Allyson Lister Andy Brown Duncan Hull Helen Parkinson James Malone Jon Ison Nandini Badarinarayan Robert Stevens The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains detailed information on licensing and formats as well as software applications themselves, mainly (but not limited) to the bioinformatics community. https://creativecommons.org/licenses/by/4.0/ Software Ontology The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, licensing, provenance and associated data. It contains SWO-specific classes and axioms as well as imports from: 1. BFO 2. IAO 3. OBI 4. EDAM 2023-03-05 editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred label editor preferred label editor preferred term editor preferred term editor preferred term~editor preferred label 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. A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> IAO example of usage example of usage definition definition textual definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition textual definition term editor 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 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> term editor alternative label alternative term A label for a class or property that can be used to refer to the class or property instead of the preferred rdfs:label. Alternative labels should be used to indicate community- or context-specific labels, abbreviations, shorthand forms and the like. An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) OBO Operations committee PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). alternative label alternative term alternative term 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 PERSON:Daniel Schober Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source term tracker item the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ An IRI or similar locator for a request or discussion of an ontology term. Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg The 'tracker item' can associate a tracker with a specific ontology term. term tracker item imported from For external terms/classes, the ontology from which the term was imported PERSON:Alan Ruttenberg PERSON:Melanie Courtot GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from term replaced by Use on obsolete terms, relating the term to another term that can be used as a substitute Person:Alan Ruttenberg Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL is a defining property chain axiom If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. is a defining property chain axiom where second argument is reflexive 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. An entity responsible for making contributions to the content of the resource. Contributor Contributor description Mark Miller 2018-05-11T13:47:29Z license title The version in which a class or property has been made obsolete EFO Development Team obsoleted in version is defined by is defined by This is an experimental annotation label label deprecated Allyson Lister 14.9.22: Added as a temporary workaround with issues relating to equivalentClass axioms between IAO software and SWO software. 'is about' relates an information entity to other entities in which the information entity holds some information which dscribes some facet of the other entity, such as the arrow direction on a sign. IAO James Malone Alan Ruttenberg is about is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of part of http://www.obofoundry.org/ro/#OBO_REL:part_of has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part has part realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. 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. is preceded by preceded_by http://www.obofoundry.org/ro/#OBO_REL:preceded_by preceded by precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. precedes This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. 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. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about has_specified_input has_specified_input see is_input_of example_of_usage The inverse property of is_specified_input_of 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: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay 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. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of has_specified_output has_specified_output The inverse property of is_specified_output_of PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_manufactured_by 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) 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. 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. Alan Ruttenberg Liju Fan has_make has_manufacturer OBI is manufactured by is_manufactured_by is_specified_output_of 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 PERSON:Bjoern Peters is_specified_output_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' 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. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by inheres in this fragility inheres in this vase this fragility is a characteristic of this vase this red color inheres in this apple this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility Inverse of characteristic_of a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of has characteristic participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in Andy Brown Please see the official RO definition for the inverse of this property, 'has participant.' participates in participates in has participant 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. this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) 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. a relation between a process and a continuant, in which the continuant is somehow involved in the process 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. has_participant http://obo-relations.googlecode.com/svn/trunk/src/ontology/core.owl http://www.obofoundry.org/ro/#OBO_REL:has_participant Andy Brown has participant has participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. has_function has function this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. has_quality has quality this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role has_role a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence has disposition inverse of has disposition This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. disposition of A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B. dos 2017-05-24T09:30:46Z has regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B. dos 2017-05-24T09:31:01Z By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'. has negative regulatory component activity A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B. dos 2017-05-24T09:31:17Z By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'. has positive regulatory component activity dos 2017-05-24T09:44:33Z A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B. has component activity w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. dos 2017-05-24T09:49:21Z has component process dos 2017-09-17T13:52:24Z Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. directly regulated by Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2. GOC:dos Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. dos 2017-09-17T13:52:38Z directly negatively regulated by Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1. GOC:dos Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. dos 2017-09-17T13:52:47Z directly positively regulated by Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1. GOC:dos A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. dos 2017-09-22T14:14:36Z This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations. has effector activity A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity. GOC:dos David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after David Osumi-Sutherland starts_at_end_of X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) immediately preceded by David Osumi-Sutherland ends_at_start_of meets X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) immediately precedes x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) overlaps true w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. has component p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. GO Regulation precludes parthood; the regulatory process may not be within the regulated process. regulates (processual) false regulates p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. negatively regulates (process to process) negatively regulates p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. positively regulates (process to process) positively regulates mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. has function realized in For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". capable of c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. has function in capable of part of true Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. consumes has input p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. produces has output A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects acts upstream of or within p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y causally upstream of, positive effect p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. causally upstream of, negative effect q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of inheres in part of characteristic of part of true A mereological relationship or a topological relationship Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships mereotopologically related to a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. catalyzes executes has is catalyzing is executing This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. This is a grouping relation that collects relations used for the purpose of connecting structure and function functionally related to this relation holds between c and p when c is part of some c', and c' is capable of p. false part of structure that is capable of true c involved_in p if and only if c enables some process p', and p' is part of p actively involved in enables part of involved in inverse of enables enabled by inverse of regulates regulated by (processual) regulated by inverse of negatively regulates negatively regulated by inverse of positively regulates positively regulated by An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. is member of member part of SIO member of has member is a mereological relation between a collection and an item. SIO has member An entity A is the 'input of' another entity B if A was put into the system, entity or software represented by B. inverse of has input Allyson Lister input of input of A piece of software can be the output of a particular software company via a software publishing process; data might be the output of a particular piece of data-producing software. An entity A is the 'output of' another entity B if it was produced as a result of the functioning of entity B. inverse of has output Allyson Lister output of output of inverse of upstream of causally downstream of immediately causally downstream of p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. indirectly activates indirectly positively regulates p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. indirectly inhibits indirectly negatively regulates relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative? The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause. https://en.wikipedia.org/wiki/Causality p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. causally upstream of p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. immediately causally upstream of p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 influences (processual) affects causally upstream of or within inverse of causally upstream of or within causally downstream of or within c involved in regulation of p if c is involved in some p' and p' regulates some p involved in regulation of c involved in regulation of p if c is involved in some p' and p' positively regulates some p involved in positive regulation of c involved in regulation of p if c is involved in some p' and p' negatively regulates some p involved in negative regulation of c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union involved in or reguates involved in or involved in regulation of A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ http://purl.obolibrary.org/obo/MI_0914 An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. binds molecularly binds with molecularly interacts with http://purl.obolibrary.org/obo/MI_0915 Axiomatization to GO to be added later An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. molecularly controls directly regulates activity of The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. directly inhibits molecularly decreases activity of directly negatively regulates activity of The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. directly activates molecularly increases activity of directly positively regulates activity of This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) is kinase activity A relationship between a material entity and a process where the material entity has some causal role that influences the process causal agent in process p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes depends on The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities causally influenced by (entity-centric) causally influenced by interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ molecular interaction relation helper property The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). causally influences (entity-centric) causally influences p directly regulates q iff p is immediately causally upstream of q and p regulates q. directly regulates (processual) directly regulates gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p has part structure that is capable of A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between material entity and a process pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. capable of regulating Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. capable of negatively regulating renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. capable of positively regulating Inverse of 'causal agent in process' process has causal agent p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. directly positively regulates (process to process) directly positively regulates p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. directly negatively regulates (process to process) directly negatively regulates Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P. 2018-01-25T23:20:13Z enables subfunction 2018-01-26T23:49:30Z acts upstream of or within, positive effect 2018-01-26T23:49:51Z acts upstream of or within, negative effect c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive 2018-01-26T23:53:14Z acts upstream of, positive effect c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative 2018-01-26T23:53:22Z acts upstream of, negative effect 2018-03-13T23:55:05Z causally upstream of or within, negative effect 2018-03-13T23:55:19Z causally upstream of or within, positive effect The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. regulates activity of p is indirectly causally upstream of q iff p is causally upstream of q and there exists some process r such that p is causally upstream of r and r is causally upstream of q. pg 2022-09-26T06:07:17Z indirectly causally upstream of p indirectly regulates q iff p is indirectly causally upstream of q and p regulates q. pg 2022-09-26T06:08:01Z indirectly regulates A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C. regulates characteristic A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C. positively regulates characteristic A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C. negatively regulates characteristic https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Replaced by rdfs:comment as no longer within the EFO release files. obsolete reason_for_obsolescence true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete is developed by true The relationship between software and a software publisher. Marked as obsolete by Allyson Lister. 0.5 This class can be entirely replaced with 'is published by', SWO_0004004. Please use SWO_0004004 instead. obsolete_is_published_by true Marked as obsolete by Allyson Lister. 1.4 This property was not in use anywhere in the ontology. Further, it had no definition and therefore its intended usage was unclear. Until a time when this property is required and an official definition created, this property is obsolete so as not to introduce inconsistent usage. has legal status true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete implements true https://github.com/allysonlister/swo/issues/59 AL 2023-03-05: Improperly created IRI (with 'efo' in the IRI) replaced by the correct form for SWO IRIs. obsolete is encoded in true 'is version of' provides a link between a 'version name' and the entity with that version. Allyson Lister For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/ is version of Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part. This property allows the linkage of two different pieces of software such that one directly executes or uses the other. The has_part relationship should instead be used to describe related but independent members of a larger software package, and 'uses platform' relationship should be used to describe which operating system(s) a particular piece of software can use. Allyson Lister uses software is implemented by is the relationship between an algorithm and a piece of software which includes an implementation of that software for use when the software is executed. James Malone is implemented by The relationship between input data which is permitted to a piece of software. James Malone AL 2.9.22: This cannot be a child of 'has specified input' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our domain and range, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely. See also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/ has specified data input The relationship between a piece of software and the data that it is possible to output. James Malone AL 2.9.22: This cannot be a child of 'has specified output' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our domain and range, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely. See also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/ has specified data output The relationship between a data and the software which can possibly take this data as input. James Malone AL 2.9.22: This cannot be a child of 'is specified input of' or 'input of' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our range and domain, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely. is specified data input of The relationship between a data and the software which can possibly produce this data as output. James Malone AL 2.9.22: This cannot be a child of 'is specified output of' or 'output of' because the restrictions on domain and range for that hierarchy would create issues for us, as both software and data item (our range and domain, respectively) are continuants. For now, the solution is to take it out of that hierarchy completely. is specified data output of Microsoft version 2007 is directly preceded by Microsoft version 2003. Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software. Allyson Lister OBO Foundry directly preceded by 'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s. Allyson Lister directly followed by 'uses platform' should be used to link a particular piece of software to one or more operating systems which that software can run on. This is in contrast to both 'uses software' (which describes one piece of software directly executing another), and has_part, which can be used to describe related but independent software in a package, for example. Allyson Lister This property, together with 'uses software', is probably best modelled as a child of has_part. Its current position in the property hierarchy is based on simplicity of use. 'uses platform' was deemed an appropriate addition (rather than making use of already extant has_part or 'uses software') due to the already present definitions of those classes which restrict their use to particular situations. uses platform is software for AL 2.9.22: When incorporating all BFO annotations, it became clear that we were using BFO 'precedes' (which was the original parent for 'directly followed by') incorrectly. 'precedes' has a range and domain of occurent, and the IAO version number class is an ICE, which is a continuant. This led to an inconsistent ontology. To fix this for now, we have created a new class that performs a similar function to BFO 'precedes' but without the domain/range restrictions. followed by AL 2.9.22: When incorporating all BFO annotations, it became clear that we were using BFO 'precedes' and 'preceded by' (which was the original parent for 'directly preceded by') incorrectly. 'precedes' has a range and domain of occurent, and the IAO version number class is an ICE, which is a continuant. This led to an inconsistent ontology. To fix this for now, we have created a new class (and this, its inverse) that performs a similar function to BFO 'precedes' but without the domain/range restrictions. follows The relationship between a software and software developer. is developed by implements is the relationship between software and an algorithm that is defined for use within that software when executed. James Malone implements Linking a type of software to its particular programming language. Is encoded in is an "is about" relationship which describes the type of encoding used for the referenced class. Allyson Lister is encoded in relationship between an entity and a version name or number For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/ has version Provides a method of asserting what type of interactions are possible for the class in question. The interface must be from the 'software interface' hierarchy. Allyson Lister Andy Brown Andy Brown has interface Has format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification. Allyson Lister has format specification Marked as obsolete by Allyson Lister. James Malone 0.3 is developed by and is_developed_by. The former is from the core file and originally had no identifier (though it is now identified via SWO_0004003), and the latter is from the original file (SWO_0000394). SWO_0000394 was retained and SWO_0004003 marked as obsolete as SWO_0004003 had no usages while SWO_0000394 has many usages. Finally, the underscores were removed from the label of SWO_0000394 so it would conform to our naming scheme. Please use SWO_0000394 instead. obsolete_is developed by true 'is published by' elucidates the relationship between a piece of software or a data format specification and its owning organization. Please note that this is not the same as authorship of the software. For instance, affy is published within Bioconductor, but has its own distinct authorship list. Allyson Lister James Malone is published by Stores those object properties which are no longer appropriate for use within SWO. Marked as obsolete by Allyson Lister Allyson Lister obsolete object property is executed in defines the relationship between a software class and an appropriate process in the information processing hierarchy. Specifically, it allows the linking of a particular piece of software to a process of a particular purpose, Allyson Lister Allyson Lister OBI is executed in Marked as obsolete by Allyson Lister. 0.3 There is an object property duplication for is specified output of, where one is from OBI (OBI_0000312) and one is from SWO (SWO_9000058); additionally, the reasoner infers these two object properties as equivalent. Both are the inverse properties for has specified output. It makes sense to retain the OBI object property. The SWO class URI was renamed to the OBI term URI (to make the moving of the axioms across to the OBI term simple), and then an SWO class with the original URI was marked as obsolete. Please use OBI_0000312 instead. obsolete_is specified output of true Axioms using the 'has clause' property, e.g. C 'has clause' C1, provide links from the left hand class to the instances within the 'license clause' hierarchy. This provides a way to more precisely assert the constraints of the licensing applied. Allyson Lister has clause The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between software and a software license. has license The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it. is license for The format for BioPAX Manchester OWL syntax is an alternative format of the BioPAX RDF/XML format. With both a domain and range of 'data format specification', this property provides a means of stating that two different data format specifications are valid specifications for the same type of data. Allyson Lister is alternative format of 'is compatible license of' provides a method of marking two software licenses as compatible and without conflicts, e.g. that the Apache License version 2 is compatible with GNU GPL version 3. If two licenses are connected with this property, it means code released under one license can be released with code from the other license in a larger program. http://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean, accessed 12 June 2013. Allyson Lister is compatible license of 'has declared status' provides a way to assert the developmental status of a class, such as whether it is stable or under development. Is especially useful for software that might not be complete or stable yet, and when combined with version information. Allyson Lister has declared status 1.4 Exact equivalence with RO class http://purl.obolibrary.org/obo/RO_0000057, to the extent that the inverse of RO_0000057 was already present in this ontology as the inverse of this SWO class. obsolete_has_participant true The inverse property. 'part of', contains the full official RO definition. has part has_part Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part. 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.) This property can be used to describe related but independent members of a larger software package. In other cases, where parts of a larger software package are independent of one another in development but one piece of software executes another directly, please use "uses software". OBO Foundry RO part of Should be used to link a particular class (e.g. a piece of software or an algorithm) with a publication(s) which act as the primary reference(s) for that class. Allyson Lister has documentation The location from where the software can be downloaded. Allyson Lister Allyson Lister has download location The URL of the homepage for the resource this property is associated with. Allyson Lister has website homepage Andy Brown The official date of release of software has release date Andy Brown A URL for a source of support information about software has support URL An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. Ontologies Ontology A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment. Heat map Heatmap Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification. Gene product profile Gene product quantification data Gene transcription profile Gene transcription quantification data Microarray data Non-coding RNA profile Non-coding RNA quantification data RNA profile RNA quantification data RNA-seq data Transcriptome profile Transcriptome quantification data mRNA profile mRNA quantification data Gene expression data Microarray data Biological or biomedical data has been rendered into an image, typically for display on screen. Image data Image Groupings of gene expression profiles according to a clustering algorithm. Clustered gene expression profiles PDBML Format of Taverna workflows. Taverna workflow format newick FASTA format Genbank entry format. GenBank GenBank format GFF Textual format html, or HyperText Markup Language in full, is a data format specification is a markup language for web pages and is the publishing language of the World Wide Web. http://www.w3.org/TR/html401/ James Malone HTML Extensible Markup Language (XML) is a standard set of rules for encoding documents in a machine-readable form defined by the W3C. James Malone XML binary format OBO format is the text file format used by OBO-Edit, the open source, platform-independent application for viewing and editing ontologies. OBO flat file format OBO Flat File Format Systems Biology Markup Language (SBML) is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. Systems Biology Markup Language http://sbml.org SBML BED format The PSI-MI format is an acronym for the Proteomics Standards Initiative - Molecular Interaction format. It provides an XML standard for molecular interactions and is supported by many molecular interaction databases and tools. PSI-MI format PSI-MIF Modified from http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012. Allyson Lister MAGE-ML MAGE-TAB is a tab delimited data format comprimising of ADF file for array design, IDFfor experimental design, SDRF for sample data relationships and associated data files. http://www.mged.org/mage-tab/ A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. MAGE-TAB CopasiML, the native format of COPASI. CopasiML Search or query a data resource and retrieve entries and / or annotation. Database retrieval Query Query and retrieval Annotate a genome sequence with terms from a controlled vocabulary. Metagenome annotation Genome annotation Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. Mathematical modelling Modelling and simulation data visualization algorithm data cleaning algorithm data selection algorithm data integration algorithm A data processing task is an information processing objective that specifies the objective that a data processing algorithm execution process needs to achieve when executed on a dataset to produce as output a new dataset. data processing task data construction algorithm Generalization specification of a directive informational entity class that specifies the type of generalization. It includes information about the types of data used to produced the generalization and the language in which the generalization is expressed. OntoDM generalization specification Allyson Lister A data processing algorithm is an algorithm that has as its objective a data processing task and has data items both as input and output. data processing algorithm http://purl.obolibrary.org/obo/OBI_0200111 1.7 AL 25.9.19: Already obsoleted in originating ontology (OntoDM) so added here so people could see the history of the term. data visualization task is information processing objective achieved by a data visualization algorithm execution process. data visualization task true A planned process that has specified output a software product and that involves the creation of source code. Mathias Brochhausen William R. Hogan http://en.wikipedia.org/wiki/Software_development A planned process resulting in a software product involving the creation of source code. software development creating a data set A planned process that has a data set as its specified output. William R. Hogan data set creation dataset creation dataset creating entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) continuant Continuant continuant An 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. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] occurrent Occurrent An entity that has temporal parts and that happens, unfolds or develops through time. BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in 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. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] sdc SpecificallyDependentContinuant specifically dependent continuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella A 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. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n &gt; 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i &lt; j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] material MaterialEntity material entity material entity Collection of random bacteria, a chair, dorsal surface of the body. a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being 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. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. BFO A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. molecular function GO:0003674 Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. molecular_function A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process. GOC:pdt A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. jl 2012-09-19T15:05:24Z Wikipedia:Biological_process biological process physiological process single organism process single-organism process GO:0008150 Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. GOC:pdt true Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. Reactome:R-HSA-6788855 Reactome:R-HSA-6788867 phosphokinase activity GO:0016301 Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term. kinase activity Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule. ISBN:0198506732 Reactome:R-HSA-6788855 FN3KRP phosphorylates PsiAm, RibAm Reactome:R-HSA-6788867 FN3K phosphorylates ketosamines measurement unit label Examples of measurement unit labels are liters, inches, weight per volume. A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. 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. PERSON: Alan Ruttenberg PERSON: Melanie Courtot measurement unit label objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. 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. 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." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification Pour the contents of flask 1 into flask 2 A directive information entity that describes an action the bearer will take. Alan Ruttenberg OBI Plan and Planned Process branch action specification datum 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 http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n GROUP: IAO 9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. datum label software 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 PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Chris Stoeckert PERSON: Melanie Courtot GROUP: OBI software http://www.ebi.ac.uk/swo/SWO_0000001 programming language R, Perl, Java A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. person:Alan Ruttenberg person:Chris Stoeckert IAO OBI_0000058 group:OBI programming language programming language data item Data items include counts of things, analyte concentrations, and statistical summaries. 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. 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. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ 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 data data item http://www.ontobee.org/browser/rdf.php?o=IAO&iri=http://purl.obolibrary.org/obo/IAO_0000027 symbol a serial number such as "12324X" a stop sign a written proper name such as "OBI" An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. 20091104, MC: this needs work and will most probably change 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). PERSON: James A. Overton PERSON: Jonathan Rees based on Oxford English Dictionary symbol information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). 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. PERSON: Chris Stoeckert IAO OBI_0000142 information content entity information content entity An information content entity whose concretizations indicate to their bearer how to realize them in a process. 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. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO 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 PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity dot plot Dot plot of SSC-H and FSC-H. 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. person:Allyson Lister person:Chris Stoeckert OBI_0000123 group:OBI dot plot 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. PERSON: Lawrence Hunter person:Alan Ruttenberg person:Allyson Lister OBI_0000240 group:OBI graph algorithm PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. 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. A plan specification which describes the inputs and 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. Philippe Rocca-Serra PlanAndPlannedProcess Branch IAO OBI_0000270 adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) algorithm algorithm curation status specification 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. Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting) PERSON:Bill Bug GROUP:OBI:<http://purl.obolibrary.org/obo/obi> OBI_0000266 curation status specification source code module The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script. A source code module is a directive information entity that specifies, using a programming language, some algorithm. person:Alan Ruttenberg person:Chris Stoeckert OBI_0000039 group:OBI source code module data format specification A data format specification is the information content borne by the document published defining the specification. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" PERSON: Alan Ruttenberg PlanAndPlannedProcess Branch OBI branch derived OBI_0000187 data format specification data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). 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. 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 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set 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. person:Alan Ruttenberg person:Allyson person:Chris Stoeckert OBI_0000030 group:OBI image data about an ontology part Data about an ontology part is a data item about a part of an ontology, for example a term Person:Alan Ruttenberg data about an ontology part plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 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. 2014-03-31: A plan specification can have other parts, such as conditional specifications. 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg Clint Dowland OBI Plan and Planned Process branch OBI_0000344 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 plan specification https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 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. 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 GROUP: IAO version name version number material information bearer A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier. a brain a hard drive A material entity in which a concretization of an information content entity inheres. GROUP: IAO material information bearer histogram A histogram is a report graph which is a statistical description of a distribution in terms of occurrence frequencies of different event classes. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI 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. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot GROUP:OBI heatmap dendrogram Dendrograms are often used in computational biology to illustrate the clustering of genes. 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. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot WEB: http://en.wikipedia.org/wiki/Dendrogram dendrogram scatter plot Comparison of gene expression values in two samples can be displayed in a 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. PERSON:Chris Stoeckert PERSON:James Malone PERSON:Melanie Courtot scattergraph WEB: http://en.wikipedia.org/wiki/Scatterplot scatter plot obsolescence reason specification The reason for which a term has been deprecated. 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. The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology. PERSON: Alan Ruttenberg PERSON: Melanie Courtot obsolescence reason specification figure Any picture, diagram or table An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something. PERSON: Lawrence Hunter figure diagram A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space. A figure that expresses one or more propositions PERSON: Lawrence Hunter diagram document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document denotator type The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities. A denotator type indicates how a term should be interpreted from an ontological perspective. Alan Ruttenberg Barry Smith, Werner Ceusters denotator type Viruses Viruses Euteleostomi bony vertebrates Euteleostomi Bacteria eubacteria Bacteria Archaea Archaea Eukaryota eucaryotes eukaryotes Eukaryota Euarchontoglires Euarchontoglires Tetrapoda tetrapods Tetrapoda Amniota amniotes Amniota Opisthokonta Opisthokonta Metazoa metazoans multicellular animals Metazoa Bilateria Bilateria Mammalia mammals Mammalia Vertebrata <vertebrates> Vertebrata vertebrates Vertebrata <vertebrates> Homo sapiens human human being Homo sapiens planned process planned process Injecting mice with a vaccine in order to test its efficacy A process that realizes a plan which is the concretization of a plan specification. '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.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process regulator role Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805 a regulatory role involved with making and/or enforcing relevant legislation and governmental orders Person:Jennifer Fostel regulator OBI regulator role regulatory role Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008 a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body. GROUP: Role branch OBI, CDISC govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent regulatory role material supplier role Jackson Labs is an organization which provide mice as experimental material a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation. Supplier role is a special kind of service, e.g. biobank PERSON:Jennifer Fostel material provider role supplier material supplier role classified data set 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. PERSON: James Malone PERSON: Monnie McGee data set with assigned class labels classified data set 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 material processing A cell lysis, production of a cloning vector, creating a buffer. A planned process which results in physical changes in a specified input material PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca Serra material transformation OBI branch derived material processing specimen role 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. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 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. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. 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. GROUP: Role Branch OBI specimen role organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear 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. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization organization regulatory agency The US Environmental Protection Agency A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government. GROUP: OBI Biomaterial Branch WEB: en.wikipedia.org/wiki/Regulator regulatory agency material transformation objective The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS. an objective specifiction that creates an specific output object from input materials. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra artifact creation objective GROUP: OBI PlanAndPlannedProcess Branch material transformation objective 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 Manufacturing implies reproducibility and responsibility AR This includes a single scientist making a processed material for personal use. PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing manufacturing objective is the objective to manufacture a material of a certain function (device) PERSON: Bjoern Peters PERSON: Frank Gibson PERSON: Jennifer Fostel PERSON: Melanie Courtot PERSON: Philippe Rocca-Serra GROUP: OBI PlanAndPlannedProcess Branch manufacturing objective manufacturer role With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role. Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process. GROUP: Role Branch OBI manufacturer role clustered data set A clustered data set is the output of a K means clustering data transformation 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. PERSON: James Malone PERSON: Monnie McGee data set with assigned discovered class labels AR thinks could be a data item instead clustered data set specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a 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. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process class prediction data transformation A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction. James Malone supervised classification data transformation PERSON: James Malone class prediction data transformation specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective 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 Ryan Brinkman SVM PERSON: Ryan Brinkman support vector machine 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 decision tree building data transformation A decision tree building data transformation is a data transformation that has objective decision tree induction. James Malone PERSON: James Malone decision tree building data transformation GenePattern software a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks. James Malone Person:Helen Parkinson WEB: http://www.broadinstitute.org/cancer/software/genepattern/ GenePattern software peak matching Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold James Malone Ryan Brinkman PERSON: Ryan Brinkman peak matching k-nearest neighbors 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 k-NN PERSON: James Malone k-nearest neighbors CART A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure. James Malone classification and regression trees BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining. CART statistical model validation 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 A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set. Helen Parkinson http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 statistical model validation manufacturer A person or organization that has a manufacturer role manufacturer service provider role Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer. is a role which inheres in a person or organization and is realized in in a planned process which provides access to training, materials or execution of protocols for an organization or person PERSON:Helen Parkinson service provider role processed specimen A tissue sample that has been sliced and stained for a histology study. A blood specimen that has been centrifuged to obtain the white blood cells. A specimen that has been intentionally physically modified. Bjoern Peters Bjoern Peters A tissue sample that has been sliced and stained for a histology study. processed specimen categorical label 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. A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale. Bjoern Peters Bjoern Peters categorical label questionnaire A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study. JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. JZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. Need to clarify if this is a document or a directive information entity (or what their connection is)) PERSON: Jessica Turner Merriam-Webster questionnaire categorical value specification A value specification that is specifies one category out of a fixed number of nominal categories PERSON:Bjoern Peters categorical value specification value specification The value of 'positive' in a classification scheme of "positive or negative"; the value of '20g' on the quantitative scale of mass. An information content entity that specifies a value within a classification scheme or on a quantitative scale. This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement. PERSON:Bjoern Peters value specification collection of specimens Blood cells collected from multiple donors over the course of a study. A material entity that has two or more specimens as its parts. Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/ Person: Chris Stoeckert, Jie Zheng OBIB, OBI Biobank collection of specimens histologic grade according to AJCC 7th edition G1:Well differentiated G4: Undifferentiated A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade according to AJCC 7th edition histologic grade according to the Fuhrman Nuclear Grading System A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System. Chris Stoeckert, Helena Ellis Histologic Grade (Fuhrman Nuclear Grading System) NCI BBRB, OBI NCI BBRB histologic grade according to the Fuhrman Nuclear Grading System histologic grade for ovarian tumor A categorical value specification that is a histologic grade assigned to a ovarian tumor. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor histologic grade for ovarian tumor according to a two-tier grading system A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors. Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to a two-tier grading system histologic grade for ovarian tumor according to the World Health Organization A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO). Chris Stoeckert, Helena Ellis NCI BBRB, OBI NCI BBRB histologic grade for ovarian tumor according to the World Health Organization pathologic primary tumor stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for colon and rectum according to AJCC 7th edition pathologic primary tumor stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread lung primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for lung according to AJCC 7th edition pathologic primary tumor stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread kidney primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for kidney according to AJCC 7th edition pathologic primary tumor stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic primary tumor stage for ovary according to AJCC 7th edition pathologic lymph node stage for colon and rectum according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for colon and rectum according to AJCC 7th edition pathologic lymph node stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread colon lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for lung according to AJCC 7th edition pathologic lymph node stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for kidney according to AJCC 7th edition pathologic lymph node stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes. Chris Stoeckert, Helena Ellis pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic lymph node stage for ovary according to AJCC 7th edition pathologic distant metastases stage for colon according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: colon distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for colon according to AJCC 7th edition pathologic distant metastases stage for lung according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: lung distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for lung according to AJCC 7th edition pathologic distant metastases stage for kidney according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: kidney distant Metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for kidney according to AJCC 7th edition pathologic distant metastases stage for ovary according to AJCC 7th edition A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery. Chris Stoeckert, Helena Ellis M: ovarian distant metastases (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB pathologic distant metastases stage for ovary according to AJCC 7th edition clinical tumor stage group according to AJCC 7th edition A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems. Chris Stoeckert, Helena Ellis Clinical tumor stage group (AJCC 7th Edition) NCI BBRB, OBI NCI BBRB clinical tumor stage group according to AJCC 7th edition International Federation of Gynecology and Obstetrics cervical cancer stage value specification A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems. Chris Stoeckert, Helena Ellis Clinical FIGO stage NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics cervical cancer stage value specification International Federation of Gynecology and Obstetrics ovarian cancer stage value specification A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system. Chris Stoeckert, Helena Ellis Pathologic Tumor Stage Grouping for ovarian cancer (FIGO) NCI BBRB, OBI NCI BBRB International Federation of Gynecology and Obstetrics ovarian cancer stage value specification performance status value specification A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life). Chris Stoeckert, Helena Ellis Performance Status Scale https://en.wikipedia.org/wiki/Performance_status NCI BBRB performance status value specification Eastern Cooperative Oncology Group score value specification A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient. Chris Stoeckert, Helena Ellis ECOG score NCI BBRB, OBI NCI BBRB Eastern Cooperative Oncology Group score value specification Karnofsky score vaue specification A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment. Chris Stoeckert, Helena Ellis Karnofsky Score NCI BBRB, OBI NCI BBRB Karnofsky score vaue specification material supplier A person or organization that provides material supplies to other people or organizations. Rebecca Jackson https://github.com/obi-ontology/obi/issues/1289 material supplier organism animal fungus plant virus 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. 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 WEB: http://en.wikipedia.org/wiki/Organism organism specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. 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 GROUP: OBI Biomaterial Branch specimen data transformation 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 planned process that produces output data from input data. Elisabetta Manduchi Helen Parkinson James Malone Melanie Courtot Philippe Rocca-Serra Richard Scheuermann Ryan Brinkman Tina Hernandez-Boussard data analysis data processing Branch editors data transformation leave one out cross validation method 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 2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178 Person:Helen Parkinson leave one out cross validation method k-means clustering 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). Elisabetta Manduchi James Malone Philippe Rocca-Serra 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 dimensionality reduction 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 Philippe Rocca-Serra data projection PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot dimensionality reduction principal components analysis dimensionality reduction 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 Philippe Rocca-Serra pca data reduction PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot principal components analysis dimensionality reduction data visualization Generation of a heatmap from a microarray dataset An planned process that creates images, diagrams or animations from the input data. Elisabetta Manduchi James Malone Melanie Courtot Tina Boussard data encoding as image visualization PERSON: Elisabetta Manduchi PERSON: James Malone PERSON: Melanie Courtot PERSON: Tina Boussard Possible future hierarchy might include this: information_encoding >data_encoding >>image_encoding data visualization data transformation objective normalize objective An objective specification to transformation input data into output data Modified definition in 2013 Philly OBI workshop James Malone PERSON: James Malone data transformation objective partitioning data transformation A partitioning data transformation is a data transformation that has objective partitioning. James Malone PERSON: James Malone partitioning data transformation partitioning objective A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets. 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. Elisabetta Manduchi James Malone PERSON: Elisabetta Manduchi partitioning objective class discovery data transformation A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery. James Malone clustering data transformation unsupervised classification data transformation PERSON: James Malone class discovery data transformation class discovery objective A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. James Malone clustering objective discriminant analysis objective unsupervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class discovery objective class prediction 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 classification objective supervised classification objective PERSON: Elisabetta Manduchi PERSON: James Malone class prediction objective cross validation objective 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 rotation estimation objective WEB: http://en.wikipedia.org/wiki/Cross_validation cross validation objective 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 A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATO:0000001 quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities PATOC:GVG length unit A unit which is a standard measure of the distance between two points. length unit mass unit A unit which is a standard measure of the amount of matter/energy of a physical object. mass unit time unit A unit which is a standard measure of the dimension in which events occur in sequence. time unit temperature unit temperature unit substance unit substance unit concentration unit concentration unit volume unit volume unit frequency unit frequency unit volumetric flow rate unit volumetric flow rate unit rate unit rate unit http://www.ebi.ac.uk/swo/data/SWO_3000069 1.7 AL 2.10.2019: Incorrectly-formatted IRI. See also https://github.com/allysonlister/swo/issues/16 obsolete sequence feature format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete matlab software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 2-sample pooled t-test true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 50-50 MANOVA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ABarray true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'ACME' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Algorithms for Calculating Microarray Enrichment true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Affymetrix Expression Console true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AIDA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Average log expression across arrays (ALE) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ALL/AML data set true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AMDIS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ANCOVA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'ANOVA' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AP-MS data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ARACNE algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ARR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AWS algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Absolute Expression Analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Absolute Expression Analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'AffyCompatible' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'AffyExpress' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Affymetrix GCOS v1.2 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Affymetrix GeneChip Operating Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Affymetrix Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agi4x44PreProcess true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Feature Extraction 5.1.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Feature Extraction software version 7.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Feature Extraction software version 7.5 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Feature Extraction software version A.5.1.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Scan Control true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Technologies Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'AnnotationDbi' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Applied Biosystems 1700 Expression Array System Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ArrayGauge true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ArrayNorm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'ArrayTools' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ArrayVision true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ArrayVision 6.0 (Imaging Research Inc.) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Array_vision_(Interfocus) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AtlasImage true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Axon GenePix Pro 3 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BAC true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Binning clustering method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BCRANK' true Marked as obsolete by Allyson Lister. After 0.4 release. Equivalence with EDAM term "BED" (format_3003). obsolete_BED format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BGL true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BGmix' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BLAST true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Iterative Bayesian Model Averaging (BMA) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Base-Pair-Distance Kernel true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BPMAP true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BRB-ArrayTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BSgenome' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BZScan true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BaldiLongT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BasReader 3.01 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Bayesian Model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Beadstudio true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BicARE' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BioMVCClass' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'Biobase' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BiocCaseStudies' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BioConductor Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'Biostrings' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BlueFuse true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BufferedMatrix' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'BufferedMatrixMethods' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CALIB' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CAMERA' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CBS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CBS algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CDF binary format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CEL binary format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CGHbase' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CGHcall' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CGHregions' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CHP binary format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CLR algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CMA' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CMA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CORREP' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CRLMM algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Continuous Wavelet Transform (CWT)-based peak detection algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CARMAweb true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Category analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Category true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'ChemmineR' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ChipReader 3.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ChipSkipper true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ChipSkipper V0.99 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete multiscan true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affy true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affycomp true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PCMG true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Feature Extraction Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Chi-square true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Annotation-Driven Clustering true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete distance calculation true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete R software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete BCRANK true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Cosmo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete F test true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MAGE-TAB inputting software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Text data set true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CSV data set true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Non-linear functional regression model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'CoCiteStats' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CodeLink Expression Analysis Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete CodeLink Expression Scanning Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Complex Estimation Algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Cyber-T true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'DEDS' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'DFP' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Discriminant Fuzzy Pattern Algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete DFW true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Digital gene expression (DGE) datasets true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'DNAcopy' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'DynDoc' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'EBImage' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'EBarrays' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Expectation-Maximization(EM) algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Empirical Bayes rule true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Expert 2100 true Marked as obsolete by Allyson Lister. 0.5 This class had no definition, and seemed incorrectly placed as an algorithm, as from its name it seemed to only be an experimental method. obsolete_FACS ( fluorescence-activated cell sorter) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete FACS data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete FARMS true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM term format_1929. Please use this term instead. obsolete_FASTA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete FC true Marked as obsolete by Allyson Lister 0.5 Obsoleted as it was a generic term where there was no way of knowing for sure which format it was - or which version the format was in. Perhaps could have been annotated and moved, but this class was only identified after a new class (http://www.ebi.ac.uk/swo/data/SWO_3000061) had been created. Please use the new class (SWO_3000061) or its versioned children instead of this obsolete class. obsolete_FCS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'FDR' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Fixed effect model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Agilent Feature Extraction Software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Firth's bias reduction procedure true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Fischer's Exact Test true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete FoxDimmicT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GACK true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GASSCO method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GC-RMA Quantification true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GEMTools 2.4 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GEO data type true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GEO Matrix Series format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GEOmetadb true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GEOquery true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GGBase true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gamma Gamma Model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GGtools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GLAD true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GLEAMS software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GMS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GOstats true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene Recommender algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GSEABase true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GSEAlm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gamma-Gamma hierarchical model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gaussian locally weighted regression true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene-Set Enrichment Analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneData Expressionist Analyst v4.0.5 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene Pix true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix 3.0.6 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix 4.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix 4100A true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix 5.0.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 3 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 5.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 6.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 6 [Axon Instruments] true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro [Axon Instruments] true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneRegionScan true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneRfold true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneSelectMMD true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneSelector true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneSpring true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneSpringGX true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneTac Analyser true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneTraffic true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 4.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenePix Pro 3.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneticsBase true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneticsDesign true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GeneticsPed true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GenomeGraphs true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GlobalAncova true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GOSemSim true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GraphAT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GraphAlignment true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete GridGrinder true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hexagon binning algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HELP true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HEM true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Heterogeneous Error Model (HEM) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hubert’s gamma true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hidden Markov Model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hidden Variable Dynamic Modelling HVDM) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HaarSeg algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hardy-Weinberg equilibrium true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Harshlight true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Heatplus true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HilbertVis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HilbertVisGUI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hypergeometric probability true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ICS-501 (version 2.3) Image Capture System true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Iteratively ReWeighted Least Squares true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete IRanges true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ITALICS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ILLUMINA data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ImaGene4.1 software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ImaGene 3.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ImageQuant true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ImageReader true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ImaGene true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Imagene v4.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Initial microarray data processing (data filtering, local normalisation and quality control) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Jaccard’s index true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Jaguar true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete KCsmart true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete KEGGSOAP true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete KEGGgraph true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete KGML true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'KLD' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Kolmogorov Smirnov rank-sum based algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete LBE true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete LC-MS data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete LMGene true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Locally Moderated Weighted-t (LMW) method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Lognormal Normal Model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Lognormal Normal with Modied Variance Model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete LPE true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete LPEadj true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete publisher role true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Langmuir Isotherm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Laplace mixture model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Library Search Algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Loess algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Logic regression true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MAANOVA v1.2 package for MATLAB true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Median Average Difference Algorithm true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM format_3161. obsolete_MAGE-ML true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MANOR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MAQC data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MIcroarray Analysis Suite true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MicroArraySuite 5.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MATLAB language true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MAVI Pro true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Multivariate correlation estimator true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Markov Chain Monte Carlo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MCR algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MCRestimate true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MEDME true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'MI' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Mutual information matrix (MIM) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MLInterfaces true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MMD true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MVCClass true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Mahalanobis distance true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MantelCorr true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MassSpecWavelet true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MeasurementError.cor true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MergeMaid true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Mfuzz true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MiPP true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Misclassification-Penalized Posteriors (MiPP) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete MicroArraySuite 4.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Mixed model equations true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'Needleman-Wunsch' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Nested Effects Models true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Nonlinear Estimation by Iterative Partial Least Squares true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OCplus true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OLIN true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OLINgui true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Optiquant true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OrderedList true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OutlierD true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Presence-Absence calls with Negative Probesets (PANP) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PAnnBuilder true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Pearson correlation estimator true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PCpheno true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PGSEA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'PLM' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PLPE true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Probe level Locally moderated Weighted median-t (PLW) method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PPC algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PROcess true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Propagation of uncertainty in microarray analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Pathways 2.01 software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Power Law Global Error Model (PLGEM) analysis method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Probe Cell Analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete PLIER (Probe Logarithmic Error Intensity Estimate) method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete QuantArray scanner software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete QuantArray, PackaardBiochip technologies true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete QuantArray version 2 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Radial basis function true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RBGL true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete R interface to boost graph library algorithm (RBGL) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RBioinf true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Random effects model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Recursive Feature Elimination (RFE) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RLMM true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Regression model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMA+ true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMA++ true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMAExpress true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMAExpress 2.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMAExpress quantification true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RMAGEML true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RNAither true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ROC true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RWebServices true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RankProd true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RbcBook1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rdbi true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RdbiPgSQL true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rdisop true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RefPlus true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Resourcerer true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rgraphviz true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Ringo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rintact true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rmagpie true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rnw true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Robust likelihood-based survival modeling true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rosetta Resolver true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete RpsiXML true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rredland true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rtreemix true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Ruuid true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete S-Score algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Serial Analysis of Gene Expression (SAGE) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SAGx true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SAM true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SAS/STAT Software, Version 8 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SBMLR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SBMLR format true Marked as obsolete by Allyson Lister 0.4 Identical to http://www.ebi.ac.uk/swo/data/SWO_3000037 obsolete_SBML file true Marked as obsolete by Allyson Lister. 0.5 'SBML model' was classed as a child of algorithm, when this clearly isn't the case. As SWO already contained 'SBML file' (to cover the data format itself), there was no need for this class at all. The one class (SBMLR) which referenced this class had the relevant axiom deleted. For referencing the SBML format, please use the class 'SBML file'. obsolete_SBML model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SDF format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SIM true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SLGI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SLqPCR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SMAP true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SNPRMA algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SNPchip true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SPIA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Semantic Similarity Measures true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SSPA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete SVDimpute algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete software developer role true Information processing is a process in which input information is analysed or transformed in order to produce information as output. James Malone Marked as obsolete by Allyson Lister. 0.4 Present both in the original file (SWO_0000393) and in the core file (SWO_0000003), and each have different identifiers. SWO_0000393 was initially created within the originalsoftwareontology.owl and later moved to swo_core.owl. SWO_0000003 was retained and SWO_0000393 deemed obsolete. Please use SWO_0000003 instead. obsolete_Information processing true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete software developer organization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete software publisher organization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 50-50 MANOVA algorithm true Marked as obsolete by Allyson Lister. 0.4 There is one EDAM html class (EDAM_format:2331) and one SWO class (SWO_0000399) within swo_data.owl. EDAM_format:2331 was retained and SWO_0000399 deemed obsolete, as EDAM_format:2331 has a better location in the hierarchy and is an imported term. All axioms belonging to SWO_0000399 were transferred to EDAM_format:2331. Please use EDAM_format:2331 (in this ontology via its full URI http://edamontology.org/format_2331) instead. obsolete_html true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ArrayExpress Bioconductor true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene list true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Clustered data set true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete R data frame true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete R language true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ScISI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ScanAlyze true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ScanArray true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ScanArray v3.1 software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete scanning software true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Scanning software G2565AA version A6.3.1 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ShortRead true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Signaling Pathway Impact Analysis (SPIA) algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Silicon Genetics Genespring true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Similarity score true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'Smith-Waterman' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Spot quantification true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Spotfinder [TIGR] true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Spotfire true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete TAS Software true Marked as obsolete by Allyson Lister. 0.4 SWO_0000434 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000016, with the label 'TIFF', is also present, and stored within swo_data.owl. SWO_3000016 was retained and SWO_0000434 deemed obsolete, as SWO_3000016 has a better location in the hierarchy. All axioms belonging to SWO_0000434 were transferred to SWO_3000016. Please use SWO_3000016 instead. obsolete_TIFF image true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete TargetSearch true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Theodore Ts’o’s true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete TypeInfo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Variance-stabilizing transformation (VST) algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete VanillaICE true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete WilcEbam true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Wilcoxon true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete XDE true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete XDotsReader true Marked as obsolete by Allyson Lister. 0.4 5. SWO_0000448 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000005 is also present within swo_data.owl. SWO_3000005 was retained and SWO_0000448 deemed obsolete, as SWO_3000005 has a better location in the hierarchy. All axioms belonging to SWO_0000448 were transferred to SWO_3000005. Please use SWO_3000005 instead. obsolete_XML true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Xba.CQV and Xba.regions true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Array Comparative Genomic Hybridization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Acuity true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affxparser true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyContam true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyImGUI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'affyPLM' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyPara true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyQCReport true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyTiling true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'affycoretools' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affyio true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete affypdnn true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete altcdfenvs true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete annaffy true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'annotate' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete data annotation true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete annotationTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Annotation data packages true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'apComplex' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete aroma.light true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete arrayMvout true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete arrayQuality true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete arrayQualityMetrics true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete arrayWoRx 2.0 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete arrayWoRx true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Associative T method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete AvgNRRs true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'beadarray' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'beadarraySNP' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'betr' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete bgafun true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete bgx true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Bitmap object true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete bioDist true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'biocDatasets' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'biocGraph' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'biocViews' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete biomaRT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Bootstrap true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'bridge' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete cdt true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'cellHTS' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'cellHTS2' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete cghMCR true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete chamber slide format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete cls true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'clusterStab' true Marked as obsolete by Allyson Lister. 0.4 The original label for this class, 'Clustering algorithm', was used in two separate class URIs. The first was SWO_0000500, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_algorithms.owl and is an import from OntoDM (OntoDM_170075). As the SWO class contains no annotation beyond its label, and because OntoDM has more structure surrounding its algorithm classes, the OntoDM class was retained and the SWO class was deemed obsolete. The 6 usages of the SWO class were refactored to reference the OntoDM term and then the SWO class was marked as obsolete. Please use OntoDM_170075 instead. obsolete_Clustering algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'codelink' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete dataset comparison true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Concordance true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete convert true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete copa true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete cosmo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete cosmoGUI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete covdesc file true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete database creation true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete crlmm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ctc true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete dChip true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete daMA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete .data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete dcf true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete design file true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'diffGeneAnalysis' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'domainsignatures' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'dualKS' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete dyebias true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Dynamic programming algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ecolitk true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete edd true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'edgeR' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete exonmap true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'explorase' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'externalVector' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete f-test true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete factDesign true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete fbat true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete fdrame true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flagme true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowClust true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowCore true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowFlowJo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowQ true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowStats true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowUtils true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete flowViz true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gaga true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'gaggle' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gcRMA quantification true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gcrma true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gct true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'genArise' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gene2pathway true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete geneRecommender true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene array analysis algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gene expression analysis true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Gene expression dataset true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete genefilter true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete genemeta true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete geneplotter true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete genomeIntervals true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM format_2305. obsolete_gff format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Global test true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete globaltest true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gmt format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete goProfiles true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete goTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gpls true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gpr format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete graph true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gtr true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete gxl format true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM data_1636. obsolete_Heatmap true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete hexbin true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hierarchical clustering true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete hopach true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete HTML report true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Hypergeometric enrichment true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete hypergraph true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Icens true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete idiogram true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalence with EDAM data_2968 obsolete_Image true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete impute true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete iterativeBMA true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete iterativeBMAsurv true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Iterative local regression and model selection true Marked as obsolete by Allyson Lister. 0.4 The original label for this class, .java file, was used in two separate class URIs. The first was SWO_0000585, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_data.owl and is SWO_3000034. As SWO_3000034 is properly modelled as a child of 'Programming language format' this class was retained and SWO_0000585 deemed obsolete. The usages of SWO_0000585 were refactored to reference 3. SWO_3000034, and SWO_0000585 was marked as obsolete. Please use SWO_3000034 instead. obsolete_.java file true Marked as obsolete by Allyson Lister. 0.4 SWO_0000586 (jpeg) was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000017, with the label 'JPEG', is also present, and stored within swo_data.owl. SWO_3000017 was retained and SWO_ 0000586 deemed obsolete, as SWO_3000017 has a better location in the hierarchy. All axioms belonging to SWO_0000586 were transferred to SWO_3000017. Please use SWO_3000017 instead. obsolete_jpeg true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete k-cores true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete k-means true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete k-nearest neighbour classification true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete keggorth true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete lapmix true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Likelihood method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete limma true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete limmaGUI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Linear modelling true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete lma true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Local-pooled-error true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete log file true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete logicFS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete logicFS dataset true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete logitT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Logit-t algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete lumi true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete maCorrPlot true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete maDB true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete maSigPro true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete maanova true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete macat true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete made4 true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete maigesPack true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete makePlatformDesign true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete makecdfenv true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete marray true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 'MAS5' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete mas5 format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete matchprobes true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete mdqc true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete M-estimation regression true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete metaArray true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Meta data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete metahdep true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete miRNApath true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete microRNA true Marked as obsolete by Allyson Lister. Obsoleted after the 0.4 release. Equivalent to EDAM class data_2603. obsolete_Microarray data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete minet true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete mrnet algorithm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Multinomial probit regression with Gaussian Process priors true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Multiple testing true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Multivariate t mixture models true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete multtest true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Negative binomial distribution true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete nem true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Neural networks models true Marked as obsolete by Allyson Lister Obsoleted after the 0.4 release. Equivalence with EDAM format_1910. obsolete_newick true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete nnNorm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete nudge true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete occugene true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete oligo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete oligoClasses true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete OMICS data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete oneChannelGUI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ontoTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pair file true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pamr true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete panp true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete parody true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete parse true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pathRender true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pcaMethods true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pcot2 true Marked as obsolete by Allyson Lister. 0.4 SWO_0000652 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000015 is also present and stored within swo_data.owl. SWO_3000015 was retained and SWO_0000652 deemed obsolete, as SWO_3000015 has a better location in the hierarchy. All axioms belonging to SWO_0000652 were transferred to SWO_3000015. Please use SWO_3000015 instead. obsolete_pdf true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pdInfoBuilder true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pdmclass true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pedigree data file true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pgUtils true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pickgene true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete pkgDepTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete plgem true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete plier true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Graph plot true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete plw true Marked as obsolete by Allyson Lister. 0.4 SWO_0000663 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000018 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000663 deemed obsolete, as SWO_3000018 has a better location in the hierarchy. All axioms belonging to SWO_0000663 were transferred to SWO_3000018 . Please use SWO_3000018 instead. obsolete_png true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Position weight matrix (PWM ) true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ppiStats true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete prada true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete preprocessCore true Marked as obsolete by Allyson Lister. 0.4 An equivalence statement is already marked for these two classes. Removed equivalence statement as the location of the obsoleted class has been changed. SWO_0000668 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000024 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000668 deemed obsolete, as SWO_3000024 has a better location in the hierarchy. All axioms belonging to SWO_0000668 were transferred to SWO_3000024. Please use SWO_3000024 instead. obsolete_ps true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete puma true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete qPCR data true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete qpcrNorm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete qpgraph true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Quantile normalization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Quantile regression techniques true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete quantsmooth true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete qvalue true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rHVDM true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rMAT true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rama true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rank-invariant set normalization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Rank product non-parametric method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete .raw files true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rbsurv true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rda true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete reb true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rflowcyt true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete .rma format true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rsbml true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete rtracklayer true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete safe true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sagenhaft true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete seqLogo true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sigPathway true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete siggenes true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Sim method true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete simpleaffy true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete simulatorAPMS true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sizepower true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete xmapbridge true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete snapCGH true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete snpMatrix true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete spikeLI true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete spkTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete splicegear true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete splots true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete spotSegmentation true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sproc true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sqlite true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete sscore true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete ssize true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete stam true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Statistical tests true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete stepNorm true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete 't-test' true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete tilingArray true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete timecourse true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete tkWidgets true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete topGO true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete tspair true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete twilight true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete Two-stage measurement error model true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete vbmp true http://purl.obolibrary.org/obo/OBI_0200111 1.7 AL 25.9.19: Redundant with http://purl.obolibrary.org/obo/OBI_0200111 obsolete data visualization true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete vsn true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete weaver true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete webbioc true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete widgetTools true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete xcms true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete xps true 1.7 AL 1.10.2019: Improperly formatted IRI replaced with correct one. Please see https://github.com/allysonlister/swo/issues/10 for more information. obsolete yaqcaffy true Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations. James Malone Modified in parts from https://en.wikipedia.org/wiki/Software Robert Stevens AL 7.9.22: There are some reasoning oddities associated with marking IAO and SWO software as equivalent; once these are sorted out, the equivalence statement will take the place of this current parent-child relationship. software http://purl.obolibrary.org/obo/IAO_0000010 A licence is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the licence. Modified from http://en.wikipedia.org/wiki/Software_license James Malone licence software license Information processing is a process in which input information is analysed or transformed in order to produce information as output. James Malone http://purl.obolibrary.org/obo/OBI_0200000 1.7 AL 18.9.2019: This class is identical (based on its definition) with OBI 'data transformation' and is no longer required. obsolete information processing true http://office.microsoft.com/ 2007-01-30T0:00:00 Microsoft Excel 2007 is a spreadsheet editing and viewing tool. Microsoft Excel 2007 http://www.mathworks.com/products/matlab/ MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran http://www.mathworks.com/products/matlab/?s_cid=SA_trafrefpai_MLipspot_Doc_bioinfo_MATLAB Nandini Badarinarayan MATLAB http://protege.stanford.edu/ Protege 4 http://www.omnigroup.com/products/omnioutliner/ OmniOutliner is commercial outlining software for Mac OS X produced by The Omni Group OmniOutliner Racket is a Scheme-based language interpreter and programming environment Racket http://www.kakadusoftware.com Kakadu WordStar http://www.jetbrains.com/idea/ IntelliJ IDEA is a commercial Java IDE for developing software. IntelliJ IntelliJ IDEA http://www.java.com Java http://www.copasi.org COPASI is a software