diff --git a/oeo-imports/iao/archive/extract-iao-module.sh b/oeo-imports/iao/archive/extract-iao-module.sh new file mode 100644 index 0000000..0cff296 --- /dev/null +++ b/oeo-imports/iao/archive/extract-iao-module.sh @@ -0,0 +1,22 @@ +# Note: For consistent results run with ROBOT v1.91 or higher +# Download the IAO release from 2022-11-07 +curl -L https://raw.githubusercontent.com/information-artifact-ontology/IAO/v2022-11-07/iao.owl > iao-full-download.owl +# Extract the terms we want with hierarchy, This removes the domain of IAO_0000136 +robot merge --input iao-full-download.owl extract --method MIREOT --lower-terms iao-w-hierarchy.txt --intermediates all --output iao-module-temp.owl +# Remove subclass axioms from BFO classes +robot remove --input iao-module-temp.owl --term BFO:0000001 --select "self descendants" --select "" --axioms subclass --axioms annotation --signature true --exclude-term BFO:0000031 --preserve-structure false --output iao-module-temp.owl +# Extract domain of IAO_0000136 +robot merge --input iao-full-download.owl filter --term http://purl.obolibrary.org/obo/IAO_0000136 --term rdfs:domain --term http://purl.obolibrary.org/obo/IAO_0000030 --select self --axioms all --signature false --output iao-extracted-domain.owl +# Extracted module +robot merge --input iao-module-temp.owl --input iao-extracted-domain.owl --output ../../ontology/imports/iao-extracted.owl +# Remove subproperty axioms +robot remove --input ../../ontology/imports/iao-extracted.owl --axioms subproperty --output ../../ontology/imports/iao-extracted.owl +# Annotates the output with a commentary to the origin of the content +robot annotate --input ../../ontology/imports/iao-extracted.owl --annotation rdfs:comment "This file contains externally imported content from the Information Artifact Ontology (IAO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT." --output ../../ontology/imports/iao-extracted.owl +# Annotates each axiom with the ontology IRI, using prov:wasDerivedFrom +robot annotate --input ../../ontology/imports/iao-extracted.owl --annotate-derived-from true --annotate-defined-by true --output ../../ontology/imports/iao-extracted.owl +# Annotate with new ontology information +robot annotate --input ../../ontology/imports/iao-extracted.owl --ontology-iri http://openenergy-platform.org/ontology/oeo/imports/iao-extracted.owl --version-iri http://openenergy-platform.org/ontology/oeo/dev/imports/iao-extracted.owl --output ../../ontology/imports/iao-extracted.owl +rm iao-full-download.owl +rm iao-extracted-domain.owl +rm iao-module-temp.owl \ No newline at end of file diff --git a/oeo-imports/iao/iao.owl b/oeo-imports/iao/archive/iao.owl similarity index 100% rename from oeo-imports/iao/iao.owl rename to oeo-imports/iao/archive/iao.owl diff --git a/oeo-imports/iao/extract-iao-module.sh b/oeo-imports/iao/extract-iao-module.sh index 0cff296..3c918ee 100644 --- a/oeo-imports/iao/extract-iao-module.sh +++ b/oeo-imports/iao/extract-iao-module.sh @@ -1,22 +1,20 @@ # Note: For consistent results run with ROBOT v1.91 or higher # Download the IAO release from 2022-11-07 curl -L https://raw.githubusercontent.com/information-artifact-ontology/IAO/v2022-11-07/iao.owl > iao-full-download.owl -# Extract the terms we want with hierarchy, This removes the domain of IAO_0000136 -robot merge --input iao-full-download.owl extract --method MIREOT --lower-terms iao-w-hierarchy.txt --intermediates all --output iao-module-temp.owl -# Remove subclass axioms from BFO classes -robot remove --input iao-module-temp.owl --term BFO:0000001 --select "self descendants" --select "" --axioms subclass --axioms annotation --signature true --exclude-term BFO:0000031 --preserve-structure false --output iao-module-temp.owl -# Extract domain of IAO_0000136 -robot merge --input iao-full-download.owl filter --term http://purl.obolibrary.org/obo/IAO_0000136 --term rdfs:domain --term http://purl.obolibrary.org/obo/IAO_0000030 --select self --axioms all --signature false --output iao-extracted-domain.owl -# Extracted module -robot merge --input iao-module-temp.owl --input iao-extracted-domain.owl --output ../../ontology/imports/iao-extracted.owl -# Remove subproperty axioms -robot remove --input ../../ontology/imports/iao-extracted.owl --axioms subproperty --output ../../ontology/imports/iao-extracted.owl -# Annotates the output with a commentary to the origin of the content -robot annotate --input ../../ontology/imports/iao-extracted.owl --annotation rdfs:comment "This file contains externally imported content from the Information Artifact Ontology (IAO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT." --output ../../ontology/imports/iao-extracted.owl +# Extract the terms we want with hierarchy until the upper term "information content entity" (IAO_0000030). +# Warning: This removes the domain of IAO_0000136 -- tbd in oeo-import-edits +# Classification: tbd in oeo-import-edits +robot merge --input iao-full-download.owl extract --method MIREOT --lower-terms iao-w-hierarchy.txt --intermediates all --upper-term http://purl.obolibrary.org/obo/IAO_0000030 --output iao-extracted-w-hierarchy.owl +# Extract the terms we want without hierarchy +robot merge --input iao-full-download.owl extract --method MIREOT --lower-terms iao-n-hierarchy.txt --upper-term owl:topObjectProperty --intermediates none --output iao-extracted-n-hierarchy.owl +# Create Extracted module and annotate with new ontology information +robot merge --input iao-extracted-w-hierarchy.owl --input iao-extracted-n-hierarchy.owl annotate --ontology-iri http://openenergy-platform.org/ontology/oeo/imports/iao-extracted.owl --version-iri http://openenergy-platform.org/ontology/oeo/dev/imports/iao-extracted.owl --output iao-extracted.owl +# Annotates the output module with a commentary to the origin of the content +robot annotate --input iao-extracted.owl --annotation rdfs:comment "This file contains externally imported content from the Information Artifact Ontology (IAO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT from the list of selected terms (iao-extract-w-hierarchy.txt, iao-extract-n-hierarchy.txt) located in the OEO-tools repository." --output iao-extracted.owl # Annotates each axiom with the ontology IRI, using prov:wasDerivedFrom -robot annotate --input ../../ontology/imports/iao-extracted.owl --annotate-derived-from true --annotate-defined-by true --output ../../ontology/imports/iao-extracted.owl -# Annotate with new ontology information -robot annotate --input ../../ontology/imports/iao-extracted.owl --ontology-iri http://openenergy-platform.org/ontology/oeo/imports/iao-extracted.owl --version-iri http://openenergy-platform.org/ontology/oeo/dev/imports/iao-extracted.owl --output ../../ontology/imports/iao-extracted.owl +robot annotate --input iao-extracted.owl --annotate-derived-from true --annotate-defined-by true --output iao-extracted.owl +## Annotate with new ontology information +#robot annotate --input iao-extracted.owl --ontology-iri http://openenergy-platform.org/ontology/oeo/imports/iao-extracted.owl --version-iri http://openenergy-platform.org/ontology/oeo/dev/imports/iao-extracted.owl --output iao-extracted.owl rm iao-full-download.owl -rm iao-extracted-domain.owl -rm iao-module-temp.owl \ No newline at end of file +rm iao-extracted-w-hierarchy.owl +rm iao-extracted-n-hierarchy.owl diff --git a/oeo-imports/iao/iao-extracted.owl b/oeo-imports/iao/iao-extracted.owl new file mode 100644 index 0000000..bb2914d --- /dev/null +++ b/oeo-imports/iao/iao-extracted.owl @@ -0,0 +1,3731 @@ + + + + + This file contains externally imported content from the Information Artifact Ontology (IAO) for import into the Open Energy Ontology (OEO). It is automatically extracted using ROBOT from the list of selected terms (iao-extract-w-hierarchy.txt, iao-extract-n-hierarchy.txt) located in the OEO-tools repository. + + + + + + + + + + + + + editor preferred term + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + editor preferred term + + + + + + + + + + + editor preferred term + + + + + + + + + + + + The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) + + + + + + PERSON:Daniel Schober + + + + + + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + + + + + + + + + + + editor preferred term + + + + + + + + + example of usage + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + example of usage + + + + + example of usage + + + + + + + + + + + + A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold. + + + + + + PERSON:Daniel Schober + + + + + + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + + + + + + + + + + + example of usage + + + + + + + + + + + + + + + has curation status + PERSON:Alan Ruttenberg + PERSON:Bill Bug + PERSON:Melanie Courtot + + has curation status + + + + + + + + + + + has curation status + + + + + + PERSON:Alan Ruttenberg + + + + + + PERSON:Bill Bug + + + + + + PERSON:Melanie Courtot + + + + + + has curation status + + + + + + + + + definition + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition + + + + + + + + + + + definition + + + + + + + + + + + + The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. + + + + + + 2012-04-05: +Barry Smith + +The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. + +Can you fix to something like: + +A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. + +Alan Ruttenberg + +Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. + +On the specifics of the proposed definition: + +We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. + +Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. + +We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. + + + + + + PERSON:Daniel Schober + + + + + + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + + + + + + + + + + + definition + + + + + + + + + editor note + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + + editor note + + + + + + + + + + + editor note + + + + + + + + + + + + An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. + + + + + + PERSON:Daniel Schober + + + + + + GROUP:OBI:<http://purl.obofoundry.org/obo/obi> + + + + + + + + + + + + editor note + + + + + + + + + term editor + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + term editor + + + + + + + + + + + term editor + + + + + + + + + + + + Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people + + + + + + 20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115. + + + + + + PERSON:Daniel Schober + + + + + + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + + + + + + + + + + + term editor + + + + + + + + + alternative label + + 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. + OBO Operations committee + PERSON:Daniel Schober + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + + alternative label + + + + + + + + + + + alternative label + + + + + + + + + + + + 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. + + + + + + OBO Operations committee + + + + + + PERSON:Daniel Schober + + + + + + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + + + + + Consider re-defing to: An alternative name for a class or property which can mean the same thing as the preferred name (semantically equivalent, narrow, broad or related). + + + + + + alternative label + + + + + + + + + definition source + + Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + PERSON:Daniel Schober + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + definition source + + + + + + + + + + + definition source + + + + + + + + + + + + Formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 + + + + + + PERSON:Daniel Schober + + + + + + Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w + + + + + + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + + + + + + + + + + + definition source + + + + + + + + + curator note + + An administrative note of use for a curator but of no use for a user + PERSON:Alan Ruttenberg + + curator note + + + + + + + + + + + curator note + + + + + + + + + + + + An administrative note of use for a curator but of no use for a user + + + + + + PERSON:Alan Ruttenberg + + + + + + + + + + + + curator note + + + + + + + + + term tracker item + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + An IRI or similar locator for a request or discussion of an ontology term. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'tracker item' can associate a tracker with a specific ontology term. + + term tracker item + + + + + + + + + + + term tracker item + + + + + + the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ + + + + + + + + + + + + An IRI or similar locator for a request or discussion of an ontology term. + + + + + + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + + + + + + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + + + + + + The 'tracker item' can associate a tracker with a specific ontology term. + + + + + + term tracker item + + + + + + + + + ontology term requester + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + The 'term requester' can credit the person, organization or project who request the ontology term. + + ontology term requester + + + + + + + + + + + ontology term requester + + + + + + + + + + + + The name of the person, project, or organization that motivated inclusion of an ontology term by requesting its addition. + + + + + + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + + + + + + Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg + + + + + + The 'term requester' can credit the person, organization or project who request the ontology term. + + + + + + ontology term requester + + + + + + + + + imported from + + For external terms/classes, the ontology from which the term was imported + PERSON:Alan Ruttenberg + PERSON:Melanie Courtot + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + imported from + + + + + + + + + + + imported from + + + + + + + + + + + + For external terms/classes, the ontology from which the term was imported + + + + + + PERSON:Alan Ruttenberg + + + + + + PERSON:Melanie Courtot + + + + + + GROUP:OBI:<http://purl.obolibrary.org/obo/obi> + + + + + + + + + + + + imported from + + + + + + + + + may be identical to + 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. + David Osumi-Sutherland + #40 + VFB + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + + may be identical to + + + + + + + + + + + may be identical to + + + + + + 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. + + + + + + David Osumi-Sutherland + + + + + + #40 + + + + + + VFB + + + + + + Edges asserting this should be annotated with to record evidence supporting the assertion and its provenance. + + + + + + may be identical to + + + + + + + + + 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. + + temporal interpretation + + + + + + + + + + + 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. + + + + + + temporal interpretation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + has part + my body has part my brain (continuant parthood, two material entities) + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + this year has part this day (occurrent parthood) + a core relation that holds between a whole and its part + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + has_part + + + has part + + + + + + + + + + + + + + + + + has part + + + + + + my body has part my brain (continuant parthood, two material entities) + + + + + + my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) + + + + + + this year has part this day (occurrent parthood) + + + + + + a core relation that holds between a whole and its part + + + + + + Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. + + + + + + Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ + + + + + + Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) + +A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. + + + + + + has_part + + + + + + + + + + + + has part + + + + + + + + + + This document is about information artifacts and their representations + + A (currently) primitive relation that relates an information artifact to an entity. + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + person:Alan Ruttenberg + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + + is about + + + + + + + + + + + + + + + + + This document is about information artifacts and their representations + + + + + + + + + + + + A (currently) primitive relation that relates an information artifact to an entity. + + + + + + 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. + +We will try to build it back up by elaborating the various subproperties that are more precisely defined. + +Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. + + + + + + person:Alan Ruttenberg + + + + + + Smith, Ceusters, Ruttenberg, 2000 years of philosophy + + + + + + is about + + + + + + + + + + + relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken + Alan Ruttenberg + + has time stamp + + + + + + + + + + + + + + + + + + + + + + + relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken + + + + + + Alan Ruttenberg + + + + + + has time stamp + + + + + + + + + + + + + + + + + + + + + + + + + + + + + objective specification + In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. + + A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. + 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." + 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. + Answers the question, why did you do this experiment? + PERSON: Alan Ruttenberg + PERSON: Barry Smith + PERSON: Bjoern Peters + PERSON: Jennifer Fostel + goal specification + OBI Plan and Planned Process/Roles Branch + OBI_0000217 + + objective specification + + + + + + + + + + + + + + + + + objective specification + + + + + + In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. + + + + + + + + + + + + A directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. + + + + + + 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." + + + + + + 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. + + + + + + Answers the question, why did you do this experiment? + + + + + + PERSON: Alan Ruttenberg + + + + + + PERSON: Barry Smith + + + + + + PERSON: Bjoern Peters + + + + + + PERSON: Jennifer Fostel + + + + + + goal specification + + + + + + OBI Plan and Planned Process/Roles Branch + + + + + + OBI_0000217 + + + + + + objective specification + + + + + + + + + + Pour the contents of flask 1 into flask 2 + + A directive information entity that describes an action the bearer will take. + Alan Ruttenberg + OBI Plan and Planned Process branch + + action specification + + + + + + + + + + + + + + + + + Pour the contents of flask 1 into flask 2 + + + + + + + + + + + + A directive information entity that describes an action the bearer will take. + + + + + + Alan Ruttenberg + + + + + + OBI Plan and Planned Process branch + + + + + + action specification + + + + + + + + + + software + + Software is a plan specification composed of a series of instructions that can be +interpreted by or directly executed by a processing unit. + see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + PERSON: Chris Stoeckert + PERSON: Melanie Courtot + GROUP: OBI + + software + + + + + + + + + + + + + + + + + software + + + + + + + + + + + + Software is a plan specification composed of a series of instructions that can be +interpreted by or directly executed by a processing unit. + + + + + + see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178 + + + + + + PERSON: Alan Ruttenberg + + + + + + PERSON: Bjoern Peters + + + + + + PERSON: Chris Stoeckert + + + + + + PERSON: Melanie Courtot + + + + + + GROUP: OBI + + + + + + software + + + + + + + + + journal article + Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. + + A report that is published in a journal. + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + OBI_0000159 + group:OBI + + journal article + + + + + + + + + + + journal article + + + + + + Examples are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number. + + + + + + + + + + + + A report that is published in a journal. + + + + + + PERSON: Alan Ruttenberg + + + + + + PERSON: Chris Stoeckert + + + + + + OBI_0000159 + + + + + + group:OBI + + + + + + journal article + + + + + + + + + + programming language + R, Perl, Java + + A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. + person:Alan Ruttenberg + person:Chris Stoeckert + OBI_0000058 + group:OBI + + programming language + + + + + + + + + + + + + + + + + programming language + + + + + + R, Perl, Java + + + + + + + + + + + + A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. + + + + + + person:Alan Ruttenberg + + + + + + person:Chris Stoeckert + + + + + + OBI_0000058 + + + + + + group:OBI + + + + + + programming language + + + + + + + + + + data item + Data items include counts of things, analyte concentrations, and statistical summaries. + + An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Jonathan Rees + data + + data item + + + + + + + + + + + + + + + + + data item + + + + + + Data items include counts of things, analyte concentrations, and statistical summaries. + + + + + + + + + + + + An information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + + + + + + 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. + + + + + + 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. + + + + + + 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. + + + + + + 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ + + + + + + JAR: datum -- well, this will be very tricky to define, but maybe some +information-like stuff that might be put into a computer and that is +meant, by someone, to denote and/or to be interpreted by some +process... I would include lists, tables, sentences... I think I might +defer to Barry, or to Brian Cantwell Smith + +JAR: A data item is an approximately justified approximately true approximate belief + + + + + + PERSON: Alan Ruttenberg + + + + + + PERSON: Chris Stoeckert + + + + + + PERSON: Jonathan Rees + + + + + + data + + + + + + data item + + + + + + + + + + symbol + a serial number such as "12324X" + a stop sign + a written proper name such as "OBI" + + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + 20091104, MC: this needs work and will most probably change + 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). + PERSON: James A. Overton + PERSON: Jonathan Rees + based on Oxford English Dictionary + + symbol + + + + + + + + + + + + + + + + + symbol + + + + + + a serial number such as "12324X" + + + + + + a stop sign + + + + + + a written proper name such as "OBI" + + + + + + + + + + + + An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity. + + + + + + 20091104, MC: this needs work and will most probably change + + + + + + 2014-03-31: We would like to have a deeper analysis of 'mark' and 'sign' in the future (see https://github.com/information-artifact-ontology/IAO/issues/154). + + + + + + PERSON: James A. Overton + + + + + + PERSON: Jonathan Rees + + + + + + based on Oxford English Dictionary + + + + + + symbol + + + + + + + + + information content entity + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + A generically dependent continuant that is about some thing. + 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + PERSON: Chris Stoeckert + OBI_0000142 + + information content entity + + + + + + + + + + + information content entity + + + + + + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + + + + + + + + + + + A generically dependent continuant that is about some thing. + + + + + + 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). + + + + + + information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). + +Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. + + + + + + PERSON: Chris Stoeckert + + + + + + OBI_0000142 + + + + + + information content entity + + + + + + + + + + + An information content entity whose concretizations indicate to their bearer how to realize them in a process. + 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. + 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO + Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan + PERSON: Alan Ruttenberg + PERSON: Bjoern Peters + + directive information entity + + + + + + + + + + + + + + + + + + + + + + + An information content entity whose concretizations indicate to their bearer how to realize them in a process. + + + + + + 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + + + + + + 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. + + + + + + 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO + + + + + + Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan + + + + + + PERSON: Alan Ruttenberg + + + + + + PERSON: Bjoern Peters + + + + + + directive information entity + + + + + + + + + + algorithm + PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. + + A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. + Philippe Rocca-Serra + PlanAndPlannedProcess Branch + OBI_0000270 + adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) + + algorithm + + + + + + + + + + + + + + + + + algorithm + + + + + + PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies. + + + + + + + + + + + + A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. + + + + + + Philippe Rocca-Serra + + + + + + PlanAndPlannedProcess Branch + + + + + + OBI_0000270 + + + + + + adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg) + + + + + + algorithm + + + + + + + + + + report + Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. + + 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). + 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on +something that has completed." Should it be restricted to those things +that are completed? For example, a progress report is (usually) about +something that definitely has *not* been completed, or may include +(only) projections. I think the definition would not suffer if the +whole sentence is deleted. + 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. + 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion + 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 + PERSON: Alan Ruttenberg + PERSON: Chris Stoeckert + PERSON: Melanie Courtot + GROUP: OBI + OBI_0000099 + + report + + + + + + + + + + + + + + + + + report + + + + + + Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article. + + + + + + + + + + + + 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). + + + + + + 2009-03-16: comment from Darren Natale: I am slightly uneasy with the sentence "Topic of the report is on +something that has completed." Should it be restricted to those things +that are completed? For example, a progress report is (usually) about +something that definitely has *not* been completed, or may include +(only) projections. I think the definition would not suffer if the +whole sentence is deleted. + + + + + + 2009-03-16: this was report of results with definition: A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so. + + + + + + 2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI. + + + + + + 2009-08-10 Alan Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by 'document'. Alan restored as there are OBI dependencies and this merits further discussion + + + + + + 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 + + + + + + PERSON: Alan Ruttenberg + + + + + + PERSON: Chris Stoeckert + + + + + + PERSON: Melanie Courtot + + + + + + GROUP: OBI + + + + + + OBI_0000099 + + + + + + report + + + + + + + + + + data format specification + + A data format specification is the information content borne by the document published defining the specification. +Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file + 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes +information. Example: The ISO document specifying what encompasses an +XML document; The instructions in a XSD file" + PERSON: Alan Ruttenberg + PlanAndPlannedProcess Branch + OBI branch derived + OBI_0000187 + + data format specification + + + + + + + + + + + + + + + + + data format specification + + + + + + + + + + + + A data format specification is the information content borne by the document published defining the specification. +Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file + + + + + + 2009-03-16: provenance: term imported from OBI_0000187, which had original definition "A data format specification is a plan which organizes +information. Example: The ISO document specifying what encompasses an +XML document; The instructions in a XSD file" + + + + + + PERSON: Alan Ruttenberg + + + + + + PlanAndPlannedProcess Branch + + + + + + OBI branch derived + + + + + + OBI_0000187 + + + + + + data format specification + + + + + + + + + + data set + Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). + + A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. + 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type + 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. + person:Allyson Lister + person:Chris Stoeckert + OBI_0000042 + group:OBI + + data set + + + + + + + + + + + + + + + + + data set + + + + + + Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). + + + + + + + + + + + + A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. + + + + + + 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type + + + + + + 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. + + + + + + person:Allyson Lister + + + + + + person:Chris Stoeckert + + + + + + OBI_0000042 + + + + + + group:OBI + + + + + + data set + + + + + + + + + + plan specification + PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. + + A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. + 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + 2014-03-31: A plan specification can have other parts, such as conditional specifications. + 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. + Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved + Alan Ruttenberg + Clint Dowland + OBI Plan and Planned Process branch + OBI_0000344 + 2/3/2009 Comment from OBI review. + +Action specification not well enough specified. +Conditional specification not well enough specified. +Question whether all plan specifications have objective specifications. + +Request that IAO either clarify these or change definitions not to use them + + plan specification + https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 + + + + + + + + + + + + + + + + + plan specification + + + + + + PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. + + + + + + + + + + + + A directive information entity with action specifications and objective specifications as parts, and that may be concretized as a realizable entity that, if realized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. + + + + + + 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. + + + + + + 2014-03-31: A plan specification can have other parts, such as conditional specifications. + + + + + + 2022-01-16 Updated definition to that proposed by Clint Dowloand, IAO Issue 231. + + + + + + Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved + + + + + + Alan Ruttenberg + + + + + + Clint Dowland + + + + + + OBI Plan and Planned Process branch + + + + + + OBI_0000344 + + + + + + 2/3/2009 Comment from OBI review. + +Action specification not well enough specified. +Conditional specification not well enough specified. +Question whether all plan specifications have objective specifications. + +Request that IAO either clarify these or change definitions not to use them + + + + + + plan specification + + + + + + https://github.com/information-artifact-ontology/IAO/issues/231#issuecomment-1010455131 + + + + + + + + + + measurement datum + 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,}. + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + 2/2/2009 is_specified_output of some assay? + person:Chris Stoeckert + OBI_0000305 + group:OBI + + measurement datum + + + + + + + + + + + + + + + + + measurement datum + + + + + + 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,}. + + + + + + + + + + + + A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. + + + + + + 2/2/2009 is_specified_output of some assay? + + + + + + person:Chris Stoeckert + + + + + + OBI_0000305 + + + + + + group:OBI + + + + + + measurement datum + + + + + + + + + + version number + + A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. + Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version + GROUP: IAO + + version number + + + + + + + + + + + + + + + + + version number + + + + + + + + + + + + A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. + + + + + + Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version + + + + + + GROUP: IAO + + + + + + version number + + + + + + + + + + textual entity + Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities + + A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. + AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. + MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. + PERSON: Lawrence Hunter + text + + textual entity + + + + + + + + + + + + + + + + + textual entity + + + + + + Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities + + + + + + + + + + + + A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. + + + + + + AR, (IAO call 2009-09-01): a document as a whole is not typically a textual entity, because it has pictures in it - rather there are parts of it that are textual entities. Examples: The title, paragraph 2 sentence 7, etc. + + + + + + MC, 2009-09-14 (following IAO call 2009-09-01): textual entities live at the FRBR (http://en.wikipedia.org/wiki/Functional_Requirements_for_Bibliographic_Records) manifestation level. Everything is significant: line break, pdf and html versions of same document are different textual entities. + + + + + + PERSON: Lawrence Hunter + + + + + + text + + + + + + textual entity + + + + + + + + + + document + A journal article, patent application, laboratory notebook, or a book + + A collection of information content entities intended to be understood together as a whole + PERSON: Lawrence Hunter + + document + + + + + + + + + + + + + + + + + document + + + + + + A journal article, patent application, laboratory notebook, or a book + + + + + + + + + + + + A collection of information content entities intended to be understood together as a whole + + + + + + PERSON: Lawrence Hunter + + + + + + document + + + + + + + + + + document part + An abstract, introduction, method or results section. + + An information content entity that is part of a document. + PERSON: Lawrence Hunter + + document part + + + + + + + + + + + + + + + + + document part + + + + + + An abstract, introduction, method or results section. + + + + + + + + + + + + An information content entity that is part of a document. + + + + + + PERSON: Lawrence Hunter + + + + + + document part + + + + + + + + + + + A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude + 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 + Alan Ruttenberg + AR notes: We need to discuss whether it should include site. + + cartesian spatial coordinate datum + http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 + + + + + + + + + + + + + + + + + + + + + + + A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude + + + + + + 2009-08-18 Alan Ruttenberg - question to BFO list about whether the BFO sense of the lower dimensional regions is that they are always part of actual space (the three dimensional sort) http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 + + + + + + Alan Ruttenberg + + + + + + AR notes: We need to discuss whether it should include site. + + + + + + cartesian spatial coordinate datum + + + + + + http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617 + + + + + + + + + + + A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region + Alan Ruttenberg + + one dimensional cartesian spatial coordinate datum + + + + + + + + + + + + + + + + + + + + + + + A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region + + + + + + Alan Ruttenberg + + + + + + one dimensional cartesian spatial coordinate datum + + + + + + + + + + + A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region + Alan Ruttenberg + + two dimensional cartesian spatial coordinate datum + + + + + + + + + + + + + + + + + + + + + + + A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region + + + + + + Alan Ruttenberg + + + + + + two dimensional cartesian spatial coordinate datum + + + + + + + + + + + A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region + Alan Ruttenberg + + three dimensional cartesian spatial coordinate datum + + + + + + + + + + + + + + + + + + + + + + + A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region + + + + + + Alan Ruttenberg + + + + + + three dimensional cartesian spatial coordinate datum + + + + + + + + + + + + time stamped measurement datum + + + + + + + + + + + + + + + + + + + + + + + time stamped measurement datum + + + + + + + + + + written name + "Bill Clinton" + "The Eiffel Tower" + "United States of America" + + A textual entity that denotes a particular in reality. + PERSON: Bill Hogan + https://github.com/information-artifact-ontology/IAO/issues/114 + 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. + + written name + + + + + + + + + + + + + + + + + written name + + + + + + "Bill Clinton" + + + + + + "The Eiffel Tower" + + + + + + "United States of America" + + + + + + + + + + + + A textual entity that denotes a particular in reality. + + + + + + PERSON: Bill Hogan + + + + + + https://github.com/information-artifact-ontology/IAO/issues/114 + + + + + + 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. + + + + + + written name + + + + + + + + + + + A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + + software method + + + + + + + + + + + + + + + + + + + + + + + A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task. + + + + + + PERSON: Melanie Courtot + + + + + + PERSON: Michel Dumontier + + + + + + https://github.com/information-artifact-ontology/IAO/issues/80 + + + + + + software method + + + + + + + + + + + A software module is software composed of a collection of software methods. + PERSON: Melanei Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + + software module + + + + + + + + + + + + + + + + + + + + + + + A software module is software composed of a collection of software methods. + + + + + + PERSON: Melanei Courtot + + + + + + PERSON: Michel Dumontier + + + + + + https://github.com/information-artifact-ontology/IAO/issues/80 + + + + + + software module + + + + + + + + + + + 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. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + + software library + + + + + + + + + + + + + + + + + + + + + + + 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. + + + + + + PERSON: Melanie Courtot + + + + + + PERSON: Michel Dumontier + + + + + + https://github.com/information-artifact-ontology/IAO/issues/80 + + + + + + software library + + + + + + + + + + + A software application is software that can be directly executed by some processing unit. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + + software application + + + + + + + + + + + + + + + + + + + + + + + A software application is software that can be directly executed by some processing unit. + + + + + + PERSON: Melanie Courtot + + + + + + PERSON: Michel Dumontier + + + + + + https://github.com/information-artifact-ontology/IAO/issues/80 + + + + + + software application + + + + + + + + + + + A software script is software whose instructions can be executed using a software interpreter. + PERSON: Melanie Courtot + PERSON: Michel Dumontier + https://github.com/information-artifact-ontology/IAO/issues/80 + + software script + + + + + + + + + + + + + + + + + + + + + + + A software script is software whose instructions can be executed using a software interpreter. + + + + + + PERSON: Melanie Courtot + + + + + + PERSON: Michel Dumontier + + + + + + https://github.com/information-artifact-ontology/IAO/issues/80 + + + + + + software script + + + + + + + + + + study design + 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. + + + study design + + + + + + + + + + + + + + + + + study design + + + + + + 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. + + + + + + + + + + + + study design + + + + + + + + diff --git a/oeo-imports/iao/iao-n-hierarchy.txt b/oeo-imports/iao/iao-n-hierarchy.txt new file mode 100644 index 0000000..4c0a5ae --- /dev/null +++ b/oeo-imports/iao/iao-n-hierarchy.txt @@ -0,0 +1 @@ +http://purl.obolibrary.org/obo/IAO_0000013 # journal article \ No newline at end of file diff --git a/oeo-imports/iao/iao-w-hierarchy.txt b/oeo-imports/iao/iao-w-hierarchy.txt index 1bbd6ab..f9d6ac7 100644 --- a/oeo-imports/iao/iao-w-hierarchy.txt +++ b/oeo-imports/iao/iao-w-hierarchy.txt @@ -1,14 +1,35 @@ -http://purl.obolibrary.org/obo/IAO_0000136 -http://purl.obolibrary.org/obo/IAO_0000010 -http://purl.obolibrary.org/obo/IAO_0000025 -http://purl.obolibrary.org/obo/IAO_0000028 -http://purl.obolibrary.org/obo/IAO_0000030 -http://purl.obolibrary.org/obo/IAO_0000033 -http://purl.obolibrary.org/obo/IAO_0000064 -http://purl.obolibrary.org/obo/IAO_0000088 -http://purl.obolibrary.org/obo/IAO_0000100 -http://purl.obolibrary.org/obo/IAO_0000104 -http://purl.obolibrary.org/obo/IAO_0000300 -http://purl.obolibrary.org/obo/IAO_0000310 -http://purl.obolibrary.org/obo/IAO_0000590 -http://purl.obolibrary.org/obo/IAO_0000233 \ No newline at end of file +http://purl.obolibrary.org/obo/IAO_0000136 # is about +http://purl.obolibrary.org/obo/IAO_0000010 # software +http://purl.obolibrary.org/obo/IAO_0000025 # programming language +http://purl.obolibrary.org/obo/IAO_0000028 # symbol +http://purl.obolibrary.org/obo/IAO_0000030 # information content entity +http://purl.obolibrary.org/obo/IAO_0000033 # directive information entity +http://purl.obolibrary.org/obo/IAO_0000064 # algorithm +http://purl.obolibrary.org/obo/IAO_0000088 # report +http://purl.obolibrary.org/obo/IAO_0000100 # data set +http://purl.obolibrary.org/obo/IAO_0000104 # plan specification +http://purl.obolibrary.org/obo/IAO_0000300 # textual entity +http://purl.obolibrary.org/obo/IAO_0000310 # document +http://purl.obolibrary.org/obo/IAO_0000590 # written name +http://purl.obolibrary.org/obo/IAO_0000233 # term tracker item + +http://purl.obolibrary.org/obo/IAO_0000582 # time stamped measurement datum +http://purl.obolibrary.org/obo/IAO_0000007 # action specification +http://purl.obolibrary.org/obo/IAO_0000098 # data format specification +http://purl.obolibrary.org/obo/IAO_0000005 # objective specification +http://purl.obolibrary.org/obo/OBI_0500000 # study design +http://purl.obolibrary.org/obo/IAO_0000594 # software application +http://purl.obolibrary.org/obo/IAO_0000593 # software library +http://purl.obolibrary.org/obo/IAO_0000591 # software method +http://purl.obolibrary.org/obo/IAO_0000592 # software module +http://purl.obolibrary.org/obo/IAO_0000595 # software script +http://purl.obolibrary.org/obo/IAO_0000314 # document part # subclasses requireds? +http://purl.obolibrary.org/obo/IAO_0000129 # version number +http://purl.obolibrary.org/obo/IAO_0000400 # cartesian spatial coordinate datum +http://purl.obolibrary.org/obo/IAO_0000401 # one dimensional cartesian spatial coordinate datum +http://purl.obolibrary.org/obo/IAO_0000402 # two dimensional cartesian spatial coordinate datum +http://purl.obolibrary.org/obo/IAO_0000403 # three dimensional cartesian spatial coordinate datum + +http://purl.obolibrary.org/obo/IAO_0006011 # may be identical to +http://purl.obolibrary.org/obo/IAO_0000581 # has time stamp + \ No newline at end of file diff --git a/oeo-imports/omo/omo-w-hierarchy.txt b/oeo-imports/omo/omo-w-hierarchy.txt index 6ed8743..bf243dd 100644 --- a/oeo-imports/omo/omo-w-hierarchy.txt +++ b/oeo-imports/omo/omo-w-hierarchy.txt @@ -1,8 +1,8 @@ -http://purl.obolibrary.org/obo/IAO_0000027 -http://purl.obolibrary.org/obo/IAO_0000112 -http://purl.obolibrary.org/obo/IAO_0000115 -http://purl.obolibrary.org/obo/IAO_0000116 -http://purl.obolibrary.org/obo/IAO_0000118 -http://purl.obolibrary.org/obo/IAO_0000119 -http://purl.obolibrary.org/obo/IAO_0006011 +http://purl.obolibrary.org/obo/IAO_0000027 # data item +http://purl.obolibrary.org/obo/IAO_0000112 # example of usage +http://purl.obolibrary.org/obo/IAO_0000115 # definition +http://purl.obolibrary.org/obo/IAO_0000116 # editor note +http://purl.obolibrary.org/obo/IAO_0000118 # alternative label +http://purl.obolibrary.org/obo/IAO_0000119 # definition source +http://purl.obolibrary.org/obo/IAO_0006011 # may be identical to