[information-artifact-ontology] r716 committed - Update top-level ontologies used by IAO from BFO 1.1 to BFO 2.0 classe...

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Revision: 716
Author: zheng...@gmail.com
Date: Mon Feb 16 15:30:55 2015 UTC
Log: Update top-level ontologies used by IAO from BFO 1.1 to BFO 2.0
classes only and from OBO-REL to RO core
The conversion related files including mapping and transition notes are
under 'BFO 1.1 to 2.0 conversion' directory
Import external terms using OntoFox. The ontoFox input file is
under 'ontoFox' directory
https://code.google.com/p/information-artifact-ontology/source/detail?r=716

Added:
/trunk/src/ontology/BFO 1.1 to 2.0 conversion
/trunk/src/ontology/BFO 1.1 to 2.0 conversion/mapping.txt
/trunk/src/ontology/BFO 1.1 to 2.0 conversion/notes.txt
/trunk/src/ontology/BFO 1.1 to 2.0 conversion/termsMapping.xlsx
/trunk/src/ontology/import-OBO.owl
/trunk/src/ontology/ontoFox
/trunk/src/ontology/ontoFox/OntoFox-input.txt
Modified:
/trunk/src/ontology/IAO.owl
/trunk/src/ontology/externalByHand.owl
/trunk/src/ontology/iao-main.owl
/trunk/src/ontology/ontology-metadata.owl

=======================================
--- /dev/null
+++ /trunk/src/ontology/BFO 1.1 to 2.0 conversion/mapping.txt Mon Feb 16
15:30:55 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
+++ /trunk/src/ontology/BFO 1.1 to 2.0 conversion/notes.txt Mon Feb 16
15:30:55 2015 UTC
@@ -0,0 +1,26 @@
+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/releases/2015-02-11/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
+
+
+Current development version IAO has following OWL files:
+ - IAO.owl (import BFO2 classes only, RO core, and iao-main.owl,
ontology-metadata.owl,import-OBO.owl,externalByHand.owl and obsolete.owl)
+ - iao-main.owl (same as IAO.owl but excludes obsolete.owl)
+ - ontology-metadata.owl
+ - import-OBO.owl
+ - externalByHand.owl
+ - obsolete.owl
+
+
+
=======================================
--- /dev/null
+++ /trunk/src/ontology/BFO 1.1 to 2.0 conversion/termsMapping.xlsx Mon Feb
16 15:30:55 2015 UTC
Binary file, no diff available.
=======================================
--- /dev/null
+++ /trunk/src/ontology/import-OBO.owl Mon Feb 16 15:30:55 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
+++ /trunk/src/ontology/ontoFox/OntoFox-input.txt Mon Feb 16 15:30:55 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
+
=======================================
--- /trunk/src/ontology/IAO.owl Mon Jul 2 16:51:22 2012 UTC
+++ /trunk/src/ontology/IAO.owl Mon Feb 16 15:30:55 2015 UTC
@@ -1,41 +1,66 @@
<?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: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/releases/2015-02-11/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">
- <obo:IAO_0000603
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IAO_0021000-IAO_0021999</obo:IAO_0000603>
- </rdf:Description>
+ <IAO_0000603
rdf:datatype="http://www.w3.org/2001/XMLSchema#string">IAO_0021000-IAO_0021999</IAO_0000603>
+ </rdf:Description>
+</rdf:RDF>
+
+

-</rdf:RDF>
+

=======================================
--- /trunk/src/ontology/externalByHand.owl Thu Jun 5 23:12:18 2014 UTC
+++ /trunk/src/ontology/externalByHand.owl Mon Feb 16 15:30:55 2015 UTC
@@ -2,28 +2,15 @@
<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>
-
+ 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: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>

@@ -110,84 +57,17 @@


<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>
=======================================
--- /trunk/src/ontology/iao-main.owl Thu Jun 5 20:04:16 2014 UTC
+++ /trunk/src/ontology/iao-main.owl Mon Feb 16 15:30:55 2015 UTC
@@ -1,39 +1,26 @@
<?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#">
+ 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>
- <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://purl.obolibrary.org/obo/bfo/2014-05-03/classes-only.owl"/>
+ <owl:imports
rdf:resource="http://purl.obolibrary.org/obo/ro/releases/2015-02-11/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/external.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/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>

@@ -46,59 +33,128 @@

///////////////////////////////////////////////////////////////////////////////////////
-->

+
+
+
+ 
+
<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
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://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
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_0000412">
- <rdfs:label xml:lang="en">imported from</rdfs:label>
+
+
+
+ 
+
+ <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_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
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_0000111">
- <rdfs:label xml:lang="en">editor preferred term</rdfs:label>
+
+
+
+ 
+
+ <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"/>

@@ -110,6 +166,18 @@

///////////////////////////////////////////////////////////////////////////////////////
-->

+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000050"/>
+
+
+
+ 
+
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/BFO_0000051"/>

@@ -118,8 +186,8 @@
<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"/>
- <rdfs:subPropertyOf
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
</owl:ObjectProperty>

@@ -221,9 +289,9 @@
<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"/>
- <rdfs:range
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
</owl:ObjectProperty>

@@ -234,9 +302,9 @@
<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"/>
- <rdfs:subPropertyOf
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
</owl:ObjectProperty>

@@ -247,10 +315,10 @@
<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"/>
- <rdfs:range
rdf:resource="http://www.ifomis.org/bfo/1.1/span#Process"/>
</owl:ObjectProperty>

@@ -302,10 +370,10 @@
<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"/>
- <rdfs:subPropertyOf
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
</owl:ObjectProperty>

@@ -316,9 +384,9 @@
<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:subPropertyOf
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
<rdfs:range>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
@@ -337,30 +405,7 @@

<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>
-
-



@@ -368,23 +413,21 @@

- 
+ 

- <owl:ObjectProperty
rdf:about="http://purl.org/obo/owl/OBO_REL#bearer_of"/>
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/RO_0000053"/>

- 
+ 

- <owl:ObjectProperty
rdf:about="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ <owl:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/RO_0000058"/>

- 
+ 

- <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:ObjectProperty
rdf:about="http://purl.obolibrary.org/obo/RO_0000059"/>

@@ -454,6 +497,48 @@

+ 
+
+ <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"/>
@@ -610,9 +695,9 @@
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description
rdf:about="http://www.ifomis.org/bfo/1.1/snap#Quality"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/BFO_0000019"/>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000294"/>
+ <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>
@@ -726,11 +811,11 @@

<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
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://www.ifomis.org/bfo/1.1#Entity"/>
+ <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>
@@ -797,7 +882,7 @@
<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: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>
@@ -1055,13 +1140,13 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000033"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000005"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000007"/>
</owl:Restriction>
</rdfs:subClassOf>
@@ -1186,12 +1271,12 @@
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description
rdf:about="http://www.ifomis.org/bfo/1.1/snap#MaterialEntity"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://purl.org/obo/owl/OBO_REL#bearer_of"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<owl:someValuesFrom>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000294"/>
+ <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:someValuesFrom>
@@ -1322,12 +1407,12 @@
<owl:equivalentClass>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description
rdf:about="http://www.ifomis.org/bfo/1.1/snap#MaterialEntity"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/BFO_0000040"/>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://purl.org/obo/owl/OBO_REL#bearer_of"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<owl:someValuesFrom>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000294"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/RO_0000059"/>
<owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000185"/>
</owl:Restriction>
</owl:someValuesFrom>
@@ -1574,7 +1659,7 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#part_of"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000310"/>
</owl:Restriction>
</rdfs:subClassOf>
@@ -1689,7 +1774,7 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000314"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000301"/>
</owl:Restriction>
</rdfs:subClassOf>
@@ -1709,7 +1794,7 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000314"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000302"/>
</owl:Restriction>
</rdfs:subClassOf>
@@ -1729,7 +1814,7 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000314"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000303"/>
</owl:Restriction>
</rdfs:subClassOf>
@@ -1867,7 +1952,7 @@
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
- <owl:someValuesFrom
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#ZeroDimensionalRegion"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000018"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
@@ -1876,9 +1961,9 @@
<owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
</owl:Restriction>
</rdfs:subClassOf>
+ <obo:IAO_0000115 xml:lang="en">A cartesian spatial coordinate
datum is a representation of a point in a spatial region, in which equal
changes in the magnitude of a coordinate value denote length qualities with
the same magnitude</obo:IAO_0000115>
<obo:IAO_0000232>AR notes: We need to discuss whether it should
include site.</obo:IAO_0000232>
<obo:IAO_0000116 xml:lang="en">2009-08-18 Alan Ruttenberg -
question to BFO list about whether the BFO sense of the lower dimensional
regions is that they are always part of actual space (the three dimensional
sort)
http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617</obo:IAO_0000116>
- <obo:IAO_0000115 xml:lang="en">A cartesian spatial coordinate
datum is a representation of a point in a spatial region, in which equal
changes in the magnitude of a coordinate value denote length qualities with
the same magnitude</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<rdfs:seeAlso
xml:lang="en">http://groups.google.com/group/bfo-discuss/browse_thread/thread/9d04e717e39fb617</rdfs:seeAlso>
<obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
@@ -1893,26 +1978,26 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
<rdfs:subClassOf>
<owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000404"/>
+ <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
+ </owl:Restriction>
+ </rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
<owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description
rdf:about="http://www.ifomis.org/bfo/1.1/snap#ZeroDimensionalRegion"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/BFO_0000018"/>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#part_of"/>
- <owl:someValuesFrom
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#OneDimensionalRegion"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000026"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000404"/>
- <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
- </owl:Restriction>
- </rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A cartesion spatial coordinate
datum that uses one value to specify a position along a one dimensional
spatial region</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
@@ -1943,10 +2028,10 @@
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description
rdf:about="http://www.ifomis.org/bfo/1.1/snap#ZeroDimensionalRegion"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/BFO_0000018"/>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#part_of"/>
- <owl:someValuesFrom
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#TwoDimensionalRegion"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000009"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
@@ -1967,20 +2052,14 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000400"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000406"/>
- <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
<owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
<owl:someValuesFrom>
<owl:Class>
<owl:intersectionOf rdf:parseType="Collection">
- <rdf:Description
rdf:about="http://www.ifomis.org/bfo/1.1/snap#ZeroDimensionalRegion"/>
+ <rdf:Description
rdf:about="http://purl.obolibrary.org/obo/BFO_0000018"/>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#part_of"/>
- <owl:someValuesFrom
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#ThreeDimensionalRegion"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000028"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
@@ -1999,6 +2078,12 @@
<owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
</owl:Restriction>
</rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000406"/>
+ <owl:cardinality
rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
+ </owl:Restriction>
+ </rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A cartesion spatial coordinate
datum that uses three values to specify a position within a three
dimensional spatial region</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
@@ -2086,7 +2171,7 @@
</owl:Restriction>
<owl:Restriction>
<owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000413"/>
- <owl:allValuesFrom
rdf:resource="http://www.ifomis.org/bfo/1.1/span#Process"/>
+ <owl:allValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
</owl:Restriction>
</owl:intersectionOf>
</owl:Class>
@@ -2135,7 +2220,7 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/IAO_0000442">
<rdfs:label xml:lang="en">author role</rdfs:label>
- <rdfs:subClassOf
rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Role"/>
+ <rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000023"/>
<obo:IAO_0000115 xml:lang="en">A role inhering in a person or
organization that is realized when the bearer participates in the work
which is the basis of the document, in the writing of the document, and
signs it with their name.</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>
@@ -2221,14 +2306,14 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
- <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000577"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000579"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_participant"/>
- <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000579"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000577"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000118>assigning a CRID</obo:IAO_0000118>
@@ -2250,14 +2335,14 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
- <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000579"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_participant"/>
- <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000579"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
@@ -2266,8 +2351,8 @@
<owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000577"/>
</owl:Restriction>
</rdfs:subClassOf>
+ <obo:IAO_0000112>Articles in Pubmed are reviewed by curators who
add MESH terms to the Pubmed records in order to categorize them better and
improve the ability to search for them. </obo:IAO_0000112>
<obo:IAO_0000118>associating information with a CRID in the CRID
registry</obo:IAO_0000118>
- <obo:IAO_0000112>Articles in Pubmed are reviewed by curators who
add MESH terms to the Pubmed records in order to categorize them better and
improve the ability to search for them. </obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A planned process in which a CRID
registry associates an information content entity with a CRID
symbol</obo:IAO_0000115>
<obo:IAO_0000117 xml:lang="en">PERSON:Alan
Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000114
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
@@ -2282,7 +2367,7 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000028"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#part_of"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000050"/>
<owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000578"/>
</owl:Restriction>
</rdfs:subClassOf>
@@ -2306,13 +2391,7 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
- <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000577"/>
- </owl:Restriction>
- </rdfs:subClassOf>
- <rdfs:subClassOf>
- <owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom>
<owl:Restriction>
<owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000219"/>
@@ -2321,6 +2400,12 @@
</owl:someValuesFrom>
</owl:Restriction>
</rdfs:subClassOf>
+ <rdfs:subClassOf>
+ <owl:Restriction>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000577"/>
+ </owl:Restriction>
+ </rdfs:subClassOf>
<obo:IAO_0000118>CRID</obo:IAO_0000118>
<obo:IAO_0000116 xml:lang="en">2014-05-05: In defining this term
we take no position on what the CRID denotes. In particular do not assume
it denotes a *record* in the CRID registry (since the registry might not
have 'records').</obo:IAO_0000116>
<obo:IAO_0000116 xml:lang="en">Alan, IAO call 20101124:
potentially the CRID denotes the instance it was associated with during
creation.
@@ -2363,29 +2448,29 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000011"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
- <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000577"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000293"/>
- <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000577"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/OBI_0000299"/>
+ <owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000030"/>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_participant"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/RO_0000057"/>
<owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000579"/>
</owl:Restriction>
</rdfs:subClassOf>
+ <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: Melanie
Courtot</obo:IAO_0000117>
<obo:IAO_0000118>looking up a CRID</obo:IAO_0000118>
<obo:IAO_0000112>Going to the PubMed website and entering a PubMed
ID in order to retrieve the Pubmed information associated with that ID.
</obo:IAO_0000112>
<obo:IAO_0000115 xml:lang="en">A planned process in which a
request to a CRID registry is made to return the information associated
with a CRID symbol</obo:IAO_0000115>
- <obo:IAO_0000117 xml:lang="en">PERSON: Alan
Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000117 xml:lang="en">PERSON: Bill Hogan</obo:IAO_0000117>
- <obo:IAO_0000117 xml:lang="en">PERSON: Bjoern
Peters</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_0000120"/>
</owl:Class>

@@ -2422,7 +2507,7 @@
<rdfs:subClassOf
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000100"/>
<rdfs:subClassOf>
<owl:Restriction>
- <owl:onProperty
rdf:resource="http://www.obofoundry.org/ro/ro.owl#has_part"/>
+ <owl:onProperty
rdf:resource="http://purl.obolibrary.org/obo/BFO_0000051"/>
<owl:someValuesFrom
rdf:resource="http://purl.obolibrary.org/obo/IAO_0000582"/>
</owl:Restriction>
</rdfs:subClassOf>
@@ -2556,5 +2641,5 @@

-
+

=======================================
--- /trunk/src/ontology/ontology-metadata.owl Tue Jan 14 22:53:41 2014 UTC
+++ /trunk/src/ontology/ontology-metadata.owl Mon Feb 16 15:30:55 2015 UTC
@@ -1,361 +1,99 @@
<?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>
+<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>
+

- <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:
+
+ 
+
+
+
+
+ 
+
+ <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.
+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:

@@ -363,154 +101,740 @@

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.
+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.
+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
+ <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)"
+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>
+ <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"
+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,
+ '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>
+ '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,
+ '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>
+ '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: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>
+
+
***The diff for this file has been truncated for email.***

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