{ "graphs" : [ { "id" : "http://purl.obolibrary.org/obo/omrse.json", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Barry Smith" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Chris Stoeckert" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Daniel Welch" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Jie Zheng" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "John W. Judkins" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sam Smith" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Selja Seppälä" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William D. Duncan" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Yongqun He" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Shariq Tariq" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Swetha Garimalla" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "William Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/description", "val" : "The Ontology for Modeling and Representation of Social Entities (OMRSE) is an OBO Foundry ontology that represents the various entities that arise from human social interactions, such as social acts, social roles, social groups, and organizations." }, { "pred" : "http://purl.org/dc/elements/1.1/title", "val" : "Ontology for Modeling and Representation of Social Entities" }, { "pred" : "http://purl.org/dc/terms/license", "val" : "https://creativecommons.org/licenses/by/4.0/" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#comment", "val" : "This ontology grew out of efforts to represent the reality underlying the demographic information required by the US federal government's \"meaningful use\" criteria for electronic medical records and a presentation by Dr. William Hogan at the Electronic Health Record of the Future conference in Buffalo, NY http://ontology.buffalo.edu/EHR/Demographics_Hogan_Buffalo_2010_09_22.ppt" }, { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", "val" : "2024-03-22" } ], "version" : "http://purl.obolibrary.org/obo/omrse/releases/2024-03-22/omrse.json" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "example to be eventually removed" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000078", "lbl" : "curation status specification", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "curation status specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Bill Bug" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000266" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000103", "lbl" : "failed exploratory term", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "failed exploratory term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000225", "lbl" : "obsolescence reason specification", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "obsolescence reason specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" } ] } }, { "id" : "http://www.w3.org/2002/07/owl#Thing" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000120", "lbl" : "metadata complete", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "metadata complete" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000121", "lbl" : "organizational term", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "organizational term" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", "lbl" : "ready for release", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ready for release" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000123", "lbl" : "metadata incomplete", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "metadata incomplete" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000124", "lbl" : "uncurated", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "uncurated" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", "lbl" : "pending final vetting", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "pending final vetting" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "placeholder removed" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "terms merged" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000228", "lbl" : "term imported", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term imported" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000229", "lbl" : "term split", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term split" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000410", "lbl" : "universal", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "universal" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000409", "lbl" : "denotator type", "type" : "CLASS", "meta" : { "definition" : { "val" : "A denotator type indicates how a term should be interpreted from an ontological perspective." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "denotator type" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Barry Smith, Werner Ceusters" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000420", "lbl" : "defined class", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "defined class" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000421", "lbl" : "named class expression", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "named class expression" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000423", "lbl" : "to be replaced with external ontology term", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Terms with this status should eventually replaced with a term from another ontology." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "to be replaced with external ontology term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", "lbl" : "requires discussion", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "requires discussion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0001000", "lbl" : "out of scope", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "http://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0001002", "lbl" : "domain entity does not exist", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "The term was added to the ontology on the assumption it was a valid domain entity, but it turns out the entity does not exist in reality." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This obsolesence reason should be used conservatively. For example: Obsoleting class that describes a breed of cow based on a record in an existing database, that was later retracted as faulty (breed does not exist). Do not use this term to obsolete a historic concept (that was once valid, but not anymore). " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "http://orcid.org/0000-0002-4142-7153" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/136" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "https://orcid.org/0000-0002-4142-7153" } ] } }, { "id" : "http://purl.obolibary.org/obo/IAO_0021001", "lbl" : "obsolete_deontic document act", "type" : "CLASS", "meta" : { "definition" : { "val" : "A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my filling in an immigration form, a judge's signing and stamping a court order" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000226" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000008", "lbl" : "software development", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process that has specified output a software product and that involves the creation of source code." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://en.wikipedia.org/wiki/Software_development" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A planned process resulting in a software product involving the creation of source code." } ] } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000032", "lbl" : "count", "type" : "CLASS", "meta" : { "definition" : { "val" : "A measurement datum that is the output of counting." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A measurement datum that is the output of counting." } ] } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000033", "lbl" : "counting", "type" : "CLASS", "meta" : { "definition" : { "val" : "The planned process of finding the number of elements in a finite set of objects." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://en.wikipedia.org/wiki/Counting" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "The planned process of finding the number of elements in a finite set of objects." } ] } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000480", "lbl" : "geographical migration of organism", "type" : "CLASS", "meta" : { "definition" : { "val" : "A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A behavior of one or more organisms that is characterized by the displacement from one geographic region to some target geographic region, and is the realization of either a biological function or (a concretization of) an objective specification." } ] } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000522", "lbl" : "source code repository", "type" : "CLASS", "meta" : { "definition" : { "val" : "A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc." }, "comments" : [ "Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "software source code version control repository" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000524", "lbl" : "compiling software", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process that converts human-written or curated software into a machine-executable or interpretable set of instructions." }, "comments" : [ "It's compiling \"software\" (scare quotes) and not \"source code\" because you can compile Java bytecode to machine code, and Java bytecode is not technically \"source code\". Compiling source code would be a subclass of this class (as would compiling Java bytecode, etc.).", "Source code can be automatically generated to some extent, but we're assuming humans still curate it minimally. Also, in the case of Java and its JVM, it's machine interpretable instructions, not directly executable. Ditto for other languages with intermediate form like Java byte code." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "process of compiling software" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000532", "lbl" : "human travel", "type" : "CLASS", "meta" : { "definition" : { "val" : "A geographical migration of an organism belonging to the species Homo sapiens." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/APOLLO_SV_00000796", "lbl" : "dataset creating", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process that has a data set as its specified output." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "creating a data set" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data set creation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "dataset creation" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000001", "lbl" : "entity", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "entity" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Julius Caesar" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Verdi’s Requiem" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the Second World War" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "your body mass index" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", "lbl" : "continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "continuant" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Continuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000003", "lbl" : "occurrent", "type" : "CLASS", "meta" : { "definition" : { "val" : "An entity that has temporal parts and that happens, unfolds or develops through time." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "occurrent" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Occurrent" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000004", "lbl" : "independent continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "comments" : [ "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "ic" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "IndependentContinuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a chair" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a heart" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a leg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a molecule" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a spatial region" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an atom" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an orchestra." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the bottom right portion of a human torso" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the interior of your mouth" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000006", "lbl" : "spatial region", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "s-region" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "SpatialRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: Spatial regions do not participate in processes." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000008", "lbl" : "temporal region", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "t-region" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "TemporalRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000009", "lbl" : "two-dimensional spatial region", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "2d-s-region" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "TwoDimensionalSpatialRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an infinitely thin plane in space." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the surface of a sphere-shaped part of space" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000011", "lbl" : "spatiotemporal region", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "st-region" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "SpatiotemporalRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the spatiotemporal region occupied by a human life" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the spatiotemporal region occupied by a process of cellular meiosis." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the spatiotemporal region occupied by the development of a cancer tumor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every spatiotemporal region occupies_spatiotemporal_region itself." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000015", "lbl" : "process", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "comments" : [ "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "process" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Process" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a process of cell-division, \\ a beating of the heart" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a process of meiosis" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a process of sleeping" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the course of a disease" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the flight of a bird" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the life of an organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "your process of aging." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000016", "lbl" : "disposition", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "disposition" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Disposition" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an atom of element X has the disposition to decay to an atom of element Y" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "certain people have a predisposition to colon cancer" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "children are innately disposed to categorize objects in certain ways." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000017", "lbl" : "realizable entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "realizable" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "RealizableEntity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the disposition of this piece of metal to conduct electricity." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the disposition of your blood to coagulate" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of your reproductive organs" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of being a doctor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of this boundary to delineate where Utah and Colorado meet" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000018", "lbl" : "zero-dimensional spatial region", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "0d-s-region" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "ZeroDimensionalSpatialRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000019", "lbl" : "quality", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "quality" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Quality" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the ambient temperature of this portion of air" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the color of a tomato" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the length of the circumference of your waist" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the mass of this piece of gold." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the shape of your nose" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the shape of your nostril" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000020", "lbl" : "specifically dependent continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "sdc" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "SpecificallyDependentContinuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "of one-sided specifically dependent continuants: the mass of this tomato" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the disposition of this fish to decay" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of this heart: to pump blood" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the mutual dependence of proton donors and acceptors in chemical reactions [79" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the pink color of a medium rare piece of grilled filet mignon at its center" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of being a doctor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the shape of this hole." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the smell of this portion of mozzarella" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000023", "lbl" : "role", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "role" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the priest role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of a boundary to demarcate two neighboring administrative territories" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of a building in serving as a military target" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of a stone in marking a property boundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role of subject in a clinical trial" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the student role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000024", "lbl" : "fiat object part", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "fiat-object-part" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "FiatObjectPart" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the FMA:regional parts of an intact human body." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the Western hemisphere of the Earth" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the division of the brain into regions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the division of the planet into hemispheres" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the dorsal and ventral surfaces of the body" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the upper and lower lobes of the left lung" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000026", "lbl" : "one-dimensional spatial region", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "1d-s-region" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "OneDimensionalSpatialRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an edge of a cube-shaped portion of space." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000027", "lbl" : "object aggregate", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "object-aggregate" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "ObjectAggregate" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a collection of cells in a blood biobank." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a swarm of bees is an aggregate of members who are linked together through natural bonds" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a symphony orchestra" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "defined by fiat: the aggregate of members of an organization" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "defined through physical attachment: the aggregate of atoms in a lump of granite" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "defined via attributive delimitations such as: the patients in this hospital" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the aggregate of bearings in a constant velocity axle joint" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the aggregate of blood cells in your body" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the nitrogen atoms in the atmosphere" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the restaurants in Palo Alto" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "your collection of Meissen ceramic plates." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000028", "lbl" : "three-dimensional spatial region", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "3d-s-region" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "ThreeDimensionalSpatialRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a cube-shaped region of space" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a sphere-shaped region of space," }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000029", "lbl" : "site", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "site" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Site" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Manhattan Canyon)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a hole in the interior of a portion of cheese" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a rabbit hole" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an air traffic control region defined in the airspace above an airport" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the Grand Canyon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the Piazza San Marco" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the cockpit of an aircraft" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the hold of a ship" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the interior of a kangaroo pouch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the interior of the trunk of your car" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the interior of your bedroom" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the interior of your office" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the interior of your refrigerator" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the lumen of your gut" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "your left nostril (a fiat part – the opening – of your left nasal cavity)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000030", "lbl" : "object", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "object" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Object" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "atom" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "cell" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "cells and organisms" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "engineered artifacts" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "grain of sand" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "molecule" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "organelle" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "planet" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "solid portions of matter" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "star" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: an object is a maximal causally unified material entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001])" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000031", "lbl" : "generically dependent continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "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])" }, "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "gdc" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "GenericallyDependentContinuant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000034", "lbl" : "function", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "function" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "Function" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of a hammer to drive in nails" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of a heart pacemaker to regulate the beating of a heart through electricity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the function of amylase in saliva to break down starch into sugar" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000035", "lbl" : "process boundary", "type" : "CLASS", "meta" : { "definition" : { "val" : "p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "p-boundary" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "ProcessBoundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the boundary between the 2nd and 3rd year of your life." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000038", "lbl" : "one-dimensional temporal region", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "1d-t-region" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "OneDimensionalTemporalRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the temporal region during which a process occurs." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000040", "lbl" : "material entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "material" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "MaterialEntity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a flame" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a forest fire" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a human being" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a hurricane" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a photon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a puff of smoke" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a sea wave" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a tornado" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an aggregate of human beings." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an energy wave" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "an epidemic" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the undetached arm of a human being" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(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] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", "lbl" : "part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a core relation that holds between a part and its whole" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_gp2term", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is part of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my brain is part of my body (continuant parthood, two material entities)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this day is part of this year (occurrent parthood)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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.)\n\nA 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'." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "part_of" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000002" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000003" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000004" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000017" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000019" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000020" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0040042", "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:PartOf" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.obofoundry.org/ro/#OBO_REL:part_of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Part_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", "lbl" : "has part", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a core relation that holds between a whole and its part" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has part" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my body has part my brain (continuant parthood, two material entities)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this year has part this day (occurrent parthood)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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.)\n\nA 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'." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_part" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000054", "lbl" : "realized in", "type" : "PROPERTY", "meta" : { "comments" : [ "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" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "realized in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this disease is realized in this disease course" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this fragility is realized in this shattering" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this investigator role is realized in this investigation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is realized by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "realized_in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "[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])" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000055", "lbl" : "realizes", "type" : "PROPERTY", "meta" : { "comments" : [ "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" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "realizes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this disease course realizes this disease" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this investigation realizes this investigator role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this shattering realizes this fragility" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "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])" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000062", "lbl" : "preceded by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "preceded by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is preceded by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preceded_by" }, { "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000063", "lbl" : "precedes", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "precedes" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000066", "lbl" : "occurs in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, "comments" : [ "Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant" ], "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "occurs in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "occurs_in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "unfolds in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "unfolds_in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Occurs_in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000067", "lbl" : "contains process", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "site of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000140", "lbl" : "continuant fiat boundary", "type" : "CLASS", "meta" : { "definition" : { "val" : "b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "cf-boundary" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "ContinuantFiatBoundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000601", "val" : "Every continuant fiat boundary is located at some spatial region at every time at which it exists" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "immaterial" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "ImmaterialEntity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000142", "lbl" : "one-dimensional continuant fiat boundary", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "1d-cf-boundary" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "OneDimensionalContinuantFiatBoundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The Equator" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "all geopolitical boundaries" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "all lines of latitude and longitude" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the median sulcus of your tongue" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000144", "lbl" : "process profile", "type" : "CLASS", "meta" : { "definition" : { "val" : "b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "process-profile" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "ProcessProfile" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000145", "lbl" : "relational quality", "type" : "CLASS", "meta" : { "definition" : { "val" : "b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "r-quality" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "RelationalQuality" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a marriage bond, an instance of requited love, an obligation between one person and another." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000146", "lbl" : "two-dimensional continuant fiat boundary", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "2d-cf-boundary" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "TwoDimensionalContinuantFiatBoundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000147", "lbl" : "zero-dimensional continuant fiat boundary", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "0d-cf-boundary" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "ZeroDimensionalContinuantFiatBoundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the geographic North Pole" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the point of origin of some spatial coordinate system." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000148", "lbl" : "zero-dimensional temporal region", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "0d-t-region" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "ZeroDimensionalTemporalRegion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a temporal region that is occupied by a process boundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "right now" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the moment at which a child is born" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the moment at which a finger is detached in an industrial accident" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the moment of death." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "temporal instant." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000602", "val" : "(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] " }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000179", "lbl" : "BFO OWL specification label", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Really of interest to developers only" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000180", "lbl" : "BFO CLIF specification label", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Really of interest to developers only" } ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000182", "lbl" : "history", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/BFO_0000179", "val" : "history" }, { "pred" : "http://purl.obolibrary.org/obo/BFO_0000180", "val" : "History" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/bfo.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/FMA_49443", "lbl" : "Anatomical cluster", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/FMA_55457", "lbl" : "vocal fold", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/FMA_64854", "lbl" : "Subdivision of larynx", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/FMA_64989", "lbl" : "Heterogeneous cluster", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/FMA_67135", "lbl" : "Anatomical structure", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/FMA_67165", "lbl" : "Material anatomical entity", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/GEO_000000400", "lbl" : "governmental organization", "type" : "CLASS", "meta" : { "definition" : { "val" : "An organization that governs the people living in a particular geographical region or aggregate of geographical regions. The geographical region it governs can change over time (such as the westward expansion of the United States and the addition of Hawaii). \n\nNote: this definition was taken over from \"geopolitical organization\"." }, "comments" : [ "IMPORTANT: The label \"geopolitical organization\" was previously used for OMRSE_00000044 (governmental organization). \"geopoli organization\" is a label for a new and different class." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Amanda Hicks" } ] } }, { "id" : "http://purl.obolibrary.org/obo/GO_0003674", "lbl" : "molecular_function", "type" : "CLASS", "meta" : { "definition" : { "val" : "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.", "xrefs" : [ "GOC:pdt" ] }, "comments" : [ "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." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecular function" } ] } }, { "id" : "http://purl.obolibrary.org/obo/GO_0007610", "lbl" : "behavior", "type" : "CLASS", "meta" : { "definition" : { "val" : "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity.", "xrefs" : [ "GOC:ems", "GOC:jl", "ISBN:0395448956", "PMID:20160973" ] }, "comments" : [ "1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews.\n2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis)." ], "xrefs" : [ { "val" : "Wikipedia:Behavior" } ] } }, { "id" : "http://purl.obolibrary.org/obo/GO_0008150", "lbl" : "biological_process", "type" : "CLASS", "meta" : { "definition" : { "val" : "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. 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.", "xrefs" : [ "GOC:pdt" ] }, "comments" : [ "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." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "biological process" }, { "pred" : "hasExactSynonym", "val" : "physiological process" }, { "pred" : "hasRelatedSynonym", "val" : "single organism process" }, { "pred" : "hasRelatedSynonym", "val" : "single-organism process" } ], "xrefs" : [ { "val" : "Wikipedia:Biological_process" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "jl" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2012-09-19T15:05:24Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/GO_0016301", "lbl" : "kinase activity", "type" : "CLASS", "meta" : { "definition" : { "val" : "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.", "xrefs" : [ "ISBN:0198506732" ] }, "comments" : [ "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." ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "phosphokinase activity" } ], "xrefs" : [ { "val" : "Reactome:R-HSA-6788855" }, { "val" : "Reactome:R-HSA-6788867" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000001", "lbl" : "conditional specification", "type" : "CLASS", "meta" : { "definition" : { "val" : "A directive information entity that specifies what should happen if the trigger condition is fulfilled." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "conditional specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PlanAndPlannedProcess Branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI branch derived" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000349" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000003", "lbl" : "measurement unit label", "type" : "CLASS", "meta" : { "definition" : { "val" : "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "measurement unit label" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples of measurement unit labels are liters, inches, weight per volume." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: provenance: a term measurement unit was\nproposed for OBI (OBI_0000176) , edited by Chris Stoeckert and\nCristian Cocos, and subsequently moved to IAO where the objective for\nwhich the original term was defined was satisfied with the definition\nof this, different, term." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000004", "lbl" : "has measurement value", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000005", "lbl" : "objective specification", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "objective specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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.\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Answers the question, why did you do this experiment?" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Barry Smith" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jennifer Fostel" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "goal specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI Plan and Planned Process/Roles Branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000217" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000006", "lbl" : "narrative object", "type" : "CLASS", "meta" : { "definition" : { "val" : "A narrative object is an information content entity that is a set of propositions." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "narrative object" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples of narrative objects are reports, journal articles, and patents submission." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000013" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000007", "lbl" : "action specification", "type" : "CLASS", "meta" : { "definition" : { "val" : "A directive information entity that describes an action the bearer will take." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Pour the contents of flask 1 into flask 2" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI Plan and Planned Process branch" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000008", "lbl" : "obsolete_artifact", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000009", "lbl" : "datum label", "type" : "CLASS", "meta" : { "definition" : { "val" : "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" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "datum label" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "GROUP: IAO" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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. \n" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000010", "lbl" : "software", "type" : "CLASS", "meta" : { "definition" : { "val" : "Software is a plan specification composed of a series of instructions that can be \ninterpreted by or directly executed by a processing unit." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "software" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP: OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000012", "lbl" : "obsolete2_digital entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "obsolete_digital entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\n\nSuperclass was 'digitial quality'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000261" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000013", "lbl" : "journal article", "type" : "CLASS", "meta" : { "definition" : { "val" : "A report that is published in a journal." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "journal article" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000159" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000015", "lbl" : "information carrier", "type" : "CLASS", "meta" : { "definition" : { "val" : "A quality of an information bearer that imparts the information content" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "information carrier" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000017", "lbl" : "model number", "type" : "CLASS", "meta" : { "definition" : { "val" : "A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "model number" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "manufactered items may have more than one model number, sometimes by rebranding, or because companies are sold and the products issued new model numbers" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person: Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000018", "lbl" : "obsolete_material_entity", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000226" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000019", "lbl" : "obsolete2_binary digital entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "binary digital entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "MS Word document, ZIP file, DICOM file, JPEG file" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nSuperclass was 'digital entity'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "digital_entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000244" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000024", "lbl" : "obsolete_unit of measure", "type" : "CLASS", "meta" : { "definition" : { "val" : "a unit of measure is the quality of some material entity compared to which another quality is some multiple of." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The length of a ruler." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000025", "lbl" : "programming language", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "programming language" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "R, Perl, Java" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000058" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000027", "lbl" : "data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Data items include counts of things, analyte concentrations, and statistical summaries." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jonathan Rees" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000028", "lbl" : "symbol", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "symbol" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a serial number such as \"12324X\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a stop sign" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a written proper name such as \"OBI\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "20091104, MC: this needs work and will most probably change" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: James A. Overton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jonathan Rees" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "based on Oxford English Dictionary" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000029", "lbl" : "numeral", "type" : "CLASS", "meta" : { "definition" : { "val" : "A symbol that denotes a number." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "numeral" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jonathan Rees" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000030", "lbl" : "information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A generically dependent continuant that is about some thing." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "information content entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples of information content entites include journal articles, data, graphical layouts, and graphs." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000142" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000031", "lbl" : "integer numeral", "type" : "CLASS", "meta" : { "definition" : { "val" : "A numeral that denotes an integer" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "integer numeral" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jonathan Rees" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000032", "lbl" : "scalar measurement datum", "type" : "CLASS", "meta" : { "definition" : { "val" : "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "10 feet. 3 ml." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in\nthis case we explicitly refer to the singular form" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000033", "lbl" : "directive information entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity whose concretizations indicate to their bearer how to realize them in a process." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bjoern Peters" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000034", "lbl" : "time trigger", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "time trigger" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000124" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PlanAndPlannedProcess Branch" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000035", "lbl" : "obsolete_study interpretation", "type" : "CLASS", "meta" : { "definition" : { "val" : "A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "obsolete_study interpretation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: definition was \"A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application.\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The obsoleting of narrative object required a modest change in the definition of this term. Circularity with \"interpretation... interprets\" has been removed, using \"about the implications\" instead." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Lawrence Hunter" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jennifer Fostel" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "conclusion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000005" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000037", "lbl" : "dot plot", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "dot plot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Dot plot of SSC-H and FSC-H." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000002" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Allyson Lister" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000038", "lbl" : "graph", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "graph" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Allyson Lister" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000240" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000039", "lbl" : "has measurement unit label", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000047", "lbl" : "obsolete2_text based digital entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A text based digital entity is a digital entity that is encoded so that it only contains text characters." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "text based digital entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "XML file, C++ source code file" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nsuperclass was 'digital document'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "digital_entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000132" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000055", "lbl" : "rule", "type" : "CLASS", "meta" : { "definition" : { "val" : "A rule is an executable which guides, defines, restricts actions." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "rule" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "example to be added" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MSI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PRS" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0500021" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "PRS" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000057", "lbl" : "contour plot", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "contour plot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Contour plot of SSC-H, FSC-H, and FL1-H." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000002" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "generically_dependent_continuants" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Allyson Lister" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000246" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:Flow Cytometry community" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000059", "lbl" : "obsolete2_report figure", "type" : "CLASS", "meta" : { "definition" : { "val" : "A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "report figure" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000124" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Replaced by defined version of figure" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Allyson Lister" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000027" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000064", "lbl" : "algorithm", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "algorithm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Philippe Rocca-Serra" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PlanAndPlannedProcess Branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000270" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000065", "lbl" : "software interpreter", "type" : "CLASS", "meta" : { "definition" : { "val" : "A software interpreter is a software application that executes some specified input software." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "software interpreter" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "R program, Perl interpreter, Java virtual machine" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000199" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000079", "lbl" : "density plot", "type" : "CLASS", "meta" : { "definition" : { "val" : "A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "density plot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Density plot of SSC-H and FSC-H." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000002" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Allyson Lister" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000179" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:Flow Cytometry community" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000088", "lbl" : "report", "type" : "CLASS", "meta" : { "definition" : { "val" : "A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "report" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence \"Topic of the report is on \nsomething that has completed.\" Should it be restricted to those things \nthat are completed? For example, a progress report is (usually) about \nsomething that definitely has *not* been completed, or may include \n(only) projections. I think the definition would not suffer if the \nwhole sentence is deleted." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP: OBI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000099" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000091", "lbl" : "obsolete_report element", "type" : "CLASS", "meta" : { "definition" : { "val" : "A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "report element" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: needs some more work (clarify relations)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: was report display element with definition: A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity' and 'figure'. Alan restored as there are OBI dependencies and this merits further discussion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Replaced by textual entity and figure" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Allyson Lister" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000001" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000093", "lbl" : "obsolete2_binary executable", "type" : "CLASS", "meta" : { "definition" : { "val" : "Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "binary executable" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nsuperclass was 'digital entity'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Jennifer Fostel" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000222" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000096", "lbl" : "source code module", "type" : "CLASS", "meta" : { "definition" : { "val" : "A source code module is a directive information entity that specifies, using a programming language, some algorithm." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "source code module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000039" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000097", "lbl" : "obsolete_report table", "type" : "CLASS", "meta" : { "definition" : { "val" : "A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "report table" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000002" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'textual entity table'. Alan restored as there are OBI dependencies and this merits further discussion" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Allyson Lister" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000265" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000098", "lbl" : "data format specification", "type" : "CLASS", "meta" : { "definition" : { "val" : "A data format specification is the information content borne by the document published defining the specification.\nExample: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data format specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-03-16: provenance: term imported from OBI_0000187, which had original definition \"A data format specification is a plan which organizes\ninformation. Example: The ISO document specifying what encompasses an\nXML document; The instructions in a XSD file\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PlanAndPlannedProcess Branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI branch derived" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000187" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000100", "lbl" : "data set", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data set" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Allyson Lister" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000042" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000101", "lbl" : "image", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "image" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Allyson" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000030" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000102", "lbl" : "data about an ontology part", "type" : "CLASS", "meta" : { "definition" : { "val" : "Data about an ontology part is a data item about a part of an ontology, for example a term" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data about an ontology part" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000104", "lbl" : "plan specification", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "comments" : [ "2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2014-03-31: A plan specification can have other parts, such as conditional specifications." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Clint Dowland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI Plan and Planned Process branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000344" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000105", "lbl" : "obsolete2_digital document", "type" : "CLASS", "meta" : { "definition" : { "val" : "A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "digital document" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4\nsuperclass was 'digial entity'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Jennifer Fostel" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000195" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000109", "lbl" : "measurement datum", "type" : "CLASS", "meta" : { "definition" : { "val" : "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "measurement datum" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2/2/2009 is_specified_output of some assay?" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000305" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "group:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000111", "lbl" : "editor preferred term", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "editor preferred term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000112", "lbl" : "example of usage", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "example of usage" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000113", "lbl" : "in branch", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An annotation property indicating which module the terms belong to. This is currently experimental and not implemented yet." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "in branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "GROUP:OBI" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI_0000277" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000114", "lbl" : "has curation status", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has curation status" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Bill Bug" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", "lbl" : "textual definition", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "definition" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe 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.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour 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. \n\nOn the specifics of the proposed definition:\n\nWe 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. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe 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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe 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.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour 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. \n\nOn the specifics of the proposed definition:\n\nWe 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. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe 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. " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000116", "lbl" : "editor note", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "editor note" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000117", "lbl" : "term editor", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term editor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000118", "lbl" : "alternative term", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "comments" : [ "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)." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "alternative label" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "OBO Operations committee" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000119", "lbl" : "definition source", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "definition source" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Daniel Schober" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI:" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000128", "lbl" : "obsolete_identifier", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000121" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.\n\nNote: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group \"identifiying\" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000226" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000129", "lbl" : "version number", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "version number" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "GROUP: IAO" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000131", "lbl" : "serial number", "type" : "CLASS", "meta" : { "definition" : { "val" : "A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "serial number" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "GROUP: IAO" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000132", "lbl" : "lot number", "type" : "CLASS", "meta" : { "definition" : { "val" : "A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "lot number" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "GROUP: IAO" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "batch number" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000135", "lbl" : "obsolete_specifically denotes", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c specifically denotes r =def \nr is a portion of reality\n& c is a particular quality\n& c depends specifically on some independent continuant b \n& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. \n\nMarked means there is a changed or additional quality of the bearer - the quality is the information carrier.\n\nCase 1\nMemory trace as mark created when reading some description of some friend. The trace can denote.\n\nCase 2\nPattern of ink arrayed on paper as mark when writing down a friend's name\n\nCase 3\nPattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink.\n\nHere the ink + paper is the independent continuant and the carrier is the pattern in the ink.\n\nc = pattern in the ink\nb = paper + ink\nr = friend" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "8/6/2009 Alan Ruttenberg: The suggestions is to deprecate specific and generically denotes in favor of a single denote relationship that corresponds to the generic sense" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000136", "lbl" : "is about", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A (currently) primitive relation that relates an information artifact to an entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "This document is about information artifacts and their representations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome 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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000140", "lbl" : "setting datum", "type" : "CLASS", "meta" : { "definition" : { "val" : "A settings datum is a datum that denotes some configuration of an instrument." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2/3/2009 Feedback from OBI\n\nThis should be a \"setting specification\". There is a question of whether it is information about a realizable or not.\n\nPro other specification are about realizables.\nCons sometimes specifies a quality which is not a realizable." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Alan grouped these in placeholder for the moment. Name by analogy to measurement datum." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000141", "lbl" : "obsolete_digital quality", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "3/22/2009 Alan Ruttenberg, obsoleted per http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Need to rework digital entity. Digital quality was suggested by Barry." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000142", "lbl" : "mentions", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An information artifact IA mentions an entity E exactly when it has a component/part that denotes E" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "7/6/2009 Alan Ruttenberg. P4 RC1 munges our GCI so remove it for now: mentions some entity equivalentTo has_part some ('generically denotes' some entity)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "7/6/2009 Alan Ruttenberg: Add this relation following conversation with Jonathan Rees that N&S GCI for is_about was too strong. Really it was simply sufficient. To effect this change we introduce this relation, which is subproperty of is_about, and have previous GCI use this relation \"mentions\" in it's (logical) definition" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jonathan Rees" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person: Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000143", "lbl" : "mentioned by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of the relation 'mentions'" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "http://orcid.org/0000-0002-8844-9165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/250" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2022-01-28T07:20:08Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000144", "lbl" : "conclusion textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "conclusion textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "that fucoidan has a small statistically significant effect on AT3 level but no useful clinical effect as in-vivo anticoagulant, a paraphrase of part of the last paragraph of the discussion section of the paper 'Pilot clinical study to evaluate the anticoagulant activity of fucoidan', by Lowenthal et. al.PMID:19696660" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009/10/23 Alan Ruttenberg: We need to work on the definition still" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000178", "lbl" : "material information bearer", "type" : "CLASS", "meta" : { "definition" : { "val" : "A material entity in which a concretization of an information content entity inheres." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "material information bearer" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a brain" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a hard drive" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "GROUP: IAO" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000179", "lbl" : "histogram", "type" : "CLASS", "meta" : { "definition" : { "val" : "A histogram is a report graph which is a statistical description of a\ndistribution in terms of occurrence frequencies of different event classes." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "histogram" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:James Malone" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000180", "lbl" : "heatmap", "type" : "CLASS", "meta" : { "definition" : { "val" : "A heatmap is a report graph which is a graphical representation of data\nwhere the values taken by a variable(s) are shown as colors in a\ntwo-dimensional map." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "heatmap" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:James Malone" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000181", "lbl" : "Venn diagram", "type" : "CLASS", "meta" : { "definition" : { "val" : "A Venn diagram is a report graph showing all hypothetically possible\nlogical relations between a finite collection of sets." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "Venn diagram" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:James Malone" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://en.wikipedia.org/wiki/Venn_diagram" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000182", "lbl" : "obsolete_survival curve", "type" : "CLASS", "meta" : { "definition" : { "val" : "A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "obsolete_survival curve" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:James Malone" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://www.graphpad.com/www/book/survive.htm" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000183", "lbl" : "dendrogram", "type" : "CLASS", "meta" : { "definition" : { "val" : "A dendrogram is a report graph which is a tree diagram\nfrequently used to illustrate the arrangement of the clusters produced by a\nclustering algorithm." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "dendrogram" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Dendrograms are often used in computational biology to\nillustrate the clustering of genes." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:James Malone" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://en.wikipedia.org/wiki/Dendrogram" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000184", "lbl" : "scatter plot", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "scatter plot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Comparison of gene expression values in two samples can be displayed in a scatter plot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Chris Stoeckert" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:James Malone" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "scattergraph" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://en.wikipedia.org/wiki/Scatterplot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000185", "lbl" : "photograph", "type" : "CLASS", "meta" : { "definition" : { "val" : "A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Joanne Luciano" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://en.wiktionary.org/wiki/photograph" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000186", "lbl" : "photographic print", "type" : "CLASS", "meta" : { "definition" : { "val" : "A photographic print is a material entity upon which a photograph generically depends." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "photographic print" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000219", "lbl" : "denotes", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. Freedictionary.com sense 3: To signify directly; refer to specifically" }, "comments" : [ "" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.\ng denotes r =def \nr is a portion of reality\nthere is some c that is a concretization of g \nevery c that is a concretization of g specifically denotes r" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000220", "lbl" : "obsolete_materially denotes", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "see https://github.com/information-artifact-ontology/IAO/issues/25&q=denote" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000221", "lbl" : "is quality measurement of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "8/6/2009 Alan Ruttenberg: The strategy is to be rather specific with this relationship. There are other kinds of measurements that are not of qualities, such as those that measure time. We will add these as separate properties for the moment and see about generalizing later" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "From the second IAO workshop [Alan Ruttenberg 8/6/2009: not completely current, though bringing in comparison is probably important]\n\nThis one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.\n\nWerner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details.\n--\nFrom the second IAO workshop, various comments, [commented on by Alan Ruttenberg 8/6/2009]\n\nunit of measure is a quality, e.g. the length of a ruler.\n\n[We decided to hedge on what units of measure are, instead talking about measurement unit labels, which are the information content entities that are about whatever measurement units are. For IAO we need that information entity in any case. See the term measurement unit label]\n\n[Some struggling with the various subflavors of is_about. We subsequently removed the relation represents, and describes until and only when we have a better theory]\n\na represents b means either a denotes b or a describes\n\ndescribe:\na describes b means a is about b and a allows an inference of at least one quality of b\n\nWe have had a long discussion about denotes versus describes." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "From the second IAO workshop: An attempt at tieing the quality to the measurement datum more carefully.\n\na is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "From the second meeting on IAO:\n\nAn attempt at defining assay using Barry's \"reliability\" wording\n\nassay:\nprocess and has_input some material entity\nand has_output some information content entity \nand which is such that instances of this process type reliably generate \noutputs that describes the input." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it \"measuring\" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.\n\nWerner suggests a solution based on \"Magnitudes\" a proposal for which we are awaiting details." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000222", "lbl" : "obsolete_describes", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000223", "lbl" : "obsolete_represents", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000224", "lbl" : "obsolete_core", "type" : "INDIVIDUAL", "meta" : { "definition" : { "val" : "Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000226" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000230", "lbl" : "obsolete_other", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used if none of the existing instances cover the reason for obsolescence. An editor note should indicate this new reason." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We expect to be able to mine these new reasons and add instances as required." } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000231", "lbl" : "has obsolescence reason", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has obsolescence reason" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000232", "lbl" : "curator note", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An administrative note of use for a curator but of no use for a user" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "curator note" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000233", "lbl" : "term tracker item", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An IRI or similar locator for a request or discussion of an ontology term." }, "comments" : [ "The 'tracker item' can associate a tracker with a specific ontology term." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term tracker item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000234", "lbl" : "ontology term requester", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition." }, "comments" : [ "The 'term requester' can credit the person, organization or project who request the ontology term." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ontology term requester" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000235", "lbl" : "denoted by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of the relation 'denotes'" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person: Jie Zheng, Chris Stoeckert, Mike Conlon" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/206" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000300", "lbl" : "textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "text" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000301", "lbl" : "citation", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity intended to identify a particular publication." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "citation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Verspoor, K., Cohen, KB., Hunter, L. Textual characteristics of traditional and Open Access scientific journals are similar, BMC Bioinformatics 2009, 10:183." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000302", "lbl" : "author identification", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity intended to identify a particular author" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "author identification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "L. Hunter" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000303", "lbl" : "institutional identification", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity intended to identify a particular institution" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "institutional identification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "University of Colorado Denver School of Medicine" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000304", "lbl" : "caption", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity that describes a figure" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "caption" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Figure 1: A system diagram describing the modules of the Hanalyzer. Reading methods (green) take external sources of knowledge (blue) and extract information from them, either by parsing structured data or biomedical language processing to extract information from unstructured data. Reading modules are responsible for tracking the provenance of all knowledge. Reasoning methods (yellow) enrich the knowledge that results from reading by, for example, noting two genes that are annotated to the same ontology term or database entry. All knowledge sources, read or reasoned, are assigned a reliability score, and all are combined using that score into a knowledge network (orange) that represents the integration of all sorts of relationship between a pair of genes and a combined reliability score. A data network (also orange) is created from experimental results to be analyzed. The reporting modules (pink) integrate the data and knowledge networks, producing visualizations that can be queried with the associated drill-down tool." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000305", "lbl" : "document title", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity that names a document" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "document title" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Textual characteristics of traditional and Open Access scientific journals are similar" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000306", "lbl" : "table", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "table" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "| T F\n--+-----\nT | T F\nF | F F" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000307", "lbl" : "table of abbreviations", "type" : "CLASS", "meta" : { "definition" : { "val" : "A table where the constituent texts are abbreviations and their expansions" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "table of abbreviations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "IAO information artifact ontology\nOBI ontology of biomedical investiations\nGO gene ontology" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000308", "lbl" : "figure", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "figure" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Any picture, diagram or table" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000309", "lbl" : "diagram", "type" : "CLASS", "meta" : { "definition" : { "val" : "A figure that expresses one or more propositions" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "diagram" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000310", "lbl" : "document", "type" : "CLASS", "meta" : { "definition" : { "val" : "A collection of information content entities intended to be understood together as a whole" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "document" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A journal article, patent application, laboratory notebook, or a book" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Lawrence Hunter" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000311", "lbl" : "publication", "type" : "CLASS", "meta" : { "definition" : { "val" : "A document that is the output of a publishing process." }, "comments" : [ "Revisit the term in Octorber 2020. 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the values represent a point" ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000408", "lbl" : "length measurement datum", "type" : "CLASS", "meta" : { "definition" : { "val" : "A scalar measurement datum that is the result of measurement of length quality" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000411", "lbl" : "is denotator type", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relates an class defined in an ontology, to the type of it's denotator" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is denotator type" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "In OWL 2 add AnnotationPropertyRange('is denotator type' 'denotator type')" }, { "pred" : 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"PROPERTY", "meta" : { "definition" : { "val" : "relates a process to a time-measurement-datum that represents the duration of the process" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000414", "lbl" : "mass measurement datum", "type" : "CLASS", "meta" : { "definition" : { "val" : "A scalar measurement datum that is the result of measurement of mass quality" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009/09/28 Alan Ruttenberg. 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Fucoidan-use-case" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000416", "lbl" : "time measurement datum", "type" : "CLASS", "meta" : { "definition" : { "val" : "A scalar measurement datum that is the result of measuring a temporal interval" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000417", "lbl" : "is quality measured as", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of the relation of is quality measurement of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009/10/19 Alan Ruttenberg. 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See issue https://github.com/information-artifact-ontology/IAO/issues/59" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000424", "lbl" : "expand expression to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "expand expression to" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000425", "lbl" : "expand assertion to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A macro expansion tag applied to an annotation property which can be expanded into a more detailed axiom." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "expand assertion to" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "ObjectProperty: RO???\nLabel: spatially disjoint from\nAnnotations: expand_assertion_to \"DisjointClasses: (http://purl.obolibrary.org/obo/BFO_0000051 some ?X) (http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000426", "lbl" : "first order logic expression", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "first order logic expression" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000427", "lbl" : "antisymmetric property", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Use boolean value xsd:true to indicate that the property is an antisymmetric property" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "antisymmetric property" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "part_of antisymmetric property xsd:true" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000429", "lbl" : "email address", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "email address" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Alan Ruttenberg 1/3/2012 - Provisional id, see issue at https://github.com/information-artifact-ontology/IAO/issues/130&thanks=130&ts=1325636583" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Chris Stoeckart" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000442", "lbl" : "author role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "author role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000443", "lbl" : "data item extraction from journal article", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000444", "lbl" : "publishing process", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process of making information, such as literature, music, and software etc., available to the public for sale or for free." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person: Jie Zheng" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Publishing" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/232" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "VEuPathDB" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000445", "lbl" : "document in preparation for publication", "type" : "CLASS", "meta" : { "definition" : { "val" : "A document that is in preparation for submission to be published." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jie Zheng" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "EFO_0001795 in preparation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/232" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "VEuPathDB" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000572", "lbl" : "documenting", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process in which a document is created or added to by including the specified input in it." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Recording the current temperature in a laboratory notebook. 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A license plate number registered at the DMV to be belonging to a specific vehicle and owner. Placing a barcode on a product and entering information in a database that this barcode is assigned." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2014-05-05: It is the CRID registry that assigns CRIDs, not the users of the registry." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "assigning a CRID" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000575", "lbl" : "associating information with a centrally registered identifier in its registry", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process in which a CRID registry associates an information content entity with a CRID symbol" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Articles in Pubmed are reviewed by curators who add MESH terms to the Pubmed records in order to categorize them better and improve the ability to search for them. " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "associating information with a CRID in the CRID registry" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000576", "lbl" : "obsolete_establishing a CRID registry", "type" : "CLASS", "meta" : { "definition" : { "val" : "a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MC, 20101124: deprecated following discussion at IAO call 20101124. Term was deemed not necessary - no use case for now." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000577", "lbl" : "centrally registered identifier symbol", "type" : "CLASS", "meta" : { "definition" : { "val" : "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "CRID symbol" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Original proposal from Bjoern, discussions at IAO calls" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000578", "lbl" : "centrally registered identifier", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The sentence \"The article has Pubmed ID 12345.\" contains a CRID that has two parts: one part is the CRID symbol, which is '12345'; the other part denotes the CRID registry, which is Pubmed." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2014-05-05: In defining this term we take no position on what the CRID denotes. In particular do not assume it denotes a *record* in the CRID registry (since the registry might not have 'records')." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Alan, IAO call 20101124: potentially the CRID denotes the instance it was associated with during creation." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note, IAO call 20101124: URIs are not always CRID, as not centrally registered. We acknowledge that CRID is a subset of a larger identifier class, but this subset fulfills our current needs. OBI PURLs are CRID as they are registered with OCLC. UPCs (Universal Product Codes from AC Nielsen)are not CRID as they are not centrally registered." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "CRID" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Original proposal from Bjoern, discussions at IAO calls" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000579", "lbl" : "centrally registered identifier registry", "type" : "CLASS", "meta" : { "definition" : { "val" : "A code set of CRID records, each consisting of a CRID symbol and additional information which was recorded in the code set through an assigning a centrally registered identifier process." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "PubMed is a CRID registry. It has a code set of PubMed identifiers associated with journal articles. " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Justin Whorton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "CRID registry" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Original proposal from Bjoern, discussions at IAO calls" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/237" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000580", "lbl" : "looking up a centrally registered identifier", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Going to the PubMed website and entering a PubMed ID in order to retrieve the Pubmed information associated with that ID. " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "looking up a CRID" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000581", "lbl" : "has time stamp", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000582", "lbl" : "time stamped measurement datum", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000583", "lbl" : "has measurement datum", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "relates a time stamped measurement datum to the measurement datum that was measured" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000584", "lbl" : "time sampled measurement data set", "type" : "CLASS", "meta" : { "definition" : { "val" : "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pmid:20604925 - time-lapse live cell microscopy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "experimental time series" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000589", "lbl" : "OBO foundry unique label", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An alternative name for a class or property which is unique across the OBO Foundry." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "OBO foundry unique label" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The intended usage of that property is as follow: OBO foundry unique labels are automatically generated based on regular expressions provided by each ontology, so that SO could specify unique label = 'sequence ' + [label], etc. , MA could specify 'mouse + [label]' etc. Upon importing terms, ontology developers can choose to use the 'OBO foundry unique label' for an imported term or not. The same applies to tools ." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP:OBO Foundry " } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000590", "lbl" : "written name", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity that denotes a particular in reality." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "written name" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "\"Bill Clinton\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "\"The Eiffel Tower\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "\"United States of America\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://github.com/information-artifact-ontology/IAO/issues/114" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "The qualifier \"written\" is to set it apart from spoken names. Also, note the restrictions to particulars. We are not naming universals. We could however, be naming, attributive collections which are particulars, so \"All people located in the boundaries of the city of Little Rock, AR on June 18, 2011 at 9:50a CDT\" would be a name." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000591", "lbl" : "software method", "type" : "CLASS", "meta" : { "definition" : { "val" : "A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Michel Dumontier" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://github.com/information-artifact-ontology/IAO/issues/80" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000592", "lbl" : "software module", "type" : "CLASS", "meta" : { "definition" : { "val" : "A software module is software composed of a collection of software methods." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanei Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Michel Dumontier" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://github.com/information-artifact-ontology/IAO/issues/80" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000593", "lbl" : "software library", "type" : "CLASS", "meta" : { "definition" : { "val" : "A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Michel Dumontier" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://github.com/information-artifact-ontology/IAO/issues/80" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000594", "lbl" : "software application", "type" : "CLASS", "meta" : { "definition" : { "val" : "A software application is software that can be directly executed by some processing unit." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Michel Dumontier" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://github.com/information-artifact-ontology/IAO/issues/80" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000595", "lbl" : "software script", "type" : "CLASS", "meta" : { "definition" : { "val" : "A software script is software whose instructions can be executed using a software interpreter." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Michel Dumontier" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://github.com/information-artifact-ontology/IAO/issues/80" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000596", "lbl" : "has ID digit count", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relates an ontology used to record id policy to the number of digits in the URI. The URI is: the 'has ID prefix\" annotation property value concatenated with an integer in the id range (left padded with \"0\"s to make this many digits)" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has ID digit count" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000597", "lbl" : "has ID range allocated to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relates a datatype that encodes a range of integers to the name of the person or organization who can use those ids constructed in that range to define new terms" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has ID range allocated" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Datatype: idrange:1\nAnnotations: 'has ID range allocated to': \"Chris Mungall\"\nEquivalentTo: xsd:integer[> 2151 , <= 2300]\n" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000598", "lbl" : "has ID policy for", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relating an ontology used to record id policy to the ontology namespace whose policy it manages" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has ID policy for" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000599", "lbl" : "has ID prefix", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relates an ontology used to record id policy to a prefix concatenated with an integer in the id range (left padded with \"0\"s to make this many digits) to construct an ID for a term being created." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has ID prefix" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Ontology: \n Annotations: \n 'has ID prefix': \"http://purl.obolibrary.org/obo/RO_\"\n 'has ID digit count' : 7,\n rdfs:label \"RO id policy\"\n 'has ID policy for': \"RO\"" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000600", "lbl" : "elucidation", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "elucidation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Barry Smith" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "Primitive terms in a highest-level ontology such as BFO are terms which are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000601", "lbl" : "has associated axiom(nl)", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has associated axiom(nl)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An axiom associated with a term expressed using natural language" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000602", "lbl" : "has associated axiom(fol)", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has associated axiom(fol)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An axiom expressed in first order logic using CLIF syntax" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000603", "lbl" : "is allocated id range", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relates an ontology IRI to an (inclusive) range of IRIs in an OBO name space. The range is give as, e.g. \"IAO_0020000-IAO_0020999\"" }, "comments" : [ "Add as annotation triples in the granting ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is allocated id range" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000604", "lbl" : "retired from use as of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "relates a class of CRID to the date after which further instances should not be made, according to the central authority" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "retired from use as of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "In OWL 2 add AnnotationPropertyRange xsd:dateTimeStamp" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000605", "lbl" : "abbreviation textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity listing abbreviations and their expansions that are used in a document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "abbreviation textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "From Shiba et al. Acta Neuropathol Commun. 2013; 1: 45. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893467/):\n\nBAC: Bacterial artificial chromosome; CR: Calretinin; GFAP: Glial fibrillary acidic protein; MAP: Microtubule-associated protein; MRI: Magnetic resonance imaging; NSC: Neural stem cell; PDA: Patent ductus arteriosus; PMG: Polymicrogyria; PNH: Periventricular nodular heterotopia; VSD: Ventricular septal defect." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000606", "lbl" : "abbreviations section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document where abbreviations and their long-forms used within the document are listed." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "abbreviations section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'abbreviations' in a typical scientific journal article." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "abbreviation and acronyms" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "abbreviation list" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "abbreviations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "abbreviations and acronyms" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "abbreviations list" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "abbreviations used" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "definitions for abbreviations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "list of abbreviations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "list of abbreviations used" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "non-standard abbreviations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "nonstandard abbreviations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "nonstandard abbreviations and acronyms" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/234" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000607", "lbl" : "author information section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "author information section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'author information' in a typical scientific journal article, e.g. in Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "author information" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "authors’ information" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "biographies" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "contributor information" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/234" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000608", "lbl" : "author information textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "author information textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "From Takon. Ann Gen Psychiatry. 2011; 10: 25. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204268/):\n\nIT [the author] is the lead paediatrician for ADHD services in East Hertfordshire, UK, where she runs a weekly joint ADHD clinic with the Child and Adolescent psychiatrist and works within an ADHD specialist team. IT also sees children with other neurodisability issues who may have comorbid ADHD, where the presentation may be more complex and challenging to manage. IT has vast experience in managing children with complex ADHD. She has 18 years of experience in paediatrics and also has extensive experience in the use of psychopharmacologic agents in managing children with ADHD." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000609", "lbl" : "author summary section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "author summary section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'synopsis' in a typical scientific journal article, e.g. in Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "author summary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "summary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "synopsis" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000610", "lbl" : "author summary textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "author summary textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "From Pendse et al. BMC Genomics. 2013; 14: 136. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3608171/):\n\n\nThe search for genetic risk factors for common human diseases often relies on the use of linkage and association studies to establish correlation between genomic markers and disease risk. These studies require additional functional evaluation of candidate genes, including their possible interaction with diet and environment. The number of candidate genes is typically large and the development of appropriate genetic tools in mammalian systems is slow. By contrast, large-scale genetic screens, using widely available genetic tools, are routinely conducted in the fruit fly Drosophila melanogaster. In this study, we used Drosophila to screen candidate genes identified in human genome-wide scans as associated with risk of metabolic abnormalities such as type 2 diabetes. We show that a number of human candidate genes have fly orthologs that play an important role in Drosophila tolerance to high dietary sucrose. We further explored some of the specific metabolic abnormalities that can result when these genes’ activities are reduced in flies, focusing on a gene we call dHHEX (CG7056), the fly ortholog of human HHEX." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000611", "lbl" : "availability section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "availability section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "availability" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "availability of data" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data archiving" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data availability" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data availability statement" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data sharing statement" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/234" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000612", "lbl" : "availability textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "availability textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):\n\nProject home page:http://krux.googlecode.com" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000613", "lbl" : "case report section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document about the medical history of a specific patient as it relates to the topic of the document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "case report section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'case report' in a typical scientific journal article, e.g. in Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "case presentation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "case report" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000614", "lbl" : "case report textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity that expresses a detailed account of a portion of the medical history for a specific patient." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "case report textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Excerpt from Taglia et al. Acta Myol. 2012 Dec; 31(3): 201–203. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631801/):\n\nThe patient is a 50-year-old man. His medical history was not contributory. At the age of 37 years, he complained of persistent fatigue and dyspnoea even for modest efforts and oedema of lower limbs. The patient was examined at the department of internal medicine of the local hospital, and hospitalised with a diagnosis of dilated cardiomyopathy probably consequence of a myocarditis process. Soon after he was transferred to the cardiologic department of the regional hospital, and pharmacologically treated for heart failure and pulmonary hypertension." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000615", "lbl" : "conclusion section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document used to summarize the findings discussed in the document. 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(http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1553-2712/homepage/ForAuthors.html)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000633", "lbl" : "materials section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document about the materials required to reproduce the content of the document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "materials section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'materials' in a typical scientific journal article, e.g. Nguyen et al. BMC Bioinformatics. 2010; 11: 279. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2889936/)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "materials" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000634", "lbl" : "notes section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document containing typically short notes about the document itself and/or the authors. Often the notes section contains subsections related to funding, competing interests, ethical approval, etc." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "notes section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'notes' in a typical scientific journal article, e.g. McLean et al. Br J Gen Pract. 2014 Jul; 64(624): e440–e447 (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073730/):" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "notes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000635", "lbl" : "patients section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document about the patients that participated in a study." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "patients section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'patients' in a typical scientific journal article, e.g. in Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000636", "lbl" : "patients textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity expressing information regarding the patients used in a study." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "patients textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Excerpt from Citak et al. Acta Orthop. 2013 Jun; 84(3): 326–327. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3715825/):\n\nBetween January 1996 and February 2012, we treated 4 patients with interprosthetic femoral fractures (3 of them women) (Figure 2) using a custom-made interposition device (Waldemar Link GmbH, Hamburg, Germany) (Figure 1). Mean age was 74 (59–86) years. The fractures occurred mean 18 (13–28) years after primary THA and mean 14 (10–17) years after primary TKA. At the latest follow-up, after mean 8 (0.5–16) years, revision surgery with a total femur replacement was required in 1 case due to aseptic loosening. No other complications requiring revision surgery occurred." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000637", "lbl" : "pre-publication history section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "pre-publication history section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'pre-publication history' in a typical scientific journal article, e.g. in Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "notice of republication" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "pre-publication history" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000638", "lbl" : "pre-publication history textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "pre-publication history textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "From Xiao et al. BMC Anesthesiol. 2013; 13: 33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016475/):\n\nThe pre-publication history for this paper can be accessed here:\nhttp://www.biomedcentral.com/1471-2253/13/33/prepub" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000639", "lbl" : "related work section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document about work in other publications that is relevant to the content of the document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "related work section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'related work' in a typical scientific journal article, e.g. Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "related literature" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "related work" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000640", "lbl" : "related work textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity that discusses work from other publications and expresses their relevancy to the content of a document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "related work textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Excerpt from Žitnik and Zupan. Bioinformatics. 2015 Jun 15; 31(12): i230–i239. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542780/):\n\nOur work presented here is similar in spirit to our recently developed methodology for data fusion via collective matrix factorization (Žitnik and Zupan, 2015).\n\n" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000641", "lbl" : "requirements section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "requirements section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'availability and requirements' in a typical scientific journal article, e.g. Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "requirements" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000642", "lbl" : "requirements textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity that expresses the requirements necessary to use a resource, e.g. software." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "requirements textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "From Qi et al. BMC Bioinformatics. 2014; 15: 11. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3897912/):\n\n• Operating systems: Platform independent\n\n• Programming language: Matlab, R, Python\n\n• Other requirements: None\n\n• License: GNU GPL v3\n\n• Any restrictions to use by non-academics: None" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000643", "lbl" : "statistical analysis textual entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A textual entity documenting statistical analysis tools and techniques employed." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "statistical analysis textual entity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "From Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/):\n\nData were captured into EPI-DATA (version 3.1), cleaned and then exported to Stata version 10 for analysis. Continuous variables were summarised as mean (± standard deviation) and median (inter-quartile range), and presented in the tables. Categorical data were analysed using frequency and percentages, and results are presented in frequency tables and bar charts. Test of significance (p-value) was determined using the chi-square test. A p-value of less than 0.05 was considered significant." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000644", "lbl" : "statistical analysis section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of the document used to describe the statistical methodologies employed in the work presented in the document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "statistical analysis section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'statistical analysis' in a typical scientific journal article, e.g. Mondo et al. Cardiovasc J Afr. 2013 Mar; 24(2): 28–33. (http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3734881/)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "statistical analysis" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000645", "lbl" : "tables section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A part of a document that contains one or more tables." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "tables section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The section labelled 'tables' in a typical scientific journal article." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bill Baumgartner" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "tables" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/183" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000646", "lbl" : "postal code", "type" : "CLASS", "meta" : { "definition" : { "val" : "An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000647", "lbl" : "Postal delivery route", "type" : "CLASS", "meta" : { "definition" : { "val" : "A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000648", "lbl" : "zone improvement plan code", "type" : "CLASS", "meta" : { "definition" : { "val" : "A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ZIP code" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000650", "lbl" : "database extract, transform, and load process", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "database extract, transform, and load process" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Alan Ruttenberg 12/21/16: Maybe this definition instead: A planned process which takes as input a database and copies concretizations from the first, optionally transforms then copies the result to the second" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Alan Ruttenberg 12/21/16: We don't define database in IAO, currently, as the bare word is ambiguous. Reasonable interpretations of the word might be the material entity, an information structure, an information content entity. However this definition commits, at least, to there being some material thing which bear concretizations of information entities and that there are new concretizations created during the process. We consider the ETL process in terms of information entities rather than the concretizations. No committment is made as to whether the specified output." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ETL" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB:https://en.wikipedia.org/wiki/Extract,_transform,_load" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/187" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "https://github.com/information-artifact-ontology/IAO" }, { "pred" : "http://xmlns.com/foaf/0.1/page", "val" : "https://en.wikipedia.org/wiki/Extract,_transform,_load" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000700", "lbl" : "has ontology root term", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has ontology root term" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Nicolas Matentzoglu" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000701", "lbl" : "descriptive data section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A document part that lists and defines data variables, describes data characteristics (e.g. missing data information) and any assumptions and simplifications made." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "descriptive data section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chen Yang" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jie Zheng" }, { "pred" : 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"http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jie Zheng" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://www.equator-network.org/reporting-guidelines/consort/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://www.equator-network.org/reporting-guidelines/prisma/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://www.equator-network.org/reporting-guidelines/strobe/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/235" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "ONE ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000703", "lbl" : "research participants section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A document part that describes human subject(s) that participated in a study (e.g. inclusion & exclusion criteria, recruitment methods, reasons for non-participation, grouping and randomisation, methods of follow-up, etc.)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "research participants section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chen Yang" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jie Zheng" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://www.equator-network.org/reporting-guidelines/consort/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://www.equator-network.org/reporting-guidelines/prisma/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://www.equator-network.org/reporting-guidelines/strobe-nut/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/235" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "ONE ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000704", "lbl" : "measurement methods section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A methods section that describes details of data assessment methods (data measurement)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "measurement methods section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chen Yang" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jie Zheng" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://www.equator-network.org/reporting-guidelines/strobe/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/235" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "ONE ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000705", "lbl" : "research settings section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A document part that describes the physical/social/cultural conditions around a research trial." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "research settings section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chen Yang" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jie Zheng" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://www.ncbi.nlm.nih.gov/books/NBK262175/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/235" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "ONE ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000706", "lbl" : "study bias section", "type" : "CLASS", "meta" : { "definition" : { "val" : "A study limitations section that describes systematic error introduced into sampling or testing by selecting or encouraging one outcome or answer over others." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "study bias section" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Chen Yang" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jie Zheng" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "DOI: 10.1097/PRS.0b013e3181de24bc" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/235" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "ONE ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000707", "lbl" : "graphical abstract", "type" : "CLASS", "meta" : { "definition" : { "val" : "An abstract that is pictorial summary of the main findings described in the document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "graphical abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Jie Zheng" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Tim Beck" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "visual abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://www.elsevier.com/authors/journal-authors/graphical-abstract" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/234" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "Biomedical literature NLP project" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000708", "lbl" : "ORCID identifier", "type" : "CLASS", "meta" : { "definition" : { "val" : "A centrally registered identifier that is issued by ORCID (https://orcid.org/) and used to persistantly identify oneself as a human researcher or contributor." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"You can connect your iD with your professional information — affiliations, grants, publications, peer review, and more. You can use your iD to share your information with other systems, ensuring you get recognition for all your contributions, saving you time and hassle, and reducing the risk of errors.\" [https://orcid.org/]" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This class was originally defined in Apollo_SV (http://purl.obolibrary.org/obo/APOLLO_SV_00000496) but due to it being more in scope of IAO, it was decided to add it to IAO and deprecate its Apollo_SV equivalent. (2022-10-25)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "http://orcid.org/0000-0002-1595-3213" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ORCID ID" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ORCiD" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "Open Researcher and Contributor ID" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "Open Researcher and Contributor Identifier" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://orcid.org/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/259" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0006011", "lbl" : "may be identical to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A annotation relationship between two terms in an ontology that may refer to the same (natural) type but where more evidence is required before terms are merged." }, "comments" : [ "Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "may be identical to" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "#40" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "VFB" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0006012", "lbl" : "scheduled for obsoletion on or after", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Used when the class or object is scheduled for obsoletion/deprecation on or after a particular date." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "scheduled for obsoletion on or after" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall, Jie Zheng" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/15532" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/32" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", "val" : "GO ontology" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0010000", "lbl" : "has axiom label", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has axiom id" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A URI that is intended to be unique label for an axiom used for tracking change to the ontology. For an axiom expressed in different languages, each expression is given the same URI" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", "val" : "http://purl.obolibrary.org/obo/iao.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020000", "lbl" : "identifier", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." }, "comments" : [ "Sep 29, 2016: The current definition has been amended from the previous version: \"A proper name is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity.\" to more accuratly reflect the necessary and sufficient condition on the class. (MB)" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "identifier" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Justin Whorton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "proper name" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/237" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020001", "lbl" : "grapheme", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity that is a fundamental unit in a written language." }, "comments" : [ "Grapheme is not about anything and hence is likely to not be an information content entity. If a new subclass of GDC for information structure entities is created it should move there." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "alphabetic letters, Chinese characters, numerical digits, punctuation marks, and the individual symbols of any of the world's writing systems" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Justin Whorton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://en.wikipedia.org/wiki/Grapheme" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/237" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020002", "lbl" : "utterance", "type" : "CLASS", "meta" : { "definition" : { "val" : "An utterance is an information content entity that is a complete unit of speech in spoken language. " }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Wikipedia: http://en.wikipedia.org/wiki/Utterance" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020003", "lbl" : "mechanical wave quality", "type" : "CLASS", "meta" : { "definition" : { "val" : "An attributive collection of qualities inhering in energy when transported through a medium in a wave." }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020004", "lbl" : "writing quality", "type" : "CLASS", "meta" : { "definition" : { "val" : "is a quality that is the concretization of graphemes and inheres in a material object." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020005", "lbl" : "writing bearer", "type" : "CLASS", "meta" : { "definition" : { "val" : "is a material information bearer that bears the concretization of graphemes." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pieces of paper, tables, walls, floors, driveways, highway signs, computer screens, skin, tablets of clay, rocks, sheets of metal (license plates), sheets of papyrus, etc. clouds of smoke in skywriting," }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020006", "lbl" : "portion of energy", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020007", "lbl" : "sound energy", "type" : "CLASS", "meta" : { "definition" : { "val" : "Energy that is transported in a sound wave." }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020008", "lbl" : "utterance energy", "type" : "CLASS", "meta" : { "definition" : { "val" : "Sound energy bearing the concretization of an utterance and being the output of an uttering process. " } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020009", "lbl" : "oscillating", "type" : "CLASS", "meta" : { "definition" : { "val" : "Oscillating is a processual that shows repetitive variation, typically in time, of some measured quality about a central value (often a point of equilibrium) or between two or more different states." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://en.wikipedia.org/wiki/Oscillation" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020010", "lbl" : "identifier creating process", "type" : "CLASS", "meta" : { "definition" : { "val" : "An identifier creating process is a planned process that provides a reference to an individual entity shared by a group of subscribers to refer to that individual entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Justin Whorton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "dubbing process" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "naming" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/237" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020011", "lbl" : "utterance process", "type" : "CLASS", "meta" : { "definition" : { "val" : "is a planned process of making speech sounds which may or may not have an actual language involved. " }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://en.wiktionary.org/wiki/utter" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020012", "lbl" : "obsolete_designates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x designates y, if for any given group of language users, x is an information content entity, is about y, and represents y in a linguistic context.." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000228" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/IAO_0000219" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020013", "lbl" : "is_borrowed_reference_to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is_borrowed_reference_for y, if x is a proper name that is used to refer to one individual among a specific group after the dubbing process took place." }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020014", "lbl" : "is_fixing_reference_to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x is_fixed_reference_for y, if x is an utterance or graphemes concretized as writing quality inhering in some independent continuant that is used to single out one individual and refer to the latter among a specific group after the." }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020015", "lbl" : "personal name", "type" : "CLASS", "meta" : { "definition" : { "val" : "An identifier referring to an individual entity that is ascribed personhood by the user of the identifier." }, "comments" : [ "Personal names \"today usually comprises a given name bestowed at birth or at a young age plus a surname. It is nearly universal for a human to have a name; except in rare cases, for example feral children growing up in isolation, or infants orphaned by natural disaster for whom no written record survives.[citation needed] The Convention on the Rights of the Child specifies that a child has the right from birth to a name. Certain isolated tribes, such as the Machiguenga of the Amazon, also lack personal names.\" (http://en.wikipedia.org/wiki/Personal_name)", "Personal names to not include names of fictional characters, e.g. Sherlock Holmes.", "Sep 29, 2016: The comment that including the wikipedia definition of personal name is not to be interpreted in a way that restricts this class to only contain strings of letters. A numerical or alphanumerical identifier that denotes a human is being is a personal name, too. (MB)" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Justin Whorton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://en.wikipedia.org/wiki/Personal_name" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/237" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020016", "lbl" : "given name", "type" : "CLASS", "meta" : { "definition" : { "val" : "A personal name that specifies and differentiates between members of a group of individuals, especially in a family, all of whose members usually share the same family name (surname). A given name is purposefully given, usually by a child's parents at or near birth, in contrast to an inherited one such as a family name" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Justin Whorton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "first name" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://en.wikipedia.org/wiki/Given_name" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/237" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020017", "lbl" : "family name", "type" : "CLASS", "meta" : { "definition" : { "val" : "An identifier that is typically a part of a person's name which has been passed, according to law or custom, from one or both parents to their children." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Justin Whorton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "last name" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "surname" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://en.wikipedia.org/wiki/Family_name" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/237" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020018", "lbl" : "is designated by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p1 is designated by p2, if p2 is an information content entity that represents p1 in a linguistic context." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020019", "lbl" : "IUI", "type" : "PROPERTY", "meta" : { "comments" : [ "An annotation to be applied to individuals only. Value is a GUID/UUID for use in a referent tracking system." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "instance unique identifier" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020020", "lbl" : "code set", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity that is a collection of other information content entities that has been created to identify or annotate things in a specified domain, and where the intention of its creators is that the collection has a one-to-one correspondence with those things." }, "comments" : [ "Code sets might include non-entities/things (e.g. missing thumbs).", "Does not imply absence vs. presence of any taxonomy.", "Does not imply that aggregated entities denote particulars, universals, or defined classes (a.k.a. attributive collections) or even that they denote only one of these three types of entities.", "Each aggregated entity is often (but not necessarily) associated with a text string—variously called a “description,” “name,” “title,” or “label”—that helps humans reach the target of denotation.\n\nWhen there is no such string, it is almost always because the entities take the form of human language words. For example, a “sex” or “gender” code set could contain “MALE” and “FEMALE,” or even “M” and “F” (by convention, we understand what these mean).", "For National Drug Codes (NDCs) and similar code sets, there doesn’t even have to be a single, fully-concretized copy somewhere (for example, for NDCs there is no centralized database or repository where they all live as one instance of concretization of code set). The code set can be “distributively” concretized. This seems like an unusual exception, but it also likely applies to Universal Product Codes (UPCs) and their follow on Global Trade Item Numbers (GTINs).", "For each given domain, there can potentially exist multiple code sets. The multiplicity of code sets is partially due to the different specific purposes of those code sets.", "Many code sets are created for a specific purpose in addition to merely identifying or annotating core ideas of a specified domain.", "The information content entities do not denote each other." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Justin Whorton" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "code map" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "code system" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "codeset" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "coding system" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "controlled vocabulary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/IAO/issues/237" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matt Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020021", "lbl" : "identity document", "type" : "CLASS", "meta" : { "definition" : { "val" : "A document that denotes some identity and is concretized by the bearer of some credential role." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Amanda Hicks" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020022", "lbl" : "documented identity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A documented identity is the aggregate of all data items about an entity. Notice that a documented identity is not itself a document since a document is intended to be understood as a whole and data items about an individual are usually scattered across different documents." }, "comments" : [ "is an aggregate of ICEs also an ICE? yes\nIs part_of the appropriate relation to use for data items and documented identities?" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Amanda Hicks" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020023", "lbl" : "authentication", "type" : "CLASS", "meta" : { "definition" : { "val" : "Authentication is the act of checking or verifying an identity claim (that is either tacit or explicit).\n" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : " I order a beer and the bartender authenticates my age by looking at my DOB on my driver's license. I sign into my email account, and the system authenticates my permission to read the email by checking the password I enter against my password listed in the database." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Amanda Hicks" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020024", "lbl" : "credential role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role that inheres in a concretization of an identity document and is realized by an authentication process." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Amanda Hicks" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020025", "lbl" : "obsolete obligor role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "obligor role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Sam's obligor role realized by him taking Nigel to lunch after promising to do so; Sarah's obligor role realized by paying the purchase price to Layla after signing the contract specifying that she is buying a piece of land from Layla." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Sarah Bost" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "duty holder role (IAO:210016)" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020026", "lbl" : "obsolete obligee role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role that is the specified output of an obligation generating social act and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "obligee role" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Nigel's obligee role realized by Sam taking him out for lunch after Sam so promised; Layla's obligee role realized by receiving the money after signing a contract in which Sarah obtained a piece of land in exchange for a specified sum of money." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Sarah Bost" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "claimant role (IAO:0021013)" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0020027", "lbl" : "owner role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role in a human social process that is based on a social act and whose bearer exercises exclusive control over a property, where this control is permitted by one or more deontic roles, which are parts of the owner role." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Tammy's owner role with regards to the house on 234 Evergreen Terrace; Walter's owner role with regards to the intellectual property on his movie script" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBIB/ICO community" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://github.com/d-acts/d-acts/issues/29" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021000", "lbl" : "obsolete_claim", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000226" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021001", "lbl" : "deontic document act", "type" : "CLASS", "meta" : { "definition" : { "val" : "A deontic declaration creating or revoking a deontic role by lawfully manipulating (signing, stamping, publishing) a document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my filling in an immigration form, a judge's signing and stamping a court order" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021002", "lbl" : "obsolete_document act", "type" : "CLASS", "meta" : { "definition" : { "val" : "A social act creating, revoking or transferring a socio-legal generically dependent continuant or a role by validating (signing, stamping, publishing) a document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my filling in an immigration form, a judge's signing and stamping a court order" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibary.org/obo/IAO_0021001" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021003", "lbl" : "social act", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process that is carried out by a conscious being or an organization, and is self-generated, directed towards another conscious being or an aggregate of conscious beings, an organization or an aggregate of organizations, and that is in need of being perceived." }, "comments" : [ "The phrase \"in need of being perceived\" does not imply that only planned processes that are in fact perceived can be social acts. Reinach clarifies that by exemplifying these matters for commands: \"The command is according to its essence in need of being heard (vernehmungsbedürtig\". It can of course happen that commands are given without being heard. Then they fail to fulfil their purpose. They are like thrown spears which fall to the ground without hitting their target.\" (A. Reinach: The Apriori Foundations of the Civil Law.\" Edited by J. Crosby, Heusenstamm: ontos Verlag, 2012).\nReinach clearly does not imply that a command that does not fulfill its prupose would not be a command.\nThanks to W.R. Hogan for finding the Reinach quote." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Colonel Klink giving Sergeant Schultz an order, Jake promising Jill to take her to the junior prom" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021004", "lbl" : "obsolete_socio-legal generically dependent continuant", "type" : "CLASS", "meta" : { "definition" : { "val" : "Socio-legal generically dependent continuants are generically dependent continuants that come into existence through social acts and that if they get concretized are concretized as realizable entities." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the claim of a piece of land, the obligation to pay rent to the owner of a rental property" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021005", "lbl" : "obsolete_deontic declaration", "type" : "CLASS", "meta" : { "definition" : { "val" : "A social act that brings about, transfers or revokes a socio-legal generically dependent continuant or brings about or transforms a role. Declarations do not depend on words spoken or written, but sometimes are merely actions, for instance the signing of a document." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "deontic declaration" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my consenting verbally to buy a used TV set for $ 500, John Robie's taking of Mrs. Steven's jewels, Jane Doe's revoking of informed consent over the phone, John Doe signing an employment contract." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "declaration" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "status function declaration" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021006", "lbl" : "obsolete obligee role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021007", "lbl" : "document act input document", "type" : "CLASS", "meta" : { "definition" : { "val" : "A document that is intended to be the specified input in a document act. It has a plan specification as a part that specifies the intended socio-legal entities that are created through the document (objective specification) and the way in which the document act is to be performed (by signing, by stamping, etc.) (action specification)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021008", "lbl" : "deontic role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role that inheres in an agent and which is externally grounded in the normative expectations that other agents within a social context have concerning how that agent should behave." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Neil Otte" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021009", "lbl" : "deontic declaration", "type" : "CLASS", "meta" : { "definition" : { "val" : "A social act that creates or revokes a deontic role." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021010", "lbl" : "obsolete_obligation", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000226" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021011", "lbl" : "legally revokes", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "d socio-legally revokes s if s participates in d and at the end of d s no longer exists.\nIt is important to note that this going out of existence of s is complete and unlike the going out of existence for material entities which basically always are transformed into something else. After the declaration nothing is left of the socio-legal generically dependent continuant in question." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021012", "lbl" : "obsolete_legally transfers", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "d socio-legally transfers l if l participates in d and d has specified input (concretization of l)1 and specified output (concretization of l)2, where (concretization of l)1 and (concretization of l)2 are not identical." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021013", "lbl" : "claimant role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A deontic role that inheres in an agent A, that mutually depends on the existence of a duty holder role borne by agent B, and that specifies B doing or abstaining from C, or providing or surrendering C to A." }, "comments" : [ "Claimant roles can either be discharged by one act of fulfilling a duty (e.g. when I pay back $5 owed to a friend) or they can remain intact and require ongoing adhering to a duty. \nhttps://plato.stanford.edu/entries/rights/#FormRighHohfAnalSyst discuss the claim of a child to freedom from abuse. That claim remains in existence and the duty to not abuse the child needs to be continuously be acted upon, by a multitude of agents (which all have a duty holder role). This claim is mutually dependent on the duty to abstain from abusing the child." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "J. Neil Otte" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://plato.stanford.edu/entries/rights/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021014", "lbl" : "obsolete_declaration executive role", "type" : "CLASS", "meta" : { "definition" : { "val" : "The role borne by a human being, an organization or an aggregate of either of both that is realized by being the active participant in a declaration." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000226" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021015", "lbl" : "obsolete_document template creator role", "type" : "CLASS", "meta" : { "definition" : { "val" : "The role of a human being or an aggregate of human beings preparing the initial document to undergo a document act, thus creating a socio-legal generically dependent continuant." }, "comments" : [ "not that the \"template\" does not need to be a template at all. It can be a document that is getting stamped and signed and by these acts creating some socio-legal generically dependent continuants." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the role borne by the US Citizen and Immigration Service realized by providing the template form for entering the US as a non-resident alien, the role of a guideline committee in putting together a clinical guideline" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000226" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021016", "lbl" : "duty holder role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A deontic role that inheres in an agent A, that mutually depends on the existence of a claimant role borne by agent B, and that specifies A doing or abstaining from some acition C, or providing or surrendering C to B." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "J. Neil Otte" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://plato.stanford.edu/entries/rights/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021017", "lbl" : "obsolete_claimant role", "type" : "CLASS", "meta" : { "definition" : { "val" : "The role of a human being or an aggregate of human beings concretizing a claim." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000226" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021018", "lbl" : "obsolete_obligator role", "type" : "CLASS", "meta" : { "definition" : { "val" : "The role of a human being or an aggregate of human beings concretizing an obligation." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000226" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021019", "lbl" : "privilege holder role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A deontic role that inheres in an agent A, that specifies that no agent B bears a claimant role against A doing C." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "J. Neil Otte" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://plato.stanford.edu/entries/rights/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021020", "lbl" : "obsolete_declaration target", "type" : "CLASS", "meta" : { "definition" : { "val" : "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "me as a bearer of a spouse role, which participates in a document act, John Doe as bearer of a debtor role, which participates in a document act" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021021", "lbl" : "document act template creator role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role that inheres in a human being or organization or aggregate of any of the aforementioned that prepares a document that is the specified input to a document act and is the input document of a document act." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The role of the U.S. Citizenship and Immigration Service realized by the creation of an immigration form that is being filled in, the role of a national professional association realized by the creation of a clinical guideline that is to be certified" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021022", "lbl" : "deontic declaration performer role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a declaration." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "declaration performer role" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021023", "lbl" : "power role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A deontic role that, if realized, is realized by its bearer’s creating, altering, or annulling some deontic role." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "J. Neil Otte" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Hohfeld, WN: Fundamental Legal Conceptions as Applied in Judicial Reasoning. Yale University Press, 1919." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://plato.stanford.edu/entries/rights/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021030", "lbl" : "obsoleted_document act target", "type" : "CLASS", "meta" : { "definition" : { "val" : "The human being or organization or aggregate of any of the aforementioned that is the bearer of a concretization of a socio-legal generically dependent continuant brought about by or transferred in a specific document act." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021031", "lbl" : "document act performer role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role inhering in a human being or an organization or an aggregate of any of the aforementioned that is realized by the bearer being the agent in a document act." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a judge's role of signing a court order" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021032", "lbl" : "obsolete_obligee role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Sarah Bost" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021033", "lbl" : "obsolete_obligor role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the providing part of a process that fulfills the previously agreed upon requirements." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Sarah Bost" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000231", "val" : "http://purl.obolibrary.org/obo/IAO_0000103" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021102", "lbl" : "standing declaration", "type" : "CLASS", "meta" : { "definition" : { "val" : "A social act that postulates a socio-legal fact for a specified group of people or organizations." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "enactment" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0021300", "lbl" : "obsolete obligor role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role that is either the specified output of an obligation generating social act or the concretization of a transferable obligation and that is realized by it's bearer being the receiving part of a process that fulfills the previously agreed upon requirements." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "John Judkins" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0100001", "lbl" : "term replaced by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, "comments" : [ "Add as annotation triples in the granting ontology" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "term replaced by" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Alan Ruttenberg" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000000", "lbl" : "ontology module", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "I have placed this under 'data about an ontology part', but this can be discussed. I think this is OK if 'part' is interpreted reflexively, as an ontology module is the whole ontology rather than part of it." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ontology file" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This class and it's subclasses are applied to OWL ontologies. Using an rdf:type triple will result in problems with OWL-DL. I propose that dcterms:type is instead used to connect an ontology URI with a class from this hierarchy. The class hierarchy is not disjoint, so multiple assertions can be made about a single ontology." } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000001", "lbl" : "base ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "base ontology module" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/INCATools/ontology-starter-kit/issues/50" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000002", "lbl" : "editors ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "editors ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "source ontology module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000003", "lbl" : "main release ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "main release ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: Add logical axioms that state that a main release ontology module is derived from (directly or indirectly) an editors module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000004", "lbl" : "bridge ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "bridge ontology module" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/inter-anatomy-ontology-bridge-ontologies" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000005", "lbl" : "import ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "A subset ontology module that is intended to be imported from another ontology." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "import ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: add axioms that indicate this is the output of a module extraction process." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "import file" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://robot.obolibrary.org/extract" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000006", "lbl" : "subset ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "subset ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ontology slim" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "subset ontology" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://robot.obolibrary.org/filter" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://www.geneontology.org/page/go-slim-and-subset-guide" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000007", "lbl" : "curation subset ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "curation subset ontology module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000008", "lbl" : "analysis subset ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "An ontology module that is intended for usage in analysis or discovery applications." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "analysis ontology module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000009", "lbl" : "single layer subset ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "single layer ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ribbon subset" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000010", "lbl" : "exclusion subset ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "exclusion subset ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "antislim" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000011", "lbl" : "external import ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "external import ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "external import" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000012", "lbl" : "species subset ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "species subset ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "taxon subset" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000013", "lbl" : "reasoned ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "reasoned ontology module" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://robot.obolibrary.org/reason" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000014", "lbl" : "generated ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "generated ontology module" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO: Add axioms (using PROV-O?) that indicate this is the output-of some reasoning process" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000015", "lbl" : "template generated ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "An ontology module that is automatically generated from a template specification and fillers for slots in that template." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "template generated ontology module" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://robot.obolibrary.org/template" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://doi.org/10.1186/s13326-017-0126-0" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/dosumis/dead_simple_owl_design_patterns/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000016", "lbl" : "taxonomic bridge ontology module", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "taxonomic bridge ontology module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000017", "lbl" : "ontology module subsetted by expressivity", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ontology module subsetted by expressivity" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000018", "lbl" : "obo basic subset ontology module", "type" : "CLASS", "meta" : { "definition" : { "val" : "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "obo basic subset ontology module" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://owlcollab.github.io/oboformat/doc/obo-syntax.html#6.2" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000019", "lbl" : "ontology module subsetted by OWL profile", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ontology module subsetted by OWL profile" } ] } }, { "id" : "http://purl.obolibrary.org/obo/IAO_8000020", "lbl" : "EL++ ontology module", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "EL++ ontology module" } ] } }, { "id" : "http://purl.obolibrary.org/obo/MF_0000030", "lbl" : "representation", "type" : "CLASS", "meta" : { "definition" : { "val" : "A dependent continuant which is about a portion of reality." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.jbiomedsem.com/content/1/1/10" } ] } }, { "id" : "http://purl.obolibrary.org/obo/MF_0000031", "lbl" : "cognitive representation", "type" : "CLASS", "meta" : { "definition" : { "val" : "A representation which specifically depends on an anatomical structure in the cognitive system of an organism." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.jbiomedsem.com/content/1/1/10" } ] } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_9606", "lbl" : "Homo sapiens", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "Homo sapiens" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "human being" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ncbitaxon.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OAE_0000002", "lbl" : "medical intervention", "type" : "CLASS", "meta" : { "definition" : { "val" : "medical intervention is a planned process that has the goal of diagnosing, preventing or relieving illness or injury." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The act of intervening, interfering or interceding with the intent of modifying the outcome. In medicine, an intervention is usually undertaken to help treat or cure a condition. For example, \"Acupuncture as a therapeutic intervention is widely practiced in the United States,\" \nReference:\nhttp://www.medterms.com/script/main/art.asp?articlekey=34214 . Some interventions can be used for diagnosis. " }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "YH" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://wiki.answers.com/Q/What_is_medical_intervention" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OAE_0000067", "lbl" : "surgery", "type" : "CLASS", "meta" : { "definition" : { "val" : "Surgery is a medical procedure that uses operative manual and instrumental techniques on a patient to investigate and/or treat a pathological condition such as disease or injury, to help improve bodily function or appearance. The key difference between a surgery and a general procedure is the need for an incision. Making an incision, or cutting into the skin to gain access to the body’s deeper tissues or organs, is a defining characteristic of surgery." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "YH, SS" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "surgical procedure" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://en.wikipedia.org/wiki/Surgery" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm" }, { "pred" : "http://purl.obolibrary.org/obo/OAE_0004334", "val" : "10042609" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OAE_0002807", "lbl" : "medical procedure", "type" : "CLASS", "meta" : { "definition" : { "val" : "a medical intervention that refers to any series of pre-defined steps that should be followed to achieve a desired result." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "YH, SS" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://www.wisegeekhealth.com/what-is-the-difference-between-a-surgery-and-a-procedure.htm" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OAE_0004334", "lbl" : "has_MedDRA_id", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/OBIB_0000667", "lbl" : "survey data", "type" : "CLASS", "meta" : { "definition" : { "val" : "A data item that contains the outcome of a survey." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alice Nzinga" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBIB_0000701", "lbl" : "survey plan specification", "type" : "CLASS", "meta" : { "definition" : { "val" : "A plan specification that is realized by process of gathering information (e.g. by asking questions)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alice Nzinga" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBIB_0000710", "lbl" : "survey execution", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process that realizes the concretization of a survey to generate an output(survey data.)" } } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000011", "lbl" : "planned process", "type" : "CLASS", "meta" : { "definition" : { "val" : "A process that realizes a plan which is the concretization of a plan specification." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "planned process" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "planned process" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Injecting mice with a vaccine in order to test its efficacy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "'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.)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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 \nobjectives is a planned process." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "branch derived" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "6/11/9: Edited at workshop. Used to include: is initiated by an agent" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000066", "lbl" : "investigation", "type" : "CLASS", "meta" : { "definition" : { "val" : "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "investigation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000245", "lbl" : "organization", "type" : "CLASS", "meta" : { "definition" : { "val" : "An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "organization" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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:\n\n1) there are organization_member_roles (president, treasurer, branch\neditor), with individual persons as bearers\n\n2) there are organization_roles (employer, owner, vendor, patent holder)\n\n3) an organization has a charter / rules / bylaws, which specify what roles\nthere are, how they should be realized, and how to modify the\ncharter/rules/bylaws themselves.\n\nIt is debatable what the organization itself is (some kind of dependent\ncontinuant or an aggregate of people). This also determines who/what the\nbearer of organization_roles' are. My personal favorite is still to define\norganization as a kind of 'legal entity', but thinking it through leads to\nall kinds of questions that are clearly outside the scope of OBI.\n\nInterestingly enough, it does not seem to matter much where we place\norganization itself, as long as we can subclass it (University, Corporation,\nGovernment Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,\nW3C, University of Oklahoma), and have it play roles.\n\nThis leads to my proposal: We define organization through the statements 1 -\n3 above, but without an 'is a' statement for now. We can leave it in its\ncurrent place in the is_a hierarchy (material entity) or move it up to\n'continuant'. We leave further clarifications to BFO, and close this issue\nfor now." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Philippe Rocca-Serra" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Susanna Sansone" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GROUP: OBI" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000293", "lbl" : "has_specified_input", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The inverse property of is_specified_input_of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has_specified_input" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has_specified_input" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "see is_input_of example_of_usage" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Larry Hunter" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Coutot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000295", "lbl" : "is_specified_input_of", "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000299", "lbl" : "has_specified_output", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The inverse property of is_specified_output_of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has_specified_output" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has_specified_output" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Larry Hunter" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON: Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000312", "lbl" : "is_specified_output_of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is_specified_output_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is_specified_output_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Bjoern Peters" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000471", "lbl" : "study design execution", "type" : "CLASS", "meta" : { "definition" : { "val" : "a planned process that carries out a study design" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "study design execution" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0000846", "lbl" : "is member of organization", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is member of organization" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000120" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2009/10/01 Alan Ruttenberg. Barry prefers generic is-member-of. Question of what the range should be. For now organization. Is organization a population? Would the same relation be used to record members of a population" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "JZ: Discussed on May 7, 2012 OBI dev call. Bjoern points out that we need to allow for organizations to be members of organizations. And agreed by the other OBI developers. So, human and organization were specified in 'Domains'. The textual definition was updated based on it." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person:Helen Parkinson" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Alan Ruttenberg" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Person:Helen Parkinson" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0001688", "lbl" : "has organization member", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Relating an organization to a legal person or organization." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has organization member" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "See tracker:\nhttps://sourceforge.net/tracker/index.php?func=detail&aid=3512902&group_id=177891&atid=886178" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Person: Jie Zheng" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0100026", "lbl" : "organism", "type" : "CLASS", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "organism" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "animal" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "fungus" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "plant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "virus" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000121" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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')" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "13-02-2009:\nOBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "GROUP: OBI Biomaterial Branch" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "WEB: http://en.wikipedia.org/wiki/Organism" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0200000", "lbl" : "data transformation", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process that produces output data from input data." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "data transformation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000122" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Elisabetta Manduchi" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Helen Parkinson" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "James Malone" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Melanie Courtot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Philippe Rocca-Serra" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Richard Scheuermann" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Ryan Brinkman" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Tina Hernandez-Boussard" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data analysis" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "data processing" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Branch editors" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0500000", "lbl" : "study design", "type" : "CLASS", "meta" : { "definition" : { "val" : "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "study design" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OBI_0600052", "lbl" : "dialysis", "type" : "CLASS", "meta" : { "definition" : { "val" : "a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "dialysis" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "PERSON:Kevin Clancy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBI branch derived" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OGMS_0000097", "lbl" : "health care encounter", "type" : "CLASS", "meta" : { "definition" : { "val" : "A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Albert Goldfain" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "creation date: 2011-02-21T09:57:44Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OGMS_0000100", "lbl" : "inpatient encounter", "type" : "CLASS", "meta" : { "definition" : { "val" : "A health care encounter involving a patient who has been admitted to a health care facility and remains in a hospital facility for at least one night." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Albert Goldfain" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "creation date: 2011-02-21T09:57:44Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OGMS_0000102", "lbl" : "injury", "type" : "CLASS", "meta" : { "definition" : { "val" : "A disorder that involves some structural damage that is immediately caused by a catastrophic external force." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'.\n\nNote: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Albert Goldfain\nSagar Jain" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5\n\nOGMS call adoption- 16 SEPT 2015\nhttps://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "creation date: 2011-09-20T09:57:44Z\nedited date: 30 SEPT 2015" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000008", "lbl" : "obsolete owns", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/OBIB_0000732" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000009", "lbl" : "obsolete administrates", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/OBIB_0000733" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000048", "lbl" : "obsolete is owned by", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Reinach, A. S�mtliche Werke. Texkritische Ausgabe, M�nchen: Philosophia Verlag, 1989, p.189-204." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/OBIB_0000735" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0000060", "lbl" : "obsolete survey data", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alice Nzinga" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/OBIB_0000667" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0001025", "lbl" : "obsolete survey plan specification", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Alice Nzinga" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/OBIB_0000701" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMIABIS_0001035", "lbl" : "obsolete survey execution", "type" : "CLASS", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/OBIB_0000710" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0001001", "lbl" : "logical characteristic of object property", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "This is an annotation used on an object property to indicate a logical characterstic beyond what is possible in OWL." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "OBO Operations call" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "http://orcid.org/0000-0001-5208-3432" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMO_0002000", "lbl" : "defined by construct", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : 10 tobacco cigerettes a day or the equivalent in other tobacco products." } } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000188", "lbl" : "answer set", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000189", "lbl" : "question text", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000190", "lbl" : "option as member of some answer set", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000191", "lbl" : "residential facility", "type" : "CLASS", "meta" : { "definition" : { "val" : "A facility that has at least one housing unit as part in which a person or persons live" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "residential facility" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Emma Norris" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Modified version of definition provided by Human Behaviour Change Project" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000192", "lbl" : "obsolete communication", "type" : "CLASS", "meta" : { "definition" : { "val" : "A process in which some participant shares some information content entity about some state of that participant with some other participant." }, "comments" : [ "The term 'participant' in the definition need not refer to a human agent." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000193", "lbl" : "obsolete linguistic competence", "type" : "CLASS", "meta" : { "definition" : { "val" : "A disposition inhering in a material entity that, if realized, is realized by that material entity’s communicating via some linguistic concretization." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000194", "lbl" : "obsolete language", "type" : "CLASS", "meta" : { "definition" : { "val" : "A disposition inhering in a linguistic community that (i) is a maximal aggregate of communicatively compatible linguistic competences, and (ii) if realized, is realized by any and all realizations of those linguistic competences." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "S. Clint Dowland" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000195", "lbl" : "linguistic community", "type" : "CLASS", "meta" : { "definition" : { "val" : "A maximal aggregate of material entities such that each member bears a linguistic competence for the same language." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000196", "lbl" : "obsolete expression of preferred language", "type" : "CLASS", "meta" : { "definition" : { "val" : "A communication in which some participant states a preference for some communicative process to be in a certain language, and that has a concretization of a preferred language information content entity as its specified output." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000197", "lbl" : "obsolete preferred language information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity that (i) is about some person, some language, and some linguistic competence; and (ii) conveys the language with which that person prefers to communicate within some given context." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000198", "lbl" : "information content entity-request process", "type" : "CLASS", "meta" : { "definition" : { "val" : "a communication in which some participant requests of some other participant an information content entity about some portion of reality" }, "comments" : [ "As with the parent class, 'participant' in the definition need not refer to a human agent.", "The medium and grammatical form are irrelevant. For example, the request may be written or spoken, and while it may be in the form of a question, it need not be." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000199", "lbl" : "information content entity request about ethnic identity", "type" : "CLASS", "meta" : { "definition" : { "val" : "an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the ethnic identity of that other participant" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000200", "lbl" : "information content entity request about racial identity", "type" : "CLASS", "meta" : { "definition" : { "val" : "an information content entity-request process in which some participant requests of some other participant an information content entity that indicates the racial identity of that other participant" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000201", "lbl" : "admission process", "type" : "CLASS", "meta" : { "definition" : { "val" : "A deontic document act in which a patient is registered with a health care provider for the purpose of receiving care in an inpatient encounter." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Amanda Hicks" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000202", "lbl" : "cancer summary staging", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process of determining the extent to which a cancer disease has developed by growing and spreading throughout an organism." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "cancer summary staging" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The cancer summary staging performed on patient John Doe's clinical picture." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "tumor summary staging" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000203", "lbl" : "cancer summary staging code", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity that is the specified output of cancer summary staging." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "cancer summary staging code" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The cancer summary staging code that is the outcome of the cancer summary staging performed on patient John Doe's clinical picture." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "tumor summary staging code" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000204", "lbl" : "social identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity that is intended to be a truthful statement about some person and whether that person identifies as some particular aspect of social identity—such as a gender, an ethnicity, a race, or a sexual orientation—where the sense of identifying may correspond to either (i) an aspect of one’s cognitive representation of oneself, (ii) how one prefers to be regarded by others within some social context, or (iii) how one chooses to present oneself to others within some social context." }, "comments" : [ "We include (i)-(iii) to acknowledge that there are different senses of \"identify\" that are relevant here, and that we may not always be sure which sense the person concretizing the social identity information content entity intended. While (i) concerns how one thinks of oneself, (ii) and (iii) are more focused on one's interactions with others. Importantly, some choose not to share with others how they identify in the sense of (i). For example, one can consider oneself to be some certain gender without either wanting others to know or choosing to present oneself in a corresponding way. We distinguish (ii) and (iii) because one can prefer to be regarded some certain way without attempting to present oneself in any corresponding way." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000205", "lbl" : "ethnic identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A social identity information content entity that is about whether some person identifies as some ethnicity." }, "comments" : [ "Ethnicity is separate from but related to racial identity. It refers more to identifying with a particular culture than with individuals similar in physical appearance. It includes things like Hispanic ethnicity (which spans many nations) and national cultural identities like Irish and ethnic groups within nations such as Catalan and Armenian." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000206", "lbl" : "OMB ethnic identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An ethnic identity information content entity that uses OMB terminology for ethnicity or terminology that is strictly mapped onto the OMB ethnicity terms." }, "comments" : [ "OMB dichotomizes ethnicity into Hispanic or Latino and Not Hispanic or Latino, and ignores all other forms of ethnicity." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000207", "lbl" : "OMB Hispanic or Latino identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An OMB ethnic identity information content entity that is about some person's identifying as Hispanic or Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race." }, "comments" : [ "It comprehends people of Portuguese culture or origin in Brazil." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000208", "lbl" : "OMB not Hispanic or Latino identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An OMB ethnic identity information content entity that is about some person's identifying as neither Hispanic nor Latino, which are intended to mean being of Cuban, Mexican, Puerto Rican, South or Central American, or other Spanish culture or origin, regardless of race." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000209", "lbl" : "gender identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A social identity information content entity that is about whether some person identifies as some gender." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000210", "lbl" : "female gender identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A gender identity information content entity that is about some person's identifying as female in gender." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000211", "lbl" : "male gender identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A gender identity information content entity that is about some person's identifying as male in gender." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000212", "lbl" : "non-binary identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A gender identity information content entity that is about some person's identifying as non-binary in gender." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000213", "lbl" : "racial identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A social identity information content entity that is about whether some person identifies as some race." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000214", "lbl" : "OMB racial identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A racial identity information content entity that uses OMB terminology and definitions for race or terminology that is strictly mapped onto the OMB race terms." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000215", "lbl" : "OMB American Indian or Alaska Native identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An OMB racial identity information content entity that is about some person's identifying as American Indian or Alaska Native, which is intended to mean having origins in any of the original peoples of North and South America (including Central America), and maintains tribal affiliation or community attachment." }, "comments" : [ "This definition corresponds to that used by OMB. It is worth noting that the OMB definition from which this one is derived is problematic, in that it implies that one's race cannot be Native American or Alaskan Native unless one maintains tribal affiliations or community attachment." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000216", "lbl" : "OMB Asian identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An OMB racial identity information content entity that is about some person's identifying as Asian, which is intended to mean having origins in any of the original peoples of the Far East, Southeast Asia, or the Indian subcontinent." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000217", "lbl" : "OMB black or African American identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An OMB racial identity information content entity that is about some person's identifying as black or African American which is intended to mean having origins in any of the black racial groups of Africa." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000218", "lbl" : "OMB Native Hawaiian or other Pacific Islander identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An OMB racial identity information content entity that is about some person's identifying as Native Hawaiian or other Pacific Islander, which is intended to mean having origins in any of the original peoples of Hawaii, Guam, Samoa, or other Pacific Islands." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000219", "lbl" : "OMB white identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An OMB racial identity information content entity that is about some person's identifying as white which is intended to mean having origins in any of the original peoples of Europe, the Middle East, or North Africa." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000220", "lbl" : "sexual orientation identity information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "A social identity information content entity that is about whether some person identifies as having some sexual orientation." }, "basicPropertyValues" : [ { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Amanda Hicks" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000221", "lbl" : "residence ZIP code information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity that is about some geographical region, in which a postal delivery route denoted by a particular ZIP code is realized, and that is the specified output of a disclosure of residence." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Hansi Zhang" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000222", "lbl" : "debt obligation", "type" : "CLASS", "meta" : { "definition" : { "val" : "A directive information entity that prescribes that something will be transferred from some human or organization that is the bearer of a duty holder role to another human or organization that is the bearer of a claimant role." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "debt obligation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Three Arrows Capital declared bankruptcy on July 1, 2022 after defaulting on a $665 million debt obligation owed to Voyager Digital." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000223", "lbl" : "disclosure of residence", "type" : "CLASS", "meta" : { "definition" : { "val" : "A social act that creates an information content entity that is about some geographical region in which a human being dwells." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Hansi Zhang" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000224", "lbl" : "electronic health record data set", "type" : "CLASS", "meta" : { "definition" : { "val" : "A data set whose members are obtained from one or more electronic health records." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "EHR data set" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Alan Ruttenberg" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brocchausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000225", "lbl" : "health care claim data set", "type" : "CLASS", "meta" : { "definition" : { "val" : "A data set whose members are the specified output of some process of adjudicating health care insurance claims (and whose inputs are at least partly some members of a health care billing data set)." }, "comments" : [ "It covers prescription claims because pharmacies bill insurance companies for patients’ prescriptions via submitting insurance claims.", "The insurance claim is submitted to the insurance company by either the patient or the provider. It is not necessarily always the provider, although in the United States, it typically is.", "The outcome of the adjudication of a claim in the claims dataset could be favorable or unfavorable for the healthcare provider, the patient, or both. 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Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000501", "lbl" : "income data item", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000502", "lbl" : "government assistance health care plan data item", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000503", "lbl" : "health care plan data item", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000504", "lbl" : "government assistance income data item", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000505", "lbl" : "WIC data item", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000506", "lbl" : "socio-economic data item", "type" : "CLASS" }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00000507", "lbl" : "obsolete non-binary gender identity datum", "type" : "CLASS", "meta" : { "definition" : { "val" : "A gender identity datum resulting from a gender identification process in which ‘non binary’ is selected based on the participant's subjective sense of gender." }, "comments" : [ "Alternatively: A gender identity datum stating that a person's subjective sense of gender is non-binary.)\n\nExamples of usage: ‘Non-binary’, ‘Trigender’, ‘Agender’, ‘Genderfluid’, ‘2’ (intended to refer to a non-binary gender role)" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "non-binary gender identity datum" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Paul Fabry" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "non-binary gender identity information content entity" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002025", "lbl" : "ISO 639-1 code", "type" : "PROPERTY", "meta" : { "comments" : [ "ISO 639-1 assigns two-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-1 code that designates them in that standard system." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ISO 639-1 code" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002026", "lbl" : "ISO 639-2/B code", "type" : "PROPERTY", "meta" : { "comments" : [ "ISO 639-2/B assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-2/B ('B' is for \"bibliographic applications\") code that designates them in that standard system." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ISO 639-2/B code" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002027", "lbl" : "ISO 639-2/T code", "type" : "PROPERTY", "meta" : { "comments" : [ "ISO 639-2/T assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-2/T ('T' is for \"terminology applications\") code that designates them in that standard system." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ISO 639-2/T code" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002028", "lbl" : "ISO 639-3 code", "type" : "PROPERTY", "meta" : { "comments" : [ "ISO 639-3 assigns three-character identifiers to individual human languages. This annotation property is for use in annotating OWL2 individuals in OMRSE that represent languages with their appropriate ISO 639-3 code that designates them in that standard system." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "ISO 639-3 code" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002029", "lbl" : "education process", "type" : "CLASS", "meta" : { "definition" : { "val" : "A planned process with an active participant who acquires mental representations of information content entities (ICEs), which had no previous mental representation in the cognitive system, and through repeated use or application of these ICEs either (1) becomes the bearer of a new instance of some type of capability, and the participant was not previously the bearer of that instance of that type of capability, (2) \"improves\" an existing capability as demonstrated through realization(s) of that capability, and/or (3) loses a capability whose realization is considered negative." }, "comments" : [ "An interesting question is whether there must be another participant who is the \"educator\". Some might object that many people are \"self taught\". A real case of being self taught is the first person who learned to play a stringed instrument, or to spin a ball on the tip of a finger. There was no previous information about that type of skill. The ICEs acquired are via one's sensory systems (vision, proprioception, auditory, etc.).\n\nOn the other hand, in the case of those who are self-taught by reading books or watching videos, or acquiring some other form of ICEs concretized outside their brain, one argument might be that the author of those ICEs somehow \"plays a role\" in the education, although they cannot participate in the education process itself (If I read Aristotle, and through repeated application of the information I acquire through doing so, develop the ability to write better ontology definitions, surely Aristotle did not actively participate in my particular education process, although he did influence it in a very real way).", "The loss of a \"bad\" capability is something like losing a bad golf swing and replacing it with a good one. Also a capability to disrupt the classroom might be something an educating process diminishes possibly to the point of \"removal\" in a student.\n\nThis addition to the definition notwithstanding, we do not intend to incorporate the receipt of punishment into the definition of educating." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "educating" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "learning process" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An act of acquiring new information and repeatedly applying that information to develop a new skill, improve an existing skill, and/or losing a skill at doing something \"bad\"." } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002030", "lbl" : "educational objective", "type" : "CLASS", "meta" : { "definition" : { "val" : "An objective specification that describes the type of capability or capabilities to be imparted or improved by its realization, which is an educating (education process)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "educational objective specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "An objective specification that describes the new knowledge & skill(s) to be obtained via an education process." } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002031", "lbl" : "educational program", "type" : "CLASS", "meta" : { "definition" : { "val" : "A plan specification with an educational objective specification as part." }, "comments" : [ "Very broad. Covers everything from grade school to high school to college to graduate education, a MOOC, an individual course, a tutorial at a conference, a continuing education course or program, an informed consent video, etc, etc." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "educational plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "A plan specification with one or more educational objectives." } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002032", "lbl" : "completing a program of education", "type" : "CLASS", "meta" : { "definition" : { "val" : "An educating that realizes a concretization of some program of education." }, "comments" : [ "Note that parent class 'educating' and referenced class 'program of education' are defined elsewhere in this education module of OMRSE.", "This class refers extremely broadly to the successful realization of any program of education: a single course, first grade, MD, PhD, high school, the ninth grade, getting a black belt in karate, getting a master mechanic certification, a bachelor's degree, a masters degree, a graduate certificate, early childhood education program, and even getting a certificate at the end of some week-long workshop, summer camp, a certifcate from a cooking class, an actuarial certification." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "completing a program of education" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002033", "lbl" : "early childhood education plan specification", "type" : "CLASS", "meta" : { "definition" : { "val" : "An educational program whose intended active participant, when a concretization of it is realized, is a human child of age birth to 8 years or a human fetus prior to birth." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "early childhood education program" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "pre-K education program" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "prekindergarten education program" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "preschool education program" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://apps.who.int/iris/bitstream/handle/10665/69729/a91213.pdf?sequence" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002034", "lbl" : "primary education program", "type" : "CLASS", "meta" : { "definition" : { "val" : "An education plan specification with one or more primary education objective specifications as parts, and these are the only objective specifications it has as parts." }, "comments" : [ "In the united states, also called \"elementary education\"", "It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only primary education objectives as parts, and we have to introduce the double negative in the class axiom.", "Primary education provides learning and educational activities typically designed to provide students with fundamental skills in reading, writing and mathematics (i.e. literacy and numeracy), and to establish a sound foundation for learning and solid understanding of core areas of knowledge and personal development, preparing for lower secondary education. It aims at learning at a basic level of complexity with little if any specialisation." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "primary education plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "elementary education" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002035", "lbl" : "primary education objective", "type" : "CLASS", "meta" : { "definition" : { "val" : "An education objective specification that has a concretization that, when realized, results in the active participant's acquisition and development of fundamental skills in reading, writing and mathematics (i.e. literacy and numeracy)." }, "comments" : [ "By the end of primary education, the student has established a sound foundation for learning and solid understanding of core areas of knowledge and personal development, preparing for lower secondary education. It aims at learning at a basic level of complexity with little if any specialisation." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "primary education objective specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://uis.unesco.org/en/glossary-term/primary-education-isced-1" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002036", "lbl" : "lower secondary education objective", "type" : "CLASS", "meta" : { "definition" : { "val" : "An education objective specification that has a concretization that, when realized, confers to the active participant skills and knowledge in subject areas more specialized than basic reading, writing, and mathematics, with the overall goal of laying the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities." }, "comments" : [ "Examples of specific subjects could--but are not necessarily required to--include biology, history, science, literature, music, art. Programs at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.", "Programmes at ISCED level 2, or ‘lower secondary’ education, are typically designed to build upon the fundamental teaching and learning processes which begin at ISCED level 1. Usually, the educational aim is to lay the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities. Programmes at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "lower secondary education objective specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://uis.unesco.org/en/glossary-term/lower-secondary-education-isced-2" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002037", "lbl" : "awarding an academic degree", "type" : "CLASS", "meta" : { "definition" : { "val" : "A deontic document act that has as specified output an academic degree and that confers on recipient of the academic degree the recognition and the claims and obligations that accompany the degree." }, "comments" : [ "Different degrees have different claims and obligations associated with them. For example, having a medical degree (either M.D. or D.O.) entitles a person to sit for stage 3 of the US Medical Licensing Exam (otherwise one may not take the exam)." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "awarding of an academic degree" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002038", "lbl" : "basic education program", "type" : "CLASS", "meta" : { "definition" : { "val" : "An education plan specification that has as part both a primary educational objective specification and a lower secondary educational objective specification." }, "comments" : [ "Most nations in the world mandate that children complete at least a basic education program. Some nations go further and include upper secondary education after basic education.", "Whole range of educational activities, taking place in various settings, that aim to meet basic learning needs as defined in the World Declaration on Education for All (Jomtien, Thailand, 1990). According to ISCED standard, basic education comprises primary education (first stage of basic education) and lower secondary education (second stage). It also covers a wide variety of non-formal and informal public and private activities intended to meet the basic learning needs of people of all ages." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "basic education plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://uis.unesco.org/en/glossary-term/basic-education" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002039", "lbl" : "lower secondary education program", "type" : "CLASS", "meta" : { "definition" : { "val" : "An education plan specification with one or more lower secondary education objective specifications as parts, and these are the only objective specifications it has as parts." }, "comments" : [ "It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only lower secondary education objectives as parts, and we have to introduce the double negative in the class axiom.", "Programmes at ISCED level 2, or ‘lower secondary’ education, are typically designed to build upon the fundamental teaching and learning processes which begin at ISCED level 1. Usually, the educational aim is to lay the foundation for lifelong learning and human development on which education systems may systematically expand further educational opportunities. Programmes at this level are usually organized around a more subject-oriented curriculum, introducing theoretical concepts across a broad range of subjects.", "Requires successful completion of a primary education program as a pre-requisite." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "lower secondary education plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002040", "lbl" : "upper secondary education objective", "type" : "CLASS", "meta" : { "definition" : { "val" : "An educational objective specification that has a concretization that, when realized, confers on the active participant skills and knowledge that prepare them for tertiary education, or employment, or both." }, "comments" : [ "Programmes at ISCED level 3, or ‘upper secondary’ education, are typically designed to complete secondary education in preparation for tertiary education, or to provide skills relevant to employment, or both. Programmes at this level offer students more varied, specialised and in-depth instruction than programmes at lower secondary education (ISCED level 2). They are more differentiated, with an increased range of options and streams available." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "upper secondary education objective specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://uis.unesco.org/en/glossary-term/upper-secondary-education-isced-3" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002041", "lbl" : "upper secondary education program", "type" : "CLASS", "meta" : { "definition" : { "val" : "An education plan specification with one or more upper secondary education objective specifications as parts, and these are the only objective specifications it has as parts." }, "comments" : [ "It can still have action specifications as parts, and possibly other ICEs as parts. That's why we cannot say it has only lower secondary education objectives as parts, and we have to introduce the double negative in the class axiom.", "Programmes at ISCED level 3, or ‘upper secondary’ education, are typically designed to complete secondary education in preparation for tertiary education, or to provide skills relevant to employment, or both. Programmes at this level offer students more varied, specialised and in-depth instruction than programmes at lower secondary education (ISCED level 2). They are more differentiated, with an increased range of options and streams available.", "Requires successful completion of a lower secondary education program as a pre-requisite." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "upper secondary education plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002042", "lbl" : "higher education program", "type" : "CLASS", "meta" : { "comments" : [ "Includes college, university, community college, professional schools (MD, RN, PharmD, PT, OT, DDS, dental hygienist, etc.), and so on.", "Refers to all higher education beyond secondary education, and thus encompasses ISCED levels 5 and above, which will eventually be subclasses of this one.", "Requires successful completion of a secondary education program as a pre-requisite." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "higher education plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "post-secondary education plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "post-secondary education program" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002043", "lbl" : "higher education objective", "type" : "CLASS", "meta" : { "definition" : { "val" : "An educational objective specification that has a concretization that, when realized, confers on the active participant skills and knowledge in a specialized discipline, and culminates in the awarding of an academic degree." }, "comments" : [ "Refers to all education beyond secondary education that leads to the awarding of an academic degree." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "higher education objective specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "post-secondary education objective" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002044", "lbl" : "vocational education objective", "type" : "CLASS", "meta" : { "definition" : { "val" : "An educational objective specification that has a concretization that, when realized, is realized by a process that confers on the active participant knowledge and skills required to realize a particular type of employee role for a given occupation or trade." }, "comments" : [ "Usually the skills are a major focus moreso than in other types of education. For example, auto mechanics, plumbers, and electricians." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "vocational education objective specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-isced-2011-en.pdf" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002045", "lbl" : "highest level of education data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "A socio-economic data item that is about a person and their completion of an education program (and its type), where that education program is the last one in a sequence (of education programs) that the person has completed, where each education program completed except the last one is a pre-requisite to the education program completed after it." }, "comments" : [ "This data item in a typical attribute-value system such as table, XML, JSON takes values like \"secondary education\", \"Associate Degree\", \"Bachelor Degree\", \"High School\", and so on." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "highest level of education socio-economic data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002046", "lbl" : "vocational education program", "type" : "CLASS", "meta" : { "definition" : { "val" : "An educational plan specification that has a vocational objective specification as part." }, "comments" : [ "Vocational education programs are designed for learners to acquire the knowledge, skills and competencies specific to a particular occupation, trade, or class of occupations or trades. Such programs may have work-based components (e.g. apprenticeships, dual-system education programmes). Successful completion of such programs leads to labor market-relevant, vocational qualifications acknowledged as occupationally-oriented by the relevant national authorities and/or the labor market." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "vocational education plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://uis.unesco.org/sites/default/files/documents/international-standard-classification-of-education-isced-2011-en.pdf" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002047", "lbl" : "kindergarten education program", "type" : "CLASS", "meta" : { "definition" : { "val" : "A primary education plan specification that specifies the competencies and information content entities that should be acquired by students in the first year of primary education in the United States." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "kindergarten education plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2020-09-02T12:38:43Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002048", "lbl" : "undergraduate higher education program", "type" : "CLASS", "meta" : { "definition" : { "val" : "A higher education plan specification that specifies the awarding of an associates or bachelors degree in the United States or equivalent degrees in other nations, and specifies as a pre-requisite the completion of some secondary education program." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "undergraduate higher education plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "undergraduate education program" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2020-09-02T12:52:46Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002049", "lbl" : "graduate higher education program", "type" : "CLASS", "meta" : { "definition" : { "val" : "A higher education plan specification that specifies the awarding of a graduate certificate or degree, and specifies as a pre-requisite the awarding of an undergraduate degree." }, "comments" : [ "Graduate degrees include masters, PhD, MD, PharmD, and other post-graduate professional degrees. To distinguish MS/PhD from the professional ones, subclass this class.", "The prerequisite degree is at the bachelors level or equivalent. An associates degree is almost never sufficient for entry into graduate education programs." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "graduate higher education plan specification" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "graduate education program" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2020-09-02T13:01:34Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002050", "lbl" : "highest level of education is grades 1 through 6 data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of first through sixth grade." }, "comments" : [ "Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.\n\nIt indicates completion of some to all of primary education in the United States." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "highest level of education is completion of grades one through six socio-economic data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2020-09-02T13:23:46Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002051", "lbl" : "highest level of education is grades 7 through 9 data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of seventh (7th) through ninth (9th) grade." }, "comments" : [ "Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.\n\nIt indicates completion of some to all of lower secondary education in the United States." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "highest level of education is completion of grades seven through nine socio-economic data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2020-09-02T13:27:15Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002052", "lbl" : "highest level of education is grades 10 through 12 data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is in the range of tenth (10th) through twelfth (12th) grade." }, "comments" : [ "Note: this broad, very loose level of grouping emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.\n\nIt indicates completion of some to all of upper secondary education in the United States." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "highest level of education is completion of grades ten through twelve socio-economic data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2020-09-02T13:27:50Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002053", "lbl" : "highest level of education is completion of undergraduate degree data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some undergraduate degree." }, "comments" : [ "Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "highest level of education is completion of some undergraduate degree socio-economic data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2020-09-02T13:28:27Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002054", "lbl" : "highest level of education is completion of graduate certificate or degree data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some graduate certificate or degree." }, "comments" : [ "Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "highest level of education is completion of some graduate degree socio-economic data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2020-09-02T13:28:49Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002055", "lbl" : "highest level of education is completion of vocaational education program data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is completion of some vocational education program." }, "comments" : [ "Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "highest level of education is completion of some vocational education program socio-economic data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2020-09-02T13:29:28Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002056", "lbl" : "highest level of education is completion of kindergarten data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is pre-kindergarten." }, "comments" : [ "Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI.\n\nIt indicates that a person has completed only early childhood education and nothing more." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "highest level of education is completion of kindergarten socio-economic data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2020-09-02T13:47:38Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002057", "lbl" : "highest level of education is completion of pre-kindergarten data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "A highest level of education socio-economic data item that represents the fact that the highest level of education achieved by an individual in the United States is kindergarten." }, "comments" : [ "Note: The requirement for this class emerged as an early requirement from the SODA project, funded by a PCORI Methods Grant, at the University of Florida with Dr. Yonghui Wu as PI." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "highest level of education is completion of pre-kindergarten socio-economic data item" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/creator", "val" : "http://orcid.org/0000-0002-9881-1017" }, { "pred" : "http://purl.org/dc/elements/1.1/date", "val" : "2020-09-02T13:48:10Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002058", "lbl" : "linguistic literacy competence", "type" : "CLASS", "meta" : { "definition" : { "val" : "A disposition borne by a human being that (1) has a linguistic competence as a dispositional part and (2) if realized, is realized by the bearer's achievement of some personal goal." }, "comments" : [ "Other dispositions that it can and likely does have as dispositional parts include cultural competencies, interpersonal competencies, competencies for navigating a society's systems of laws, claims, obligations, deontic declarations, and norms of financial and other economic exchange.", "The realization of this disposition by definition realizes the bearer's linguistic competence that is a dispositional part of this disposition. The realization of the linguistic competence would be an occurrent part of the realization of this disposition (and not a temporal part).", "Whereas linguistic competence may be afforded to non-human agents, literacy is nearly always considered in the context of human beings." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "language literacy competence" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "human literacy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "linguistic literacy" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Jiang Bian" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Xi Yang" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Yonghui Wu" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002059", "lbl" : "caregiver role", "type" : "CLASS", "meta" : { "definition" : { "val" : "A human social role that, if realized, is realized in providing assistance in the activities of daily living of another human being who possesses reduced capability to complete some of these activities alone." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "John Judkins" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002060", "lbl" : "family relationship", "type" : "CLASS", "meta" : { "definition" : { "val" : "A relational quality that inheres within two or more persons related as members of a domestic group, or a number of domestic groups linked through descent from a common ancestor, marriage, or adoption." }, "comments" : [ "We are also intending on including other family arrangements. This is something we are working on." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ERO_0002033" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "John Judkins" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002061", "lbl" : "monetary personal income data item", "type" : "CLASS", "meta" : { "definition" : { "val" : "A data item that is about the sum of earnings for some person(s) from various forms of payment or profits." }, "comments" : [ "We use the phrase ‘some person’ in the definition because this class can be about an individual's or a household's earnings. Similarly, we use 'personal income' in the label because the term is typically restricted to individuals and households. This class is also restricted to being about monetary forms of income." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Examples of monetary forms of payment include: wages, salary, or tips; interest generated by capital; dividends earned; lottery, game, or contest monetary winnings; alimony; royalties; trusts; pensions; receipt of rental payments; unemployment payments; social security payments; worker's compensation; social security payments; or profit from entrepreneurial activities." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Chris Stoeckert" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002062", "lbl" : "concretization-utilization process", "type" : "CLASS", "meta" : { "definition" : { "val" : "Process in which some participant utilizes some specifically dependent continuant as a concretization of some generically dependent continuant." }, "comments" : [ "Instances include any process that brings it about that some specifically dependent continuant begins to stand in a concretization relation to some generically dependent continuant, as well as any process in which someone makes use of a pre-established concretization relation. To be clear, instances do not include using concretizations of words or letters for purposes that do not make use of the concretization relations in which they stand (for example, hanging up a sign in a foreign language as a decoration because one likes the colors, despite having no idea what the sign says).", "Instances include, but are not limited to, processes that bring about cognitive concretizations." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Taking notes on a meeting is an example in which the concretization relation is newly established, since the SDCs that concretize the GDCs come into existence as the notes are written. In contrast, using slides prepared by someone else in order to convey information during a presentation is a case of using a concretization in which the performer neither brings the concretizing SDCs into existence nor is responsible for their standing in the concretization relation to the relevant GDCs. A nonlinguistic example is drawing the logo of one’s favorite brand, in which one creates a pattern that concretizes a GDC that is also concretized by patterns on products of the brand." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002063", "lbl" : "linguistic concretization-utilization process", "type" : "CLASS", "meta" : { "definition" : { "val" : "A concretization-utilization process in which the utilized specifically dependent continuant concretizes the generically dependent through use of some language." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002064", "lbl" : "concretization-interpretation process", "type" : "CLASS", "meta" : { "definition" : { "val" : "Process in which some participant infers that some particular specifically dependent continuant stands in the concretization relation to some particular generically dependent continuant." }, "comments" : [ "The interpretation need not be accurate. It may even be the case that the specifically dependent continuant has not previously concretized anything." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "For example, reading a text message that says, “It is raining outside,” and inferring that the words on the screen are meant to convey information about the weather. The pattern on the screen that corresponds to the words is the SDC, and the ICE about the rain is the GDC. Or, hearing your spouse say, “Can you come to the kitchen?” and then knowing that your spouse wants you to come to the kitchen. You have interpreted the patterns of the sound as concretizing a GDC about what your spouse wants. Or, seeing a drawing of a basketball player and inferring—perhaps incorrectly—that it is of Michael Jordan." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002065", "lbl" : "linguistic concretization-interpretation process", "type" : "CLASS", "meta" : { "definition" : { "val" : "A concretization-interpretation process in which the specifically dependent continuant is inferred to concretize the generically dependent continuant in a way that makes use of some language." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Sarah Bost" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002066", "lbl" : "linguistic competence", "type" : "CLASS", "meta" : { "definition" : { "val" : "A disposition that inheres in some material entity and is such that that, if realized, it is realized by either some linguistic concretization-utilization process or some linguistic concretization-interpretation process." }, "comments" : [ "When realized in a concretization-utilization process, the only relevant concretization may in some cases be a cognitive one, but that suffices to realize a linguistic competence. For example, suppose one begins to write a letter, planning out the words ahead of time, but is interrupted before beginning to write and never resumes. During the process of planning out the words and what one intends to communicate, one is already concretizing words cognitively, as well as considering which combinations of words one can use to concretize additional generically dependent continuants. In doing so, one performs processes that realize one's linguistic competence, without producing any concretizations other than those cognitive ones." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002068", "lbl" : "communication", "type" : "CLASS", "meta" : { "definition" : { "val" : "A process in which some participant shares some generically dependent continuant with some other participant. The former utilizes some specifically dependent continuant that concretizes the generically dependent continuant intended to be shared, while the latter interprets that specifically dependent continuant to concretize some particular generically dependent continuant, aiming to accurately infer the other participant’s intent." }, "comments" : [ "For example, if you tell someone, “It is raining,” you produce sounds that have patterns that concretize information about the weather. Your utilization of that concretization is part of the communication. When the other person hears you, they interpret those patterns to concretize something, which may or may not be the same as what you intended to convey. In other words, they interpret the sounds you produce to have meanings associated with them, and that interpretation process is another part of the communication. If a process does not have a part of each type, it is not a communication.", "The interpretation need not correspond exactly to what was intended by the other participant.", "The term 'participant' in the definition need not refer to a human agent." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002069", "lbl" : "language", "type" : "CLASS", "meta" : { "definition" : { "val" : "A disposition that (i) is an aggregate of linguistic competences, considered as forming a distinct group on the basis of perceived common characteristics, such as mutual intelligibility among their bearers, in addition to historical or cultural factors; (ii) if realized, is realized in any and all realizations of those linguistic competences; and (iii) inheres in a linguistic community." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "William R. Hogan" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "S. Clint Dowland" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002070", "lbl" : "disclosure of preferred language", "type" : "CLASS", "meta" : { "definition" : { "val" : "A communication in which some participant states a preference for some communicative process to be in a certain language, via some concretization of some preferred language information content entity." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002071", "lbl" : "preferred language information content entity", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity that is about some person and some language, and that conveys the language with which that person prefers to communicate within some given context." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Matthew Diller" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "S. Clint Dowland" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "William R. Hogan" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OMRSE_00002072", "lbl" : "role in human social processes", "type" : "CLASS", "meta" : { "definition" : { "val" : "A role that inheres in some entity that is realized in a social act." }, "comments" : [ "Previous definition: A role played by an entity in human social processes." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Matthew Diller" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/omrse/releases/2023-10-08/omrse.owl" }, { "pred" : "http://purl.org/dc/elements/1.1/contributor", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OOSTT_00000030", "lbl" : "OOSTT user-centered description", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A description of an OOSTT class that is aimed at the OOSTT user community and not meant to be definition for use in ontology development, curation or maintenance." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OOSTT_00000074", "lbl" : "academic degree", "type" : "CLASS", "meta" : { "definition" : { "val" : "An information content entity that is the specified outcome of and documents the sucessful completion of a tertiary education program." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "John Judkins" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/OOSTT_00000030", "val" : "Recognized degree awarded after successful completion of a college or post-graduate porgram." } ] } }, { "id" : "http://purl.obolibrary.org/obo/OOSTT_00000081", "lbl" : "associate degree", "type" : "CLASS", "meta" : { "definition" : { "val" : "An academic degree awarded by colleges and universities upon completion of a program of study lasting two years." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "John Judkins" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/w/index.php?title=Associate_degree&oldid=723897149" }, { "pred" : "http://purl.obolibrary.org/obo/OOSTT_00000030", "val" : "Recognition awarded after completion of a specific curriculum from an accredited tertiary education provider that falls between high school and bachelor's degree program." } ] } }, { "id" : "http://purl.obolibrary.org/obo/OOSTT_00000082", "lbl" : "master's degree", "type" : "CLASS", "meta" : { "definition" : { "val" : "An academic degree awarded by universities upon completion of a course of study demonstrating a mastery or high-order overview of a specific field of study or area of professional practice.[1] Within the area studied, graduates are posited to possess advanced knowledge of a specialized body of theoretical and applied topics; high order skills in analysis, critical evaluation, or professional application; and the ability to solve complex problems and think rigorously and independently." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "John Judkins" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/w/index.php?title=Master%27s_degree&oldid=726036185" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OOSTT_00000083", "lbl" : "bachelor's degree", "type" : "CLASS", "meta" : { "definition" : { "val" : "An academic degree awarded by colleges and universities upon completion of a course of study lasting three to seven years." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "John Judkins" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/w/index.php?title=Bachelor%27s_degree&oldid=725713923" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OOSTT_00000084", "lbl" : "bachelor's of nursing degree", "type" : "CLASS", "meta" : { "definition" : { "val" : "An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a bachelor's of nursing program." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "John Judkins" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/w/index.php?title=Bachelor_of_Science_in_Nursing&oldid=725962822" } ] } }, { "id" : "http://purl.obolibrary.org/obo/OOSTT_00000086", "lbl" : "master's in the science of nursing degree", "type" : "CLASS", "meta" : { "definition" : { "val" : "An academic degree in the science and principles of nursing, granted by an accredited tertiary education provider after the successful completion of a master's of nursing program." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "John Judkins" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Mathias Brochhausen" }, { "pred" : "http://purl.obolibrary.org/obo/OOSTT_00000030", "val" : "An advanced academic degree in the principles and practices of nursing, with a focus on administration, education, or advanced nursing practice, granted by an accredited college or university after the successful completion of a master's of nursing program." } ] } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000001", "lbl" : "quality", "type" : "CLASS", "meta" : { "definition" : { "val" : "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities", "xrefs" : [ "PATOC:GVG" ] } } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000051", "lbl" : "morphology", "type" : "CLASS", "meta" : { "definition" : { "val" : "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "morphology" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/pato.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000122", "lbl" : "length", "type" : "CLASS", "meta" : { "definition" : { "val" : "A 1-D extent quality which is equal to the distance between two points." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "length" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/pato.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0000125", "lbl" : "mass", "type" : "CLASS", "meta" : { "definition" : { "val" : "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "mass" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/pato.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001018", "lbl" : "physical quality", "type" : "CLASS", "meta" : { "definition" : { "val" : "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "physical quality" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/pato.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001025", "lbl" : "pressure", "type" : "CLASS", "meta" : { "subsets" : [ "http://purl.org/obo/owl/obo#attribute_slim" ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", "val" : "_:genid2147485205" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasDefinition", "val" : "_:genid2147485206" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" } ] } }, { "id" : "http://purl.obolibrary.org/obo/PATO_0001241", "lbl" : "physical object quality", "type" : "CLASS", "meta" : { "definition" : { "val" : "A quality which inheres in a continuant." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "physical object quality" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/pato.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/PCO_0000020", "lbl" : "family", "type" : "CLASS", "meta" : { "definition" : { "val" : "A domestic group, or a number of domestic groups linked through descent (demonstrated or stipulated) from a common ancestor, marriage, or adoption." }, "comments" : [ "Family membership through marriage or adoption apply primarily to human families. In most species, family membership is defined by common anscestry." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000123" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Needs axioms for family relationships." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25173" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000052", "lbl" : "characteristic of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "inheres in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this fragility is a characteristic of this vase" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this red color is a characteristic of this apple" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "inheres_in" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000053", "lbl" : "has characteristic", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of characteristic_of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "bearer of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this apple is bearer of this red color" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this vase is bearer of this fragility" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "bearer_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is bearer of" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000056", "lbl" : "participates in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a continuant and a process, in which the continuant is somehow involved in the process" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "participates in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this blood clot participates in this blood coagulation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this input material (or this output material) participates in this process" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this investigator participates in this investigation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "participates_in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000057", "lbl" : "has_participant", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a process and a continuant, in which the continuant is somehow involved in the process" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "has participant" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this blood coagulation has participant this blood clot" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this investigation has participant this investigator" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this process has participant this input material (or this output material)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_participant" }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" }, { "pred" : "http://purl.org/dc/terms/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:has_participant" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000058", "lbl" : "is concretized as", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is concretized as" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000059", "lbl" : "concretizes", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "concretizes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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)." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/obi.owl" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000079", "lbl" : "function of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" }, "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this catalysis function is a function of this enzyme" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "function_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is function of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000080", "lbl" : "quality of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" }, "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this red color is a quality of this apple" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "A quality inheres in its bearer at all times for which the quality exists." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is quality of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "quality_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000081", "lbl" : "role of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" }, "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this investigator role is a role of this person" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is role of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "role_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000085", "lbl" : "has function", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_function" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000086", "lbl" : "has quality", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this apple has quality this red color" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_quality" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000087", "lbl" : "has role", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this person has role this investigator role (more colloquially: this person has this role of investigator)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_role" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000091", "lbl" : "has disposition", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0000092", "lbl" : "disposition of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of has disposition" }, "comments" : [ "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." ], "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001000", "lbl" : "derives from", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this cell derives from this parent cell (cell division)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this nucleus derives from this parent nucleus (nuclear division)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "derives_from" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001001", "lbl" : "derives into", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this parent cell derives into this cell (cell division)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this parent nucleus derives into this nucleus (nuclear division)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "derives_into" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001015", "lbl" : "location of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "is location of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my head is the location of my brain" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this cage is the location of this rat" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "location_of" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001025", "lbl" : "located in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", "val" : "located in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my brain is located in my head" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "this rat is located in this cage" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "located_in" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://purl.org/dc/elements/1.1/source", "val" : "http://www.obofoundry.org/ro/#OBO_REL:located_in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0001900", "lbl" : "temporal interpretation", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002000", "lbl" : "2D boundary of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "the surface of my skin is a 2D boundary of my body" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "2D_boundary_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "boundary of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is 2D boundary of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is boundary of" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002002", "lbl" : "has 2D boundary", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "my body has 2D boundary the surface of my skin" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has boundary" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has_2D_boundary" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002012", "lbl" : "occurrent part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A part of relation that applies only between occurrents." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002013", "lbl" : "has regulatory component activity", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:30:46Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002014", "lbl" : "has negative regulatory component activity", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "comments" : [ "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'." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:01Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002015", "lbl" : "has positive regulatory component activity", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "comments" : [ "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'." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:31:17Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002017", "lbl" : "has component activity", "type" : "PROPERTY", "meta" : { "comments" : [ "A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:44:33Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002018", "lbl" : "has component process", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-05-24T09:49:21Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002022", "lbl" : "directly regulated by", "type" : "PROPERTY", "meta" : { "comments" : [ "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." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:24Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002023", "lbl" : "directly negatively regulated by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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.", "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:38Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002024", "lbl" : "directly positively regulated by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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.", "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-17T13:52:47Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002025", "lbl" : "has effector activity", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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.", "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations." ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-09-22T14:14:36Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002081", "lbl" : "before or simultaneous with", "type" : "PROPERTY", "meta" : { "comments" : [ "Primitive instance level timing relation between events" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "<=" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002083", "lbl" : "before", "type" : "PROPERTY", "meta" : { "comments" : [ "t1 before t2 iff:= t1 before_or_simulataneous_with t2 and not (t1 simultaeous_with t2)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002086", "lbl" : "ends after", "type" : "PROPERTY", "meta" : { "comments" : [ "X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002087", "lbl" : "immediately preceded by", "type" : "PROPERTY", "meta" : { "comments" : [ "X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "starts_at_end_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002090", "lbl" : "immediately precedes", "type" : "PROPERTY", "meta" : { "comments" : [ "X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)" ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "David Osumi-Sutherland" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ends_at_start_of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "meets" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/BFO_0000063" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002131", "lbl" : "overlaps", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x overlaps y if and only if there exists some z such that x has part z and z part of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002180", "lbl" : "has component", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:Componency" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", "lbl" : "regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0001-7476-6306" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-3837-8864" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "GO" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "regulates (processual)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", "val" : "false" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002212", "lbl" : "negatively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "negatively regulates (process to process)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002213", "lbl" : "positively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "positively regulates (process to process)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002215", "lbl" : "capable of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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. " }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function realized in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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)\"." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002216", "lbl" : "capable of part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has function in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002217", "lbl" : "obsolete actively participates in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "OBSOLETE x actively participates in y if and only if x participates in y and x realizes some active role" }, "comments" : [ "Obsoleted as the inverse property was obsoleted." ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "agent in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002608" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002218", "lbl" : "obsolete has active participant", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x has participant y if and only if x realizes some active role that inheres in y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "'heart development' has active participant some Shh protein" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This may be obsoleted and replaced by the original 'has agent' relation" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has agent" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000412", "val" : "http://purl.obolibrary.org/obo/ro.owl" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0100001", "val" : "http://purl.obolibrary.org/obo/RO_0002500" } ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002222", "lbl" : "temporally related to", "type" : "PROPERTY", "meta" : { "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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." }, { "pred" : "http://purl.org/dc/terms/source", "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002223", "lbl" : "starts", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of starts with" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "Allen" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002224", "lbl" : "starts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(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." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "started by" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002229", "lbl" : "ends", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of ends with" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002230", "lbl" : "ends with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(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." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "Chris Mungall" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "finished by" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002231", "lbl" : "has start location", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "starts with process that occurs in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002232", "lbl" : "has end location", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "ends with process that occurs in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002233", "lbl" : "has input", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "consumes" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Has_input" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002234", "lbl" : "has output", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "produces" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Has_output" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002263", "lbl" : "acts upstream of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "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." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002264", "lbl" : "acts upstream of or within", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "affects" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002304", "lbl" : "causally upstream of, positive effect", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "comments" : [ "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" ], "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002411" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Causally_upstream_of,_positive_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002305", "lbl" : "causally upstream of, negative effect", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" }, { "pred" : "http://purl.org/dc/terms/creator", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Causally_upstream_of,_negative_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002314", "lbl" : "characteristic of part of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "inheres in part of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002323", "lbl" : "mereotopologically related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A mereological relationship or a topological relationship" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", "lbl" : "enables", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c enables p iff c is capable of p and c acts to execute p." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "catalyzes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "has" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is catalyzing" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is executing" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enables" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002328", "lbl" : "functionally related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002329", "lbl" : "part of structure that is capable of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "false" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002331", "lbl" : "involved in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "actively involved in" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "enables part of" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002333", "lbl" : "enabled by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of enables" }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enabled_by" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002334", "lbl" : "regulated by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of regulates" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "regulated by (processual)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002335", "lbl" : "negatively regulated by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of negatively regulates" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002336", "lbl" : "positively regulated by", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of positively regulates" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002350", "lbl" : "member of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "is member of is a mereological relation between a item and a collection." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An organism that is a member of a population of organisms" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "is member of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "member part of" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "SIO" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002351", "lbl" : "has member", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "has member is a mereological relation between a collection and an item." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "SIO" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0001900", "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002352", "lbl" : "input of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of has input" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002353", "lbl" : "output of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of has output" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002404", "lbl" : "causally downstream of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of upstream of" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002405", "lbl" : "immediately causally downstream of", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", "val" : "http://purl.obolibrary.org/obo/IAO_0000428" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002407", "lbl" : "indirectly positively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "indirectly activates" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002213" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002409", "lbl" : "indirectly negatively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "indirectly inhibits" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002579", "val" : "http://purl.obolibrary.org/obo/RO_0002212" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002410", "lbl" : "causally related to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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.", "xrefs" : [ "https://en.wikipedia.org/wiki/Causality" ] }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe 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.\n\nFor 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.\n\nFor 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.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002411", "lbl" : "causally upstream of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002412", "lbl" : "immediately causally upstream of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002411" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002418", "lbl" : "causally upstream of or within", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "affects" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "influences (processual)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002427", "lbl" : "causally downstream of or within", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "inverse of causally upstream of or within" }, "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002428", "lbl" : "involved in regulation of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", "lbl" : "involved in positive regulation of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002430", "lbl" : "involved in negative regulation of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002431", "lbl" : "involved in or involved in regulation of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "OWL does not allow defining object properties via a Union" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "involved in or reguates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002432", "lbl" : "is active in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure.", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "enables activity in" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A protein that enables activity in a cytosol." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "executes activity in" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Is_active_in" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", "lbl" : "interacts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "in pairwise interaction with" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Considering relabeling as 'pairwise interacts with'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "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." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" }, { "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", "val" : "http://purl.obolibrary.org/obo/MI_0914" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002436", "lbl" : "molecularly interacts with", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "binds" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "molecularly binds with" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000353" }, { "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", "val" : "http://purl.obolibrary.org/obo/MI_0915" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002447", "lbl" : "phosphorylates", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002448", "lbl" : "directly regulates activity of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly controls" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002449", "lbl" : "directly negatively regulates activity of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly decreases activity of" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-4639-4431" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly inhibits" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002450", "lbl" : "directly positively regulates activity of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly increases activity of" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-4639-4431" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", "val" : "directly activates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002479", "lbl" : "has part that occurs in", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002481", "lbl" : "is kinase activity", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002500", "lbl" : "causal agent in process", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002501", "lbl" : "causal relation between processes", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002502", "lbl" : "depends on", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002506", "lbl" : "causal relation between entities", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "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" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002559", "lbl" : "causally influenced by", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "causally influenced by (entity-centric)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "lbl" : "interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002564", "lbl" : "molecular interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002566", "lbl" : "causally influences", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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)." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-4639-4431" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "causally influences (entity-centric)" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002577", "lbl" : "system", "type" : "CLASS", "meta" : { "definition" : { "val" : "A material entity consisting of multiple components that are causally integrated." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://www.jbiomedsem.com/content/4/1/43" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002578", "lbl" : "directly regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p directly regulates q iff p is immediately causally upstream of q and p regulates q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly regulates (processual)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002575", "val" : "http://purl.obolibrary.org/obo/RO_0002211" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002581", "lbl" : "is a defining property chain axiom", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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" } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002582", "lbl" : "is a defining property chain axiom where second argument is reflexive", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002584", "lbl" : "has part structure that is capable of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002595", "lbl" : "causal relation between material entity and a process", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002596", "lbl" : "capable of regulating", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "pyrethroid -> growth" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002597", "lbl" : "capable of negatively regulating", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002598", "lbl" : "capable of positively regulating", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "renin -> arteriolar smooth muscle contraction" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002608", "lbl" : "process has causal agent", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Inverse of 'causal agent in process'" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002629", "lbl" : "directly positively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly positively regulates (process to process)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Directly_positively_regulates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002630", "lbl" : "directly negatively regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", "val" : "directly negatively regulates (process to process)" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Directly_negatively_regulates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0003000", "lbl" : "produces", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "a produces b if some process that occurs_in a has_output b, where a and b are material entities. 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"http://purl.obolibrary.org/obo/IAO_0000125" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0001-9114-8737" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004028", "lbl" : "realized in response to stimulus", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2017-12-26T19:45:49Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004031", "lbl" : "enables subfunction", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-25T23:20:13Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004032", "lbl" : "acts upstream of or within, positive effect", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002264" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:49:30Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : 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"http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002263" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-01-26T23:53:22Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of,_negative_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004046", "lbl" : "causally upstream of or within, negative effect", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002418" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:05Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_negative_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004047", "lbl" : "causally upstream of or within, positive effect", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004049", "val" : "http://purl.obolibrary.org/obo/RO_0002418" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2018-03-13T23:55:19Z" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004096", "lbl" : "DEPRECATED inheres 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See comments on that relation for more information." ], "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0004097", "lbl" : "DEPRECATED bearer of", "type" : "PROPERTY", "meta" : { "deprecated" : true } }, { "id" : "http://purl.obolibrary.org/obo/RO_0009501", "lbl" : "realized in response to", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "triggered by process", "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph." }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-6996-0040" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-7073-9172" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0002-8461-9745" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://docs.google.com/document/d/1KWhZxVBhIPkV6_daHta0h6UyHbjY2eIrnON1WIRGgdY/edit" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0010001", "lbl" : "generically depends on", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "A generically dependent continuant *b* generically depends on an independent continuant *c* at time *t* means: there inheres in *c* a specifically deendent continuant which concretizes *b* at *t*." }, "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "g-depends on" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Genetic information generically depend on molecules of DNA." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The novel *War and Peace* generically depends on this copy of the novel." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The pattern shared by chess boards generically depends on any chess board." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "The score of a symphony g-depends on a copy of the score." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "This pdf file generically depends on this server." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "[072-ISO]" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0010002", "lbl" : "is carrier of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "*b* is carrier of *c* at time *t* if and only if *c* *g-depends on* *b* at *t*" }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "Molecules of DNA are carriers of genetic information." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "This copy of *War and Peace* is carrier of the novel written by Tolstoy." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", "val" : "This hard drive is carrier of these data items." }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", "val" : "[072-ISO]" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0011002", "lbl" : "regulates activity of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012011", "lbl" : "indirectly causally upstream of", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "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." }, "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0003-1813-6857" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2022-09-26T06:07:17Z" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012012", "lbl" : "indirectly regulates", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "p 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