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brianjlowe 2013-10-03 16:38:24 -04:00
parent 601a0674ab
commit e21b3e7077
31 changed files with 3300 additions and 889 deletions
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rdf/tbox/filegraph/research-resource-iao.owl
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@ -85,7 +85,7 @@
<!-- http://purl.obolibrary.org/obo/IAO_0000003 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000003">
<rdfs:label xml:lang="en">measurement unit label</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000009"/>
<obo:IAO_0000116 xml:lang="en">2009-03-16: provenance: a term measurement unit was
proposed for OBI (OBI_0000176) , edited by Chris Stoeckert and
@ -107,7 +107,7 @@ of this, different, term.</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000005 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000005">
<rdfs:label xml:lang="en">objective specification</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000116 xml:lang="en">Answers the question, why did you do this experiment?</obo:IAO_0000116>
<obo:IAO_0000119 xml:lang="en">OBI Plan and Planned Process/Roles Branch</obo:IAO_0000119>
@ -128,7 +128,7 @@ of this, different, term.</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000007 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000007">
<rdfs:label xml:lang="en">action specification</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">OBI Plan and Planned Process branch</obo:IAO_0000119>
@ -143,10 +143,7 @@ of this, different, term.</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000009 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000009">
<rdfs:label xml:lang="en">datum label</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000232>9/22/11 BP: changed the rdfs:label for this class from &apos;label&apos; to &apos;datum label&apos; 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.
</obo:IAO_0000232>
<obo:IAO_0000115 xml:lang="en">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</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">GROUP: IAO</obo:IAO_0000117>
<obo:IAO_0000111 xml:lang="en">datum label</obo:IAO_0000111>
@ -160,7 +157,7 @@ of this, different, term.</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000027 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000027">
<rdfs:label xml:lang="en">data item</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
@ -188,7 +185,7 @@ JAR: A data item is an approximately justified approximately true approximate be
<!-- http://purl.obolibrary.org/obo/IAO_0000030 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030">
<rdfs:label xml:lang="en">information content entity</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
<rdfs:subClassOf>
<owl:Restriction>
@ -213,7 +210,7 @@ Previous. An information content entity is a non-realizable information entity t
<!-- http://purl.obolibrary.org/obo/IAO_0000032 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000032">
<rdfs:label xml:lang="en">scalar measurement datum</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
<obo:IAO_0000112 xml:lang="en">10 feet. 3 ml.</obo:IAO_0000112>
<obo:IAO_0000116 xml:lang="en">2009-03-16: we decided to keep datum singular in scalar measurement datum, as in
@ -230,7 +227,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000033 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000033">
<rdfs:label xml:lang="en">directive information entity</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000116 xml:lang="en">8/6/2009 Alan Ruttenberg: Changed label from &quot;information entity about a realizable&quot; after discussions at ICBO</obo:IAO_0000116>
<obo:IAO_0000115 xml:lang="en">An information content entity whose concretizations indicate to their bearer how to realize them in a process.</obo:IAO_0000115>
@ -246,7 +243,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000078 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000078">
<rdfs:label xml:lang="en">curation status specification</rdfs:label>
<owl:equivalentClass>
<owl:Class>
<owl:oneOf rdf:parseType="Collection">
@ -277,7 +274,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000102 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000102">
<rdfs:label xml:lang="en">data about an ontology part</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">data about an ontology part is a data item about a part of an ontology, for example a term</obo:IAO_0000115>
@ -288,7 +285,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000104 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000104">
<rdfs:label xml:lang="en">plan specification</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<obo:IAO_0000116 xml:lang="en">2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was &quot; a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan&quot;. 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.</obo:IAO_0000116>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
@ -307,7 +304,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000109 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000109">
<rdfs:label xml:lang="en">measurement datum</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000027"/>
<obo:IAO_0000116 xml:lang="en">2/2/2009 is_specified_output of some assay?</obo:IAO_0000116>
<obo:IAO_0000115 xml:lang="en">A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device.</obo:IAO_0000115>
@ -324,7 +321,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000144 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000144">
<rdfs:label xml:lang="en">conclusion textual entity</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000116 xml:lang="en">2009/09/28 Alan Ruttenberg. Fucoidan-use-case</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">2009/10/23 Alan Ruttenberg: We need to work on the definition still</obo:IAO_0000116>
@ -341,7 +338,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000225 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000225">
<rdfs:label xml:lang="en">obsolescence reason specification</rdfs:label>
<owl:equivalentClass>
<owl:Class>
<owl:oneOf rdf:parseType="Collection">
@ -367,7 +364,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000300 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000300">
<rdfs:label xml:lang="en">textual entity</rdfs:label>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
@ -383,7 +380,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<!-- http://purl.obolibrary.org/obo/IAO_0000409 -->
<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000409">
<rdfs:label xml:lang="en">denotator type</rdfs:label>
<owl:equivalentClass>
<owl:Class>
<owl:oneOf rdf:parseType="Collection">
@ -470,7 +467,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000002">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<rdfs:label xml:lang="en">example to be eventually removed</rdfs:label>
</owl:NamedIndividual>
@ -479,7 +476,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000103">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
<rdfs:label xml:lang="en">failed exploratory term</rdfs:label>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Person:Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">The term was used used in an attempt to structure part of the ontology but in retrospect failed to do a good job</obo:IAO_0000115>
</owl:NamedIndividual>
@ -490,7 +487,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000120">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<rdfs:label xml:lang="en">metadata complete</rdfs:label>
<obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
</owl:NamedIndividual>
@ -500,7 +497,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000121">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<rdfs:label xml:lang="en">organizational term</rdfs:label>
<obo:IAO_0000115 xml:lang="en">term created to ease viewing/sort terms for development purpose, and will not be included in a release</obo:IAO_0000115>
</owl:NamedIndividual>
@ -510,7 +507,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000122">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<rdfs:label xml:lang="en">ready for release</rdfs:label>
<obo:IAO_0000115 xml:lang="en">Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking &quot;ready_for_release&quot; should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed &quot;ready_for_release&quot; will also derived from a chain of ancestor classes that are also &quot;ready_for_release.&quot;</obo:IAO_0000115>
</owl:NamedIndividual>
@ -520,7 +517,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000123">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<rdfs:label xml:lang="en">metadata incomplete</rdfs:label>
<obo:IAO_0000115 xml:lang="en">Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.</obo:IAO_0000115>
</owl:NamedIndividual>
@ -530,7 +527,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000124">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<rdfs:label xml:lang="en">uncurated</rdfs:label>
<obo:IAO_0000115 xml:lang="en">Nothing done yet beyond assigning a unique class ID and proposing a preferred term.</obo:IAO_0000115>
</owl:NamedIndividual>
@ -540,7 +537,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000125">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<rdfs:label xml:lang="en">pending final vetting</rdfs:label>
<obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
</owl:NamedIndividual>
@ -550,7 +547,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000224">
<rdf:type rdf:resource="http://www.geneontology.org/formats/oboInOwl#Subset"/>
<rdfs:label xml:lang="en">core</rdfs:label>
<obo:IAO_0000115 xml:lang="en">Core is an instance of a grouping of terms from an ontology or ontologies. It is used by the ontology to identify main classes.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Melanie Courtot</obo:IAO_0000117>
@ -562,7 +559,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000226">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
<rdfs:label xml:lang="en">placeholder removed</rdfs:label>
</owl:NamedIndividual>
@ -571,7 +568,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000227">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
<rdfs:label xml:lang="en">terms merged</rdfs:label>
<obo:IAO_0000116 xml:lang="en">An editor note should explain what were the merged terms and the reason for the merge.</obo:IAO_0000116>
</owl:NamedIndividual>
@ -581,7 +578,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000228">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
<rdfs:label xml:lang="en">term imported</rdfs:label>
<obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
</owl:NamedIndividual>
@ -591,7 +588,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000229">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
<rdfs:label xml:lang="en">term split</rdfs:label>
<obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
</owl:NamedIndividual>
@ -601,7 +598,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000410">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000409"/>
<rdfs:label xml:lang="en">universal</rdfs:label>
<obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf</obo:IAO_0000119>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hard to give a definition for. Intuitively a &quot;natural kind&quot; 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.</obo:IAO_0000116>
@ -613,7 +610,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000420">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000409"/>
<rdfs:label xml:lang="en">defined class</rdfs:label>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">&quot;definitions&quot;, 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.</obo:IAO_0000116>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal</obo:IAO_0000117>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan Ruttenberg</obo:IAO_0000117>
@ -625,7 +622,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000421">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000409"/>
<rdfs:label xml:lang="en">named class expression</rdfs:label>
<obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A named class expression is a logical expression that is given a name. The name can be used in place of the expression.</obo:IAO_0000115>
<obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000116 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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</obo:IAO_0000116>
@ -637,7 +634,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000423">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<rdfs:label xml:lang="en">to be replaced with external ontology term</rdfs:label>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000115 xml:lang="en">Terms with this status should eventually replaced with a term from another ontology.</obo:IAO_0000115>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
@ -649,7 +646,7 @@ this case we explicitly refer to the singular form</obo:IAO_0000116>
<owl:NamedIndividual rdf:about="http://purl.obolibrary.org/obo/IAO_0000428">
<rdf:type rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
<rdfs:label xml:lang="en">requires discussion</rdfs:label>
<obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>