[information-artifact-ontology] r713 committed - a merged version of IAO for review purpose

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Revision: 713
Author: zheng...@gmail.com
Date: Sat Jan 3 07:29:14 2015 UTC
Log: a merged version of IAO for review purpose
https://code.google.com/p/information-artifact-ontology/source/detail?r=713

Added:
/branches/2015-01-02/ontology-BFO2/iao_merged.owl

=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/iao_merged.owl Sat Jan 3 07:29:14
2015 UTC
@@ -0,0 +1,5835 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/iao_merged.owl#"
+ xml:base="http://purl.obolibrary.org/obo/iao_merged.owl"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:obo="http://purl.obolibrary.org/obo/"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
+ xmlns:foaf="http://xmlns.com/foaf/0.1/"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
+ <owl:Ontology
rdf:about="http://purl.obolibrary.org/obo/iao_merged.owl">
+ <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">An information
artifact is, loosely, a dependent continuant or its bearer that is created
as the result of one or more intentional processes. Examples: uniprot, the
english language, the contents of this document or a printout of it, the
temperature measurements from a weather balloon. For more information, see
the project home page at
http://code.google.com/p/information-artifact-ontology/</rdfs:comment>
+ <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IDs allocated to
related efforts: PNO: IAO_0020000-IAO_0020999, D_ACTS:
IAO_0021000-IAO_0021999</rdfs:comment>
+ <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IDs allocated to
subdomains of IAO. pno.owl: IAO_0020000-IAO_0020999, d-acts.owl:
IAO_0021000-IAO_0021999</rdfs:comment>
+ <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This is a
transitional artifact for discussion, not to be used for
production</rdfs:comment>
+ <protege:defaultLanguage
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
+ <owl:versionInfo xml:lang="en">$Revision$</owl:versionInfo>
+ <rdfs:seeAlso
rdf:resource="http://code.google.com/p/information-artifact-ontology/"/>
+ <owl:imports
rdf:resource="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl"/>
+ </owl:Ontology>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://protege.stanford.edu/plugins/owl/protege#defaultLanguage"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000179">
+ <rdfs:label xml:lang="en">BFO OWL specification label</rdfs:label>
+ <obo:IAO_0000232 xml:lang="en">Really of interest to developers
only</obo:IAO_0000232>
+ <obo:IAO_0000115 xml:lang="en">Relates an entity in the ontology
to the name of the variable that is used to represent it in the code that
generates the BFO OWL file from the lispy specification.</obo:IAO_0000115>
+ <rdfs:subPropertyOf
rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000180">
+ <rdfs:label xml:lang="en">BFO CLIF specification label</rdfs:label>
+ <obo:IAO_0000119>Person:Alan Ruttenberg</obo:IAO_0000119>
+ <obo:IAO_0000232 xml:lang="en">Really of interest to developers
only</obo:IAO_0000232>
+ <obo:IAO_0000115 xml:lang="en">Relates an entity in the ontology
to the term that is used to represent it in the the CLIF specification of
BFO2</obo:IAO_0000115>
+ <rdfs:subPropertyOf
rdf:resource="http://www.w3.org/2000/01/rdf-schema#label"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
+ <rdfs:label xml:lang="en">editor preferred label</rdfs:label>
+ <rdfs:label>editor preferred term</rdfs:label>
+ <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+ <obo:IAO_0000111>editor preferred term</obo:IAO_0000111>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Daniel
Schober</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">The concise, meaningful, and
human-friendly name for a class or property preferred by the ontology
developers. (US-English)</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">editor preferred
label</obo:IAO_0000111>
+ <obo:IAO_0000111 xml:lang="en">editor preferred
term</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000112">
+ <rdfs:label xml:lang="en">example of usage</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">A phrase describing how a class
name should be used. May also include other kinds of examples that
facilitate immediate understanding of a class semantics, such as widely
known prototypical subclasses or instances of the class. Although essential
for high level terms, examples for low level terms (e.g., Affymetrix HU133
array) are not</obo:IAO_0000115>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Daniel
Schober</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">example</obo:IAO_0000111>
+ <obo:IAO_0000111 xml:lang="en">example of usage</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000113">
+ <rdfs:label xml:lang="en">in branch</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">An annotation property indicating
which module the terms belong to. This is currently experimental and not
implemented yet.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">GROUP:OBI</obo:IAO_0000117>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000277</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">in branch</obo:IAO_0000111>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000114">
+ <rdfs:label xml:lang="en">has curation status</rdfs:label>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000281</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Bill Bug</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Melanie
Courtot</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">has curation
status</obo:IAO_0000111>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</rdfs:label>
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">textual
definition</rdfs:label>
+ <rdfs:label>definition</rdfs:label>
+ <rdfs:label xml:lang="en">definition</rdfs:label>
+ <obo:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">definition</obo:IAO_0000111>
+ <obo:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">textual
definition</obo:IAO_0000111>
+ <obo:IAO_0000116 xml:lang="en">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. </obo:IAO_0000116>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000115 xml:lang="en">The official definition, explaining
the meaning of a class or property. Shall be Aristotelian, formalized and
normalized. Can be augmented with colloquial definitions.</obo:IAO_0000115>
+ <obo:IAO_0000111>definition</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Daniel
Schober</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">The official OBI definition,
explaining the meaning of a class or property. Shall be Aristotelian,
formalized and normalized. Can be augmented with colloquial
definitions.</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">definition</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
+ <rdfs:label xml:lang="en">editor note</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obfoundry.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Daniel
Schober</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">editor note</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
+ <rdfs:label xml:lang="en">term editor</rdfs:label>
+ <obo:IAO_0000116 xml:lang="en">20110707, MC: label update to term
editor and definition modified accordingly. See
http://code.google.com/p/information-artifact-ontology/issues/detail?id=115.</obo:IAO_0000116>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000115 xml:lang="en">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</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Daniel
Schober</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">term editor</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
+ <rdfs:label xml:lang="en">alternative term</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">An alternative name for a class or
property which means the same thing as the preferred name (semantically
equivalent)</obo:IAO_0000115>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Daniel
Schober</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">alternative term</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
+ <rdfs:label xml:lang="en">definition source</rdfs:label>
+ <obo:IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Discussion on
obo-discuss mailing-list, see http://bit.ly/hgm99w</obo:IAO_0000119>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Daniel
Schober</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">definition source</obo:IAO_0000111>
+ <obo:IAO_0000115 xml:lang="en">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</obo:IAO_0000115>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000231">
+ <rdfs:label xml:lang="en">has obsolescence reason</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Melanie
Courtot</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">Relates an annotation property to
an obsolescence reason. The values of obsolescence reasons come from a list
of predefined terms, instances of the class obsolescence reason
specification.</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">has obsolescence
reason</obo:IAO_0000111>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000232">
+ <rdfs:label xml:lang="en">curator note</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">An administrative note of use for a
curator but of no use for a user</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">curator note</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000411">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is denotator
type</rdfs:label>
+ <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">In OWL 2 add
AnnotationPropertyRange('is denotator type' 'denotator
type')</obo:IAO_0000116>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">relates an class
defined in an ontology, to the type of it's denotator</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">is denotator type</obo:IAO_0000111>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
+ <rdfs:label xml:lang="en">imported from</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">For external terms/classes, the
ontology from which the term was imported</obo:IAO_0000115>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Melanie
Courtot</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">imported from</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000424">
+ <rdfs:label xml:lang="en">expand expression to</rdfs:label>
+ <obo:IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Chris
Mungall</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">A macro expansion tag applied to an
object property (or possibly a data property) which can be used by a
macro-expansion engine to generate more complex expressions from simpler
ones</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">ObjectProperty: RO_0002104
+Label: has plasma membrane part
+Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051
some (http://purl.org/obo/owl/GO#GO_0005886 and
http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
+</obo:IAO_0000112>
+ <obo:IAO_0000111 xml:lang="en">expand expression
to</obo:IAO_0000111>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000425">
+ <rdfs:label xml:lang="en">expand assertion to</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">A macro expansion tag applied to an
annotation property which can be expanded into a more detailed
axiom.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">Chris Mungall</obo:IAO_0000117>
+ <obo:IAO_0000112 xml:lang="en">ObjectProperty: RO???
+Label: spatially disjoint from
+Annotations: expand_assertion_to "DisjointClasses:
(http://purl.obolibrary.org/obo/BFO_0000051 some ?X)
(http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)"
+</obo:IAO_0000112>
+ <obo:IAO_0000111 xml:lang="en">expand assertion
to</obo:IAO_0000111>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000426">
+ <rdfs:label xml:lang="en">first order logic expression</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">first order logic
expression</obo:IAO_0000111>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000427">
+ <rdfs:label xml:lang="en">antisymmetric property</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">antisymmetric
property</obo:IAO_0000111>
+ <obo:IAO_0000112 xml:lang="en">part_of antisymmetric property
xsd:true</obo:IAO_0000112>
+ <obo:IAO_0000115 xml:lang="en">use boolean value xsd:true to
indicate that the property is an antisymmetric property</obo:IAO_0000115>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000589">
+ <rdfs:label xml:lang="en">OBO foundry unique label</rdfs:label>
+ <obo:IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The intended usage
of that property is as follow: OBO foundry unique labels are automatically
generated based on regular expressions provided by each ontology, so that
SO could specify unique label = 'sequence ' + [label], etc. , MA
could specify 'mouse + [label]' etc. Upon importing terms,
ontology developers can choose to use the 'OBO foundry unique
label' for an imported term or not. The same applies to
tools .</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">An alternative name for a class or
property which is unique across the OBO Foundry.</obo:IAO_0000115>
+ <obo:IAO_0000119 xml:lang="en">GROUP:OBO Foundry
<http://obofoundry.org/></obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">OBO foundry unique
label</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Bjoern
Peters</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Chris
Mungall</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Melanie
Courtot</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000596">
+ <rdfs:label xml:lang="en">has ID digit count</rdfs:label>
+ <obo:IAO_0000112>Ontology:
<http://purl.obolibrary.org/obo/ro/idrange/>
+ Annotations:
+ 'has ID prefix':
"http://purl.obolibrary.org/obo/RO_"
+ 'has ID digit count' : 7,
+ rdfs:label "RO id policy"
+ 'has ID policy for': "RO"</obo:IAO_0000112>
+ <obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000115>Relates an ontology used to record id policy to
the number of digits in the URI. The URI is: the 'has ID prefix"
annotation property value concatenated with an integer in the id range
(left padded with "0"s to make this many digits)</obo:IAO_0000115>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000597">
+ <rdfs:label xml:lang="en">has ID range allocated to</rdfs:label>
+ <obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000115>Relates a datatype that encodes a range of
integers to the name of the person or organization who can use those ids
constructed in that range to define new terms</obo:IAO_0000115>
+ <obo:IAO_0000112>Datatype: idrange:1
+Annotations: 'has ID range allocated to': "Chris
Mungall"
+EquivalentTo: xsd:integer[> 2151 , <= 2300]
+</obo:IAO_0000112>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000598">
+ <rdfs:label>has ID policy for</rdfs:label>
+ <obo:IAO_0000115>Relating an ontology used to record id policy to
the ontology namespace whose policy it manages</obo:IAO_0000115>
+ <obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000112>Ontology:
<http://purl.obolibrary.org/obo/ro/idrange/>
+ Annotations:
+ 'has ID prefix':
"http://purl.obolibrary.org/obo/RO_"
+ 'has ID digit count' : 7,
+ rdfs:label "RO id policy"
+ 'has ID policy for': "RO"</obo:IAO_0000112>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000599">
+ <rdfs:label xml:lang="en">has ID prefix</rdfs:label>
+ <obo:IAO_0000115>Relates an ontology used to record id policy to a
prefix concatenated with an integer in the id range (left padded with
"0"s to make this many digits) to construct an ID for a term
being created.</obo:IAO_0000115>
+ <obo:IAO_0000112>Ontology:
<http://purl.obolibrary.org/obo/ro/idrange/>
+ Annotations:
+ 'has ID prefix':
"http://purl.obolibrary.org/obo/RO_"
+ 'has ID digit count' : 7,
+ rdfs:label "RO id policy"
+ 'has ID policy for': "RO"</obo:IAO_0000112>
+ <obo:IAO_0000117>Person:Alan Ruttenberg</obo:IAO_0000117>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000600">
+ <rdfs:label xml:lang="en">elucidation</rdfs:label>
+ <obo:IAO_0000119 xml:lang="en">Person:Barry Smith</obo:IAO_0000119>
+ <obo:IAO_0000600 xml:lang="en">Primitive terms in a highest-level
ontology such as BFO are terms which are so basic to our understanding of
reality that there is no way of defining them in a non-circular fashion.
For these, therefore, we can provide only elucidations, supplemented by
examples and by axioms</obo:IAO_0000600>
+ <obo:IAO_0000111 xml:lang="en">elucidation</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">person:Alan
Ruttenberg</obo:IAO_0000117>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000601">
+ <rdfs:label xml:lang="en">has associated axiom(nl)</rdfs:label>
+ <obo:IAO_0000600 xml:lang="en">An axiom associated with a term
expressed using natural language</obo:IAO_0000600>
+ <obo:IAO_0000119 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">has associated
axiom(nl)</obo:IAO_0000111>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000602">
+ <rdfs:label xml:lang="en">has associated axiom(fol)</rdfs:label>
+ <obo:IAO_0000600 xml:lang="en">An axiom expressed in first order
logic using CLIF syntax</obo:IAO_0000600>
+ <obo:IAO_0000117 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000119 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">has associated
axiom(fol)</obo:IAO_0000111>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000603">
+ <rdfs:label xml:lang="en">is allocated id range</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">Add as annotation triples in the
granting ontology</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">Relates an ontology IRI to an
(inclusive) range of IRIs in an OBO name space. The range is give as, e.g.
"IAO_0020000-IAO_0020999"</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">is allocated id
range</obo:IAO_0000111>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000604">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">retired from use as
of</rdfs:label>
+ <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">In OWL 2 add
AnnotationPropertyRange xsd:dateTimeStamp</obo:IAO_0000116>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">relates a class of
CRID to the date after which further instances should not be made,
according to the central authority</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">retired from use as
of</obo:IAO_0000111>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0010000">
+ <rdfs:label xml:lang="en">has axiom label</rdfs:label>
+ <obo:IAO_0000600 xml:lang="en">A URI that is intended to be unique
label for an axiom used for tracking change to the ontology. For an axiom
expressed in different languages, each expression is given the same
URI</obo:IAO_0000600>
+ <obo:IAO_0000119 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">has axiom id</obo:IAO_0000111>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0100001">
+ <rdfs:label xml:lang="en">term replaced by</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">Add as annotation triples in the
granting ontology</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000119 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000119>
+ <obo:IAO_0000115 xml:lang="en">Use on obsolete terms, relating the
term to another term that can be used as a substitute</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">term replaced by</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/RO_0001900">
+ <rdfs:label xml:lang="en">temporal interpretation</rdfs:label>
+ <foaf:page
rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">https://code.google.com/p/obo-relations/wiki/ROAndTime</foaf:page>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.org/dc/elements/1.1/contributor"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.org/dc/elements/1.1/creator"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.org/dc/elements/1.1/member"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.org/dc/elements/1.1/publisher"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.org/dc/elements/1.1/source"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.org/dc/elements/1.1/title"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://www.geneontology.org/formats/oboInOwl#shorthand">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">shorthand</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://www.w3.org/2000/01/rdf-schema#comment"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://www.w3.org/2000/01/rdf-schema#isDefinedBy"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://www.w3.org/2000/01/rdf-schema#seeAlso"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://www.w3.org/2002/07/owl#versionInfo"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://xmlns.com/foaf/0.1/homepage"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="http://xmlns.com/foaf/0.1/page"/>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000050">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+ <rdfs:label xml:lang="en">part of</rdfs:label>
+ <obo:IAO_0000116 xml:lang="en">Ambiguous between
continuant-parthood and occurrent-parthood</obo:IAO_0000116>
+
<rdfs:seeAlso>http://www.obofoundry.org/ro/#OBO_REL:part_of</rdfs:seeAlso>
+ <obo:IAO_0000111 xml:lang="en">is part of</obo:IAO_0000111>
+ <obo:IAO_0000118 xml:lang="en">part_of</obo:IAO_0000118>
+ <owl:inverseOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+ <obo:RO_0001900
rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000051">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+ <rdfs:label xml:lang="en">has part</rdfs:label>
+ <obo:IAO_0000116 xml:lang="en">Ambiguous between
continuant-parthood and occurrent-parthood</obo:IAO_0000116>
+ <obo:IAO_0000111 xml:lang="en">has part</obo:IAO_0000111>
+ <obo:IAO_0000118 xml:lang="en">has_part</obo:IAO_0000118>
+ <obo:RO_0001900
rdf:resource="http://purl.obolibrary.org/obo/RO_0001901"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000054">
+ <rdfs:label xml:lang="en">realized in</rdfs:label>
+ <obo:IAO_0000118 xml:lang="en">is realized by</obo:IAO_0000118>
+ <obo:IAO_0000111 xml:lang="en">realized in</obo:IAO_0000111>
+ <obo:IAO_0000118 xml:lang="en">realized_in</obo:IAO_0000118>
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000055">
+ <rdfs:label xml:lang="en">realizes</rdfs:label>
+ <obo:IAO_0000111 xml:lang="en">realizes</obo:IAO_0000111>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+ <owl:inverseOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000054"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000066">
+ <rdfs:label xml:lang="en">occurs in</rdfs:label>
+ <obo:IAO_0000118 xml:lang="en">Intended meaning:
+domain: occurrent
+range: independent continuant
+time: atemporal</obo:IAO_0000118>
+ <obo:IAO_0000111 xml:lang="en">occurs in</obo:IAO_0000111>
+ <obo:IAO_0000118 xml:lang="en">occurs_in</obo:IAO_0000118>
+ <obo:IAO_0000118 xml:lang="en">unfolds in</obo:IAO_0000118>
+ <obo:IAO_0000118 xml:lang="en">unfolds_in</obo:IAO_0000118>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
+ <owl:inverseOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000067"/>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/BFO_0000066"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
+ </owl:propertyChainAxiom>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/BFO_0000066"/>
+ </owl:propertyChainAxiom>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000067">
+ <rdfs:label xml:lang="en">contains process</rdfs:label>
+ <obo:IAO_0000111 xml:lang="en">site of</obo:IAO_0000111>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000039">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
+ <rdfs:label xml:lang="en">has measurement unit label</rdfs:label>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000135">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_specifically
denotes</rdfs:label>
+ <obo:IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8/6/2009 Alan
Ruttenberg: The suggestions is to deprecate specific and generically
denotes in favor of a single denote relationship that corresponds to the
generic sense</obo:IAO_0000116>
+ <obo:IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smith, Ceusters,
Ruttenberg, 2000 years of philosophy</obo:IAO_0000119>
+ <obo:IAO_0000112
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The process of
creation is, for example, writing down on paper the name of a friend by
deliberately creating a certain pattern using ink.
+
+Here the ink + paper is the independent continuant and the carrier is the
pattern in the ink.
+
+c = pattern in the ink
+b = paper + ink
+r = friend</obo:IAO_0000112>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">c specifically
denotes r =def
+r is a portion of reality
+& c is a particular quality
+& c depends specifically on some independent continuant b
+& b acquired c as the result of the achievement of an objective to
enable pointing to r repeatedly.
+
+Marked means there is a changed or additional quality of the bearer - the
quality is the information carrier.
+
+Case 1
+Memory trace as mark created when reading some description of some friend.
The trace can denote.
+
+Case 2
+Pattern of ink arrayed on paper as mark when writing down a friend's
name
+
+Case 3
+Pattern of magnetic domains on scattered pieces of a hard disk platter as
mark when saving a file.</obo:IAO_0000115>
+ <obo:IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see
http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote</obo:IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <obo:IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <rdfs:subPropertyOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000136">
+ <rdfs:label xml:lang="en">is about</rdfs:label>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000119 xml:lang="en">Smith, Ceusters, Ruttenberg, 2000
years of philosophy</obo:IAO_0000119>
+ <obo:IAO_0000112 xml:lang="en">This document is about information
artifacts and their representations</obo:IAO_0000112>
+ <obo:IAO_0000115 xml:lang="en">is_about is a (currently) primitive
relation that relates an information artifact to an
entity.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">person:Alan
Ruttenberg</obo:IAO_0000117>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000142">
+ <rdfs:label xml:lang="en">mentions</rdfs:label>
+ <obo:IAO_0000116 xml:lang="en">7/6/2009 Alan Ruttenberg. P4 RC1
munges our GCI so remove it for now: mentions some entity equivalentTo
has_part some ('generically denotes' some
entity)</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">7/6/2009 Alan Ruttenberg: Add this
relation following conversation with Jonathan Rees that N&S GCI for
is_about was too strong. Really it was simply sufficient. To effect this
change we introduce this relation, which is subproperty of is_about, and
have previous GCI use this relation "mentions" in it's
(logical) definition</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">An information artifact IA mentions
an entity E exactly when it has a component/part that denotes
E</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Jonathan
Rees</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">Person: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000219">
+ <rdfs:label xml:lang="en">denotes</rdfs:label>
+ <rdfs:comment xml:lang="en"></rdfs:comment>
+ <obo:IAO_0000116 xml:lang="en">2009-11-10 Alan Ruttenberg. Old
definition said the following to emphasize the generic nature of this
relation. We no longer have 'specifically denotes', which would
have been primitive, so make this relation primitive.
+g denotes r =def
+r is a portion of reality
+there is some c that is a concretization of g
+every c that is a concretization of g specifically denotes
r</obo:IAO_0000116>
+ <obo:IAO_0000112 xml:lang="en">A person's name denotes the
person. A variable name in a computer program denotes some piece of memory.
Lexically equivalent strings can denote different things, for instance
"Alan" can denote different people. In each case of use, there is
a case of the denotation relation obtaining, between "Alan" and
the person that is being named.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">Conversations with Barry Smith,
Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James
Malone, Bill Hogan</obo:IAO_0000119>
+ <obo:IAO_0000115 xml:lang="en">denotes is a primitive,
instance-level, relation obtaining between an information content entity
and some portion of reality. Denotation is what happens when someone
creates an information content entity E in order to specifically refer to
something. The only relation between E and the thing is that E can be used
to 'pick out' the thing. This relation connects those two
together. Freedictionary.com sense 3: To signify directly; refer to
specifically</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">person:Alan
Ruttenberg</obo:IAO_0000117>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000220">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_materially
denotes</rdfs:label>
+ <obo:IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">see
http://code.google.com/p/information-artifact-ontology/issues/detail?id=25&q=denote</obo:IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <obo:IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <rdfs:subPropertyOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000221">
+ <rdfs:label xml:lang="en">is quality measurement of</rdfs:label>
+ <obo:IAO_0000116 xml:lang="en">8/6/2009 Alan Ruttenberg: The
strategy is to be rather specific with this relationship. There are other
kinds of measurements that are not of qualities, such as those that measure
time. We will add these as separate properties for the moment and see about
generalizing later</obo:IAO_0000116>
+ <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000116 xml:lang="en">From the second IAO workshop [Alan
Ruttenberg 8/6/2009: not completely current, though bringing in comparison
is probably important]
+
+This one is the one we are struggling with at the moment. The issue is
what a measurement measures. On the one hand saying that it measures the
quality would include it "measuring" the bearer = referring to
the bearer in the measurement. However this makes comparisons of two
different things not possible. On the other hand not having it inhere in
the bearer, on the face of it, breaks the audit trail.
+
+Werner suggests a solution based on "Magnitudes" a proposal for
which we are awaiting details.
+--
+From the second IAO workshop, various comments, [commented on by Alan
Ruttenberg 8/6/2009]
+
+unit of measure is a quality, e.g. the length of a ruler.
+
+[We decided to hedge on what units of measure are, instead talking about
measurement unit labels, which are the information content entities that
are about whatever measurement units are. For IAO we need that information
entity in any case. See the term measurement unit label]
+
+[Some struggling with the various subflavors of is_about. We subsequently
removed the relation represents, and describes until and only when we have
a better theory]
+
+a represents b means either a denotes b or a describes
+
+describe:
+a describes b means a is about b and a allows an inference of at least one
quality of b
+
+We have had a long discussion about denotes versus
describes.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">From the second IAO workshop: An
attempt at tieing the quality to the measurement datum more carefully.
+
+a is a magnitude means a is a determinate quality particular inhering in
some bearer b existing at a time t that can be represented/denoted by an
information content entity e that has parts denoting a unit of measure, a
number, and b. The unit of measure is an instance of the determinable
quality.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">From the second meeting on IAO:
+
+An attempt at defining assay using Barry's "reliability"
wording
+
+assay:
+process and has_input some material entity
+and has_output some information content entity
+and which is such that instances of this process type reliably generate
+outputs that describes the input.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">This one is the one we are
struggling with at the moment. The issue is what a measurement measures. On
the one hand saying that it measures the quality would include it
"measuring" the bearer = referring to the bearer in the
measurement. However this makes comparisons of two different things not
possible. On the other hand not having it inhere in the bearer, on the face
of it, breaks the audit trail.
+
+Werner suggests a solution based on "Magnitudes" a proposal for
which we are awaiting details.</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">m is a quality measurement of q at
t when
+q is a quality
+there is a measurement process p that has specified output m, a
measurement datum, that is about q</obo:IAO_0000115>
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000222">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_describes</rdfs:label>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <obo:IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <rdfs:subPropertyOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000223">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_represents</rdfs:label>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <obo:IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <rdfs:subPropertyOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000407">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
+ <rdfs:label xml:lang="en">has coordinate unit label</rdfs:label>
+ <rdfs:comment xml:lang="en">relating a cartesian spatial
coordinate datum to a unit label that together with the values represent a
point</rdfs:comment>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/UO_0000001"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000413">
+ <rdfs:label xml:lang="en">is duration of</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">relates a process to a
time-measurement-datum that represents the duration of the
process</obo:IAO_0000115>
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000416"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000417">
+ <rdfs:label xml:lang="en">is quality measured as</rdfs:label>
+ <obo:IAO_0000116 xml:lang="en">2009/10/19 Alan Ruttenberg. Named
'junk' relation useful in restrictions, but not a real instance
relationship</obo:IAO_0000116>
+ <obo:IAO_0000117 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">inverse of the relation of is
quality measurement of</obo:IAO_0000115>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ <owl:inverseOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000221"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000418">
+ <rdfs:label xml:lang="en">is quality specification of</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">Person:Bjoern
Peters</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">a relation between a data item and
a quality of a material entity where the material entity is the specified
output of a material transformation which achieves an objective
specification that indicates the intended value of the specified
quality.</obo:IAO_0000115>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000419">
+ <rdfs:label xml:lang="en">quality is specified as</rdfs:label>
+ <obo:IAO_0000116 xml:lang="en">2009/10/19 Alan Ruttenberg. Named
'junk' relation useful in restrictions, but not a real instance
relationship</obo:IAO_0000116>
+ <obo:IAO_0000117 xml:lang="en">Person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">Person:Bjoern
Peters</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">inverse of the relation of is
quality specification of</obo:IAO_0000115>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ <owl:inverseOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000418"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000581">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
+ <rdfs:label xml:lang="en">has time stamp</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">relates a time stamped measurement
datum to the time measurement datum that denotes the time when the
measurement was taken</obo:IAO_0000115>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000416"/>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000582"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000583">
+ <rdfs:label xml:lang="en">has measurement datum</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">relates a time stamped measurement
datum to the measurement datum that was measured</obo:IAO_0000115>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000582"/>
+ <rdfs:range>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000109"/>
+ <owl:Class>
+ <owl:complementOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000416"/>
+ </owl:Class>
+ </owl:intersectionOf>
+ </owl:Class>
+ </rdfs:range>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000293">
+ <rdfs:label xml:lang="en">has_specified_input</rdfs:label>
+ <obo:IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">8/17/09: specified
inputs of one process are not necessarily specified inputs of a larger
process that it is part of. This is in contrast to how 'has
participant' works.</obo:IAO_0000116>
+ <obo:IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern
Peters</obo:IAO_0000117>
+ <obo:IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Larry
Hunter</obo:IAO_0000117>
+ <obo:IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie
Coutot</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">A relation between a planned
process and a continuant participating in that process that is not created
during the process. The presence of the continuant during the process is
explicitly specified in the plan specification which the process realizes
the concretization of.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000111
xml:lang="en">has_specified_input</obo:IAO_0000111>
+ <obo:IAO_0000112 xml:lang="en">see is_input_of
example_of_usage</obo:IAO_0000112>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+ </owl:ObjectProperty>
***The diff for this file has been truncated for email.***

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