[information-artifact-ontology] r712 committed - Checkout SVN revision 711 and convert owl files from BFO 1.1 and OBORO...

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Revision: 712
Author: zheng...@gmail.com
Date: Sat Jan 3 07:23:58 2015 UTC
Log: Checkout SVN revision 711 and convert owl files from BFO 1.1 and
OBORO to BFO 2 classes only and RO core relations
Clean up external terms import using OntoFox
https://code.google.com/p/information-artifact-ontology/source/detail?r=712

Added:
/branches/2015-01-02
/branches/2015-01-02/doc
/branches/2015-01-02/doc/mapping.txt
/branches/2015-01-02/doc/notes.txt
/branches/2015-01-02/doc/termsMapping.xlsx
/branches/2015-01-02/doc/~$termsMapping.xlsx
/branches/2015-01-02/ontology
/branches/2015-01-02/ontology/IAO.owl
/branches/2015-01-02/ontology/external.owl
/branches/2015-01-02/ontology/externalByHand.owl
/branches/2015-01-02/ontology/externalDerived.owl
/branches/2015-01-02/ontology/iao-main.owl
/branches/2015-01-02/ontology/obsolete.owl
/branches/2015-01-02/ontology/ontology-metadata.owl
/branches/2015-01-02/ontology-BFO2
/branches/2015-01-02/ontology-BFO2/IAO.owl
/branches/2015-01-02/ontology-BFO2/catalog-v001.xml
/branches/2015-01-02/ontology-BFO2/external
/branches/2015-01-02/ontology-BFO2/external/annotations.owl
/branches/2015-01-02/ontology-BFO2/external/bfo-classes-minimal.owl
/branches/2015-01-02/ontology-BFO2/external/bfo_classes_only.owl
/branches/2015-01-02/ontology-BFO2/external/ro-core.owl
/branches/2015-01-02/ontology-BFO2/externalByHand.owl
/branches/2015-01-02/ontology-BFO2/iao-main.owl
/branches/2015-01-02/ontology-BFO2/import-OBO.owl
/branches/2015-01-02/ontology-BFO2/obsolete.owl
/branches/2015-01-02/ontology-BFO2/ontoFox
/branches/2015-01-02/ontology-BFO2/ontoFox/OntoFox-input.txt
/branches/2015-01-02/ontology-BFO2/ontology-metadata.owl

=======================================
--- /dev/null
+++ /branches/2015-01-02/doc/mapping.txt Sat Jan 3 07:23:58 2015 UTC
@@ -0,0 +1,31 @@
+http://www.ifomis.org/bfo/1.1#Entity
http://purl.obolibrary.org/obo/BFO_0000001
+http://www.ifomis.org/bfo/1.1/snap#Continuant
http://purl.obolibrary.org/obo/BFO_0000002
+http://www.ifomis.org/bfo/1.1/snap#Disposition
http://purl.obolibrary.org/obo/BFO_0000016
+http://www.ifomis.org/bfo/1.1/snap#Function
http://purl.obolibrary.org/obo/BFO_0000034
+http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant
http://purl.obolibrary.org/obo/BFO_0000031
+http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant
http://purl.obolibrary.org/obo/BFO_0000004
+http://www.ifomis.org/bfo/1.1/snap#MaterialEntity
http://purl.obolibrary.org/obo/BFO_0000040
+http://www.ifomis.org/bfo/1.1/snap#Quality
http://purl.obolibrary.org/obo/BFO_0000019
+http://www.ifomis.org/bfo/1.1/snap#RealizableEntity
http://purl.obolibrary.org/obo/BFO_0000017
+http://www.ifomis.org/bfo/1.1/snap#Role
http://purl.obolibrary.org/obo/BFO_0000023
+http://www.ifomis.org/bfo/1.1/snap#Site
http://purl.obolibrary.org/obo/BFO_0000029
+http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant
http://purl.obolibrary.org/obo/BFO_0000020
+http://www.ifomis.org/bfo/1.1/span#Occurrent
http://purl.obolibrary.org/obo/BFO_0000003
+http://www.ifomis.org/bfo/1.1/span#ProcessualEntity
http://purl.obolibrary.org/obo/BFO_0000015
+http://www.ifomis.org/bfo/1.1/span#Process
http://purl.obolibrary.org/obo/BFO_0000015
+http://www.ifomis.org/bfo/1.1/snap#ZeroDimensionalRegion
http://purl.obolibrary.org/obo/BFO_0000018
+http://www.ifomis.org/bfo/1.1/snap#OneDimensionalRegion
http://purl.obolibrary.org/obo/BFO_0000026
+http://www.ifomis.org/bfo/1.1/snap#TwoDimensionalRegion
http://purl.obolibrary.org/obo/BFO_0000009
+http://www.ifomis.org/bfo/1.1/snap#ThreeDimensionalRegion
http://purl.obolibrary.org/obo/BFO_0000028
+http://purl.org/obo/owl/OBO_REL#bearer_of
http://purl.obolibrary.org/obo/RO_0000053
+http://purl.org/obo/owl/OBO_REL#inheres_in
http://purl.obolibrary.org/obo/RO_0000052
+http://www.obofoundry.org/ro/ro.owl#has_part
http://purl.obolibrary.org/obo/BFO_0000051
+http://www.obofoundry.org/ro/ro.owl#part_of
http://purl.obolibrary.org/obo/BFO_0000050
+http://www.obofoundry.org/ro/ro.owl#has_participant
http://purl.obolibrary.org/obo/RO_0000057
+http://www.obofoundry.org/ro/ro.owl#participates_in
http://purl.obolibrary.org/obo/RO_0000056
+http://purl.obolibrary.org/obo/OBI_0000294
http://purl.obolibrary.org/obo/RO_0000059
+http://purl.obolibrary.org/obo/OBI_0000297
http://purl.obolibrary.org/obo/RO_0000058
+http://purl.obolibrary.org/obo/OBI_0000300
http://purl.obolibrary.org/obo/BFO_0000054
+http://purl.obolibrary.org/obo/OBI_0000308
http://purl.obolibrary.org/obo/BFO_0000055
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/doc/notes.txt Sat Jan 3 07:23:58 2015 UTC
@@ -0,0 +1,14 @@
+1. Update term URIs of BFO and RO/OBI relations using doc/mapping.txt file
+
+2. Import classes from external resources using OntoFox based on MIREOT
strategy, generated import-OBO.owl
+
+3. Change <owl:import> in IAO.owl and iao-main.owl, replace import
external.owl and externalDerived.owl by import-OBO.owl
+
+4. Clean up ontology headers including removing unused xmlns and
owl:import of BFO 1.1 and RO and add import of BFO2.0 class only and RO
core relations
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/bfo/2014-05-03/classes-only.owl"/>
+ <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/core.owl"/>
+
+
+5. Remove any axioms related to imported terms in iao-main.owl
+
+6. Add domain and range of ObjectiveProperties manually in
externalByHand.owl since includes domain/range settings using OntoFox need
to include all axioms recursively which will bring in unwanted classes and
propteries
=======================================
--- /dev/null
+++ /branches/2015-01-02/doc/termsMapping.xlsx Sat Jan 3 07:23:58 2015 UTC
Binary file, no diff available.
=======================================
--- /dev/null
+++ /branches/2015-01-02/doc/~$termsMapping.xlsx Sat Jan 3 07:23:58 2015
UTC
@@ -0,0 +1,3 @@
+
+Windows User
+ W i n d o w s U s e r

=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology/IAO.owl Sat Jan 3 07:23:58 2015 UTC
@@ -0,0 +1,41 @@
+<?xml version="1.0"?>
+<rdf:RDF
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns:obo="http://purl.obolibrary.org/obo/"
+ xmlns="http://purl.obolibrary.org/obo/"
+ xml:base="http://purl.obolibrary.org/obo/iao/dev/iao.owl">
+ <owl:Ontology rdf:about="">
+ <rdfs:seeAlso>
+ <owl:Thing
rdf:about="http://code.google.com/p/information-artifact-ontology/"/>
+ </rdfs:seeAlso>
+ <owl:versionInfo xml:lang="en">$Revision$</owl:versionInfo>
+ <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>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/obsolete.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/iao-main.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/externalDerived.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/external.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/externalByHand.owl"/>
+ <owl:imports><owl:Ontology
rdf:about="http://www.obofoundry.org/ro/ro.owl"/></owl:imports>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl"/>
+ <owl:imports
rdf:resource="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl"/>
+ <owl:imports rdf:resource="http://www.ifomis.org/bfo/1.1"/>
+ <protege:defaultLanguage
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
+ <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>
+ </owl:Ontology>
+ <owl:AnnotationProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000603"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/iao/pno.owl">
+ <obo:IAO_0000603
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IAO_0020000-IAO_0020999</obo:IAO_0000603>
+ </rdf:Description>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/iao/d-acts.owl">
+ <obo:IAO_0000603
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IAO_0021000-IAO_0021999</obo:IAO_0000603>
+ </rdf:Description>
+
+</rdf:RDF>
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology/external.owl Sat Jan 3 07:23:58 2015 UTC
@@ -0,0 +1,99 @@
+<?xml version="1.0"?>
+<rdf:RDF
+
xmlns:protege-dc="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl#"
+ xmlns:ro="http://www.obofoundry.org/ro/ro.owl#"
+ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
+ xmlns:dcterms="http://purl.org/dc/terms/"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns:rotoo="http://purl.org/obo/owl/ro#"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#"
+ xmlns:bfo="http://www.ifomis.org/bfo/1.1#"
+ xmlns:robfo="http://purl.org/obo/owl/ro_bfo_bridge/1.1#"
+ xmlns:swrl="http://www.w3.org/2003/11/swrl#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
+ xmlns:span="http://www.ifomis.org/bfo/1.1/span#"
+ xmlns="http://purl.obolibrary.org/obo/"
+ xml:base="http://purl.obolibrary.org/obo/iao/dev/external.owl">
+ <owl:Ontology rdf:about="">
+ <owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >$Revision: 80 $</owl:versionInfo>
+ </owl:Ontology>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000066">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011"/>
+ </rdfs:subClassOf>
+ <IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000104"/>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000002">
+ <IAO_0000412 rdf:resource="http://purl.org/obo/owl/UO"/>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000471">
+ <IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0500000">
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
+ <IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000003">
+ <IAO_0000412 rdf:resource="http://purl.org/obo/owl/UO"/>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011">
+ <IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+ <rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/span#ProcessualEntity"/>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000001">
+ <IAO_0000412 rdf:resource="http://purl.org/obo/owl/UO"/>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000122">
+ <rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
+ <IAO_0000412 rdf:resource="http://purl.org/obo/owl/PATO"/>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000125">
+ <rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
+ <IAO_0000412 rdf:resource="http://purl.org/obo/owl/PATO"/>
+ </owl:Class>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000114">
+ <rdfs:label xml:lang="en">has curation status</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
+ <rdfs:label xml:lang="en">term editor</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
+ <rdfs:label xml:lang="en">definition source</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
+ <rdfs:label xml:lang="en">imported from</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000112">
+ <rdfs:label xml:lang="en">example of usage</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+ <rdfs:label xml:lang="en">definition</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
+ <rdfs:label xml:lang="en">alternative term</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
+ <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
+ <rdfs:label xml:lang="en">editor note</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000113">
+ <rdfs:label xml:lang="en">in branch</rdfs:label>
+ </owl:AnnotationProperty>
+</rdf:RDF>
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology/externalByHand.owl Sat Jan 3 07:23:58
2015 UTC
@@ -0,0 +1,256 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/"
+ xml:base="http://purl.obolibrary.org/obo/"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+
xmlns:protege-dc="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl#"
+ xmlns:ro="http://www.obofoundry.org/ro/ro.owl#"
+ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
+ xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
+ xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#"
+ xmlns:rotoo="http://purl.org/obo/owl/ro#"
+ xmlns:bfo="http://www.ifomis.org/bfo/1.1#"
+ xmlns:dcterms="http://purl.org/dc/terms/"
+ xmlns:obo="http://purl.obolibrary.org/obo/"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:swrl="http://www.w3.org/2003/11/swrl#"
+ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
+ 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:robfo="http://purl.org/obo/owl/ro_bfo_bridge/1.1#"
+ xmlns:OBO_REL="http://purl.org/obo/owl/OBO_REL#"
+ xmlns:span="http://www.ifomis.org/bfo/1.1/span#">
+ <owl:Ontology
rdf:about="http://purl.obolibrary.org/obo/iao/dev/externalByHand.owl">
+ <owl:versionInfo
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">$Revision: 80
$</owl:versionInfo>
+ </owl:Ontology>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+ <rdfs:label xml:lang="en">definition</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
+ <rdfs:label xml:lang="en">editor note</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000113">
+ <rdfs:label xml:lang="en">in branch</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
+ <rdfs:label xml:lang="en">imported from</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000114">
+ <rdfs:label xml:lang="en">has curation status</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
+ <rdfs:label xml:lang="en">definition source</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
+ <rdfs:label xml:lang="en">term editor</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
+ <rdfs:label xml:lang="en">alternative term</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
+ <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000112">
+ <rdfs:label xml:lang="en">example of usage</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000293">
+ <rdfs:label xml:lang="en">has_specified_input</rdfs:label>
+ <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.</IAO_0000116>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern
Peters</IAO_0000117>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Larry
Hunter</IAO_0000117>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie
Coutot</IAO_0000117>
+ <IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_specified_input</IAO_0000111>
+ <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.</IAO_0000115>
+ <IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</IAO_0000117>
+ <IAO_0000112 xml:lang="en">see is_input_of
example_of_usage</IAO_0000112>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+ <rdfs:subPropertyOf
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_participant"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000299">
+ <rdfs:label xml:lang="en">has_specified_output</rdfs:label>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Bjoern
Peters</IAO_0000117>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Larry
Hunter</IAO_0000117>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie
Courtot</IAO_0000117>
+ <IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_specified_output</IAO_0000111>
+ <IAO_0000115 xml:lang="en">A relation between a planned process
and a continuant participating in that process. The presence of the
continuant at the end of the process is explicitly specified in the
objective specification which the process realizes the concretization
of.</IAO_0000115>
+ <IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</IAO_0000117>
+ <owl:inverseOf
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
+ <rdfs:subPropertyOf
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_participant"/>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000300">
+ <rdfs:label xml:lang="en">is_realized_by</rdfs:label>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP:OBI:<http://obi.sourceforge.net></IAO_0000117>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Chris
Mungall</IAO_0000117>
+ <IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Relation between a
realizable and a process. Reciprocal relation of realizes
[GOC:cjm]</IAO_0000115>
+ <IAO_0000118
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">executed_during</IAO_0000118>
+ <IAO_0000118
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">has_realization</IAO_0000118>
+ <IAO_0000118
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is_realized_as</IAO_0000118>
+ <IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is_realized_by</IAO_0000111>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:range
rdf:resource="http://www.ifomis.org/bfo/1.1/span#ProcessualEntity"/>
+ <rdfs:domain
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#RealizableEntity"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000312">
+ <rdfs:label xml:lang="en">is_specified_output_of</rdfs:label>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Bjoern
Peters</IAO_0000117>
+ <IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">is_specified_output_of</IAO_0000111>
+ <IAO_0000115 xml:lang="en">A relation between a planned process
and a continuant participating in that process. The presence of the
continuant at the end of the process is explicitly specified in the
objective specification which the process realizes the concretization
of.</IAO_0000115>
+ <IAO_0000117 xml:lang="en">Alan Ruttenberg</IAO_0000117>
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+ <rdfs:subPropertyOf
rdf:resource="http://www.obofoundry.org/ro/ro.owl#participates_in"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.org/obo/owl/OBO_REL#bearer_of">
+ <rdfs:range
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant"/>
+ <rdfs:domain
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.org/obo/owl/OBO_REL#inheres_in">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">inheres
in</rdfs:label>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This clarifies that
only specifically dependent continuants inhere in (specifically) one
independent continuant over all time. For GDCs, there in implicitly
inherence to all the independent continuants in which the concretizations
inhere. Should add a 'cardinality 1' restriction to the
definition of specifically dependent continuant.</IAO_0000116>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">This relation
belongs in BFO/RO, and will be in BFO 2</IAO_0000116>
+ <owl:inverseOf
rdf:resource="http://purl.org/obo/owl/OBO_REL#bearer_of"/>
+ <rdfs:range
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant"/>
+ <rdfs:domain
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://www.obofoundry.org/ro/ro.owl#has_participant"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://www.obofoundry.org/ro/ro.owl#participates_in"/>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/GAZ_00000448">
+ <rdfs:label xml:lang="en">geographical location</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Site"/>
+ <IAO_0000115>A reference to a place on the Earth, by its name or
by its geographical location.</IAO_0000115>
+ <IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/GAZ"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011"/>
+
+
+
+ 
+
+ <owl:Class
rdf:about="http://www.ifomis.org/bfo/1.1/snap#IndependentContinuant"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://www.ifomis.org/bfo/1.1/snap#Site"/>
+
+
+
+ 
+
+ <owl:Class
rdf:about="http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant"/>
+
+
+
+ 
+
+ <owl:Class
rdf:about="http://www.ifomis.org/bfo/1.1/span#ProcessualEntity"/>
+
+
+
+ 
+
+ <owl:Class
rdf:about="http://www.ifomis.org/bfo/1.1/snap#RealizableEntity"/>
+
+
+
+</rdf:RDF>
+
+
+
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology/externalDerived.owl Sat Jan 3 07:23:58
2015 UTC
@@ -0,0 +1,173 @@
+<?xml version="1.0"?>
+<rdf:RDF
xmlns="http://purl.obolibrary.org/obo/iao/dev/externalDerived.owl#"
+ xml:base="http://purl.obolibrary.org/obo/iao/dev/externalDerived.owl"
+ xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#"
+
xmlns:protege-dc="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:dcterms="http://purl.org/dc/terms/"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:rotoo="http://purl.org/obo/owl/ro#"
+ xmlns:daml="http://www.daml.org/2001/03/daml+oil#"
+ xmlns:robfo="http://purl.org/obo/owl/ro_bfo_bridge/1.1#"
+ xmlns:obi="http://purl.obolibrary.org/obo/"
+ xmlns:ro="http://www.obofoundry.org/ro/ro.owl#"
+ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
+ xmlns:bfo="http://www.ifomis.org/bfo/1.1#"
+ xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
+ xmlns:swrl="http://www.w3.org/2003/11/swrl#"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
+ xmlns:span="http://www.ifomis.org/bfo/1.1/span#">
+ <owl:Ontology
rdf:about="http://purl.obolibrary.org/obo/iao/dev/externalDerived.owl">
+ <owl:versionInfo
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">$Revision: 80
$</owl:versionInfo>
+ </owl:Ontology>
+
+
+
+ 
+
+ <rdf:Description
rdf:about="http://www.w3.org/2002/07/owl#versionInfo"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000113">
+ <rdfs:label xml:lang="en">in branch</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
+ <rdfs:label xml:lang="en">editor note</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
+ <rdfs:label xml:lang="en">term editor</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000112">
+ <rdfs:label xml:lang="en">example of usage</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
+ <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000114">
+ <rdfs:label xml:lang="en">has curation status</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
+ <rdfs:label xml:lang="en">alternative term</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
+ <rdfs:label xml:lang="en">imported from</rdfs:label>
+ </owl:AnnotationProperty>
+ <rdf:Description
rdf:about="http://www.w3.org/2000/01/rdf-schema#label"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+ <rdfs:label xml:lang="en">definition</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
+ <rdfs:label xml:lang="en">definition source</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011">
+ <rdfs:label xml:lang="en">planned process</rdfs:label>
+ <obi:IAO_0000115 xml:lang="en">A processual entity that realizes a
plan which is the concretization of a plan specification.</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">planned process</obi:IAO_0000111>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000066">
+ <rdfs:label xml:lang="en">investigation</rdfs:label>
+ <obi:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a planned process
that consists of parts: planning, study design execution, documentation and
which produce conclusion(s).</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">investigation</obi:IAO_0000111>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000471">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study design
execution</rdfs:label>
+ <obi:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a planned process
that realizes the concretization of a study design</obi:IAO_0000115>
+ <obi:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study design
execution</obi:IAO_0000111>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0500000">
+ <rdfs:label xml:lang="en">study design</rdfs:label>
+ <obi:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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.</obi:IAO_0000115>
+ <obi:IAO_0000111 xml:lang="en">study design</obi:IAO_0000111>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000122">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">length</rdfs:label>
+ <obi:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">length</obi:IAO_0000111>
+ <obi:IAO_0000115 xml:lang="en">A 1-D extent quality which is equal
to the distance between two points.</obi:IAO_0000115>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000125">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass</rdfs:label>
+ <obi:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass</obi:IAO_0000111>
+ <obi:IAO_0000115 xml:lang="en">A physical quality that inheres in
a bearer by virtue of the proportion of the bearer's amount of
matter.</obi:IAO_0000115>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000001">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">length
unit</rdfs:label>
+ <obi:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">length
unit</obi:IAO_0000111>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000002">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass
unit</rdfs:label>
+ <obi:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass
unit</obi:IAO_0000111>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000003">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">time
unit</rdfs:label>
+ <obi:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">time
unit</obi:IAO_0000111>
+ </owl:Class>
+</rdf:RDF>
+
+
+
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology/iao-main.owl Sat Jan 3 07:23:58 2015 UTC
@@ -0,0 +1,2560 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/iao/dev/iao-main.owl#"
+ xml:base="http://purl.obolibrary.org/obo/iao/dev/iao-main.owl"
+ xmlns:ro="http://www.obofoundry.org/ro/ro.owl#"
+ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
+ xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
+ xmlns:iao="http://purl.obolibrary.org/obo/iao/"
+ xmlns:p1="http://purl.obolibrary.org/obo/iao/ontology-metadata.owl#"
+ xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#"
+ xmlns:daml="http://www.daml.org/2001/03/daml+oil#"
+ xmlns:owl2="http://www.w3.org/2006/12/owl2#"
+ xmlns:bfo="http://www.ifomis.org/bfo/1.1#"
+
xmlns:obo2="http://purl.obolibrary.org/obo/iao/dev/iao-main.owl#http://purl.obolibrary.org/obo/"
+ xmlns:obo="http://purl.obolibrary.org/obo/"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:swrl="http://www.w3.org/2003/11/swrl#"
+ xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
+ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
+ 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:OBO_REL="http://purl.org/obo/owl/OBO_REL#"
+ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
+ xmlns:span="http://www.ifomis.org/bfo/1.1/span#">
+ <owl:Ontology
rdf:about="http://purl.obolibrary.org/obo/iao/dev/iao-main.owl">
+ <protege:defaultLanguage
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
+ <owl:versionInfo xml:lang="en">$Revision$</owl:versionInfo>
+ <rdfs:comment xml:lang="en">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: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:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/external.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/externalByHand.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/externalDerived.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl"/>
+ <owl:imports rdf:resource="http://www.ifomis.org/bfo/1.1"/>
+ <owl:imports rdf:resource="http://www.obofoundry.org/ro/ro.owl"/>
+ </owl:Ontology>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://protege.stanford.edu/plugins/owl/protege#defaultLanguage"/>
+ <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#comment"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+ <rdfs:label xml:lang="en">definition</rdfs:label>
+ </owl:AnnotationProperty>
+ <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://purl.obolibrary.org/obo/IAO_0000116">
+ <rdfs:label xml:lang="en">editor note</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000113">
+ <rdfs:label xml:lang="en">in branch</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000114">
+ <rdfs:label xml:lang="en">has curation status</rdfs:label>
+ </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_0000412">
+ <rdfs:label xml:lang="en">imported from</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
+ <rdfs:label xml:lang="en">definition source</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
+ <rdfs:label xml:lang="en">term editor</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000231">
+ <rdfs:label xml:lang="en">has obsolescence reason</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
+ <rdfs:label xml:lang="en">alternative term</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
+ <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+
+
+
+ 
+
+
+
+
+ 
+
+ <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:range
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
+ <rdfs:subPropertyOf
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ </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_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:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000109"/>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+ <rdfs:range
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
+ </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:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/UO_0000001"/>
+ <rdfs:subPropertyOf
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ </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>
+ <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"/>
+ <rdfs:range
rdf:resource="http://www.ifomis.org/bfo/1.1/span#Process"/>
+ </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>
+ <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"/>
+ <rdfs:subPropertyOf
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ </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>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000582"/>
+ <rdfs:subPropertyOf
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ <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"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000294">
+ <rdfs:label xml:lang="en">is_concretization_of</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">a relationship between a
generically dependent continuant and at least one specifically dependent
continuant upon which it existentially depends</obo:IAO_0000115>
+ <rdfs:range
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant"/>
+ <rdfs:domain
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000297">
+ <rdfs:label xml:lang="en">is_concretized_as</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">a relationship between a
generically dependent continuant and at least one specifically dependent
continuant upon which it existentially depends</obo:IAO_0000115>
+ <owl:inverseOf
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000294"/>
+ <rdfs:domain
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant"/>
+ <rdfs:range
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#SpecificallyDependentContinuant"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000299"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.org/obo/owl/OBO_REL#bearer_of"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://www.obofoundry.org/ro/ro.owl#part_of">
+ <obo:IAO_0000116 xml:lang="en">There is controversy about this
relation intended to represent the relation between some arbitrary physical
thing that is used as a represention/proxy/pointer to something
else</obo:IAO_0000116>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:DatatypeProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000004">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
+ <rdfs:label xml:lang="en">has measurement value</rdfs:label>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000032"/>
+ <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+ </owl:DatatypeProperty>
+
+
+
+ 
+
+ <owl:DatatypeProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000404">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
+ <rdfs:label xml:lang="en">has x coordinate value</rdfs:label>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
+ <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+ </owl:DatatypeProperty>
+
+
+
+ 
+
+ <owl:DatatypeProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000405">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
+ <rdfs:label xml:lang="en">has z coordinate value</rdfs:label>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
+ <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+ </owl:DatatypeProperty>
+
+
+
+ 
+
+ <owl:DatatypeProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000406">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
+ <rdfs:label xml:lang="en">has y coordinate value</rdfs:label>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
+ <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+ </owl:DatatypeProperty>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/GAZ_00000448"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000001">
+ <rdfs:label xml:lang="en">conditional specification</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
+ <obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000349</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess
Branch</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">a directive information entity that
specifies what should happen if the trigger condition is
fulfilled</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">conditional
specification</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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
+Cristian Cocos, and subsequently moved to IAO where the objective for
+which the original term was defined was satisfied with the definition
+of this, different, term.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">2009-03-16: review of this term
done during during the OBI workshop winter 2009 and the current definition
was considered acceptable for use in OBI. If there is a need to modify this
definition please notify OBI.</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">A measurement unit label is as a
label that is part of a scalar measurement datum and denotes a unit of
measure.</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">Examples of measurement unit labels
are liters, inches, weight per volume.</obo:IAO_0000112>
+ <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">measurement unit
label</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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">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."</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">Answers the question, why did you
do this experiment?</obo:IAO_0000116>
+ <obo:IAO_0000112 xml:lang="en">In the protocol of a ChIP assay the
objective specification says to identify protein and DNA
interaction.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI Plan and Planned Process/Roles
Branch</obo:IAO_0000119>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000217</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Barry
Smith</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Bjoern
Peters</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Jennifer
Fostel</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
+ <obo:IAO_0000118 xml:lang="en">goal specification</obo:IAO_0000118>
+ <obo:IAO_0000111 xml:lang="en">objective
specification</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000006">
+ <rdfs:label xml:lang="en">narrative object</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+ <obo:IAO_0000116 xml:lang="en">2009-08-10 Alan Ruttenberg: Larry
Hunter suggests that this be obsoleted and replaced by 'textual
entity' and 'figure'. Alan restored as there are OBI
dependencies and this merits further discussion</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">A narrative object is an
information content entity that is a set of propositions.</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">Examples of narrative objects are
reports, journal articles, and patents submission.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000013</obo:IAO_0000119>
+ <obo:IAO_0000116 xml:lang="en">agree - DENRIE. Issue(alan) do we
only mean text? What about a story told by mime. Does music count? (no)
what about an oral report. Regarding definition, saying it is a set of
propositions means we loose the idea that wording matters. Maybe adjust
saying a narrative object has some relationshop to a set of
propositions</obo:IAO_0000116>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">narrative object</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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>
+ <obo:IAO_0000112 xml:lang="en">Pour the contents of flask 1 into
flask 2</obo:IAO_0000112>
+ <obo:IAO_0000115 xml:lang="en">a directive information entity that
describes an action the bearer will take</obo:IAO_0000115>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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 'label' to 'datum label' to convey that this class
is not intended to cover all kinds of labels (stickers, radiolabels, etc.),
and not even all kind of textual labels, but rather the kind of labels
occuring in a datum.
+</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>
+ <obo:IAO_0000116
xml:lang="en">http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n</obo:IAO_0000116>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000010">
+ <rdfs:label xml:lang="en">software</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
+ <obo:IAO_0000119 xml:lang="en">GROUP: OBI</obo:IAO_0000119>
+ <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
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Melanie
Courtot</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">Software is a plan specification
composed of a series of instructions that can be
+interpreted by or directly executed by a processing unit.</obo:IAO_0000115>
+ <obo:IAO_0000116 xml:lang="en">see sourceforge tracker discussion
at
http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178</obo:IAO_0000116>
+ <obo:IAO_0000111 xml:lang="en">software</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000013">
+ <rdfs:label xml:lang="en">journal article</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000088"/>
+ <obo:IAO_0000112 xml:lang="en">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.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000159</obo:IAO_0000119>
+ <obo:IAO_0000115 xml:lang="en">a report that is published in a
journal</obo:IAO_0000115>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">journal article</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000015">
+ <rdfs:label xml:lang="en">information carrier</rdfs:label>
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <rdf:Description
rdf:about="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
+ <owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000294"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ <obo:IAO_0000116 xml:lang="en">12/15/09: There is a concern that
some ways that carry information may be processes rather than qualities,
such as in a 'delayed wave carrier'.</obo:IAO_0000116>
+ <obo:IAO_0000116>2014-03-10: We are not certain that all
information carriers are qualities. There was a discussion of dropping
it.</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">A quality of an information bearer
that imparts the information content</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">In the case of a printed paperback
novel the physicality of the ink and of the paper form part of the
information bearer. The qualities of appearing black and having a certain
pattern for the ink and appearing white for the paper form part of the
information carrier in this case.</obo:IAO_0000112>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000119 xml:lang="en">Smith, Ceusters, Ruttenberg, 2000
years of philosophy</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">information
carrier</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000017">
+ <rdfs:label xml:lang="en">model number</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000028"/>
+ <obo:IAO_0000115 xml:lang="en">A model number is an information
content entity specifically borne by catalogs, design specifications,
advertising materials, inventory systems and similar that is about
manufactured objects of the same class. The model number is an alternative
term for the class. The manufactered objects may or may not also bear the
model number. Model numbers can be encoded in a variety of other
information objects, such as bar codes, numerals, or patterns of
dots.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">Person: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000116 xml:lang="en">manufactered items may have more
than one model number, sometimes by rebranding, or because companies are
sold and the products issued new model numbers</obo:IAO_0000116>
+ <obo:IAO_0000111 xml:lang="en">model number</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000025">
+ <rdfs:label xml:lang="en">programming language</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
+ <obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000058</obo:IAO_0000119>
+ <obo:IAO_0000112 xml:lang="en">R, Perl, Java</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">programming
language</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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>2014-03-31: See discussion at
http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/</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>
+ <obo:IAO_0000116 xml:lang="en">2009-03-16: removed datum as
alternative term as datum specifically refers to singular form, and is thus
not an exact synonym.</obo:IAO_0000116>
+ <obo:IAO_0000112 xml:lang="en">Data items include counts of
things, analyte concentrations, and statistical summaries.</obo:IAO_0000112>
+ <obo:IAO_0000116 xml:lang="en">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</obo:IAO_0000116>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Jonathan
Rees</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">a data item is 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.</obo:IAO_0000115>
+ <obo:IAO_0000118 xml:lang="en">data</obo:IAO_0000118>
+ <obo:IAO_0000111 xml:lang="en">data item</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000028">
+ <rdfs:label xml:lang="en">symbol</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+ <obo:IAO_0000116 xml:lang="en">20091104, MC: this needs work and
will most probably change</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">2014-03-31: We would like to have a
deeper analysis of 'mark' and 'sign' in the future (see
https://code.google.com/p/information-artifact-ontology/issues/detail?id=154).</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">An information content entity that
is a mark(s) or character(s) used as a conventional representation of
another entity.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON: James A.
Overton</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Jonathan
Rees</obo:IAO_0000117>
+ <obo:IAO_0000112 xml:lang="en">a serial number such as
"12324X"</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">a stop sign</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">a written proper name such as
"OBI"</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">based on Oxford English
Dictionary</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">symbol</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000029">
+ <rdfs:label xml:lang="en">numeral</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000028"/>
+ <obo:IAO_0000115 xml:lang="en">A symbol that denotes a
number.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Jonathan
Rees</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">numeral</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant"/>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+ <owl:someValuesFrom
rdf:resource="http://www.ifomis.org/bfo/1.1#Entity"/>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <obo:IAO_0000116 xml:lang="en">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).</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">A generically dependent continuant
that is about some thing.</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">Examples of information content
entites include journal articles, data, graphical layouts, and
graphs.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000142</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">information content
entity</obo:IAO_0000111>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000031">
+ <rdfs:label xml:lang="en">integer numeral</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000029"/>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Jonathan
Rees</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">a numeral that denotes an
integer</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">integer numeral</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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"/>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000039"/>
+ <owl:minCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minCardinality>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000004"/>
+ <owl:minCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minCardinality>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <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
+this case we explicitly refer to the singular form</obo:IAO_0000116>
+ <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_0000116 xml:lang="en">Would write this as: has_part some
'measurement unit label' and has_part some numeral and has_part
exactly 2, except for the fact that this won't let us take advantage
of OWL reasoning over the numbers. Instead use has measurment value
property to represent the same. Use has measurement unit label (subproperty
of has_part) so we can easily say that there is only one of
them.</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">a scalar measurement datum is a
measurement datum that is composed of two parts, numerals and a unit
label.</obo:IAO_0000115>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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"/>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+ <owl:someValuesFrom
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#RealizableEntity"/>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">8/6/2009 Alan Ruttenberg: Changed
label from "information entity about a realizable" 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>
+ <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_0000116 xml:lang="en">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</obo:IAO_0000116>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000034">
+ <rdfs:label xml:lang="en">time trigger</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000001"/>
+ <obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000331</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess
Branch</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">revisit?</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">time trigger</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000124"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000037">
+ <rdfs:label xml:lang="en">dot plot</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
+ <obo:IAO_0000115 xml:lang="en">A dot plot is a report graph which
is a graphical representation of data where each data point is represented
by a single dot placed on coordinates corresponding to data point values in
particular dimensions.</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">Dot plot of SSC-H and
FSC-H.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000123</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">dot plot</obo:IAO_0000111>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">person:Allyson
Lister</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000002"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000038">
+ <rdfs:label xml:lang="en">graph</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000309"/>
+ <obo:IAO_0000115 xml:lang="en">A diagram that presents one or more
tuples of information by mapping those tuples in to a two dimensional space
in a non arbitrary way.</obo:IAO_0000115>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000240</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Lawrence
Hunter</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">graph</obo:IAO_0000111>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Allyson
Lister</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000055">
+ <rdfs:label xml:lang="en">rule</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000001"/>
+ <obo:IAO_0000116 xml:lang="en">MSI</obo:IAO_0000116>
+ <obo:IAO_0000119 xml:lang="en">OBI_0500021</obo:IAO_0000119>
+ <obo:IAO_0000119 xml:lang="en">PRS</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PRS</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">a rule is an executable which
guides, defines, restricts actions</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">example to be
added</obo:IAO_0000112>
+ <obo:IAO_0000111 xml:lang="en">rule</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000057">
+ <rdfs:label xml:lang="en">contour plot</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
+ <obo:IAO_0000112 xml:lang="en">Contour plot of SSC-H, FSC-H, and
FL1-H.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000246</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">contour plot</obo:IAO_0000111>
+ <obo:IAO_0000116
xml:lang="en">generically_dependent_continuants</obo:IAO_0000116>
+ <obo:IAO_0000119 xml:lang="en">group:Flow Cytometry
community</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">person:Allyson
Lister</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000002"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000064">
+ <rdfs:label xml:lang="en">algorithm</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
+ <obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000270</obo:IAO_0000119>
+ <obo:IAO_0000112 xml:lang="en">PMID: 18378114.Genomics. 2008 Mar
28. LINKGEN: A new algorithm to process data in genetic linkage
studies.</obo:IAO_0000112>
+ <obo:IAO_0000117 xml:lang="en">Philippe
Rocca-Serra</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess
Branch</obo:IAO_0000117>
+ <obo:IAO_0000119 xml:lang="en">adapted from discussion on OBI list
(Matthew Pocock, Christian Cocos, Alan Ruttenberg)</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">algorithm</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000065">
+ <rdfs:label xml:lang="en">software interpreter</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000064"/>
+ <obo:IAO_0000115 xml:lang="en">A software interpreter is a
software application that executes some specified input software.
</obo:IAO_0000115>
+ <obo:IAO_0000116 xml:lang="en">Do we care? Jennifer: Yes, there
was a particular version of R that had a bug and it was fixed later. That
would imply that we mean specific version of an interpreter. So an instance
of this would be a particular version of the interpreter</obo:IAO_0000116>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000199</obo:IAO_0000119>
+ <obo:IAO_0000112 xml:lang="en">R program, Perl interpreter, Java
virtual machine</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">software
interpreter</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000079">
+ <rdfs:label xml:lang="en">density plot</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
+ <obo:IAO_0000115 xml:lang="en">A density plot is a report graph
which is a graphical representation of data where the tint of a particular
pixel corresponds to some kind of function corresponding the the amount of
data points relativelly with their distance from the the
pixel.</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">Density plot of SSC-H and
FSC-H.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000179</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">density plot</obo:IAO_0000111>
+ <obo:IAO_0000119 xml:lang="en">group:Flow Cytometry
community</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">person:Allyson
Lister</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000002"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000088">
+ <rdfs:label xml:lang="en">report</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000310"/>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">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</obo:IAO_0000116>
+ <obo:IAO_0000112 xml:lang="en">Examples of reports are gene lists
and investigation reports. These are not published (journal) articles but
may be included in a journal article.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">GROUP: OBI</obo:IAO_0000119>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000099</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_0000117 xml:lang="en">PERSON:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">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)</obo:IAO_0000115>
+ <obo:IAO_0000116 xml:lang="en">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</obo:IAO_0000116>
+ <obo:IAO_0000111 xml:lang="en">report</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000096">
+ <rdfs:label xml:lang="en">source code module</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
+ <obo:IAO_0000115 xml:lang="en">A source code module is a directive
information entity that specifies, using a programming language, some
algorithm.</obo:IAO_0000115>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000039</obo:IAO_0000119>
+ <obo:IAO_0000112 xml:lang="en">The written source code that
implements part of an algorithm. Test - if you know that it was written in
a specific language, then it can be source code module. We mean here,
roughly, the wording of a document such as a perl script.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">source code module</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000098">
+ <rdfs:label xml:lang="en">data format specification</rdfs:label>
***The diff for this file has been truncated for email.***
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology/obsolete.owl Sat Jan 3 07:23:58 2015 UTC
@@ -0,0 +1,474 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/"
+ xml:base="http://purl.obolibrary.org/obo/"
+ 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: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#">
+ <owl:Ontology
rdf:about="http://purl.obolibrary.org/obo/iao/dev/obsolete.owl">
+ <protege:defaultLanguage
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
+ <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete classes
from the information artifact ontology. see
http://code.google.com/p/information-artifact-ontology/</rdfs:comment>
+ <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://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl"/>
+ </owl:Ontology>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000113"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000118"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000231"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
+
+
+
+ 
+
+
+
+
+ 
+
+
+
+
+ 
+
+ <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>
+ <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</IAO_0000116>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan
Ruttenberg</IAO_0000117>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smith, Ceusters,
Ruttenberg, 2000 years of philosophy</IAO_0000119>
+ <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</IAO_0000112>
+ <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.</IAO_0000115>
+ <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</IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <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_0000220">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_materially
denotes</rdfs:label>
+ <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</IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <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_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>
+ <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>
+ <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://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000008">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_artifact</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000012">
+ <rdfs:label xml:lang="en">obsolete2_digital entity</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000261</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">3/22/2009 Alan Ruttenberg, obsoleted
per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
+
+Superclass was 'digitial quality'</IAO_0000116>
+ <IAO_0000115 xml:lang="en">A digital entity is an information
entity which is a collection of bits that can be interpreted by a computer.
Two digital entities are the same if they are bitwise
identical.</IAO_0000115>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000111 xml:lang="en">obsolete_digital entity</IAO_0000111>
+ <IAO_0000117 xml:lang="en">person:Chris Stoeckert</IAO_0000117>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000018">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_material_entity</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000226"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000019">
+ <rdfs:label xml:lang="en">obsolete2_binary digital
entity</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000244</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">3/22/2009 Alan Ruttenberg, obsoleted
per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
+Superclass was 'digital entity'</IAO_0000116>
+ <IAO_0000115 xml:lang="en">A binary digital entity is a digital
entity that is encoded in a way that is not easily human readable and that
contains other than text characters.</IAO_0000115>
+ <IAO_0000112 xml:lang="en">MS Word document, ZIP file, DICOM file,
JPEG file</IAO_0000112>
+ <IAO_0000111 xml:lang="en">binary digital entity</IAO_0000111>
+ <IAO_0000116 xml:lang="en">digital_entity</IAO_0000116>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">person:Chris Stoeckert</IAO_0000117>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000024">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_unit of
measure</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan
Ruttenberg</IAO_0000117>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smith, Ceusters,
Ruttenberg, 2000 years of philosophy</IAO_0000119>
+ <IAO_0000112
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The length of a
ruler.</IAO_0000112>
+ <IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a unit of measure is
the quality of some material entity compared to which another quality is
some multiple of.</IAO_0000115>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000035">
+ <rdfs:label xml:lang="en">obsolete_study
interpretation</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-03-16:
definition was "A conclusion is a narrative object which can be
published in a paper summerizing and interpreting a protocol
application."</IAO_0000116>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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.</IAO_0000116>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000005</IAO_0000119>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Alan
Ruttenberg</IAO_0000117>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie
Courtot</IAO_0000117>
+ <IAO_0000118
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">conclusion</IAO_0000118>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000115 xml:lang="en">A study interpretation is a textual
entity about the implications of a study result. Examples include
discussion of whether a hypothesis is false, whether the study failed to
address the hypothesis, and whether the study results have led to new
hypotheses</IAO_0000115>
+ <IAO_0000117 xml:lang="en">Lawrence Hunter</IAO_0000117>
+ <IAO_0000117 xml:lang="en">PERSON: Jennifer Fostel</IAO_0000117>
+ <IAO_0000116 xml:lang="en">The obsoleting of narrative object
required a modest change in the definition of this term. Circularity with
"interpretation... interprets" has been removed, using
"about the implications" instead.</IAO_0000116>
+ <IAO_0000111 xml:lang="en">obsolete_study
interpretation</IAO_0000111>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000047">
+ <rdfs:label xml:lang="en">obsolete2_text based digital
entity</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000132</IAO_0000119>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">group:OBI</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">3/22/2009 Alan Ruttenberg, obsoleted
per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
+superclass was 'digital document'</IAO_0000116>
+ <IAO_0000115 xml:lang="en">A text based digital entity is a
digital entity that is encoded so that it only contains text
characters.</IAO_0000115>
+ <IAO_0000112 xml:lang="en">XML file, C++ source code
file</IAO_0000112>
+ <IAO_0000116 xml:lang="en">digital_entity</IAO_0000116>
+ <IAO_0000117 xml:lang="en">person:Chris Stoeckert</IAO_0000117>
+ <IAO_0000111 xml:lang="en">text based digital entity</IAO_0000111>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000059">
+ <rdfs:label xml:lang="en">obsolete2_report figure</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000027</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000115 xml:lang="en">A report figure is a report display
element that has some aspect of illustration, but may be a composite of
figures, images, and other elements</IAO_0000115>
+ <IAO_0000116 xml:lang="en">I prepended the 'report ' to
make it clear that we mean parts of reports here. We may want a more
generic version of 'figure', in which case this would become a
defined class - figure and part_of some report</IAO_0000116>
+ <IAO_0000116 xml:lang="en">Replaced by defined version of
figure</IAO_0000116>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">person:Alan Ruttenberg</IAO_0000117>
+ <IAO_0000117 xml:lang="en">person:Allyson Lister</IAO_0000117>
+ <IAO_0000111 xml:lang="en">report figure</IAO_0000111>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000124"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000091">
+ <rdfs:label xml:lang="en">obsolete_report element</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-03-16: needs
some more work (clarify relations).</IAO_0000116>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-03-16: was
report display element with definition: A report display element is a
narrative object that is part of a report. Report display elements are set
off from the textual parts of a report and are typically given a label(e.g.
Figure 2) which is used to refer to the element from the text. Typically
the 2d layout is part of the identity of such elements.</IAO_0000116>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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.</IAO_0000116>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-08-10 Alan
Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by
'textual entity' and 'figure'. Alan restored as there
are OBI dependencies and this merits further discussion</IAO_0000116>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000001</IAO_0000119>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie
Courtot</IAO_0000117>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Replaced by textual
entity and figure</IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000115 xml:lang="en">A report element is a narrative object
in which information is presented and consumed by a human being, and is
part of a report. Examples of report elements are figure (dot plot), table,
text portion (may include a movie or audio clip on a web
page).</IAO_0000115>
+ <IAO_0000119 xml:lang="en">GROUP:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</IAO_0000117>
+ <IAO_0000117 xml:lang="en">PERSON: Allyson Lister</IAO_0000117>
+ <IAO_0000116 xml:lang="en">There will be some issue here about
whether these are defined classes. As intended these are meant to denote
the parts of the report that are not textual but are typically boxed and
set within the text, labelled with some identifier, and referred to in the
text</IAO_0000116>
+ <IAO_0000111 xml:lang="en">report element</IAO_0000111>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000093">
+ <rdfs:label xml:lang="en">obsolete2_binary executable</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000222</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">3/22/2009 Alan Ruttenberg, obsoleted
per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
+superclass was 'digital entity'</IAO_0000116>
+ <IAO_0000115 xml:lang="en">Binary executable is a digital entity
consisting of the binary representation of machine instructions of a
specific processor or they may be binary pseudocode for a virtual machine.
A non-source executable file is also called an object program. It is
assumed that the binary executable file contains properly-formatted
computer instructions. (derived from Wikipedia, Nov 1, 2007)</IAO_0000115>
+ <IAO_0000111 xml:lang="en">binary executable</IAO_0000111>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">person:Jennifer Fostel</IAO_0000117>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000097">
+ <rdfs:label xml:lang="en">obsolete_report table</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-08-10 Alan
Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by
'textual entity table'. Alan restored as there are OBI
dependencies and this merits further discussion</IAO_0000116>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000265</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000115 xml:lang="en">A report table is a report display
element consisting of a matrix of cells layed out in a grid, some set of
which are filled with some information content</IAO_0000115>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">person:Alan Ruttenberg</IAO_0000117>
+ <IAO_0000117 xml:lang="en">person:Allyson Lister</IAO_0000117>
+ <IAO_0000111 xml:lang="en">report table</IAO_0000111>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000002"/>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000105">
+ <rdfs:label xml:lang="en">obsolete2_digital document</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000195</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">3/22/2009 Alan Ruttenberg, obsoleted
per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
+superclass was 'digial entity'</IAO_0000116>
+ <IAO_0000115 xml:lang="en">A digital document is a digital entity
consisting of an electronic file which can be rendered into human-readable
form by one or more computational applications. The digital document does
not refer to the information content of the document but to an instance of
the file.</IAO_0000115>
+ <IAO_0000111 xml:lang="en">digital document</IAO_0000111>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">person:Jennifer Fostel</IAO_0000117>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000128">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_identifier</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">_identifier is a
container under information content entity for collecting types of terms to
indicate a specific instance or clas of what was used or participated in an
investigation. Identifiers are borne by a product or its packaging, and can
be encoded in a variety of other information objects, such as bar codes,
numerals, or patterns of dots.
+
+Note: everybody agreed that identifier is probably a too general term. We
however felt that it would be appropriate to group "identifiying"
terms under some kind of umbrella. We therefore propose to use _identifier
for that purpose. As per OBI conventions, the _ prefixing identifier
indicates that this is a helper class and shouldn't be considered as
final.</IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000121"/>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000226"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000141">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_digital
quality</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Need to rework
digital entity. Digital quality was suggested by Barry.</IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116>3/22/2009 Alan Ruttenberg, obsoleted per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4</IAO_0000116>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000182">
+ <rdfs:label xml:lang="en">obsolete_survival curve</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000115 xml:lang="en">A survival curve is a report graph
which is a graphical representation of data where the percentage of
survival is plotted as a function of time.</IAO_0000115>
+ <IAO_0000117 xml:lang="en">PERSON:Chris Stoeckert</IAO_0000117>
+ <IAO_0000117 xml:lang="en">PERSON:James Malone</IAO_0000117>
+ <IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</IAO_0000117>
+ <IAO_0000119 xml:lang="en">WEB:
http://www.graphpad.com/www/book/survive.htm</IAO_0000119>
+ <IAO_0000111 xml:lang="en">obsolete_survival curve</IAO_0000111>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000576">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_establishing
a CRID registry</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a planned process
with the objective to establish a system that allows to refer to specific
entities of a certain kind and store information about them, by
establishing a CRID registry and plan specifications for the process of 1)
assigning a CRID and 2) looking up a CRID.</IAO_0000115>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116>MC, 20101124: deprecated following discussion at IAO
call 20101124. Term was deemed not necessary - no use case for
now.</IAO_0000116>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:Thing rdf:about="http://purl.obolibrary.org/obo/IAO_0000103"/>
+
+
+
+ 
+
+ <owl:Thing rdf:about="http://purl.obolibrary.org/obo/IAO_0000226"/>
+
+
+
+ 
+
+ <owl:NamedIndividual
rdf:about="http://purl.obolibrary.org/obo/IAO_0000230">
+ <rdf:type
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
+ <rdfs:label xml:lang="en">other</rdfs:label>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">This is to be used if none of the
existing instances cover the reason for obsolescence. An editor note should
indicate this new reason.</IAO_0000116>
+ <IAO_0000116 xml:lang="en">We expect to be able to mine these new
reasons and add instances as required.</IAO_0000116>
+ </owl:NamedIndividual>
+</rdf:RDF>
+
+
+
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology/ontology-metadata.owl Sat Jan 3 07:23:58
2015 UTC
@@ -0,0 +1,516 @@
+<?xml version="1.0"?>
+<rdf:RDF
+ xmlns:owl2xml="http://www.w3.org/2006/12/owl2-xml#"
+ xmlns:snap="http://www.ifomis.org/bfo/1.1/snap#"
+ xmlns:bfo="http://www.ifomis.org/bfo/1.1#"
+ xmlns:owl2="http://www.w3.org/2006/12/owl2#"
+ xmlns:swrl="http://www.w3.org/2003/11/swrl#"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns="http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl#"
+ xmlns:ro="http://www.obofoundry.org/ro/ro.owl#"
+ xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
+ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
+ xmlns:obo="http://purl.obolibrary.org/obo/"
+ xmlns:span="http://www.ifomis.org/bfo/1.1/span#"
+ xmlns:daml="http://www.daml.org/2001/03/daml+oil#"
+ xml:base="http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl">
+ <owl:Ontology rdf:about="">
+ <protege:defaultLanguage
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >en</protege:defaultLanguage>
+ <owl:versionInfo xml:lang="en">$Revision$</owl:versionInfo>
+ </owl:Ontology>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000027">
+ <rdfs:label xml:lang="en">data item</rdfs:label>
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000409">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:oneOf rdf:parseType="Collection">
+ <obo:IAO_0000409
rdf:about="http://purl.obolibrary.org/obo/IAO_0000421">
+ <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>
+ <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>
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >named class expression</rdfs:label>
+ </obo:IAO_0000409>
+ <obo:IAO_0000409
rdf:about="http://purl.obolibrary.org/obo/IAO_0000410">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >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 "natural kind"
rather than a collection of any old things, which a class is able to be,
formally. At the meta level, universals are defined as positives, are
disjoint with their siblings, have single asserted
parents.</obo:IAO_0000116>
+ </obo:IAO_0000409>
+ <obo:IAO_0000409
rdf:about="http://purl.obolibrary.org/obo/IAO_0000420">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >defined class</rdfs:label>
+ <obo:IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >"definitions", in some readings, always are given by
necessary and sufficient conditions. So one must be careful (and this is
difficult sometimes) to distinguish between defined classes and
universal.</obo:IAO_0000116>
+ <obo:IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000115
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_0000115>
+ </obo:IAO_0000409>
+ </owl:oneOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ <obo:IAO_0000119 rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Barry Smith, Werner Ceusters</obo:IAO_0000119>
+ <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >A denotator type indicates how a term should be interpreted from an
ontological perspective.</obo:IAO_0000115>
+ <obo:IAO_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Alan Ruttenberg</obo:IAO_0000117>
+ <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >denotator type</rdfs:label>
+ <obo:IAO_0000112 rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >The Basic Formal Ontology ontology makes a distinction between
Universals and defined classes, where the formal are "natural kinds" and
the latter arbitrary collections of entities.</obo:IAO_0000112>
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#Definition">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000225">
+ <obo:IAO_0000114>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000125">
+ <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>
+ <rdfs:label xml:lang="en">pending final vetting</rdfs:label>
+ </obo:IAO_0000078>
+ </obo:IAO_0000114>
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:oneOf rdf:parseType="Collection">
+ <obo:IAO_0000225
rdf:about="http://purl.obolibrary.org/obo/IAO_0000103">
+ <obo:IAO_0000115 xml:lang="en">The term was used in an attempt
to structure part of the ontology but in retrospect failed to do a good
job</obo:IAO_0000115>
+ <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_0000225>
+ <obo:IAO_0000225
rdf:about="http://purl.obolibrary.org/obo/IAO_0000227">
+ <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>
+ <rdfs:label xml:lang="en">terms merged</rdfs:label>
+ </obo:IAO_0000225>
+ <obo:IAO_0000225
rdf:about="http://purl.obolibrary.org/obo/IAO_0000229">
+ <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>
+ </obo:IAO_0000225>
+
+ <obo:IAO_0000225
rdf:about="http://purl.obolibrary.org/obo/IAO_0000226">
+ <rdfs:label xml:lang="en">placeholder removed</rdfs:label>
+ </obo:IAO_0000225>
+ <obo:IAO_0000225
rdf:about="http://purl.obolibrary.org/obo/IAO_0000228">
+ <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>
+ <rdfs:label xml:lang="en">term imported</rdfs:label>
+ </obo:IAO_0000225>
+ </owl:oneOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ <obo:IAO_0000111 xml:lang="en">obsolescence reason
specification</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000116 xml:lang="en">The creation of this class has been
inspired in part by Werner Ceusters' paper, Applying evolutionary
terminology auditing to the Gene Ontology.</obo:IAO_0000116>
+ <rdfs:label xml:lang="en">obsolescence reason
specification</rdfs:label>
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </rdfs:subClassOf>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Melanie
Courtot</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">The reason for which a term has been
deprecated. The allowed values come from an enumerated list of predefined
terms. See the specification of these instances for more detailed
definitions of each enumerated value.</obo:IAO_0000115>
+ </owl:Class>
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#SynonymType">
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000078">
+ <obo:IAO_0000119 xml:lang="en">OBI_0000266</obo:IAO_0000119>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <obo:IAO_0000116 xml:lang="en">Better to represent curation as a
process with parts and then relate labels to that process (in IAO
meeting)</obo:IAO_0000116>
+ <obo:IAO_0000111 xml:lang="en">curation status
specification</obo:IAO_0000111>
+ <rdfs:label xml:lang="en">curation status specification</rdfs:label>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000115 xml:lang="en">The curation status of the term. The
allowed values come from an enumerated list of predefined terms. See the
specification of these instances for more detailed definitions of each
enumerated value.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Bill Bug</obo:IAO_0000117>
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:oneOf rdf:parseType="Collection">
+ <owl:NamedIndividual
rdf:about="http://purl.obolibrary.org/obo/IAO_0000428">
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <rdf:type
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
+ <obo:IAO_0000117 xml:lang="en">Alan
Ruttenberg</obo:IAO_0000117>
+ <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>
+ </owl:NamedIndividual>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000124">
+ <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>
+ </obo:IAO_0000078>
+ <owl:NamedIndividual
rdf:about="http://purl.obolibrary.org/obo/IAO_0000423">
+ <rdf:type
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000078"/>
+ <obo:IAO_0000117 xml:lang="en">Alan
Ruttenberg</obo:IAO_0000117>
+ <rdfs:label xml:lang="en">to be replaced with external
ontology term</rdfs:label>
+ <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>
+ </owl:NamedIndividual>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000122">
+ <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 "ready_for_release" should be considered likely to change
place in hierarchy, have its definition refined, or be obsoleted in the
next release. Those classes deemed "ready_for_release" will also derived
from a chain of ancestor classes that are
also "ready_for_release."</obo:IAO_0000115>
+ <rdfs:label xml:lang="en">ready for release</rdfs:label>
+ </obo:IAO_0000078>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000120">
+ <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>
+ </obo:IAO_0000078>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000002">
+ <rdfs:label xml:lang="en">example to be eventually
removed</rdfs:label>
+ </obo:IAO_0000078>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000123">
+ <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>
+ </obo:IAO_0000078>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000121">
+ <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>
+ </obo:IAO_0000078>
+ </owl:oneOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ <rdfs:subClassOf>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </rdfs:subClassOf>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000102">
+ <rdfs:label xml:lang="en">data about an ontology part</rdfs:label>
+ <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>
+ <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>
+ </owl:Class>
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#Synonym">
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </owl:Class>
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#DbXref">
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </owl:Class>
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#Subset">
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:oneOf rdf:parseType="Collection">
+ <oboInOwl:Subset
rdf:about="http://purl.obolibrary.org/obo/IAO_0000224">
+ <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: Melanie
Courtot</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Alan
Ruttenberg</obo:IAO_0000117>
+ </oboInOwl:Subset>
+ </owl:oneOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ </owl:Class>
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000030">
+ <rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#GenericallyDependentContinuant"/>
+ <rdfs:label xml:lang="en">information content entity</rdfs:label>
+ </owl:Class>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000411">
+ <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>
+ <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_0000111 xml:lang="en">is denotator type</obo:IAO_0000111>
+ <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>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000232">
+ <obo:IAO_0000111 xml:lang="en">curator note</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">An administrative note of use for a
curator but of no use for a user</obo:IAO_0000115>
+ <rdfs:label xml:lang="en">curator note</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000112">
+ <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_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:label xml:lang="en">example of usage</rdfs:label>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">example</obo:IAO_0000111>
+ </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_0000111 xml:lang="en">has obsolescence
reason</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</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>
+ </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_0000111 xml:lang="en">is allocated id range</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">Add as annotation triples in the
granting ontology</obo:IAO_0000115> <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>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0100001">
+ <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_0000115 xml:lang="en">Add as annotation triples in the
granting ontology</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">term replaced by</obo:IAO_0000111>
+ <rdfs:label xml:lang="en">term replaced by</rdfs:label>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
+ <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+ <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_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <obo:IAO_0000111 xml:lang="en">editor preferred term</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000114">
+ <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_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000281</obo:IAO_0000119>
+ <rdfs:label xml:lang="en">has curation status</rdfs:label>
+ <obo:IAO_0000111 xml:lang="en">has curation status</obo:IAO_0000111>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
+ <rdfs:label xml:lang="en">term editor</rdfs:label>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">term editor</obo:IAO_0000111>
+ <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_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_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000425">
+ <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>
+ <rdfs:label xml:lang="en">expand assertion to</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">Chris Mungall</obo:IAO_0000117>
+ <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>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">imported from</obo:IAO_0000111>
+ <obo:IAO_0000115 xml:lang="en">For external terms/classes, the
ontology from which the term was imported</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</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:label xml:lang="en">imported from</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000600">
+ <obo:IAO_0000119 xml:lang="en">Person:Barry Smith</obo:IAO_0000119>
+ <rdfs:label xml:lang="en">elucidation</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">person:Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">elucidation</obo:IAO_0000111>
+ <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>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000601">
+ <obo:IAO_0000119 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000119>
+ <rdfs:label xml:lang="en">has associated axiom(nl)</rdfs:label>
+ <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>
+ <obo:IAO_0000600 xml:lang="en">An axiom associated with a term
expressed using natural language</obo:IAO_0000600>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0010000">
+ <obo:IAO_0000119 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000119>
+ <rdfs:label xml:lang="en">has axiom label</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">has axiom id</obo:IAO_0000111>
+ <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>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000602">
+ <obo:IAO_0000119 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000119>
+ <rdfs:label xml:lang="en">has associated axiom(fol)</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">Person:Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">has associated
axiom(fol)</obo:IAO_0000111>
+ <obo:IAO_0000600 xml:lang="en">An axiom expressed in first order logic
using CLIF syntax</obo:IAO_0000600>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <rdfs:label xml:lang="en">definition</rdfs:label>
+ <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_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <obo:IAO_0000111 xml:lang="en">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>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
+ <rdfs:label xml:lang="en">alternative term</rdfs:label>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">alternative term</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <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>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000589">
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <obo:IAO_0000111 xml:lang="en">OBO foundry unique
label</obo:IAO_0000111>
+ <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_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000119 xml:lang="en">GROUP:OBO Foundry
<http://obofoundry.org/></obo:IAO_0000119>
+ <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_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_0000117 xml:lang="en">PERSON:Bjoern Peters</obo:IAO_0000117>
+ <rdfs:label xml:lang="en">OBO foundry unique label</rdfs:label>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000113">
+ <rdfs:label xml:lang="en">in branch</rdfs:label>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000277</obo:IAO_0000119>
+ <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_0000111 xml:lang="en">in branch</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">GROUP:OBI</obo:IAO_0000117>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
+ <obo:IAO_0000111 xml:lang="en">definition source</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:label xml:lang="en">definition source</rdfs:label>
+ <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_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
+ <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>
+ </owl:AnnotationProperty>
+ <owl:AllDifferent>
+ <owl:distinctMembers rdf:parseType="Collection">
+ <obo:IAO_0000225
rdf:about="http://purl.obolibrary.org/obo/IAO_0000226"/>
+ <obo:IAO_0000225
rdf:about="http://purl.obolibrary.org/obo/IAO_0000227"/>
+ <obo:IAO_0000225
rdf:about="http://purl.obolibrary.org/obo/IAO_0000228"/>
+ <obo:IAO_0000225
rdf:about="http://purl.obolibrary.org/obo/IAO_0000229"/>
+ </owl:distinctMembers>
+ </owl:AllDifferent>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000427">
+ <obo:IAO_0000115 xml:lang="en">use boolean value xsd:true to indicate
that the property is an antisymmetric property</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">part_of antisymmetric property
xsd:true</obo:IAO_0000112>
+ <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
+ <rdfs:label xml:lang="en">antisymmetric property</rdfs:label>
+ <obo:IAO_0000111 xml:lang="en">antisymmetric property</obo:IAO_0000111>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000424">
+ <obo:IAO_0000111 xml:lang="en">expand expression to</obo:IAO_0000111>
+ <rdfs:label xml:lang="en">expand expression to</rdfs:label>
+ <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_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_0000117 rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
+ >Chris Mungall</obo:IAO_0000117>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000426">
+ <obo:IAO_0000111 xml:lang="en">first order logic
expression</obo:IAO_0000111>
+ <rdfs:label xml:lang="en">first order logic expression</rdfs:label>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Alan Ruttenberg</obo:IAO_0000117>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://protege.stanford.edu/plugins/owl/protege#defaultLanguage"/>
+ <owl:AllDifferent>
+ <owl:distinctMembers rdf:parseType="Collection">
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000121"/>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000124"/>
+ <obo:IAO_0000078
rdf:about="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <owl:NamedIndividual
rdf:about="http://purl.obolibrary.org/obo/IAO_0000423"/>
+ <owl:NamedIndividual
rdf:about="http://purl.obolibrary.org/obo/IAO_0000428"/>
+ </owl:distinctMembers>
+ </owl:AllDifferent>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obfoundry.org/obo/obi></obo:IAO_0000119>
+ <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_0000111 xml:lang="en">editor note</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Daniel Schober</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:label xml:lang="en">editor note</rdfs:label>
+ </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_0000112>Datatype: idrange:1
+Annotations: 'has ID range allocated to': "Chris Mungall"
+EquivalentTo: xsd:integer[> 2151 , <= 2300]
+</obo:IAO_0000112>
+ <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>
+ </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_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_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_0000112">
+ <rdfs:label xml:lang="en">example of usage</rdfs:label>
+ </owl:AnnotationProperty>
+
+</rdf:RDF>
+
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/IAO.owl Sat Jan 3 07:23:58 2015 UTC
@@ -0,0 +1,66 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/"
+ xml:base="http://purl.obolibrary.org/obo/"
+ 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: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#">
+ <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/iao.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://purl.obolibrary.org/obo/bfo/2014-05-03/classes-only.owl"/>
+ <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/core.owl"/>
+ <owl:imports
rdf:resource="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/iao-main.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/import-OBO.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/externalByHand.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/obsolete.owl"/>
+ </owl:Ontology>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:Thing
rdf:about="http://code.google.com/p/information-artifact-ontology/"/>
+
+
+
+ 
+
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/iao/pno.owl">
+ <IAO_0000603
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IAO_0020000-IAO_0020999</IAO_0000603>
+ </rdf:Description>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/iao/d-acts.owl">
+ <IAO_0000603
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IAO_0021000-IAO_0021999</IAO_0000603>
+ </rdf:Description>
+</rdf:RDF>
+
+
+
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/catalog-v001.xml Sat Jan 3 07:23:58
2015 UTC
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<catalog prefer="public"
xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
+ <uri id="User Entered Import Resolution"
name="http://purl.obolibrary.org/obo/iao/dev/obsolete.owl"
uri="obsolete.owl"/>
+ <uri id="User Entered Import Resolution"
name="http://purl.obolibrary.org/obo/iao/dev/iao-main.owl"
uri="iao-main.owl"/>
+ <uri id="User Entered Import Resolution"
name="http://purl.obolibrary.org/obo/iao/dev/externalByHand.owl"
uri="externalByHand.owl"/>
+ <uri id="User Entered Import Resolution"
name="http://purl.obolibrary.org/obo/iao/dev/import-OBO.owl"
uri="import-OBO.owl"/>
+ <uri id="User Entered Import Resolution"
name="http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl"
uri="ontology-metadata.owl"/>
+ <uri id="User Entered Import Resolution"
name="http://purl.obolibrary.org/obo/bfo/2014-05-03/classes-only.owl"
uri="external/bfo_classes_only.owl"/>
+ <uri id="User Entered Import Resolution"
name="http://purl.obolibrary.org/obo/ro/core.owl"
uri="external/ro-core.owl"/>
+ <uri id="User Entered Import Resolution"
name="http://purl.obolibrary.org/obo/ro/annotations.owl"
uri="external/annotations.owl"/>
+ <uri id="User Entered Import Resolution"
name="http://purl.obolibrary.org/obo/ro/bfo-classes-minimal.owl"
uri="external/bfo-classes-minimal.owl"/>
+</catalog>
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/external/annotations.owl Sat Jan 3
07:23:58 2015 UTC
@@ -0,0 +1,307 @@
+<?xml version="1.0"?>
+
+
+<!DOCTYPE rdf:RDF [
+ <!ENTITY foaf "http://xmlns.com/foaf/0.1/" >
+ <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
+ <!ENTITY obo "http://purl.obolibrary.org/obo/" >
+ <!ENTITY dc "http://purl.org/dc/elements/1.1/" >
+ <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
+ <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
+ <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
+ <!ENTITY oboInOwl "http://www.geneontology.org/formats/oboInOwl#" >
+]>
+
+
+<rdf:RDF xmlns="&obo;bfo.owl#"
+ xml:base="&obo;bfo.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: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="&obo;ro/annotations.owl"/>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000111">
+ <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000112">
+ <rdfs:label xml:lang="en">example of usage</rdfs:label>
+ <obo:IAO_0000114 rdf:resource="&obo;IAO_0000122"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000114">
+ <rdfs:label xml:lang="en">has curation status</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000115">
+ <rdfs:label rdf:datatype="&xsd;string">definition</rdfs:label>
+ <rdfs:label xml:lang="en">definition</rdfs:label>
+ <obo:IAO_0000114 rdf:resource="&obo;IAO_0000122"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000116">
+ <rdfs:label xml:lang="en">editor note</rdfs:label>
+ <obo:IAO_0000114 rdf:resource="&obo;IAO_0000122"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000117">
+ <rdfs:label xml:lang="en">term editor</rdfs:label>
+ <obo:IAO_0000114 rdf:resource="&obo;IAO_0000122"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000118">
+ <rdfs:label xml:lang="en">alternative term</rdfs:label>
+ <obo:IAO_0000114 rdf:resource="&obo;IAO_0000125"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000119">
+ <rdfs:label xml:lang="en">definition source</rdfs:label>
+ <obo:IAO_0000114 rdf:resource="&obo;IAO_0000122"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000412">
+ <rdfs:label xml:lang="en">imported from</rdfs:label>
+ <obo:IAO_0000114 rdf:resource="&obo;IAO_0000125"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000424">
+ <rdfs:label xml:lang="en">expand expression to</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000425">
+ <rdfs:label xml:lang="en">expand assertion to</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;IAO_0000426">
+ <rdfs:label xml:lang="en">first order logic expression</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&obo;RO_0001900">
+ <rdfs:label xml:lang="en">temporal interpretation</rdfs:label>
+ <foaf:page
rdf:datatype="&xsd;anyURI">https://code.google.com/p/obo-relations/wiki/ROAndTime</foaf:page>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&dc;contributor"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&dc;creator"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&dc;publisher"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&dc;source"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&dc;title"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&oboInOwl;shorthand">
+ <rdfs:label rdf:datatype="&xsd;string">shorthand</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&rdfs;label"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&foaf;homepage"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty rdf:about="&foaf;page"/>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:NamedIndividual rdf:about="&obo;RO_0001901">
+ <rdfs:label xml:lang="en">axiom holds for all times</rdfs:label>
+ <obo:IAO_0000115>
+
+## Elucidation
+
+This is used when the statement/axiom is assumed to hold true
'eternally'
+
+## How to interpret (informal)
+
+First the "atemporal" FOL is derived from the OWL using the
standard
+interpretation. This axiom is temporalized by embedding the axiom
+within a for-all-times quantified sentence. The t argument is added to
+all instantiation predicates and predicates that use this relation.
+
+## Example
+
+ Class: nucleus
+ SubClassOf: part_of some cell
+
+ forall t :
+ forall n :
+ instance_of(n,Nucleus,t)
+ implies
+ exists c :
+ instance_of(c,Cell,t)
+ part_of(n,c,t)
+
+## Notes
+
+This interpretation is *not* the same as an at-all-times relation
+
+</obo:IAO_0000115>
+ </owl:NamedIndividual>
+
+
+
+ 
+
+ <owl:NamedIndividual rdf:about="&obo;RO_0001902">
+ <rdfs:label xml:lang="en">relation has no temporal
argument</rdfs:label>
+ <obo:IAO_0000115>
+
+## Elucidation
+
+This is used when the first-order logic form of the relation is
+binary, and takes no temporal argument.
+
+## Example:
+
+ Class: limb
+ SubClassOf: develops_from some lateral-plate-mesoderm
+
+ forall t, t2:
+ forall x :
+ instance_of(x,Limb,t)
+ implies
+ exists y :
+ instance_of(y,LPM,t2)
+ develops_from(x,y)
+
+
+</obo:IAO_0000115>
+ </owl:NamedIndividual>
+
+
+
+ 
+
+ <rdf:Description rdf:about="&obo;IAO_0000232">
+ <rdfs:label xml:lang="en">curator note</rdfs:label>
+ <obo:IAO_0000114 rdf:resource="&obo;IAO_0000122"/>
+ </rdf:Description>
+</rdf:RDF>
+
+
+
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/external/bfo-classes-minimal.owl Sat
Jan 3 07:23:58 2015 UTC
@@ -0,0 +1,160 @@
+<?xml version="1.0"?>
+
+
+<!DOCTYPE rdf:RDF [
+ <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
+ <!ENTITY obo "http://purl.obolibrary.org/obo/" >
+ <!ENTITY dc "http://purl.org/dc/elements/1.1/" >
+ <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
+ <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
+ <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
+]>
+
+
+<rdf:RDF xmlns="&obo;bfo.owl#"
+ xml:base="&obo;bfo.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: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#">
+ <owl:Ontology rdf:about="&obo;ro/bfo-classes-minimal.owl">
+ <owl:imports rdf:resource="&obo;ro/annotations.owl"/>
+ </owl:Ontology>
+
+
+
+ 
+
+ 
+
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Obsolete
Class</rdfs:label>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="&obo;BFO_0000002">
+ <rdfs:label xml:lang="en">continuant</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">An entity that exists in full at
any time in which it exists at all, persists through time while maintaining
its identity and has no temporal parts.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="&obo;BFO_0000003">
+ <rdfs:label xml:lang="en">occurrent</rdfs:label>
+ <obo:IAO_0000115 xml:lang="en">An entity that has temporal parts
and that happens, unfolds or develops through time.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="&obo;BFO_0000004">
+ <rdfs:label xml:lang="en">independent continuant</rdfs:label>
+ <rdfs:subClassOf rdf:resource="&obo;BFO_0000002"/>
+ <obo:IAO_0000115 xml:lang="en">A continuant that is a bearer of
quality and realizable entity entities, in which other entities inhere and
which itself cannot inhere in anything.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="&obo;BFO_0000005">
+ <rdfs:label xml:lang="en">obsolete dependent
continuant</rdfs:label>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <obo:IAO_0000115 xml:lang="en">A continuant that is either
dependent on one or other independent continuant bearers or inheres in or
is borne by other entities.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="&obo;BFO_0000015">
+ <rdfs:label xml:lang="en">process</rdfs:label>
+ <rdfs:subClassOf rdf:resource="&obo;BFO_0000003"/>
+ <obo:IAO_0000115 xml:lang="en">An occurrent that has temporal
proper parts and for some time t, p s-depends_on some material entity at
t.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="&obo;BFO_0000017">
+ <rdfs:label xml:lang="en">realizable entity</rdfs:label>
+ <rdfs:subClassOf rdf:resource="&obo;BFO_0000020"/>
+ <obo:IAO_0000115 xml:lang="en">A specifically dependent
continuant that inheres in continuant entities and are not exhibited in
full at every time in which it inheres in an entity or group of entities.
The exhibition or actualization of a realizable entity is a particular
manifestation, functioning or process that occurs under certain
circumstances.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="&obo;BFO_0000019">
+ <rdfs:label xml:lang="en">quality</rdfs:label>
+ <rdfs:subClassOf rdf:resource="&obo;BFO_0000020"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="&obo;BFO_0000020">
+ <rdfs:label xml:lang="en">specifically dependent
continuant</rdfs:label>
+ <rdfs:subClassOf rdf:resource="&obo;BFO_0000002"/>
+ <obo:IAO_0000115 xml:lang="en">A continuant that inheres in or is
borne by other entities. Every instance of A requires some specific
instance of B which must always be the same.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="&obo;BFO_0000023">
+ <rdfs:label xml:lang="en">role</rdfs:label>
+ <rdfs:subClassOf rdf:resource="&obo;BFO_0000017"/>
+ <obo:IAO_0000115 xml:lang="en">A realizable entity the
manifestation of which brings about some result or end that is not
essential to a continuant in virtue of the kind of thing that it is but
that can be served or participated in by that kind of continuant in some
kinds of natural, social or institutional contexts.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="&obo;BFO_0000031">
+ <rdfs:label xml:lang="en">generically dependent
continuant</rdfs:label>
+ <rdfs:subClassOf rdf:resource="&obo;BFO_0000002"/>
+ <obo:IAO_0000115 xml:lang="en">A continuant that is dependent on
one or other independent continuant bearers. For every instance of A
requires some instance of (an independent continuant type) B but which
instance of B serves can change from time to time.</obo:IAO_0000115>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="&obo;BFO_0000040">
+ <rdfs:label xml:lang="en">material entity</rdfs:label>
+ <rdfs:subClassOf rdf:resource="&obo;BFO_0000004"/>
+ <obo:IAO_0000115 xml:lang="en">An independent continuant that is
spatially extended whose identity is independent of that of other entities
and can be maintained through time.</obo:IAO_0000115>
+ </owl:Class>
+
+
+ <owl:Class rdf:about="&obo;BFO_0000141">
+ <rdfs:label xml:lang="en">immaterial entity</rdfs:label>
+ <rdfs:subClassOf rdf:resource="&obo;BFO_0000004"/>
+ </owl:Class>
+</rdf:RDF>
+
+
+
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/external/bfo_classes_only.owl Sat
Jan 3 07:23:58 2015 UTC
@@ -0,0 +1,1786 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/bfo.owl#"
+ xml:base="http://purl.obolibrary.org/obo/bfo.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: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#">
+ <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/bfo.owl">
+ <dc:contributor>Ron Rudnicki</dc:contributor>
+ <dc:contributor>Jonathan Bona</dc:contributor>
+ <obo:IAO_0000116>BFO 2 Reference: BFO’s treatment of continuants
and occurrents – as also its treatment of regions, rests on a dichotomy
between space and time, and on the view that there are two perspectives on
reality – earlier called the ‘SNAP’ and ‘SPAN’ perspectives, both of which
are essential to the non-reductionist representation of reality as we
understand it from the best available science [30</obo:IAO_0000116>
+ <dc:contributor>Pierre Grenon</dc:contributor>
+ <dc:contributor>Werner Ceusters</dc:contributor>
+ <dc:contributor>Ludger Jansen</dc:contributor>
+ <dc:contributor>Barry Smith</dc:contributor>
+ <dc:contributor>Chris Mungall</dc:contributor>
+ <dc:contributor>Albert Goldfain</dc:contributor>
+ <dc:contributor>Robert Rovetto</dc:contributor>
+ <dc:contributor>Larry Hunter</dc:contributor>
+ <dc:contributor>Randall Dipert</dc:contributor>
+ <dc:contributor>Mathias Brochhausen</dc:contributor>
+ <dc:contributor>Leonard Jacuzzo</dc:contributor>
+ <dc:contributor>Janna Hastings</dc:contributor>
+ <obo:IAO_0000116>BFO 2 Reference: For both terms and relational
expressions in BFO, we distinguish between primitive and defined. ‘Entity’
is an example of one such primitive term. Primitive terms in a
highest-level ontology such as BFO are terms that 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_0000116>
+ <dc:contributor>David Osumi-Sutherland</dc:contributor>
+ <dc:contributor>Mauricio Almeida</dc:contributor>
+ <dc:contributor>Bjoern Peters</dc:contributor>
+ <dc:contributor>Fabian Neuhaus</dc:contributor>
+ <dc:contributor>Mark Ressler</dc:contributor>
+ <obo:IAO_0000116>BFO 2 Reference: BFO does not claim to be a
complete coverage of all entities. It seeks only to provide coverage of
those entities studied by empirical science together with those entities
which affect or are involved in human activities such as data processing
and planning – coverage that is sufficiently broad to provide assistance to
those engaged in building domain ontologies for purposes of data annotation
[17</obo:IAO_0000116>
+ <dc:contributor>Melanie Courtot</dc:contributor>
+ <dc:contributor>Stefan Schulz</dc:contributor>
+ <dc:contributor>Bill Duncan</dc:contributor>
+ <dc:contributor>Alan Ruttenberg</dc:contributor>
+ <dc:contributor>Jie Zheng</dc:contributor>
+ <dc:contributor>James A. Overton</dc:contributor>
+ <rdfs:comment xml:lang="en">The
http://purl.obolibary.org/obo/bfo/classes-only.owl variant of BFO
("bfo_classes_only.owl") includes only the class hierarchy and
annotations from the full OWL version of BFO 2:
http://purl.obolibary.org/obo/bfo.owl ("bfo.owl"). There are no
object properties or logical axioms that use the object properties in
bfo_classes_only.owl. As the logical axioms in the bfo_classes_only.owl
variant are limited to subclass and disjoint assertions they are much
weaker than the logical axioms in bfo.owl.
+
+If you plan to use the relations that define BFO 2, you should import
bfo.owl instead of bfo_classes_only.owl. To the extent that the relations
are used without importing bfo.owl, be mindful that they should be used in
a manner consistent with their use in bfo.owl. Otherwise if your ontology
is imported by a another ontology that imports bfo.owl there may be
inconsistencies.
+
+See the BFO 2 release notes for further information about BFO 2. Please
note that the current release of bfo.owl uses temporal relations when the
subject or object is a continuant, a major change from BFO 1.</rdfs:comment>
+ <dc:contributor>Thomas Bittner</dc:contributor>
+ <rdfs:comment xml:lang="en">This is an early version of BFO
version 2 and has not yet been extensively reviewed by the project team
members. Please see the project site http://code.google.com/p/bfo/ , the
bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel ,
the bfo2 discussion group http://groups.google.com/group/bfo-devel, the
tracking google doc http://goo.gl/IlrEE, and the current version of the
bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx .
This ontology is generated from a specification at
http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/
and with the code that generates the OWL version in
http://bfo.googlecode.com/svn/trunk/src/tools/. A very early version of BFO
version 2 in CLIF is at
http://purl.obolibrary.org/obo/bfo/dev/bfo.clif</rdfs:comment>
+ <rdfs:isDefinedBy
rdf:resource="http://bfo.googlecode.com/svn/trunk/src/ontology/owl-group/specification/"/>
+ <rdfs:seeAlso
rdf:resource="http://bfo.googlecode.com/svn/trunk/src/tools/"/>
+ <foaf:homepage rdf:resource="http://code.google.com/p/bfo/"/>
+ <dc:license
rdf:resource="http://creativecommons.org/licenses/by/3.0/"/>
+ <rdfs:seeAlso
rdf:resource="http://purl.obolibrary.org/obo/bfo/dev/owl"/>
+ <rdfs:seeAlso
rdf:resource="http://groups.google.com/group/bfo-devel"/>
+ <rdfs:seeAlso
rdf:resource="http://groups.google.com/group/bfo-discuss"/>
+ <rdfs:seeAlso
rdf:resource="http://groups.google.com/group/bfo-owl-devel"/>
+ <foaf:homepage rdf:resource="http://ifomis.org/bfo"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo/2012-07-20/Reference"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo/2014-05-03/ReleaseNotes"/>
+ <owl:versionIRI
rdf:resource="http://purl.obolibrary.org/obo/bfo/2014-05-03/classes-only.owl"/>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo/dev/bfo.clif"/>
+ <foaf:mbox rdf:resource="mailto:bfo-ow...@googlegroups.com"/>
+ </owl:Ontology>
+
+
+
+ 
+
+
+
+
+ 
+
+ <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 term</rdfs:label>
+ <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>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+ <rdfs:label xml:lang="en">definition</rdfs:label>
+ <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>
+ <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>
+ <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>
+ <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>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000232">
+ <rdfs:label xml:lang="en">curator note</rdfs:label>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
+ <rdfs:label xml:lang="en">imported from</rdfs:label>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000600">
+ <rdfs:label xml:lang="en">elucidation</rdfs:label>
+ <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>
+ <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>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0010000">
+ <rdfs:label xml:lang="en">has axiom label</rdfs:label>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/iao.owl"/>
+ </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/member"/>
+
+
+
+ 
+
+ <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#seeAlso"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://xmlns.com/foaf/0.1/homepage"/>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001">
+ <rdfs:label xml:lang="en">entity</rdfs:label>
+ <obo:IAO_0000600 xml:lang="en">An entity is anything that exists
or has existed or will exist. (axiom label in BFO2 Reference:
[001-001])</obo:IAO_0000600>
+ <obo:BFO_0000180>Entity</obo:BFO_0000180>
+ <obo:IAO_0000116 xml:lang="en">Entity doesn't have a closure
axiom because the subclasses don't necessarily exhaust all
possibilites. For example Werner Ceusters 'portions of reality'
include 4 sorts, entities (as BFO construes them), universals,
configurations, and relations. It is an open question as to whether
entities as construed in BFO will at some point also include these other
portions of reality. See, for example, 'How to track absolutely
everything' at
http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf</obo:IAO_0000116>
+ <obo:IAO_0000112 xml:lang="en">Julius Caesar</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">Verdi’s Requiem</obo:IAO_0000112>
+ <obo:BFO_0000179>entity</obo:BFO_0000179>
+ <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: In all areas of
empirical inquiry we encounter general terms of two sorts. First are
general terms which refer to universals or types:animaltuberculosissurgical
procedurediseaseSecond, are general terms used to refer to groups of
entities which instantiate a given universal but do not correspond to the
extension of any subuniversal of that universal because there is nothing
intrinsic to the entities in question by virtue of which they – and only
they – are counted as belonging to the given group. Examples are: animal
purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical
procedure performed on a patient from Stockholmperson identified as
candidate for clinical trial #2056-555person who is signatory of Form
656-PPVpainting by Leonardo da VinciSuch terms, which represent what are
called ‘specializations’ in [81</obo:IAO_0000116>
+ <obo:IAO_0000112 xml:lang="en">the Second World
War</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">your body mass
index</obo:IAO_0000112>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">An entity is anything that
exists or has existed or will exist. (axiom label in BFO2 Reference:
[001-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/001-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <rdfs:comment>per discussion with Barry Smith</rdfs:comment>
+ <owl:annotatedTarget xml:lang="en">Entity doesn't have a
closure axiom because the subclasses don't necessarily exhaust all
possibilites. For example Werner Ceusters 'portions of reality'
include 4 sorts, entities (as BFO construes them), universals,
configurations, and relations. It is an open question as to whether
entities as construed in BFO will at some point also include these other
portions of reality. See, for example, 'How to track absolutely
everything' at
http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000004"/>
+ <rdfs:seeAlso
rdf:resource="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000002">
+ <rdfs:label xml:lang="en">continuant</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
+ <owl:disjointWith
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <obo:IAO_0000602>(forall (x y) (if (and (Continuant x) (exists (t)
(hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2
CLIF: [126-001] </obo:IAO_0000602>
+ <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Continuant
entities are entities which can be sliced to yield parts only along the
spatial dimension, yielding for example the parts of your table which we
call its legs, its top, its nails. ‘My desk stretches from the window to
the door. It has spatial parts, and can be sliced (in space) in two. With
respect to time, however, a thing is a continuant.’ [60, p.
240</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">Continuant doesn't have a
closure axiom because the subclasses don't necessarily exhaust all
possibilites. For example, in an expansion involving bringing in some of
Ceuster's other portions of reality, questions are raised as to
whether universals are continuants</obo:IAO_0000116>
+ <obo:BFO_0000179>continuant</obo:BFO_0000179>
+ <obo:BFO_0000180>Continuant</obo:BFO_0000180>
+ <obo:IAO_0000602>(forall (x y) (if (and (Continuant x) (exists (t)
(continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF:
[009-002] </obo:IAO_0000602>
+ <obo:IAO_0000602>(forall (x) (if (Continuant x) (Entity x))) //
axiom label in BFO2 CLIF: [008-002] </obo:IAO_0000602>
+ <obo:IAO_0000602>(forall (x) (if (Material Entity x) (exists (t)
(and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF:
[011-002] </obo:IAO_0000602>
+ <obo:IAO_0000600 xml:lang="en">A continuant is an entity that
persists, endures, or continues to exist through time while maintaining its
identity. (axiom label in BFO2 Reference: [008-002])</obo:IAO_0000600>
+ <obo:IAO_0000601 xml:lang="en">if b is a continuant and if, for
some t, c has_continuant_part b at t, then c is a continuant. (axiom label
in BFO2 Reference: [126-001])</obo:IAO_0000601>
+ <obo:IAO_0000601 xml:lang="en">if b is a continuant and if, for
some t, cis continuant_part of b at t, then c is a continuant. (axiom label
in BFO2 Reference: [009-002])</obo:IAO_0000601>
+ <obo:IAO_0000601 xml:lang="en">if b is a material entity, then
there is some temporal interval (referred to below as a one-dimensional
temporal region) during which b exists. (axiom label in BFO2 Reference:
[011-002])</obo:IAO_0000601>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x y) (if (and (Continuant x) (exists
(t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2
CLIF: [009-002] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/009-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x y) (if (and (Continuant x) (exists
(t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2
CLIF: [126-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/126-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">if b is a material entity, then
there is some temporal interval (referred to below as a one-dimensional
temporal region) during which b exists. (axiom label in BFO2 Reference:
[011-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/011-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">if b is a continuant and if,
for some t, cis continuant_part of b at t, then c is a continuant. (axiom
label in BFO2 Reference: [009-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/009-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">Continuant doesn't have a
closure axiom because the subclasses don't necessarily exhaust all
possibilites. For example, in an expansion involving bringing in some of
Ceuster's other portions of reality, questions are raised as to
whether universals are continuants</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000007"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">A continuant is an entity that
persists, endures, or continues to exist through time while maintaining its
identity. (axiom label in BFO2 Reference: [008-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/008-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (Material Entity x) (exists
(t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF:
[011-002] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/011-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (Continuant x) (Entity x)))
// axiom label in BFO2 CLIF: [008-002] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/008-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">if b is a continuant and if,
for some t, c has_continuant_part b at t, then c is a continuant. (axiom
label in BFO2 Reference: [126-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/126-001"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000003">
+ <rdfs:label xml:lang="en">occurrent</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
+ <obo:IAO_0000116>Simons uses different terminology for relations
of occurrents to regions: Denote the spatio-temporal location of a given
occurrent e by 'spn[e]' and call this region its span. We may say
an occurrent is at its span, in any larger region, and covers any smaller
region. Now suppose we have fixed a frame of reference so that we can speak
not merely of spatio-temporal but also of spatial regions (places) and
temporal regions (times). The spread of an occurrent, (relative to a frame
of reference) is the space it exactly occupies, and its spell is likewise
the time it exactly occupies. We write 'spr[e]' and `spl[e]'
respectively for the spread and spell of e, omitting mention of the
frame.</obo:IAO_0000116>
+ <obo:IAO_0000602>(forall (x) (if (Occurrent x) (exists (r) (and
(SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom
label in BFO2 CLIF: [108-001] </obo:IAO_0000602>
+ <obo:IAO_0000602>(forall (x) (iff (Occurrent x) (and (Entity x)
(exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
</obo:IAO_0000602>
+ <obo:IAO_0000600 xml:lang="en">An occurrent is an entity that
unfolds itself in time or it is the instantaneous boundary of such an
entity (for example a beginning or an ending) or it is a temporal or
spatiotemporal region which such an entity occupies_temporal_region or
occupies_spatiotemporal_region. (axiom label in BFO2 Reference:
[077-002])</obo:IAO_0000600>
+ <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: every occurrent
that is not a temporal or spatiotemporal region is s-dependent on some
independent continuant that is not a spatial region</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: s-dependence
obtains between every process and its participants in the sense that, as a
matter of necessity, this process could not have existed unless these or
those participants existed also. A process may have a succession of
participants at different phases of its unfolding. Thus there may be
different players on the field at different times during the course of a
football game; but the process which is the entire game s-depends_on all of
these players nonetheless. Some temporal parts of this process will
s-depend_on on only some of the players.</obo:IAO_0000116>
+ <obo:IAO_0000601 xml:lang="en">Every occurrent
occupies_spatiotemporal_region some spatiotemporal region. (axiom label in
BFO2 Reference: [108-001])</obo:IAO_0000601>
+ <obo:BFO_0000180>Occurrent</obo:BFO_0000180>
+ <obo:IAO_0000116 xml:lang="en">Occurrent doesn't have a
closure axiom because the subclasses don't necessarily exhaust all
possibilites. An example would be the sum of a process and the process
boundary of another process.</obo:IAO_0000116>
+ <obo:BFO_0000179>occurrent</obo:BFO_0000179>
+ <obo:IAO_0000601 xml:lang="en">b is an occurrent entity iff b is
an entity that has temporal parts. (axiom label in BFO2 Reference:
[079-001])</obo:IAO_0000601>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">Occurrent doesn't have a
closure axiom because the subclasses don't necessarily exhaust all
possibilites. An example would be the sum of a process and the process
boundary of another process.</owl:annotatedTarget>
+ <rdfs:comment>per discussion with Barry Smith</rdfs:comment>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000006"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>Simons uses different terminology for
relations of occurrents to regions: Denote the spatio-temporal location of
a given occurrent e by 'spn[e]' and call this region its span. We
may say an occurrent is at its span, in any larger region, and covers any
smaller region. Now suppose we have fixed a frame of reference so that we
can speak not merely of spatio-temporal but also of spatial regions
(places) and temporal regions (times). The spread of an occurrent,
(relative to a frame of reference) is the space it exactly occupies, and
its spell is likewise the time it exactly occupies. We write
'spr[e]' and `spl[e]' respectively for the spread and spell
of e, omitting mention of the frame.</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000012"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (Occurrent x) (exists (r)
(and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) //
axiom label in BFO2 CLIF: [108-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/108-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (iff (Occurrent x) (and (Entity
x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF:
[079-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/079-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">An occurrent is an entity that
unfolds itself in time or it is the instantaneous boundary of such an
entity (for example a beginning or an ending) or it is a temporal or
spatiotemporal region which such an entity occupies_temporal_region or
occupies_spatiotemporal_region. (axiom label in BFO2 Reference:
[077-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/077-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">b is an occurrent entity iff b
is an entity that has temporal parts. (axiom label in BFO2 Reference:
[079-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/079-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">Every occurrent
occupies_spatiotemporal_region some spatiotemporal region. (axiom label in
BFO2 Reference: [108-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/108-001"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000004">
+ <rdfs:label xml:lang="en">independent continuant</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
+ <obo:IAO_0000602>(forall (x t) (if (and (IndependentContinuant x)
(existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x
t))))) // axiom label in BFO2 CLIF: [018-002] </obo:IAO_0000602>
+ <obo:BFO_0000180>IndependentContinuant</obo:BFO_0000180>
+ <obo:BFO_0000179>ic</obo:BFO_0000179>
+ <obo:IAO_0000602>(iff (IndependentContinuant a) (and (Continuant
a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in
BFO2 CLIF: [017-002] </obo:IAO_0000602>
+ <obo:IAO_0000602>(forall (x t) (if (IndependentContinuant x)
(exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label
in BFO2 CLIF: [134-001] </obo:IAO_0000602>
+ <obo:IAO_0000601 xml:lang="en">For any independent continuant b
and any time t there is some spatial region r such that b is located_in r
at t. (axiom label in BFO2 Reference: [134-001])</obo:IAO_0000601>
+ <obo:IAO_0000601 xml:lang="en">For every independent continuant b
and time t during the region of time spanned by its life, there are
entities which s-depends_on b during t. (axiom label in BFO2 Reference:
[018-002])</obo:IAO_0000601>
+ <obo:IAO_0000112 xml:lang="en">a chair</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">a heart</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">a leg</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">a molecule</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">a spatial region</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">an atom</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">an orchestra.</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">an organism</obo:IAO_0000112>
+ <obo:IAO_0000115 xml:lang="en">b is an independent continuant =
Def. b is a continuant which is such that there is no c and no t such that
b s-depends_on c at t. (axiom label in BFO2 Reference:
[017-002])</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">the bottom right portion of a human
torso</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the interior of your
mouth</obo:IAO_0000112>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x t) (if (IndependentContinuant x)
(exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label
in BFO2 CLIF: [134-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/134-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x t) (if (and (IndependentContinuant
x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x
t))))) // axiom label in BFO2 CLIF: [018-002] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/018-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">For every independent
continuant b and time t during the region of time spanned by its life,
there are entities which s-depends_on b during t. (axiom label in BFO2
Reference: [018-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/018-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">b is an independent continuant
= Def. b is a continuant which is such that there is no c and no t such
that b s-depends_on c at t. (axiom label in BFO2 Reference:
[017-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/017-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(iff (IndependentContinuant a) (and
(Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) //
axiom label in BFO2 CLIF: [017-002] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/017-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">For any independent continuant
b and any time t there is some spatial region r such that b is located_in r
at t. (axiom label in BFO2 Reference: [134-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000004"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/134-001"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000006">
+ <rdfs:label xml:lang="en">spatial region</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000141"/>
+ <obo:IAO_0000602>(forall (x y t) (if (and (SpatialRegion x)
(continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2
CLIF: [036-001] </obo:IAO_0000602>
+ <obo:IAO_0000602>(forall (x) (if (SpatialRegion x) (Continuant
x))) // axiom label in BFO2 CLIF: [035-001] </obo:IAO_0000602>
+ <obo:IAO_0000600 xml:lang="en">A spatial region is a continuant
entity that is a continuant_part_of spaceR as defined relative to some
frame R. (axiom label in BFO2 Reference: [035-001])</obo:IAO_0000600>
+ <obo:IAO_0000601 xml:lang="en">All continuant parts of spatial
regions are spatial regions. (axiom label in BFO2 Reference:
[036-001])</obo:IAO_0000601>
+ <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Spatial regions do
not participate in processes.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">Spatial region doesn't have a
closure axiom because the subclasses don't exhaust all possibilites.
An example would be the union of a spatial point and a spatial line that
doesn't overlap the point, or two spatial lines that intersect at a
single point. In both cases the resultant spatial region is neither
0-dimensional, 1-dimensional, 2-dimensional, or
3-dimensional.</obo:IAO_0000116>
+ <obo:BFO_0000180>SpatialRegion</obo:BFO_0000180>
+ <obo:BFO_0000179>s-region</obo:BFO_0000179>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (SpatialRegion x) (Continuant
x))) // axiom label in BFO2 CLIF: [035-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000006"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/035-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x y t) (if (and (SpatialRegion x)
(continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2
CLIF: [036-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000006"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/036-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">A spatial region is a
continuant entity that is a continuant_part_of spaceR as defined relative
to some frame R. (axiom label in BFO2 Reference:
[035-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000006"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/035-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">Spatial region doesn't
have a closure axiom because the subclasses don't exhaust all
possibilites. An example would be the union of a spatial point and a
spatial line that doesn't overlap the point, or two spatial lines that
intersect at a single point. In both cases the resultant spatial region is
neither 0-dimensional, 1-dimensional, 2-dimensional, or
3-dimensional.</owl:annotatedTarget>
+ <rdfs:comment>per discussion with Barry Smith</rdfs:comment>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000006"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">All continuant parts of spatial
regions are spatial regions. (axiom label in BFO2 Reference:
[036-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000006"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/036-001"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000008">
+ <rdfs:label xml:lang="en">temporal region</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <obo:IAO_0000602>(forall (x) (if (TemporalRegion x) (Occurrent
x))) // axiom label in BFO2 CLIF: [100-001] </obo:IAO_0000602>
+ <obo:IAO_0000600 xml:lang="en">A temporal region is an occurrent
entity that is part of time as defined relative to some reference frame.
(axiom label in BFO2 Reference: [100-001])</obo:IAO_0000600>
+ <obo:IAO_0000601 xml:lang="en">Every temporal region t is such
that t occupies_temporal_region t. (axiom label in BFO2 Reference:
[119-002])</obo:IAO_0000601>
+ <obo:BFO_0000180>TemporalRegion</obo:BFO_0000180>
+ <obo:IAO_0000602>(forall (r) (if (TemporalRegion r)
(occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
</obo:IAO_0000602>
+ <obo:IAO_0000602>(forall (x y) (if (and (TemporalRegion x)
(occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF:
[101-001] </obo:IAO_0000602>
+ <obo:IAO_0000601 xml:lang="en">All parts of temporal regions are
temporal regions. (axiom label in BFO2 Reference:
[101-001])</obo:IAO_0000601>
+ <obo:IAO_0000116 xml:lang="en">Temporal region doesn't have a
closure axiom because the subclasses don't exhaust all possibilites.
An example would be the mereological sum of a temporal instant and a
temporal interval that doesn't overlap the instant. In this case the
resultant temporal region is neither 0-dimensional nor
1-dimensional</obo:IAO_0000116>
+ <obo:BFO_0000179>t-region</obo:BFO_0000179>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">Every temporal region t is such
that t occupies_temporal_region t. (axiom label in BFO2 Reference:
[119-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000008"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/119-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x y) (if (and (TemporalRegion x)
(occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF:
[101-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000008"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/101-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">A temporal region is an
occurrent entity that is part of time as defined relative to some reference
frame. (axiom label in BFO2 Reference: [100-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000008"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/100-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <rdfs:comment>per discussion with Barry Smith</rdfs:comment>
+ <owl:annotatedTarget xml:lang="en">Temporal region doesn't
have a closure axiom because the subclasses don't exhaust all
possibilites. An example would be the mereological sum of a temporal
instant and a temporal interval that doesn't overlap the instant. In
this case the resultant temporal region is neither 0-dimensional nor
1-dimensional</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000008"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000003"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">All parts of temporal regions
are temporal regions. (axiom label in BFO2 Reference:
[101-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000008"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/101-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (r) (if (TemporalRegion r)
(occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000008"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/119-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (TemporalRegion x) (Occurrent
x))) // axiom label in BFO2 CLIF: [100-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000008"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/100-001"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000009">
+ <rdfs:label xml:lang="en">two-dimensional spatial
region</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000006"/>
+ <obo:IAO_0000600 xml:lang="en">A two-dimensional spatial region is
a spatial region that is of two dimensions. (axiom label in BFO2 Reference:
[039-001])</obo:IAO_0000600>
+ <obo:BFO_0000180>TwoDimensionalSpatialRegion</obo:BFO_0000180>
+ <obo:IAO_0000602>(forall (x) (if (TwoDimensionalSpatialRegion x)
(SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
</obo:IAO_0000602>
+ <obo:BFO_0000179>2d-s-region</obo:BFO_0000179>
+ <obo:IAO_0000112 xml:lang="en">an infinitely thin plane in
space.</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the surface of a sphere-shaped part
of space</obo:IAO_0000112>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (TwoDimensionalSpatialRegion
x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000009"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/039-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">A two-dimensional spatial
region is a spatial region that is of two dimensions. (axiom label in BFO2
Reference: [039-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000009"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/039-001"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000011">
+ <rdfs:label xml:lang="en">spatiotemporal region</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <obo:IAO_0000602>(forall (x) (if (SpatioTemporalRegion x) (exists
(y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label
in BFO2 CLIF: [098-001] </obo:IAO_0000602>
+ <obo:IAO_0000602>(forall (x) (if (SpatioTemporalRegion x)
(Occurrent x))) // axiom label in BFO2 CLIF: [095-001] </obo:IAO_0000602>
+ <obo:IAO_0000602>(forall (x t) (if (SpatioTemporalRegion x)
(exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) //
axiom label in BFO2 CLIF: [099-001] </obo:IAO_0000602>
+ <obo:IAO_0000602>(forall (x y) (if (and (SpatioTemporalRegion x)
(occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2
CLIF: [096-001] </obo:IAO_0000602>
+ <obo:IAO_0000602>(forall (r) (if (SpatioTemporalRegion r)
(occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
</obo:IAO_0000602>
+ <obo:IAO_0000600 xml:lang="en">A spatiotemporal region is an
occurrent entity that is part of spacetime. (axiom label in BFO2 Reference:
[095-001])</obo:IAO_0000600>
+ <obo:BFO_0000179>st-region</obo:BFO_0000179>
+ <obo:BFO_0000180>SpatiotemporalRegion</obo:BFO_0000180>
+ <obo:IAO_0000601 xml:lang="en">All parts of spatiotemporal regions
are spatiotemporal regions. (axiom label in BFO2 Reference:
[096-001])</obo:IAO_0000601>
+ <obo:IAO_0000601 xml:lang="en">Each spatiotemporal region at any
time t projects_onto some spatial region at t. (axiom label in BFO2
Reference: [099-001])</obo:IAO_0000601>
+ <obo:IAO_0000601 xml:lang="en">Each spatiotemporal region
projects_onto some temporal region. (axiom label in BFO2 Reference:
[098-001])</obo:IAO_0000601>
+ <obo:IAO_0000601 xml:lang="en">Every spatiotemporal region
occupies_spatiotemporal_region itself.</obo:IAO_0000601>
+ <obo:IAO_0000601 xml:lang="en">Every spatiotemporal region s is
such that s occupies_spatiotemporal_region s. (axiom label in BFO2
Reference: [107-002])</obo:IAO_0000601>
+ <obo:IAO_0000112 xml:lang="en">the spatiotemporal region occupied
by a human life</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the spatiotemporal region occupied
by a process of cellular meiosis.</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the spatiotemporal region occupied
by the development of a cancer tumor</obo:IAO_0000112>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">Every spatiotemporal region s
is such that s occupies_spatiotemporal_region s. (axiom label in BFO2
Reference: [107-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/107-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (r) (if (SpatioTemporalRegion r)
(occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/107-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">All parts of spatiotemporal
regions are spatiotemporal regions. (axiom label in BFO2 Reference:
[096-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/096-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x y) (if (and (SpatioTemporalRegion
x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2
CLIF: [096-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/096-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">Each spatiotemporal region
projects_onto some temporal region. (axiom label in BFO2 Reference:
[098-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/098-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x t) (if (SpatioTemporalRegion x)
(exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) //
axiom label in BFO2 CLIF: [099-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/099-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (SpatioTemporalRegion x)
(Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/095-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">Each spatiotemporal region at
any time t projects_onto some spatial region at t. (axiom label in BFO2
Reference: [099-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/099-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (SpatioTemporalRegion x)
(exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) //
axiom label in BFO2 CLIF: [098-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/098-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">A spatiotemporal region is an
occurrent entity that is part of spacetime. (axiom label in BFO2 Reference:
[095-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000011"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/095-001"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015">
+ <rdfs:label xml:lang="en">process</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000003"/>
+ <obo:IAO_0000602>(iff (Process a) (and (Occurrent a) (exists (b)
(properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c)
(specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
</obo:IAO_0000602>
+ <obo:BFO_0000180>Process</obo:BFO_0000180>
+ <obo:IAO_0000112 xml:lang="en">a process of
meiosis</obo:IAO_0000112>
+ <obo:IAO_0000115 xml:lang="en">p is a process = Def. p is an
occurrent that has temporal proper parts and for some time t, p
s-depends_on some material entity at t. (axiom label in BFO2 Reference:
[083-003])</obo:IAO_0000115>
+ <obo:BFO_0000179>process</obo:BFO_0000179>
+ <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: The realm of
occurrents is less pervasively marked by the presence of natural units than
is the case in the realm of independent continuants. Thus there is here no
counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart.
In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material
entity’. Those natural – as contrasted with engineered, which here means:
deliberately executed – units which do exist in the realm of occurrents are
typically either parasitic on the existence of natural units on the
continuant side, or they are fiat in nature. Thus we can count lives; we
can count football games; we can count chemical reactions performed in
experiments or in chemical manufacturing. We cannot count the processes
taking place, for instance, in an episode of insect mating behavior.Even
where natural units are identifiable, for example cycles in a cyclical
process such as the beating of a heart or an organism’s sleep/wake cycle,
the processes in question form a sequence with no discontinuities (temporal
gaps) of the sort that we find for instance where billiard balls or
zebrafish or planets are separated by clear spatial gaps. Lives of
organisms are process units, but they too unfold in a continuous series
from other, prior processes such as fertilization, and they unfold in turn
in continuous series of post-life processes such as post-mortem decay.
Clear examples of boundaries of processes are almost always of the fiat
sort (midnight, a time of death as declared in an operating theater or on a
death certificate, the initiation of a state of war)</obo:IAO_0000116>
+ <obo:IAO_0000112 xml:lang="en">a process of cell-division, \ a
beating of the heart</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">a process of
sleeping</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the course of a
disease</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the flight of a
bird</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the life of an
organism</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">your process of
aging.</obo:IAO_0000112>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget>(iff (Process a) (and (Occurrent a) (exists
(b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c)
(specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/083-003"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">p is a process = Def. p is an
occurrent that has temporal proper parts and for some time t, p
s-depends_on some material entity at t. (axiom label in BFO2 Reference:
[083-003])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/083-003"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000016">
+ <rdfs:label xml:lang="en">disposition</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
+ <owl:disjointWith
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
+ <obo:IAO_0000602>(forall (x) (if (Disposition x) (and
(RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y
t)))))) // axiom label in BFO2 CLIF: [062-002] </obo:IAO_0000602>
+ <obo:BFO_0000180>Disposition</obo:BFO_0000180>
+ <obo:IAO_0000602>(forall (x t) (if (and (RealizableEntity x)
(existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x
y t))))) // axiom label in BFO2 CLIF: [063-002] </obo:IAO_0000602>
+ <obo:IAO_0000601 xml:lang="en">If b is a realizable entity then
for all t at which b exists, b s-depends_on some material entity at t.
(axiom label in BFO2 Reference: [063-002])</obo:IAO_0000601>
+ <obo:IAO_0000112 xml:lang="en">an atom of element X has the
disposition to decay to an atom of element Y</obo:IAO_0000112>
+ <obo:IAO_0000600 xml:lang="en">b is a disposition means: b is a
realizable entity & b’s bearer is some material entity & b is such
that if it ceases to exist, then its bearer is physically changed, &
b’s realization occurs when and because this bearer is in some special
physical circumstances, & this realization occurs in virtue of the
bearer’s physical make-up. (axiom label in BFO2 Reference:
[062-002])</obo:IAO_0000600>
+ <obo:IAO_0000112 xml:lang="en">certain people have a
predisposition to colon cancer</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">children are innately disposed to
categorize objects in certain ways.</obo:IAO_0000112>
+ <obo:BFO_0000179>disposition</obo:BFO_0000179>
+ <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: Dispositions exist
along a strength continuum. Weaker forms of disposition are realized in
only a fraction of triggering cases. These forms occur in a significant
number of cases of a similar type.</obo:IAO_0000116>
+ <obo:IAO_0000112 xml:lang="en">the cell wall is disposed to filter
chemicals in endocytosis and exocytosis</obo:IAO_0000112>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">If b is a realizable entity
then for all t at which b exists, b s-depends_on some material entity at t.
(axiom label in BFO2 Reference: [063-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/063-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x t) (if (and (RealizableEntity x)
(existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x
y t))))) // axiom label in BFO2 CLIF: [063-002] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/063-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (Disposition x) (and
(RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y
t)))))) // axiom label in BFO2 CLIF: [062-002] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/062-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">b is a disposition means: b is
a realizable entity & b’s bearer is some material entity & b is
such that if it ceases to exist, then its bearer is physically changed,
& b’s realization occurs when and because this bearer is in some
special physical circumstances, & this realization occurs in virtue of
the bearer’s physical make-up. (axiom label in BFO2 Reference:
[062-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000016"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/062-002"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000017">
+ <rdfs:label xml:lang="en">realizable entity</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+ <owl:disjointWith
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+ <obo:BFO_0000179>realizable</obo:BFO_0000179>
+ <obo:IAO_0000601 xml:lang="en">All realizable dependent
continuants have independent continuants that are not spatial regions as
their bearers. (axiom label in BFO2 Reference: [060-002])</obo:IAO_0000601>
+ <obo:BFO_0000180>RealizableEntity</obo:BFO_0000180>
+ <obo:IAO_0000602>(forall (x t) (if (RealizableEntity x) (exists
(y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x
t))))) // axiom label in BFO2 CLIF: [060-002] </obo:IAO_0000602>
+ <obo:IAO_0000602>(forall (x) (if (RealizableEntity x) (and
(SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant
y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2
CLIF: [058-002] </obo:IAO_0000602>
+ <obo:IAO_0000600 xml:lang="en">To say that b is a realizable
entity is to say that b is a specifically dependent continuant that inheres
in some independent continuant which is not a spatial region and is of a
type instances of which are realized in processes of a correlated type.
(axiom label in BFO2 Reference: [058-002])</obo:IAO_0000600>
+ <obo:IAO_0000112 xml:lang="en">the disposition of this piece of
metal to conduct electricity.</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the disposition of your blood to
coagulate</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the function of your reproductive
organs</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the role of being a
doctor</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the role of this boundary to
delineate where Utah and Colorado meet</obo:IAO_0000112>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">All realizable dependent
continuants have independent continuants that are not spatial regions as
their bearers. (axiom label in BFO2 Reference:
[060-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/060-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">To say that b is a realizable
entity is to say that b is a specifically dependent continuant that inheres
in some independent continuant which is not a spatial region and is of a
type instances of which are realized in processes of a correlated type.
(axiom label in BFO2 Reference: [058-002])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/058-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (RealizableEntity x) (and
(SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant
y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2
CLIF: [058-002] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/058-002"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x t) (if (RealizableEntity x)
(exists (y) (and (IndependentContinuant y) (not (SpatialRegion y))
(bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/060-002"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000018">
+ <rdfs:label xml:lang="en">zero-dimensional spatial
region</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000006"/>
+ <obo:BFO_0000179>0d-s-region</obo:BFO_0000179>
+ <obo:IAO_0000602>(forall (x) (if (ZeroDimensionalSpatialRegion x)
(SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
</obo:IAO_0000602>
+ <obo:IAO_0000600 xml:lang="en">A zero-dimensional spatial region
is a point in space. (axiom label in BFO2 Reference:
[037-001])</obo:IAO_0000600>
+ <obo:BFO_0000180>ZeroDimensionalSpatialRegion</obo:BFO_0000180>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (ZeroDimensionalSpatialRegion
x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000018"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/037-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">A zero-dimensional spatial
region is a point in space. (axiom label in BFO2 Reference:
[037-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000018"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/037-001"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000019">
+ <rdfs:label xml:lang="en">quality</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+ <obo:IAO_0000602>(forall (x) (if (Quality x)
(SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF:
[055-001] </obo:IAO_0000602>
+ <obo:IAO_0000601 xml:lang="en">If an entity is a quality at any
time that it exists, then it is a quality at every time that it exists.
(axiom label in BFO2 Reference: [105-001])</obo:IAO_0000601>
+ <obo:BFO_0000179>quality</obo:BFO_0000179>
+ <obo:BFO_0000180>Quality</obo:BFO_0000180>
+ <obo:IAO_0000602>(forall (x) (if (exists (t) (and (existsAt x t)
(Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom
label in BFO2 CLIF: [105-001] </obo:IAO_0000602>
+ <obo:IAO_0000600 xml:lang="en">a quality is a specifically
dependent continuant that, in contrast to roles and dispositions, does not
require any further process in order to be realized. (axiom label in BFO2
Reference: [055-001])</obo:IAO_0000600>
+ <obo:IAO_0000112 xml:lang="en">the ambient temperature of this
portion of air</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the color of a
tomato</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the length of the circumference of
your waist</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the mass of this piece of
gold.</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the shape of your
nose</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the shape of your
nostril</obo:IAO_0000112>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (Quality x)
(SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF:
[055-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/055-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">If an entity is a quality at
any time that it exists, then it is a quality at every time that it exists.
(axiom label in BFO2 Reference: [105-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000601"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/105-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (exists (t) (and (existsAt x
t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) //
axiom label in BFO2 CLIF: [105-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/105-001"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">a quality is a specifically
dependent continuant that, in contrast to roles and dispositions, does not
require any further process in order to be realized. (axiom label in BFO2
Reference: [055-001])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000600"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/055-001"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000020">
+ <rdfs:label xml:lang="en">specifically dependent
continuant</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000002"/>
+ <obo:BFO_0000179>sdc</obo:BFO_0000179>
+ <obo:IAO_0000602>(iff (SpecificallyDependentContinuant a) (and
(Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and
(IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt
a b t))))))) // axiom label in BFO2 CLIF: [050-003] </obo:IAO_0000602>
+ <obo:BFO_0000180>SpecificallyDependentContinuant</obo:BFO_0000180>
+ <obo:IAO_0000602>(iff (RelationalSpecificallyDependentContinuant
a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and
(not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists
(d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t))))
(specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) //
axiom label in BFO2 CLIF: [131-004] </obo:IAO_0000602>
+ <obo:IAO_0000112 xml:lang="en">Reciprocal specifically dependent
continuants: the function of this key to open this lock and the mutually
dependent disposition of this lock: to be opened by this
key</obo:IAO_0000112>
+ <obo:IAO_0000116 xml:lang="en">Specifically dependent continuant
doesn't have a closure axiom because the subclasses don't
necessarily exhaust all possibilites. We're not sure what else will
develop here, but for example there are questions such as what are
promises, obligation, etc.</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">b is a relational specifically
dependent continuant = Def. b is a specifically dependent continuant and
there are n &gt; 1 independent continuants c1, … cn which are not
spatial regions are such that for all 1 i &lt; j n, ci and cj share
no common parts, are such that for each 1 i n, b s-depends_on ci at every
time t during the course of b’s existence (axiom label in BFO2 Reference:
[131-004])</obo:IAO_0000115>
+ <obo:IAO_0000115 xml:lang="en">b is a specifically dependent
continuant = Def. b is a continuant & there is some independent
continuant c which is not a spatial region and which is such that b
s-depends_on c at every time t during the course of b’s existence. (axiom
label in BFO2 Reference: [050-003])</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">of one-sided specifically dependent
continuants: the mass of this tomato</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">of relational dependent continuants
(multiple bearers): John’s love for Mary, the ownership relation between
John and this statue, the relation of authority between John and his
subordinates.</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the disposition of this fish to
decay</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the function of this heart: to pump
blood</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the mutual dependence of proton
donors and acceptors in chemical reactions [79</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the mutual dependence of the role
predator and the role prey as played by two organisms in a given
interaction</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the pink color of a medium rare
piece of grilled filet mignon at its center</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the role of being a
doctor</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the shape of this
hole.</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the smell of this portion of
mozzarella</obo:IAO_0000112>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget>(iff
(RelationalSpecificallyDependentContinuant a) (and
(SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not
(SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d)
(and (continuantPartOfAt d b t) (continuantPartOfAt d c t))))
(specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) //
axiom label in BFO2 CLIF: [131-004] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/131-004"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">b is a relational specifically
dependent continuant = Def. b is a specifically dependent continuant and
there are n &gt; 1 independent continuants c1, … cn which are not
spatial regions are such that for all 1 i &lt; j n, ci and cj share
no common parts, are such that for each 1 i n, b s-depends_on ci at every
time t during the course of b’s existence (axiom label in BFO2 Reference:
[131-004])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/131-004"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget>(iff (SpecificallyDependentContinuant a) (and
(Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and
(IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt
a b t))))))) // axiom label in BFO2 CLIF: [050-003] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/050-003"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <owl:annotatedTarget xml:lang="en">b is a specifically dependent
continuant = Def. b is a continuant & there is some independent
continuant c which is not a spatial region and which is such that b
s-depends_on c at every time t during the course of b’s existence. (axiom
label in BFO2 Reference: [050-003])</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/050-003"/>
+ </owl:Axiom>
+ <owl:Axiom>
+ <rdfs:comment>per discussion with Barry Smith</rdfs:comment>
+ <owl:annotatedTarget xml:lang="en">Specifically dependent
continuant doesn't have a closure axiom because the subclasses
don't necessarily exhaust all possibilites. We're not sure what
else will develop here, but for example there are questions such as what
are promises, obligation, etc.</owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000116"/>
+ <obo:IAO_0010000
rdf:resource="http://purl.obolibrary.org/obo/bfo/axiom/0000005"/>
+ </owl:Axiom>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000023">
+ <rdfs:label xml:lang="en">role</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
+ <obo:BFO_0000180>Role</obo:BFO_0000180>
+ <obo:IAO_0000602>(forall (x) (if (Role x) (RealizableEntity x)))
// axiom label in BFO2 CLIF: [061-001] </obo:IAO_0000602>
+ <obo:IAO_0000112 xml:lang="en">John’s role of husband to Mary is
dependent on Mary’s role of wife to John, and both are dependent on the
object aggregate comprising John and Mary as member parts joined together
through the relational quality of being married.</obo:IAO_0000112>
+ <obo:IAO_0000600 xml:lang="en">b is a role means: b is a
realizable entity & b exists because there is some single bearer that
is in some special physical, social, or institutional set of circumstances
in which this bearer does not have to be& b is not such that, if it
ceases to exist, then the physical make-up of the bearer is thereby
changed. (axiom label in BFO2 Reference: [061-001])</obo:IAO_0000600>
+ <obo:BFO_0000179>role</obo:BFO_0000179>
+ <obo:IAO_0000116 xml:lang="en">BFO 2 Reference: One major family
of examples of non-rigid universals involves roles, and ontologies
developed for corresponding administrative purposes may consist entirely of
representatives of entities of this sort. Thus ‘professor’, defined as
follows,b instance_of professor at t =Def. there is some c, c instance_of
professor role & c inheres_in b at t.denotes a non-rigid universal and
so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These
terms are all, in the jargon of philosophy, phase sortals.) By using role
terms in definitions, we can create a BFO conformant treatment of such
entities drawing on the fact that, while an instance of professor may be
simultaneously an instance of trade union member, no instance of the type
professor role is also (at any time) an instance of the type trade union
member role (any more than any instance of the type color is at any time an
instance of the type length).If an ontology of employment positions should
be defined in terms of roles following the above pattern, this enables the
ontology to do justice to the fact that individuals instantiate the
corresponding universals – professor, sergeant, nurse – only during
certain phases in their lives.</obo:IAO_0000116>
+ <obo:IAO_0000112 xml:lang="en">the priest role</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the role of a boundary to demarcate
two neighboring administrative territories</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the role of a building in serving
as a military target</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the role of a stone in marking a
property boundary</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the role of subject in a clinical
trial</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">the student role</obo:IAO_0000112>
+ <rdfs:isDefinedBy
rdf:resource="http://purl.obolibrary.org/obo/bfo.owl"/>
+ </owl:Class>
+ <owl:Axiom>
+ <owl:annotatedTarget>(forall (x) (if (Role x) (RealizableEntity
x))) // axiom label in BFO2 CLIF: [061-001] </owl:annotatedTarget>
+ <owl:annotatedSource
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
+ <owl:annotatedProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000602"/>
***The diff for this file has been truncated for email.***
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/external/ro-core.owl Sat Jan 3
07:23:58 2015 UTC
@@ -0,0 +1,376 @@
+<?xml version="1.0"?>
+
+
+<!DOCTYPE rdf:RDF [
+ <!ENTITY foaf "http://xmlns.com/foaf/0.1/" >
+ <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
+ <!ENTITY obo "http://purl.obolibrary.org/obo/" >
+ <!ENTITY dc "http://purl.org/dc/elements/1.1/" >
+ <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
+ <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
+ <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
+]>
+
+
+<rdf:RDF xmlns="&obo;bfo.owl#"
+ xml:base="&obo;bfo.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: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#">
+ <owl:Ontology rdf:about="&obo;ro/core.owl">
+ <foaf:homepage
rdf:datatype="&xsd;anyURI">https://code.google.com/p/obo-relations/w/ROCore</foaf:homepage>
+ <owl:imports rdf:resource="&obo;ro/annotations.owl"/>
+ <owl:imports rdf:resource="&obo;ro/bfo-classes-minimal.owl"/>
+ </owl:Ontology>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;BFO_0000050">
+ <rdf:type rdf:resource="&owl;TransitiveProperty"/>
+ <rdfs:label xml:lang="en">part of</rdfs:label>
+
<rdfs:seeAlso>http://www.obofoundry.org/ro/#OBO_REL:part_of</rdfs:seeAlso>
+ <obo:IAO_0000116 xml:lang="en">Ambiguous between
continuant-parthood and occurrent-parthood</obo:IAO_0000116>
+ <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="&obo;BFO_0000051"/>
+ <obo:RO_0001900 rdf:resource="&obo;RO_0001901"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;BFO_0000051">
+ <rdf:type rdf:resource="&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="&obo;RO_0001901"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&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="&obo;BFO_0000015"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&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="&obo;BFO_0000015"/>
+ <owl:inverseOf rdf:resource="&obo;BFO_0000054"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&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="&obo;BFO_0000003"/>
+ <rdfs:range rdf:resource="&obo;BFO_0000004"/>
+ <owl:inverseOf rdf:resource="&obo;BFO_0000067"/>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="&obo;BFO_0000066"/>
+ <rdf:Description rdf:about="&obo;BFO_0000050"/>
+ </owl:propertyChainAxiom>
+ <owl:propertyChainAxiom rdf:parseType="Collection">
+ <rdf:Description rdf:about="&obo;BFO_0000050"/>
+ <rdf:Description rdf:about="&obo;BFO_0000066"/>
+ </owl:propertyChainAxiom>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&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="&obo;RO_0000052">
+ <rdfs:label xml:lang="en">inheres in</rdfs:label>
+ <obo:IAO_0000116 xml:lang="en">Intended meaning:
+domain: specifically dependent continuant
+range: independent continuant
+time: at all times
+
+A specifically dependent continuant A inheres in its independent
continuant B at all times during which A exists.</obo:IAO_0000116>
+ <obo:IAO_0000111 xml:lang="en">inheres in</obo:IAO_0000111>
+ <obo:IAO_0000118 xml:lang="en">inheres_in</obo:IAO_0000118>
+ <obo:RO_0001900 rdf:resource="&obo;RO_0001901"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0000053">
+ <rdfs:label xml:lang="en">bearer of</rdfs:label>
+ <obo:IAO_0000111 xml:lang="en">bearer of</obo:IAO_0000111>
+ <obo:IAO_0000118 xml:lang="en">bearer_of</obo:IAO_0000118>
+ <obo:IAO_0000118 xml:lang="en">is bearer of</obo:IAO_0000118>
+ <rdfs:range rdf:resource="&obo;BFO_0000020"/>
+ <owl:inverseOf rdf:resource="&obo;RO_0000052"/>
+ <obo:RO_0001900 rdf:resource="&obo;RO_0001901"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0000056">
+ <rdfs:label xml:lang="en">participates in</rdfs:label>
+ <obo:IAO_0000111 xml:lang="en">participates in</obo:IAO_0000111>
+ <obo:IAO_0000118 xml:lang="en">participates_in</obo:IAO_0000118>
+ <rdfs:domain rdf:resource="&obo;BFO_0000002"/>
+ <rdfs:range rdf:resource="&obo;BFO_0000003"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0000057">
+ <rdfs:label xml:lang="en">has participant</rdfs:label>
+ <obo:IAO_0000111 xml:lang="en">has participant</obo:IAO_0000111>
+ <obo:IAO_0000118 xml:lang="en">has_participant</obo:IAO_0000118>
+
<dc:source>http://www.obofoundry.org/ro/#OBO_REL:has_participant</dc:source>
+ <obo:IAO_0000116 xml:lang="en">Has_participant is a primitive
instance-level relation between a process, a continuant, and a time at
which the continuant participates in some way in the process. The relation
obtains, for example, when this particular process of oxygen exchange
across this particular alveolar membrane has_participant this particular
sample of hemoglobin at this particular time.</obo:IAO_0000116>
+ <rdfs:range rdf:resource="&obo;BFO_0000002"/>
+ <rdfs:domain rdf:resource="&obo;BFO_0000003"/>
+ <owl:inverseOf rdf:resource="&obo;RO_0000056"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/RO_0000058">
+ <rdfs:label xml:lang="en">is concretized as</rdfs:label>
+ <obo:IAO_0000112 xml:lang="en">A journal article is an information
artifact that inheres in some number of printed journals. For each copy of
the printed journal there is some quality that carries the journal article,
such as a pattern of ink. The journal article (a generically dependent
continuant) is concretized as the quality (a specifically dependent
continuant), and both depend on that copy of the printed journal (an
independent continuant).</obo:IAO_0000112>
+ <obo:IAO_0000115 xml:lang="en">A relationship between a
generically dependent continuant and a specifically dependent continuant,
in which the generically dependent continuant depends on some independent
continuant in virtue of the fact that the specifically dependent continuant
also depends on that same independent continuant. A generically dependent
continuant may be concretized as multiple specifically dependent
continuants.</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">An investigator reads a protocol
and forms a plan to carry out an assay. The plan is a realizable entity (a
specifically dependent continuant) that concretizes the protocol (a
generically dependent continuant), and both depend on the investigator (an
independent continuant). The plan is then realized by the assay (a
process).</obo:IAO_0000112>
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
+ <owl:inverseOf
rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/RO_0000059">
+ <rdfs:label xml:lang="en">concretizes</rdfs:label>
+ <obo:IAO_0000112 xml:lang="en">A journal article is an information
artifact that inheres in some number of printed journals. For each copy of
the printed journal there is some quality that carries the journal article,
such as a pattern of ink. The quality (a specifically dependent continuant)
concretizes the journal article (a generically dependent continuant), and
both depend on that copy of the printed journal (an independent
continuant).</obo:IAO_0000112>
+ <obo:IAO_0000115 xml:lang="en">A relationship between a
specifically dependent continuant and a generically dependent continuant,
in which the generically dependent continuant depends on some independent
continuant in virtue of the fact that the specifically dependent continuant
also depends on that same independent continuant. Multiple specifically
dependent continuants can concretize the same generically dependent
continuant.</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">An investigator reads a protocol
and forms a plan to carry out an assay. The plan is a realizable entity (a
specifically dependent continuant) that concretizes the protocol (a
generically dependent continuant), and both depend on the investigator (an
independent continuant). The plan is then realized by the assay (a
process).</obo:IAO_0000112>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000031"/>
+ <owl:inverseOf
rdf:resource="http://purl.obolibrary.org/obo/RO_0000058"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0000081">
+ <rdfs:label xml:lang="en">role of</rdfs:label>
+ <obo:IAO_0000118 xml:lang="en">is role of</obo:IAO_0000118>
+ <obo:IAO_0000118 xml:lang="en">role_of</obo:IAO_0000118>
+ <rdfs:subPropertyOf rdf:resource="&obo;RO_0000052"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0000086">
+ <rdfs:label xml:lang="en">has quality</rdfs:label>
+ <rdfs:range rdf:resource="&obo;BFO_0000019"/>
+ <rdfs:subPropertyOf rdf:resource="&obo;RO_0000053"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0000087">
+ <rdfs:label xml:lang="en">has role</rdfs:label>
+ <obo:IAO_0000118 xml:lang="en">has_role</obo:IAO_0000118>
+ <rdfs:range rdf:resource="&obo;BFO_0000023"/>
+ <rdfs:subPropertyOf rdf:resource="&obo;RO_0000053"/>
+ <owl:inverseOf rdf:resource="&obo;RO_0000081"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0001000">
+ <rdfs:label xml:lang="en">derives from</rdfs:label>
+ <obo:IAO_0000114 rdf:resource="&obo;IAO_0000125"/>
+ <rdfs:subPropertyOf rdf:resource="&owl;topObjectProperty"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0001001">
+ <rdfs:label xml:lang="en">derives into</rdfs:label>
+ <obo:IAO_0000114 rdf:resource="&obo;IAO_0000125"/>
+ <rdfs:subPropertyOf rdf:resource="&owl;topObjectProperty"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0001015">
+ <rdf:type rdf:resource="&owl;TransitiveProperty"/>
+ <rdfs:label xml:lang="en">location of</rdfs:label>
+ <obo:IAO_0000111 xml:lang="en">is location of</obo:IAO_0000111>
+ <obo:IAO_0000118 xml:lang="en">location_of</obo:IAO_0000118>
+ <obo:RO_0001900 rdf:resource="&obo;RO_0001901"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0001018">
+ <rdfs:label xml:lang="en">contained in</rdfs:label>
+ <obo:IAO_0000116>Containment is location not involving parthood,
and arises only where some immaterial continuant is
involved.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">Containment obtains in each case
between material and immaterial continuants, for instance: lung
contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence
containment is not a transitive relation. If c part_of c1 at t then we
have also, by our definition and by the axioms of mereology applied to
spatial regions, c located_in c1 at t. Thus, many examples of
instance-level location relations for continuants are in fact cases of
instance-level parthood. For material continuants location and parthood
coincide. Containment is location not involving parthood, and arises only
where some immaterial continuant is involved. To understand this relation,
we first define overlap for continuants as follows: c1 overlap c2 at t
=def for some c, c part_of c1 at t and c part_of c2 at t. The containment
relation on the instance level can then be defined (see
definition):</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">Intended meaning:
+domain: material entity
+range: spatial region or site (immaterial continuant)
+ </obo:IAO_0000116>
+ <obo:IAO_0000111 xml:lang="en">contained in</obo:IAO_0000111>
+ <obo:IAO_0000118 xml:lang="en">contained_in</obo:IAO_0000118>
+ <owl:inverseOf rdf:resource="&obo;RO_0001019"/>
+ <obo:RO_0001900 rdf:resource="&obo;RO_0001901"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0001019">
+ <rdfs:label xml:lang="en">contains</rdfs:label>
+ <obo:IAO_0000111 xml:lang="en">contains</obo:IAO_0000111>
+ <obo:RO_0001900 rdf:resource="&obo;RO_0001901"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0001025">
+ <rdf:type rdf:resource="&owl;TransitiveProperty"/>
+ <rdfs:label xml:lang="en">located in</rdfs:label>
+ <obo:IAO_0000116 xml:lang="en">Location as a relation between
instances: The primitive instance-level relation c located_in r at t
reflects the fact that each continuant is at any given time associated with
exactly one spatial region, namely its exact location. Following we can use
this relation to define a further instance-level location relation - not
between a continuant and the region which it exactly occupies, but rather
between one continuant and another. c is located in c1, in this sense,
whenever the spatial region occupied by c is part_of the spatial region
occupied by c1. Note that this relation comprehends both the relation of
exact location between one continuant and another which obtains when r and
r1 are identical (for example, when a portion of fluid exactly fills a
cavity), as well as those sorts of inexact location relations which obtain,
for example, between brain and head or between ovum and
uterus</obo:IAO_0000116>
+
<dc:source>http://www.obofoundry.org/ro/#OBO_REL:located_in</dc:source>
+ <obo:IAO_0000111 xml:lang="en">located in</obo:IAO_0000111>
+ <obo:IAO_0000118 xml:lang="en">located_in</obo:IAO_0000118>
+ <owl:inverseOf rdf:resource="&obo;RO_0001015"/>
+ <obo:RO_0001900 rdf:resource="&obo;RO_0001901"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0002000">
+ <rdfs:label xml:lang="en">boundary of</rdfs:label>
+ <obo:IAO_0000115 rdf:datatype="&xsd;string">The relationships
between a boundary (a 2D immaterial entity) and the material entity that it
delimits.</obo:IAO_0000115>
+ <obo:RO_0001900 rdf:resource="&obo;RO_0001901"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0002002">
+ <rdfs:label xml:lang="en">has boundary</rdfs:label>
+ <obo:IAO_0000115 rdf:datatype="&xsd;string">The relationship
between a material entity and the boundary (2D immaterial entity) that
delimits it.</obo:IAO_0000115>
+ <obo:RO_0001900 rdf:resource="&obo;RO_0001901"/>
+ <owl:inverseOf rdf:resource="&obo;RO_0002000"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0002350">
+ <rdfs:label xml:lang="en">member of</rdfs:label>
+ <obo:IAO_0000118>is member of</obo:IAO_0000118>
+ <obo:IAO_0000118>member part of</obo:IAO_0000118>
+ <obo:IAO_0000119>SIO</obo:IAO_0000119>
+ <obo:IAO_0000112>An organism that is a member of a population of
organisms</obo:IAO_0000112>
+ <obo:IAO_0000115>is member of is a mereological relation between a
item and a collection.</obo:IAO_0000115>
+ <rdfs:subPropertyOf rdf:resource="&obo;BFO_0000050"/>
+ <obo:RO_0001900 rdf:resource="&obo;RO_0001901"/>
+ <owl:inverseOf rdf:resource="&obo;RO_0002351"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty rdf:about="&obo;RO_0002351">
+ <rdf:type rdf:resource="&owl;IrreflexiveProperty"/>
+ <rdfs:label xml:lang="en">has member</rdfs:label>
+ <obo:IAO_0000119>SIO</obo:IAO_0000119>
+ <obo:IAO_0000115>has member is a mereological relation between a
collection and an item.</obo:IAO_0000115>
+ <rdfs:subPropertyOf rdf:resource="&obo;BFO_0000051"/>
+ <obo:RO_0001900 rdf:resource="&obo;RO_0001901"/>
+ </owl:ObjectProperty>
+</rdf:RDF>
+
+
+
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/externalByHand.owl Sat Jan 3
07:23:58 2015 UTC
@@ -0,0 +1,94 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/"
+ xml:base="http://purl.obolibrary.org/obo/"
+ xmlns:dc="http://purl.org/dc/elements/1.1/"
+ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
+ xmlns:obo="http://purl.obolibrary.org/obo/"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:swrl="http://www.w3.org/2003/11/swrl#"
+ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
+ 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#">
+ <owl:Ontology
rdf:about="http://purl.obolibrary.org/obo/iao/dev/externalByHand.owl"/>
+
+
+ 
+
+
+
+
+ 
+
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000293">
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000299">
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000312">
+ <rdfs:range
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011"/>
+
+
+
+</rdf:RDF>
+
+
+
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/iao-main.owl Sat Jan 3 07:23:58
2015 UTC
@@ -0,0 +1,2645 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/iao/dev/iao-main.owl#"
+ xml:base="http://purl.obolibrary.org/obo/iao/dev/iao-main.owl"
+ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
+ xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
+ xmlns:obo="http://purl.obolibrary.org/obo/"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:swrl="http://www.w3.org/2003/11/swrl#"
+ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
+ 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/dev/iao-main.owl">
+ <protege:defaultLanguage
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
+ <rdfs:comment xml:lang="en">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:seeAlso
rdf:resource="http://code.google.com/p/information-artifact-ontology/"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/bfo/2014-05-03/classes-only.owl"/>
+ <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/core.owl"/>
+ <owl:imports
rdf:resource="http://protege.stanford.edu/plugins/owl/dc/protege-dc.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/import-OBO.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/externalByHand.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl"/>
+ </owl:Ontology>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://protege.stanford.edu/plugins/owl/protege#defaultLanguage"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
+ <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000113">
+ <rdfs:label xml:lang="en">in branch</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000114">
+ <rdfs:label xml:lang="en">has curation status</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000115">
+ <rdfs:label xml:lang="en">definition</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000116">
+ <rdfs:label xml:lang="en">editor note</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000117">
+ <rdfs:label xml:lang="en">term editor</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000118">
+ <rdfs:label xml:lang="en">alternative term</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000119">
+ <rdfs:label xml:lang="en">definition source</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000231">
+ <rdfs:label xml:lang="en">has obsolescence reason</rdfs:label>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
+ <rdfs:label xml:lang="en">imported from</rdfs:label>
+ </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://www.w3.org/2000/01/rdf-schema#comment"/>
+
+
+
+ 
+
+ <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:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>
+
+
+
+ 
+
+ <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_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_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_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"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000299"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/RO_0000053"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/RO_0000058"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/RO_0000059"/>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:DatatypeProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000004">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
+ <rdfs:label xml:lang="en">has measurement value</rdfs:label>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000032"/>
+ <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+ </owl:DatatypeProperty>
+
+
+
+ 
+
+ <owl:DatatypeProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000404">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
+ <rdfs:label xml:lang="en">has x coordinate value</rdfs:label>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
+ <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+ </owl:DatatypeProperty>
+
+
+
+ 
+
+ <owl:DatatypeProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000405">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
+ <rdfs:label xml:lang="en">has z coordinate value</rdfs:label>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
+ <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+ </owl:DatatypeProperty>
+
+
+
+ 
+
+ <owl:DatatypeProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000406">
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>
+ <rdfs:label xml:lang="en">has y coordinate value</rdfs:label>
+ <rdfs:domain
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
+ <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#float"/>
+ </owl:DatatypeProperty>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000001"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000009"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000018"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000023"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000026"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000028"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/GAZ_00000448"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000001">
+ <rdfs:label xml:lang="en">conditional specification</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
+ <obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000349</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess
Branch</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">a directive information entity that
specifies what should happen if the trigger condition is
fulfilled</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">conditional
specification</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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
+Cristian Cocos, and subsequently moved to IAO where the objective for
+which the original term was defined was satisfied with the definition
+of this, different, term.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">2009-03-16: review of this term
done during during the OBI workshop winter 2009 and the current definition
was considered acceptable for use in OBI. If there is a need to modify this
definition please notify OBI.</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">A measurement unit label is as a
label that is part of a scalar measurement datum and denotes a unit of
measure.</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">Examples of measurement unit labels
are liters, inches, weight per volume.</obo:IAO_0000112>
+ <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">measurement unit
label</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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">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."</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">Answers the question, why did you
do this experiment?</obo:IAO_0000116>
+ <obo:IAO_0000112 xml:lang="en">In the protocol of a ChIP assay the
objective specification says to identify protein and DNA
interaction.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI Plan and Planned Process/Roles
Branch</obo:IAO_0000119>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000217</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Barry
Smith</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Bjoern
Peters</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Jennifer
Fostel</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
+ <obo:IAO_0000118 xml:lang="en">goal specification</obo:IAO_0000118>
+ <obo:IAO_0000111 xml:lang="en">objective
specification</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000006">
+ <rdfs:label xml:lang="en">narrative object</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+ <obo:IAO_0000116 xml:lang="en">2009-08-10 Alan Ruttenberg: Larry
Hunter suggests that this be obsoleted and replaced by 'textual
entity' and 'figure'. Alan restored as there are OBI
dependencies and this merits further discussion</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">A narrative object is an
information content entity that is a set of propositions.</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">Examples of narrative objects are
reports, journal articles, and patents submission.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000013</obo:IAO_0000119>
+ <obo:IAO_0000116 xml:lang="en">agree - DENRIE. Issue(alan) do we
only mean text? What about a story told by mime. Does music count? (no)
what about an oral report. Regarding definition, saying it is a set of
propositions means we loose the idea that wording matters. Maybe adjust
saying a narrative object has some relationshop to a set of
propositions</obo:IAO_0000116>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">narrative object</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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>
+ <obo:IAO_0000112 xml:lang="en">Pour the contents of flask 1 into
flask 2</obo:IAO_0000112>
+ <obo:IAO_0000115 xml:lang="en">a directive information entity that
describes an action the bearer will take</obo:IAO_0000115>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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 'label' to 'datum label' to convey that this class
is not intended to cover all kinds of labels (stickers, radiolabels, etc.),
and not even all kind of textual labels, but rather the kind of labels
occuring in a datum.
+</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>
+ <obo:IAO_0000116
xml:lang="en">http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n</obo:IAO_0000116>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000010">
+ <rdfs:label xml:lang="en">software</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
+ <obo:IAO_0000119 xml:lang="en">GROUP: OBI</obo:IAO_0000119>
+ <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
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Melanie
Courtot</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">Software is a plan specification
composed of a series of instructions that can be
+interpreted by or directly executed by a processing unit.</obo:IAO_0000115>
+ <obo:IAO_0000116 xml:lang="en">see sourceforge tracker discussion
at
http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178</obo:IAO_0000116>
+ <obo:IAO_0000111 xml:lang="en">software</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000013">
+ <rdfs:label xml:lang="en">journal article</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000088"/>
+ <obo:IAO_0000112 xml:lang="en">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.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000159</obo:IAO_0000119>
+ <obo:IAO_0000115 xml:lang="en">a report that is published in a
journal</obo:IAO_0000115>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">journal article</obo:IAO_0000111>
+ <obo:IAO_0000117 xml:lang="en">person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000015">
+ <rdfs:label xml:lang="en">information carrier</rdfs:label>
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:intersectionOf rdf:parseType="Collection">
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/BFO_0000019"/>
+ <owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+ </owl:Restriction>
+ </owl:intersectionOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ <obo:IAO_0000116 xml:lang="en">12/15/09: There is a concern that
some ways that carry information may be processes rather than qualities,
such as in a 'delayed wave carrier'.</obo:IAO_0000116>
+ <obo:IAO_0000116>2014-03-10: We are not certain that all
information carriers are qualities. There was a discussion of dropping
it.</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">A quality of an information bearer
that imparts the information content</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">In the case of a printed paperback
novel the physicality of the ink and of the paper form part of the
information bearer. The qualities of appearing black and having a certain
pattern for the ink and appearing white for the paper form part of the
information carrier in this case.</obo:IAO_0000112>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000119 xml:lang="en">Smith, Ceusters, Ruttenberg, 2000
years of philosophy</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">information
carrier</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000017">
+ <rdfs:label xml:lang="en">model number</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000028"/>
+ <obo:IAO_0000115 xml:lang="en">A model number is an information
content entity specifically borne by catalogs, design specifications,
advertising materials, inventory systems and similar that is about
manufactured objects of the same class. The model number is an alternative
term for the class. The manufactered objects may or may not also bear the
model number. Model numbers can be encoded in a variety of other
information objects, such as bar codes, numerals, or patterns of
dots.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">Person: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000116 xml:lang="en">manufactered items may have more
than one model number, sometimes by rebranding, or because companies are
sold and the products issued new model numbers</obo:IAO_0000116>
+ <obo:IAO_0000111 xml:lang="en">model number</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000025">
+ <rdfs:label xml:lang="en">programming language</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
+ <obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000058</obo:IAO_0000119>
+ <obo:IAO_0000112 xml:lang="en">R, Perl, Java</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">programming
language</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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>2014-03-31: See discussion at
http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/</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>
+ <obo:IAO_0000116 xml:lang="en">2009-03-16: removed datum as
alternative term as datum specifically refers to singular form, and is thus
not an exact synonym.</obo:IAO_0000116>
+ <obo:IAO_0000112 xml:lang="en">Data items include counts of
things, analyte concentrations, and statistical summaries.</obo:IAO_0000112>
+ <obo:IAO_0000116 xml:lang="en">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</obo:IAO_0000116>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Jonathan
Rees</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">a data item is 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.</obo:IAO_0000115>
+ <obo:IAO_0000118 xml:lang="en">data</obo:IAO_0000118>
+ <obo:IAO_0000111 xml:lang="en">data item</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000028">
+ <rdfs:label xml:lang="en">symbol</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+ <obo:IAO_0000116 xml:lang="en">20091104, MC: this needs work and
will most probably change</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">2014-03-31: We would like to have a
deeper analysis of 'mark' and 'sign' in the future (see
https://code.google.com/p/information-artifact-ontology/issues/detail?id=154).</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">An information content entity that
is a mark(s) or character(s) used as a conventional representation of
another entity.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON: James A.
Overton</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Jonathan
Rees</obo:IAO_0000117>
+ <obo:IAO_0000112 xml:lang="en">a serial number such as
"12324X"</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">a stop sign</obo:IAO_0000112>
+ <obo:IAO_0000112 xml:lang="en">a written proper name such as
"OBI"</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">based on Oxford English
Dictionary</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">symbol</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000029">
+ <rdfs:label xml:lang="en">numeral</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000028"/>
+ <obo:IAO_0000115 xml:lang="en">A symbol that denotes a
number.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Jonathan
Rees</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">numeral</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000001"/>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <obo:IAO_0000116 xml:lang="en">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).</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">A generically dependent continuant
that is about some thing.</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">Examples of information content
entites include journal articles, data, graphical layouts, and
graphs.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000142</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">information content
entity</obo:IAO_0000111>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000031">
+ <rdfs:label xml:lang="en">integer numeral</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000029"/>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Jonathan
Rees</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">a numeral that denotes an
integer</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">integer numeral</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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"/>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000039"/>
+ <owl:minCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minCardinality>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000004"/>
+ <owl:minCardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minCardinality>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <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
+this case we explicitly refer to the singular form</obo:IAO_0000116>
+ <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_0000116 xml:lang="en">Would write this as: has_part some
'measurement unit label' and has_part some numeral and has_part
exactly 2, except for the fact that this won't let us take advantage
of OWL reasoning over the numbers. Instead use has measurment value
property to represent the same. Use has measurement unit label (subproperty
of has_part) so we can easily say that there is only one of
them.</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">a scalar measurement datum is a
measurement datum that is composed of two parts, numerals and a unit
label.</obo:IAO_0000115>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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"/>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000136"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000017"/>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
+ <obo:IAO_0000116 xml:lang="en">8/6/2009 Alan Ruttenberg: Changed
label from "information entity about a realizable" 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>
+ <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_0000116 xml:lang="en">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</obo:IAO_0000116>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000034">
+ <rdfs:label xml:lang="en">time trigger</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000001"/>
+ <obo:IAO_0000119 xml:lang="en">OBI branch derived</obo:IAO_0000119>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000331</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess
Branch</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">revisit?</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">time trigger</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000124"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000037">
+ <rdfs:label xml:lang="en">dot plot</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
+ <obo:IAO_0000115 xml:lang="en">A dot plot is a report graph which
is a graphical representation of data where each data point is represented
by a single dot placed on coordinates corresponding to data point values in
particular dimensions.</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">Dot plot of SSC-H and
FSC-H.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000123</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">dot plot</obo:IAO_0000111>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">person:Allyson
Lister</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000002"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000038">
+ <rdfs:label xml:lang="en">graph</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000309"/>
+ <obo:IAO_0000115 xml:lang="en">A diagram that presents one or more
tuples of information by mapping those tuples in to a two dimensional space
in a non arbitrary way.</obo:IAO_0000115>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000240</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Lawrence
Hunter</obo:IAO_0000117>
+ <obo:IAO_0000111 xml:lang="en">graph</obo:IAO_0000111>
+ <obo:IAO_0000119 xml:lang="en">group:OBI</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">person:Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Allyson
Lister</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000055">
+ <rdfs:label xml:lang="en">rule</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000001"/>
+ <obo:IAO_0000116 xml:lang="en">MSI</obo:IAO_0000116>
+ <obo:IAO_0000119 xml:lang="en">OBI_0500021</obo:IAO_0000119>
+ <obo:IAO_0000119 xml:lang="en">PRS</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PRS</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">a rule is an executable which
guides, defines, restricts actions</obo:IAO_0000115>
+ <obo:IAO_0000112 xml:lang="en">example to be
added</obo:IAO_0000112>
+ <obo:IAO_0000111 xml:lang="en">rule</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000057">
+ <rdfs:label xml:lang="en">contour plot</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000038"/>
+ <obo:IAO_0000112 xml:lang="en">Contour plot of SSC-H, FSC-H, and
FL1-H.</obo:IAO_0000112>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000246</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">contour plot</obo:IAO_0000111>
+ <obo:IAO_0000116
xml:lang="en">generically_dependent_continuants</obo:IAO_0000116>
+ <obo:IAO_0000119 xml:lang="en">group:Flow Cytometry
community</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">person:Allyson
Lister</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">person:Chris
Stoeckert</obo:IAO_0000117>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000002"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000064">
+ <rdfs:label xml:lang="en">algorithm</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
+ <obo:IAO_0000115 xml:lang="en">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.</obo:IAO_0000115>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000270</obo:IAO_0000119>
+ <obo:IAO_0000112 xml:lang="en">PMID: 18378114.Genomics. 2008 Mar
28. LINKGEN: A new algorithm to process data in genetic linkage
studies.</obo:IAO_0000112>
+ <obo:IAO_0000117 xml:lang="en">Philippe
Rocca-Serra</obo:IAO_0000117>
+ <obo:IAO_0000117 xml:lang="en">PlanAndPlannedProcess
Branch</obo:IAO_0000117>
+ <obo:IAO_0000119 xml:lang="en">adapted from discussion on OBI list
(Matthew Pocock, Christian Cocos, Alan Ruttenberg)</obo:IAO_0000119>
+ <obo:IAO_0000111 xml:lang="en">algorithm</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
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=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/import-OBO.owl Sat Jan 3 07:23:58
2015 UTC
@@ -0,0 +1,373 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/iao/dev/import-OBO.owl#"
+ xml:base="http://purl.obolibrary.org/obo/iao/dev/import-OBO.owl"
+ xmlns:obo="http://purl.obolibrary.org/obo/"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ 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#">
+ <owl:Ontology
rdf:about="http://purl.obolibrary.org/obo/iao/dev/import-OBO.owl"/>
+
+
+
+ 
+
+ <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_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 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_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_0000111 xml:lang="en">definition</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </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"/>
+ </owl:AnnotationProperty>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000412">
+ <rdfs:label xml:lang="en">imported from</rdfs:label>
+ </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_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"/>
+ </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"/>
+ </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"/>
+ </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 of usage</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:AnnotationProperty>
+
+
+
+ 
+
+
+
+
+ 
+
+
+
+
+ 
+
+ <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:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000299">
+ <rdfs:label xml:lang="en">has_specified_output</rdfs:label>
+ <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
Courtot</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">A relation between a planned
process and a continuant participating in that process. The presence of the
continuant at the end of the process is explicitly specified in the
objective specification which the process realizes the concretization
of.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">PERSON: Alan
Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000111
xml:lang="en">has_specified_output</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <owl:inverseOf
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000312"/>
+ <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>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/OBI_0000312">
+ <rdfs:label xml:lang="en">is_specified_output_of</rdfs:label>
+ <obo:IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Bjoern
Peters</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">A relation between a planned
process and a continuant participating in that process. The presence of the
continuant at the end of the process is explicitly specified in the
objective specification which the process realizes the concretization
of.</obo:IAO_0000115>
+ <obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
+ <obo:IAO_0000111
xml:lang="en">is_specified_output_of</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdfs:subPropertyOf
rdf:resource="http://purl.obolibrary.org/obo/RO_0000056"/>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+ </owl:ObjectProperty>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/RO_0000056"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/RO_0000057"/>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000015"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000019"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000029"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/GAZ_00000448">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">geographic
location</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000029"/>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A reference to a
place on the Earth, by its name or by its geographical
location.</obo:IAO_0000115>
+ <obo:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">geographic
location</obo:IAO_0000111>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000003"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000104"/>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000011">
+ <rdfs:label xml:lang="en">planned process</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
+ <obo:IAO_0000115 xml:lang="en">A processual entity that realizes a
plan which is the concretization of a plan specification.</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">planned process</obo:IAO_0000111>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000066">
+ <rdfs:label xml:lang="en">investigation</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+ <obo:IAO_0000115 xml:lang="en">a planned process that consists of
parts: planning, study design execution, documentation and which produce
conclusion(s).</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">investigation</obo:IAO_0000111>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000471">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study design
execution</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a planned process
that realizes the concretization of a study design</obo:IAO_0000115>
+ <obo:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">study design
execution</obo:IAO_0000111>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0500000">
+ <rdfs:label xml:lang="en">study design</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000104"/>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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.</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">study design</obo:IAO_0000111>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000122">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">length</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A 1-D extent quality
which is equal to the distance between two points.</obo:IAO_0000115>
+ <obo:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">length</obo:IAO_0000111>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/PATO_0000125">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000019"/>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A physical quality
that inheres in a bearer by virtue of the proportion of the bearer's
amount of matter.</obo:IAO_0000115>
+ <obo:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass</obo:IAO_0000111>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/pato.owl"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000001">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">length
unit</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A unit which is a
standard measure of the distance between two points.</obo:IAO_0000115>
+ <obo:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">length
unit</obo:IAO_0000111>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/uo.owl"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000002">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass
unit</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A unit which is a
standard measure of the amount of matter/energy of a physical
object.</obo:IAO_0000115>
+ <obo:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mass
unit</obo:IAO_0000111>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/uo.owl"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/UO_0000003">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">time
unit</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000003"/>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A unit which is a
standard measure of the dimension in which events occur in
sequence.</obo:IAO_0000115>
+ <obo:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">time
unit</obo:IAO_0000111>
+ <obo:IAO_0000412
rdf:resource="http://purl.obolibrary.org/obo/uo.owl"/>
+ </owl:Class>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:NamedIndividual
rdf:about="http://purl.obolibrary.org/obo/GAZ_00000448">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">geographic
location</rdfs:label>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A reference to a
place on the Earth, by its name or by its geographical
location.</obo:IAO_0000115>
+ <obo:IAO_0000111
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">geographic
location</obo:IAO_0000111>
+ </owl:NamedIndividual>
+
+
+
+ 
+
+ <owl:NamedIndividual
rdf:about="http://purl.obolibrary.org/obo/IAO_0000122">
+ <rdfs:label xml:lang="en">ready for release</rdfs:label>
+ </owl:NamedIndividual>
+</rdf:RDF>
+
+
+
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/obsolete.owl Sat Jan 3 07:23:58
2015 UTC
@@ -0,0 +1,474 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://purl.obolibrary.org/obo/"
+ xml:base="http://purl.obolibrary.org/obo/"
+ 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: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#">
+ <owl:Ontology
rdf:about="http://purl.obolibrary.org/obo/iao/dev/obsolete.owl">
+ <protege:defaultLanguage
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
+ <rdfs:comment
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete classes
from the information artifact ontology. see
http://code.google.com/p/information-artifact-ontology/</rdfs:comment>
+ <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://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl"/>
+ </owl:Ontology>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000115"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000116"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000113"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000114"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000117"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000118"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000231"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000111"/>
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000112"/>
+
+
+
+ 
+
+
+
+
+ 
+
+
+
+
+ 
+
+ <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>
+ <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</IAO_0000116>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan
Ruttenberg</IAO_0000117>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smith, Ceusters,
Ruttenberg, 2000 years of philosophy</IAO_0000119>
+ <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</IAO_0000112>
+ <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.</IAO_0000115>
+ <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</IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <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_0000220">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_materially
denotes</rdfs:label>
+ <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</IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <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_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>
+ <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>
+ <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://www.geneontology.org/formats/oboInOwl#ObsoleteProperty"/>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000008">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_artifact</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000012">
+ <rdfs:label xml:lang="en">obsolete2_digital entity</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000261</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">3/22/2009 Alan Ruttenberg, obsoleted
per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
+
+Superclass was 'digitial quality'</IAO_0000116>
+ <IAO_0000115 xml:lang="en">A digital entity is an information
entity which is a collection of bits that can be interpreted by a computer.
Two digital entities are the same if they are bitwise
identical.</IAO_0000115>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000111 xml:lang="en">obsolete_digital entity</IAO_0000111>
+ <IAO_0000117 xml:lang="en">person:Chris Stoeckert</IAO_0000117>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000018">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_material_entity</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000226"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000019">
+ <rdfs:label xml:lang="en">obsolete2_binary digital
entity</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000244</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">3/22/2009 Alan Ruttenberg, obsoleted
per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
+Superclass was 'digital entity'</IAO_0000116>
+ <IAO_0000115 xml:lang="en">A binary digital entity is a digital
entity that is encoded in a way that is not easily human readable and that
contains other than text characters.</IAO_0000115>
+ <IAO_0000112 xml:lang="en">MS Word document, ZIP file, DICOM file,
JPEG file</IAO_0000112>
+ <IAO_0000111 xml:lang="en">binary digital entity</IAO_0000111>
+ <IAO_0000116 xml:lang="en">digital_entity</IAO_0000116>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">person:Chris Stoeckert</IAO_0000117>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000024">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_unit of
measure</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan
Ruttenberg</IAO_0000117>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Smith, Ceusters,
Ruttenberg, 2000 years of philosophy</IAO_0000119>
+ <IAO_0000112
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The length of a
ruler.</IAO_0000112>
+ <IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a unit of measure is
the quality of some material entity compared to which another quality is
some multiple of.</IAO_0000115>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000035">
+ <rdfs:label xml:lang="en">obsolete_study
interpretation</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-03-16:
definition was "A conclusion is a narrative object which can be
published in a paper summerizing and interpreting a protocol
application."</IAO_0000116>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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.</IAO_0000116>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000005</IAO_0000119>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Alan
Ruttenberg</IAO_0000117>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie
Courtot</IAO_0000117>
+ <IAO_0000118
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">conclusion</IAO_0000118>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000115 xml:lang="en">A study interpretation is a textual
entity about the implications of a study result. Examples include
discussion of whether a hypothesis is false, whether the study failed to
address the hypothesis, and whether the study results have led to new
hypotheses</IAO_0000115>
+ <IAO_0000117 xml:lang="en">Lawrence Hunter</IAO_0000117>
+ <IAO_0000117 xml:lang="en">PERSON: Jennifer Fostel</IAO_0000117>
+ <IAO_0000116 xml:lang="en">The obsoleting of narrative object
required a modest change in the definition of this term. Circularity with
"interpretation... interprets" has been removed, using
"about the implications" instead.</IAO_0000116>
+ <IAO_0000111 xml:lang="en">obsolete_study
interpretation</IAO_0000111>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000047">
+ <rdfs:label xml:lang="en">obsolete2_text based digital
entity</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000132</IAO_0000119>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">group:OBI</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">3/22/2009 Alan Ruttenberg, obsoleted
per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
+superclass was 'digital document'</IAO_0000116>
+ <IAO_0000115 xml:lang="en">A text based digital entity is a
digital entity that is encoded so that it only contains text
characters.</IAO_0000115>
+ <IAO_0000112 xml:lang="en">XML file, C++ source code
file</IAO_0000112>
+ <IAO_0000116 xml:lang="en">digital_entity</IAO_0000116>
+ <IAO_0000117 xml:lang="en">person:Chris Stoeckert</IAO_0000117>
+ <IAO_0000111 xml:lang="en">text based digital entity</IAO_0000111>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000059">
+ <rdfs:label xml:lang="en">obsolete2_report figure</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000027</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000115 xml:lang="en">A report figure is a report display
element that has some aspect of illustration, but may be a composite of
figures, images, and other elements</IAO_0000115>
+ <IAO_0000116 xml:lang="en">I prepended the 'report ' to
make it clear that we mean parts of reports here. We may want a more
generic version of 'figure', in which case this would become a
defined class - figure and part_of some report</IAO_0000116>
+ <IAO_0000116 xml:lang="en">Replaced by defined version of
figure</IAO_0000116>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">person:Alan Ruttenberg</IAO_0000117>
+ <IAO_0000117 xml:lang="en">person:Allyson Lister</IAO_0000117>
+ <IAO_0000111 xml:lang="en">report figure</IAO_0000111>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000124"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000091">
+ <rdfs:label xml:lang="en">obsolete_report element</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-03-16: needs
some more work (clarify relations).</IAO_0000116>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-03-16: was
report display element with definition: A report display element is a
narrative object that is part of a report. Report display elements are set
off from the textual parts of a report and are typically given a label(e.g.
Figure 2) which is used to refer to the element from the text. Typically
the 2d layout is part of the identity of such elements.</IAO_0000116>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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.</IAO_0000116>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-08-10 Alan
Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by
'textual entity' and 'figure'. Alan restored as there
are OBI dependencies and this merits further discussion</IAO_0000116>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000001</IAO_0000119>
+ <IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON: Melanie
Courtot</IAO_0000117>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Replaced by textual
entity and figure</IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000115 xml:lang="en">A report element is a narrative object
in which information is presented and consumed by a human being, and is
part of a report. Examples of report elements are figure (dot plot), table,
text portion (may include a movie or audio clip on a web
page).</IAO_0000115>
+ <IAO_0000119 xml:lang="en">GROUP:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">PERSON: Alan Ruttenberg</IAO_0000117>
+ <IAO_0000117 xml:lang="en">PERSON: Allyson Lister</IAO_0000117>
+ <IAO_0000116 xml:lang="en">There will be some issue here about
whether these are defined classes. As intended these are meant to denote
the parts of the report that are not textual but are typically boxed and
set within the text, labelled with some identifier, and referred to in the
text</IAO_0000116>
+ <IAO_0000111 xml:lang="en">report element</IAO_0000111>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000093">
+ <rdfs:label xml:lang="en">obsolete2_binary executable</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000222</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">3/22/2009 Alan Ruttenberg, obsoleted
per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
+superclass was 'digital entity'</IAO_0000116>
+ <IAO_0000115 xml:lang="en">Binary executable is a digital entity
consisting of the binary representation of machine instructions of a
specific processor or they may be binary pseudocode for a virtual machine.
A non-source executable file is also called an object program. It is
assumed that the binary executable file contains properly-formatted
computer instructions. (derived from Wikipedia, Nov 1, 2007)</IAO_0000115>
+ <IAO_0000111 xml:lang="en">binary executable</IAO_0000111>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">person:Jennifer Fostel</IAO_0000117>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000097">
+ <rdfs:label xml:lang="en">obsolete_report table</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2009-08-10 Alan
Ruttenberg: Larry Hunter suggests that this be obsoleted and replaced by
'textual entity table'. Alan restored as there are OBI
dependencies and this merits further discussion</IAO_0000116>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000265</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000115 xml:lang="en">A report table is a report display
element consisting of a matrix of cells layed out in a grid, some set of
which are filled with some information content</IAO_0000115>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">person:Alan Ruttenberg</IAO_0000117>
+ <IAO_0000117 xml:lang="en">person:Allyson Lister</IAO_0000117>
+ <IAO_0000111 xml:lang="en">report table</IAO_0000111>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000002"/>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000105">
+ <rdfs:label xml:lang="en">obsolete2_digital document</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000119
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">OBI_0000195</IAO_0000119>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">3/22/2009 Alan Ruttenberg, obsoleted
per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4
+superclass was 'digial entity'</IAO_0000116>
+ <IAO_0000115 xml:lang="en">A digital document is a digital entity
consisting of an electronic file which can be rendered into human-readable
form by one or more computational applications. The digital document does
not refer to the information content of the document but to an instance of
the file.</IAO_0000115>
+ <IAO_0000111 xml:lang="en">digital document</IAO_0000111>
+ <IAO_0000119 xml:lang="en">group:OBI</IAO_0000119>
+ <IAO_0000117 xml:lang="en">person:Jennifer Fostel</IAO_0000117>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000128">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_identifier</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">_identifier is a
container under information content entity for collecting types of terms to
indicate a specific instance or clas of what was used or participated in an
investigation. Identifiers are borne by a product or its packaging, and can
be encoded in a variety of other information objects, such as bar codes,
numerals, or patterns of dots.
+
+Note: everybody agreed that identifier is probably a too general term. We
however felt that it would be appropriate to group "identifiying"
terms under some kind of umbrella. We therefore propose to use _identifier
for that purpose. As per OBI conventions, the _ prefixing identifier
indicates that this is a helper class and shouldn't be considered as
final.</IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000121"/>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000226"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000141">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_digital
quality</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Need to rework
digital entity. Digital quality was suggested by Barry.</IAO_0000116>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116>3/22/2009 Alan Ruttenberg, obsoleted per
http://groups.google.com/group/information-ontology/browse_thread/thread/789ad4b7708d5cf4</IAO_0000116>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000182">
+ <rdfs:label xml:lang="en">obsolete_survival curve</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000115 xml:lang="en">A survival curve is a report graph
which is a graphical representation of data where the percentage of
survival is plotted as a function of time.</IAO_0000115>
+ <IAO_0000117 xml:lang="en">PERSON:Chris Stoeckert</IAO_0000117>
+ <IAO_0000117 xml:lang="en">PERSON:James Malone</IAO_0000117>
+ <IAO_0000117 xml:lang="en">PERSON:Melanie Courtot</IAO_0000117>
+ <IAO_0000119 xml:lang="en">WEB:
http://www.graphpad.com/www/book/survive.htm</IAO_0000119>
+ <IAO_0000111 xml:lang="en">obsolete_survival curve</IAO_0000111>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000576">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">obsolete_establishing
a CRID registry</rdfs:label>
+ <rdfs:subClassOf
rdf:resource="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+ <IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">a planned process
with the objective to establish a system that allows to refer to specific
entities of a certain kind and store information about them, by
establishing a CRID registry and plan specifications for the process of 1)
assigning a CRID and 2) looking up a CRID.</IAO_0000115>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116>MC, 20101124: deprecated following discussion at IAO
call 20101124. Term was deemed not necessary - no use case for
now.</IAO_0000116>
+ <IAO_0000231
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#ObsoleteClass"/>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:Thing rdf:about="http://purl.obolibrary.org/obo/IAO_0000103"/>
+
+
+
+ 
+
+ <owl:Thing rdf:about="http://purl.obolibrary.org/obo/IAO_0000226"/>
+
+
+
+ 
+
+ <owl:NamedIndividual
rdf:about="http://purl.obolibrary.org/obo/IAO_0000230">
+ <rdf:type
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000225"/>
+ <rdfs:label xml:lang="en">other</rdfs:label>
+ <owl:deprecated
rdf:datatype="http://www.w3.org/2001/XMLSchema#boolean">true</owl:deprecated>
+ <IAO_0000116 xml:lang="en">This is to be used if none of the
existing instances cover the reason for obsolescence. An editor note should
indicate this new reason.</IAO_0000116>
+ <IAO_0000116 xml:lang="en">We expect to be able to mine these new
reasons and add instances as required.</IAO_0000116>
+ </owl:NamedIndividual>
+</rdf:RDF>
+
+
+
+
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/ontoFox/OntoFox-input.txt Sat Jan 3
07:23:58 2015 UTC
@@ -0,0 +1,138 @@
+[URI of the OWL(RDF/XML) output file]
+http://purl.obolibrary.org/obo/iao/dev/import-OBO.owl
+
+[Source ontology]
+#comment here
+#List of ontologies: OBI, NCBITaxon, MP, PATO, GO, DOID, IDO, CHEBI, SO,
PRO, CL, ENVO, FMA, CARO
+OBI
+
+[Low level source term URIs]
+http://purl.obolibrary.org/obo/OBI_0000011 #planned process
+http://purl.obolibrary.org/obo/OBI_0000066 #investigation
+http://purl.obolibrary.org/obo/OBI_0000471 #study design execution
+http://purl.obolibrary.org/obo/OBI_0500000 #study design
+
+[Top level source term URIs and target direct superclass URIs]
+http://purl.obolibrary.org/obo/OBI_0000011 #planned process
+subClassOf http://purl.obolibrary.org/obo/BFO_0000015 #process
+http://purl.obolibrary.org/obo/OBI_0000066 #investigation
+subClassOf http://purl.obolibrary.org/obo/OBI_0000011
+http://purl.obolibrary.org/obo/OBI_0000471 #study design execution
+subClassOf http://purl.obolibrary.org/obo/OBI_0000011
+http://purl.obolibrary.org/obo/OBI_0500000 #study design
+subClassOf http://purl.obolibrary.org/obo/IAO_0000104
+
+[Source term retrieval setting]
+includeNoIntermediates
+
+[Source annotation URIs]
+http://www.w3.org/2000/01/rdf-schema#label
+copyTo http://purl.obolibrary.org/obo/IAO_0000111
+http://purl.obolibrary.org/obo/IAO_0000115
+
+
+###################################################
+[Source ontology]
+#comment here
+#List of ontologies: OBI, NCBITaxon, MP, PATO, GO, DOID, IDO, CHEBI, SO,
PRO, CL, ENVO, FMA, CARO
+OBI
+
+[Low level source term URIs]
+http://purl.obolibrary.org/obo/OBI_0000293 #has_specified_input
+http://purl.obolibrary.org/obo/OBI_0000299 #has_specified_output
+http://purl.obolibrary.org/obo/OBI_0000312 #is_specified_output_of
+
+[Top level source term URIs and target direct superclass URIs]
+http://purl.obolibrary.org/obo/OBI_0000293 #has_specified_input
+subPropertyOf http://purl.obolibrary.org/obo/RO_0000057 #has participant
+http://purl.obolibrary.org/obo/OBI_0000299 #has_specified_output
+subPropertyOf http://purl.obolibrary.org/obo/RO_0000057 #has participant
+http://purl.obolibrary.org/obo/OBI_0000312 #is_specified_output_of
+subPropertyOf http://purl.obolibrary.org/obo/RO_0000056 #participates in
+
+
+[Source term retrieval setting]
+
+
+[Source annotation URIs]
+includeAllAxioms
+
+
+###################################################
+
+[Source ontology]
+#comment here
+#List of ontologies: OBI, NCBITaxon, MP, PATO, GO, DOID, IDO, CHEBI, SO,
PRO, CL, ENVO, FMA, CARO
+PATO
+
+[Low level source term URIs]
+http://purl.obolibrary.org/obo/PATO_0000122 #length
+http://purl.obolibrary.org/obo/PATO_0000125 #mass
+
+[Top level source term URIs and target direct superclass URIs]
+http://purl.obolibrary.org/obo/PATO_0000122 #length
+subClassOf http://purl.obolibrary.org/obo/BFO_0000019 #quality
+http://purl.obolibrary.org/obo/PATO_0000125 #mass
+subClassOf http://purl.obolibrary.org/obo/BFO_0000019 #quality
+
+[Source term retrieval setting]
+includeNoIntermediates
+
+[Source annotation URIs]
+http://www.w3.org/2000/01/rdf-schema#label
+copyTo http://purl.obolibrary.org/obo/IAO_0000111
+http://purl.obolibrary.org/obo/IAO_0000115
+
+
+###################################################
+
+[Source ontology]
+#comment here
+#List of ontologies: OBI, NCBITaxon, MP, PATO, GO, DOID, IDO, CHEBI, SO,
PRO, CL, ENVO, FMA, CARO
+UO
+
+[Low level source term URIs]
+http://purl.obolibrary.org/obo/UO_0000001 #length unit
+http://purl.obolibrary.org/obo/UO_0000002 #mass unit
+http://purl.obolibrary.org/obo/UO_0000003 #time unit
+
+[Top level source term URIs and target direct superclass URIs]
+http://purl.obolibrary.org/obo/UO_0000001 #length unit
+subClassOf http://purl.obolibrary.org/obo/IAO_0000003
+http://purl.obolibrary.org/obo/UO_0000002 #mass unit
+subClassOf http://purl.obolibrary.org/obo/IAO_0000003
+http://purl.obolibrary.org/obo/UO_0000003 #time unit
+subClassOf http://purl.obolibrary.org/obo/IAO_0000003
+
+[Source term retrieval setting]
+includeNoIntermediates
+
+[Source annotation URIs]
+http://www.w3.org/2000/01/rdf-schema#label
+copyTo http://purl.obolibrary.org/obo/IAO_0000111
+http://purl.obolibrary.org/obo/IAO_0000115
+
+
+
+###################################################
+
+[Source ontology]
+#comment here
+#List of ontologies: OBI, NCBITaxon, MP, PATO, GO, DOID, IDO, CHEBI, SO,
PRO, CL, ENVO, FMA, CARO
+GAZ
+
+[Low level source term URIs]
+http://purl.obolibrary.org/obo/GAZ_00000448 #geographical location
+
+[Top level source term URIs and target direct superclass URIs]
+http://purl.obolibrary.org/obo/GAZ_00000448 #geographical location
+subClassOf http://purl.obolibrary.org/obo/BFO_0000029 #site
+
+[Source term retrieval setting]
+includeNoIntermediates
+
+[Source annotation URIs]
+http://www.w3.org/2000/01/rdf-schema#label
+copyTo http://purl.obolibrary.org/obo/IAO_0000111
+http://purl.obolibrary.org/obo/IAO_0000115
+
=======================================
--- /dev/null
+++ /branches/2015-01-02/ontology-BFO2/ontology-metadata.owl Sat Jan 3
07:23:58 2015 UTC
@@ -0,0 +1,840 @@
+<?xml version="1.0"?>
+<rdf:RDF
xmlns="http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl#"
+
xml:base="http://purl.obolibrary.org/obo/iao/dev/ontology-metadata.owl"
+ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
+ xmlns:xsp="http://www.owl-ontologies.com/2005/08/07/xsp.owl#"
+ xmlns:obo="http://purl.obolibrary.org/obo/"
+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+ xmlns:swrl="http://www.w3.org/2003/11/swrl#"
+ xmlns:owl="http://www.w3.org/2002/07/owl#"
+ xmlns:swrlb="http://www.w3.org/2003/11/swrlb#"
+ 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/dev/ontology-metadata.owl">
+ <protege:defaultLanguage
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">en</protege:defaultLanguage>
+ <owl:versionInfo xml:lang="en">$Revision$</owl:versionInfo>
+ </owl:Ontology>
+
+
+
+ 
+
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://protege.stanford.edu/plugins/owl/protege#defaultLanguage"/>
+
+
+
+ 
+
+ <owl:AnnotationProperty
rdf:about="http://purl.obolibrary.org/obo/IAO_0000111">
+ <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+ <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
term</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </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_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </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 xml:lang="en">definition</rdfs:label>
+ <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_0000117 xml:lang="en">PERSON:Daniel
Schober</obo:IAO_0000117>
+ <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 xml:lang="en">definition</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ </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"/>
+ </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"/>
+ </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"/>
+ </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"/>
+ </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"/>
+ </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"/>
+ </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>
+ </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>
+ </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>
+ </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_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>
+ </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:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000031"/>
+
+
+
+ 
+
+ <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"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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">
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000124"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000423"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000428"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000121"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000002"/>
+ </owl:oneOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ <obo:IAO_0000116 xml:lang="en">Better to represent curation as a
process with parts and then relate labels to that process (in IAO
meeting)</obo:IAO_0000116>
+ <obo:IAO_0000119
xml:lang="en">GROUP:OBI:<http://purl.obolibrary.org/obo/obi></obo:IAO_0000119>
+ <obo:IAO_0000119 xml:lang="en">OBI_0000266</obo:IAO_0000119>
+ <obo:IAO_0000117 xml:lang="en">PERSON:Bill Bug</obo:IAO_0000117>
+ <obo:IAO_0000115 xml:lang="en">The curation status of the term.
The allowed values come from an enumerated list of predefined terms. See
the specification of these instances for more detailed definitions of each
enumerated value.</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">curation status
specification</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <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>
+ </owl:Class>
+
+
+
+ 
+
+ <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">
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000227"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000228"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000226"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000103"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000229"/>
+ </owl:oneOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ <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_0000116 xml:lang="en">The creation of this class has been
inspired in part by Werner Ceusters' paper, Applying evolutionary
terminology auditing to the Gene Ontology.</obo:IAO_0000116>
+ <obo:IAO_0000115 xml:lang="en">The reason for which a term has
been deprecated. The allowed values come from an enumerated list of
predefined terms. See the specification of these instances for more
detailed definitions of each enumerated value.</obo:IAO_0000115>
+ <obo:IAO_0000111 xml:lang="en">obsolescence reason
specification</obo:IAO_0000111>
+ <obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000409">
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">denotator
type</rdfs:label>
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:oneOf rdf:parseType="Collection">
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000410"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000420"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000421"/>
+ </owl:oneOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ <obo:IAO_0000115
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A denotator type
indicates how a term should be interpreted from an ontological
perspective.</obo:IAO_0000115>
+ <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">Barry Smith, Werner
Ceusters</obo:IAO_0000119>
+ <obo:IAO_0000112
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">The Basic Formal
Ontology ontology makes a distinction between Universals and defined
classes, where the formal are "natural kinds" and the latter
arbitrary collections of entities.</obo:IAO_0000112>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#DbXref">
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#Definition">
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#Subset">
+ <owl:equivalentClass>
+ <owl:Class>
+ <owl:oneOf rdf:parseType="Collection">
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000224"/>
+ </owl:oneOf>
+ </owl:Class>
+ </owl:equivalentClass>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#Synonym">
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </owl:Class>
+
+
+
+ 
+
+ <owl:Class
rdf:about="http://www.geneontology.org/formats/oboInOwl#SynonymType">
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
+ </owl:Class>
+
+
+
+ 
+
+
+
+
+ 
+
+ <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>
+
+
+
+ 
+
+ <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 in an attempt to
structure part of the ontology but in retrospect failed to do a good
job</obo:IAO_0000115>
+ </owl:NamedIndividual>
+
+
+
+ 
+
+ <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>
+
+
+
+ 
+
+ <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>
+
+
+
+ 
+
+ <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 "ready_for_release" should be considered likely to change
place in hierarchy, have its definition refined, or be obsoleted in the
next release. Those classes deemed "ready_for_release" will also
derived from a chain of ancestor classes that are also
"ready_for_release."</obo:IAO_0000115>
+ </owl:NamedIndividual>
+
+
+
+ 
+
+ <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>
+
+
+
+ 
+
+ <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>
+
+
+
+ 
+
+ <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>
+
+
+
+ 
+
+ <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>
+ </owl:NamedIndividual>
+
+
+
+ 
+
+ <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>
+
+
+
+ 
+
+ <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>
+
+
+
+ 
+
+ <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>
+
+
+
+ 
+
+ <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>
+
+
+
+ 
+
+ <owl:NamedIndividual
rdf:about="http://purl.obolibrary.org/obo/IAO_0000410">
+ <rdf:type
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000409"/>
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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 "natural kind" rather than a
collection of any old things, which a class is able to be, formally. At the
meta level, universals are defined as positives, are disjoint with their
siblings, have single asserted parents.</obo:IAO_0000116>
+ </owl:NamedIndividual>
+
+
+
+ 
+
+ <owl:NamedIndividual
rdf:about="http://purl.obolibrary.org/obo/IAO_0000420">
+ <rdf:type
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000409"/>
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">defined
class</rdfs:label>
+ <obo:IAO_0000116
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">"definitions",
in some readings, always are given by necessary and sufficient conditions.
So one must be careful (and this is difficult sometimes) to distinguish
between defined classes and universal.</obo:IAO_0000116>
+ <obo:IAO_0000115
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_0000115>
+ <obo:IAO_0000117
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Alan
Ruttenberg</obo:IAO_0000117>
+ </owl:NamedIndividual>
+
+
+
+ 
+
+ <owl:NamedIndividual
rdf:about="http://purl.obolibrary.org/obo/IAO_0000421">
+ <rdf:type
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000409"/>
+ <rdfs:label
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">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>
+ </owl:NamedIndividual>
+
+
+
+ 
+
+ <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>
+ </owl:NamedIndividual>
+
+
+
+ 
+
+ <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>
+ </owl:NamedIndividual>
+
+
+
+ 
+
+ <rdf:Description>
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#AllDifferent"/>
+ <owl:distinctMembers rdf:parseType="Collection">
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000120"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000121"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000122"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000123"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000124"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000125"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000423"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000428"/>
+ </owl:distinctMembers>
+ </rdf:Description>
+ <rdf:Description>
+ <rdf:type
rdf:resource="http://www.w3.org/2002/07/owl#AllDifferent"/>
+ <owl:distinctMembers rdf:parseType="Collection">
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000226"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000227"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000228"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/IAO_0000229"/>
+ </owl:distinctMembers>
+ </rdf:Description>
+</rdf:RDF>
+
+
+
+
+

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