidae Enterobacteriales Enterobacteriales Cetartiodactyla Cetartiodactyla core eudicotyledons core eudicotyledons eurosids I eurosids I eurosids II eurosids II campanulids campanulids lamiids lamiids Acidithiobacillus ferrooxidans Acidithiobacillus ferrooxidans Bartonella koehlerae Bartonella koehlerae Metatheria Metatheria Xanthomonas axonopodis pv. citri Xanthomonas axonopodis pv. citri Macropodidae Macropodidae Macropus Macropus Mycosphaerellaceae Mycosphaerellaceae Macropus eugenii Macropus eugenii Eutheria Eutheria Anaplasmataceae Anaplasmataceae Ehrlichia Ehrlichia Ehrlichia canis Ehrlichia canis Primates Primates Methanosarcinales Methanosarcinales Platyrrhini Platyrrhini Anaplasma phagocytophilum Anaplasma phagocytophilum Callitrichinae Callitrichinae Callithrix Callithrix Callithrix jacchus Callithrix jacchus Cebidae Cebidae Noctuinae Noctuinae Catarrhini Catarrhini Cercopithecidae Cercopithecidae Cercopithecinae Cercopithecinae Macaca Macaca Macaca fascicularis Macaca fascicularis Macaca fuscata Macaca fuscata Macaca mulatta Macaca mulatta Pan Pan Pan troglodytes Pan troglodytes Pongo Pongo Pongo pygmaeus Pongo pygmaeus Hominidae Hominidae Homo Homo Homo sapiens human being Homo sapiens Canidae Canidae Canis Canis Canis familiaris Canis familiaris Vulpes Vulpes Vulpes vulpes Vulpes vulpes Felidae Felidae Felis Felis Felis catus Felis catus Ferroplasma acidarmanus Ferroplasma acidarmanus Bacteroidetes Bacteroidetes Cytophaga Cytophaga Perissodactyla Perissodactyla Equidae Equidae Equus Equus Equus caballus Equus caballus Suidae Suidae Sus Sus Sus scrofa Sus scrofa Ruminantia Ruminantia Cytophaga hutchinsonii Cytophaga hutchinsonii Festuca brevipila Festuca brevipila Festuca rubra subsp. fallax Festuca rubra subsp. fallax Festuca rubra subsp. littoralis Festuca rubra subsp. littoralis Bovidae Bovidae Bos Bos Bos taurus Bos taurus Bos indicus Bos indicus Ovis Ovis Ovis aries Ovis aries Caprinae Caprinae Tetraodon nigroviridis Tetraodon nigroviridis Rodentia Rodentia age A time quality inhering in a bearer by virtue of how long the bearer has existed. age 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 length length A 1-D extent quality which is equal to the distance between two points. mass mass A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter. temperature A physical quality of the thermal energy of a system. temperature 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 female A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes. female male A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes. male volume A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies. volume pressure A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts. pressure diluted A concentration which relatively low. diluted 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 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 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 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 quality of a single physical entity A physical object quality which inheres in a single-bearer. quality of a single physical entity quality of related physical entities A physical entity quality which exists in relation towards some other entity. quality of related physical entities mixed sex A biological sex quality inhering in a population of multiple sexes. mixed sex biomaterial purity A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial. biomaterial purity hermaphrodite A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual. hermaphrodite a mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating. a mating type (yeast) alpha mating type (yeast) A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids. alpha mating type (yeast) h minus A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus. h minus h plus A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus. h plus F mating type A bacterial mating type indicating the presence of F plasmid in a bacterial cell. F mating type F minus mating type A bacterial mating type indicating the absence of F plasmid in a bacterial cell. F minus mating type 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 haploid A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes. haploid polyploid A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes. polyploid 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 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 cellular quality A monadic quality of continuant that exists at the cellular level of organisation. cellular quality alive A viability quality inhering in a bearer by virtue of the bearer's condition before death. alive dead A viability quality inhering in a bearer by virtue of the cessation of the bearer's life. dead 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 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 radioactive A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity. radioactive 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 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 frozen A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point. frozen 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 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 circular A quality of a nucleotide polymer that has no terminal nucleotide residues. circular life cycle stage A spatiotemporal region encompassing some part of the life cycle of an organism. life cycle stage left cerebral hemisphere left cerebral hemisphere right cerebral hemisphere right cerebral hemisphere length unit length unit length unit A unit which is a standard measure of the distance between two points. length unit mass unit mass unit mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit time unit time unit time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit temperature unit A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter. temperature unit substance unit A unit which is a standardised quantity of an element or compound with uniform composition. substance unit concentration unit A unit which represents a standard measurement of how much of a given substance there is mixed with another substance. concentration unit 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 pressure unit A unit which is a standard measure of the force applied to a given area. pressure unit 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 entity continuant Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building Synonyms: endurant dependent_continuant Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities. disposition Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C. Examples: the disposition of vegetables to decay when not refrigerated, the disposition of a vase to brake if dropped, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease, the disposition of metal to conduct electricity. fiat_object_part Definition: A material entity [snap:MaterialEntity] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities. Examples: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso Synonyms: fiat substance part function Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for. Examples: the function of a birth canal to enable transport, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc., the function of reproduction in the transmission of genetic material, the digestive function of the stomach to nutriate the body, the function of a hammer to drive in nails, the function of a computer program to compute mathematical equations, the function of an automobile to provide transportation, the function of a judge in a court of law generically_dependent_continuant Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time. Examples: a certain PDF file that exists in different and in several hard drives independent_continuant Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything. Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building Synonyms: substantial entity material_entity Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. Examples: collection of random bacteria, a chair, dorsal surface of the body object Definition: A material entity [snap:MaterialEntity] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time. Examples: an organism, a heart, a chair, a lung, an apple Synonyms: substance object_aggregate Definition: A material entity [snap:MaterialEntity] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries. Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital Synonyms: substance aggregate object_boundary Comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal. Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world. Examples: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall Synonyms: substance boundary one_dimensional_region Definition: A spatial region [snap:SpatialRegion] with one dimension. Examples: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space quality Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property). Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee realizable_entity Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized. Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity role Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts. Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university site Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are site [snap:Site] entities) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class). Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities. Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria. spatial_region Comment: All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself. Comment: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion]. Comment: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities. Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities. Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe specifically_dependent_continuant Definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc. Synonyms: property, trope, mode three_dimensional_region Definition: A spatial region [snap:SpatialRegion] with three dimensions. Examples: a cube-shaped part of space, a sphere-shaped part of space two_dimensional_region Definition: A spatial region [snap:SpatialRegion] with two dimensions. Examples: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space zero_dimensional_region Definition: A spatial region [snap:SpatialRegion] with no dimensions. Examples: a point connected_spatiotemporal_region Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same spatiotemporal region [span:SpatiotemporalRegion]. Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus connected_temporal_region Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which. Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis fiat_process_part Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities. Examples: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life occurrent Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor Synonyms: perdurant process Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. Examples: the life of an organism, the process of sleeping, the process of cell-division process_aggregate Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries. Examples: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together process_boundary Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary. Examples: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery processual_context Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities. Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. Processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur. Examples: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment. processual_entity Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird scattered_spatiotemporal_region Definition: A spatiotemporal region [span:SpatiotemporalRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which. Examples: the space and time occupied by the individual games of the World Cup, the space and time occupied by the individual liaisons in a romantic affair scattered_temporal_region Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which. Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair spatiotemporal_instant Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] at a specific moment. Examples: the spatiotemporal region occupied by a single instantaneous temporal slice (part) of a process spatiotemporal_interval Definition: A connected spatiotemporal region [span:ConnectedSpatiotemporalRegion] that endures for more than a single moment of time. Examples: the spatiotemporal region occupied by a process or by a fiat processual part spatiotemporal_region Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities, that is, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself. Comment: An instance of the spatiotemporal region [span:SpatiotemporalRegion] is a part of spacetime. All parts of spacetime are spatiotemporal region [span:SpatiotemporalRegion] entities and only spatiotemporal region [span:SpatiotemporalRegion] entities are parts of spacetime. In particular, neither spatial region [snap:SpatialRegion] entities nor temporal region [span:TemporalRegion] entities are in BFO parts of spacetime. Spacetime is the entire extent of the spatiotemporal universe, a designated individual, which is thus itself a spatiotemporal region [span:SpatiotemporalRegion]. Spacetime is among occurrents the analogous of space among continuant [snap:Continuant] entities. Comment: Spacetime and spatiotemporal region [span:SpatiotemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called "absolutist" or "the container view". In BFO, the class processual context [span:ProcessualContext] allows for a so-called relational view of spacetime, that is to say, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO, the bridge between these two views is secured through the fact that instances of processual context [span:ProcessualContext] are too spatiotemporal entities. Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located. Examples: the spatiotemporal region occupied by a human life, the spatiotemporal region occupied by the development of a cancer tumor, the spatiotemporal context occupied by a process of cellular meiosis temporal_instant Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time. Examples: right now, the moment at which a finger is detached in an industrial accident, the moment at which a child is born, the moment of death temporal_interval Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time. Examples: any continuous temporal duration during which a process occurs temporal_region Comment: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant]. Comment: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself. Comment: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion]. Definition: An occurrent [span:Occurrent] that is part of time. Examples: the time it takes to run a marathon, the duration of a surgical procedure, the moment of death example to be eventually removed metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. organizational term PERSON:Alan Ruttenberg term created to ease viewing/sort terms for development purpose, and will not be included in a release ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. to be replaced with external ontology term Alan Ruttenberg Terms with this status should eventually replaced with a term from another ontology. group:OBI requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. Alan Ruttenberg group:OBI Helicos Helicos Philippe Rocca-Serra Roche Philippe Rocca-Serra Roche Illumina Illumina Philippe Rocca-Serra Li-Cor Li-Cor Philippe Rocca-Serra Applied Biosystems Applied Biosystems Philippe Rocca-Serra