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From: <mco...@us...> - 2009-01-20 01:11:29
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Revision: 1363
http://obi.svn.sourceforge.net/obi/?rev=1363&view=rev
Author: mcourtot
Date: 2009-01-20 01:11:20 +0000 (Tue, 20 Jan 2009)
Log Message:
-----------
OBI.owl in which defined classes have only N&S conditions
Added Paths:
-----------
trunk/tests/reasoning/OBI-defined.owl
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From: <mco...@us...> - 2009-01-20 00:54:13
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Revision: 1362
http://obi.svn.sourceforge.net/obi/?rev=1362&view=rev
Author: mcourtot
Date: 2009-01-20 00:54:10 +0000 (Tue, 20 Jan 2009)
Log Message:
-----------
restaured defined classes
Modified Paths:
--------------
trunk/tests/reasoning/OBI-fixed.owl
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From: <mco...@us...> - 2009-01-19 22:37:47
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Revision: 1361
http://obi.svn.sourceforge.net/obi/?rev=1361&view=rev
Author: mcourtot
Date: 2009-01-19 21:54:44 +0000 (Mon, 19 Jan 2009)
Log Message:
-----------
fixed
Added Paths:
-----------
trunk/tests/reasoning/OBI-fixed.owl
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From: <mco...@us...> - 2009-01-19 22:37:13
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Revision: 1360
http://obi.svn.sourceforge.net/obi/?rev=1360&view=rev
Author: mcourtot
Date: 2009-01-19 21:35:00 +0000 (Mon, 19 Jan 2009)
Log Message:
-----------
created test directory for reasoning trouble
Added Paths:
-----------
trunk/tests/reasoning/
trunk/tests/reasoning/OBI.owl
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From: <al...@us...> - 2009-01-18 03:44:44
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Revision: 1359
http://obi.svn.sourceforge.net/obi/?rev=1359&view=rev
Author: alanr
Date: 2009-01-18 03:44:31 +0000 (Sun, 18 Jan 2009)
Log Message:
-----------
Uncle. I added redundant definitions of the annotation properties to each and every file
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
trunk/src/ontology/branches/DataFormatSpecification.owl
trunk/src/ontology/branches/DataTransformation.owl
trunk/src/ontology/branches/DigitalEntityPlus.owl
trunk/src/ontology/branches/InstrumentAndPart.owl
trunk/src/ontology/branches/OBI-Function.owl
trunk/src/ontology/branches/Obsolete.owl
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
trunk/src/ontology/branches/Quality.owl
trunk/src/ontology/branches/Relations.owl
trunk/src/ontology/branches/Role.owl
trunk/src/ontology/branches/external-byhand.owl
trunk/src/ontology/branches/external.owl
trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/obi.obo
trunk/src/ontology/branches/obil.owl
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From: <mco...@us...> - 2009-01-17 09:06:11
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Revision: 1358
http://obi.svn.sourceforge.net/obi/?rev=1358&view=rev
Author: mcourtot
Date: 2009-01-17 09:06:07 +0000 (Sat, 17 Jan 2009)
Log Message:
-----------
following PA call with BP and JF, the following lines have benn removed in the role file:
?\194?\160<rdf:Description rdf:about="http://purl.obofoundry.org/obo/OBI_0000094">
?\194?\160?\194?\160?\194?\160<IAO_0000115 xml:lang="en">a material_application is protocol_application which has the objective to
?\194?\160?\194?\160?\194?\160produce output material(s) from input material(s)</IAO_0000115>
?\194?\160</rdf:Description>
=> extra definition for artifact material creation
?\194?\160<rdf:Description rdf:about="http://purl.obofoundry.org/obo/OBI_0200000">
?\194?\160?\194?\160?\194?\160<IAO_0000115 xml:lang="en">a protocol application which has the objective to ?\194?\160produce output data from input data</IAO_0000115>
?\194?\160</rdf:Description>
=> extra definition for data transformation
?\194?\160<rdf:Description rdf:about="http://purl.obofoundry.org/obo/OBI_0000011">
?\194?\160?\194?\160?\194?\160<rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/span#Process"/>
?\194?\160</rdf:Description>
=> assertion of ODP under Process
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <mco...@us...> - 2009-01-17 00:35:53
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Revision: 1357
http://obi.svn.sourceforge.net/obi/?rev=1357&view=rev
Author: mcourtot
Date: 2009-01-17 00:35:46 +0000 (Sat, 17 Jan 2009)
Log Message:
-----------
removed extra imports declaration
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
trunk/src/ontology/branches/Relations.owl
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From: <mco...@us...> - 2009-01-16 18:20:49
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Revision: 1356
http://obi.svn.sourceforge.net/obi/?rev=1356&view=rev
Author: mcourtot
Date: 2009-01-16 18:20:39 +0000 (Fri, 16 Jan 2009)
Log Message:
-----------
added alt term source for homo sapiens
added in branch core annotation for core terms to test extraction
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
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From: <fgi...@us...> - 2009-01-16 14:13:25
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Revision: 1355
http://obi.svn.sourceforge.net/obi/?rev=1355&view=rev
Author: fgibson_sf
Date: 2009-01-16 14:13:08 +0000 (Fri, 16 Jan 2009)
Log Message:
-----------
added the supplies relation and added it as a N condition on device
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
trunk/src/ontology/branches/Relations.owl
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From: <bjo...@us...> - 2009-01-15 22:57:12
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Revision: 1354
http://obi.svn.sourceforge.net/obi/?rev=1354&view=rev
Author: bjoernpeters
Date: 2009-01-15 22:23:20 +0000 (Thu, 15 Jan 2009)
Log Message:
-----------
- Based on the PlanAndPlannedProcess branch, cleaned up the definitions and labels of 'addition of material' terms.
- Moved all defined classes under the '_defined protocol applications', and additional asserted parents.
- Added study design execution based on request for role branch
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <jen...@us...> - 2009-01-15 19:52:05
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Revision: 1353
http://obi.svn.sourceforge.net/obi/?rev=1353&view=rev
Author: jenfostel
Date: 2009-01-15 19:51:54 +0000 (Thu, 15 Jan 2009)
Log Message:
-----------
added restrictions on study participant role to describe how the role is realized (where possible)
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <bjo...@us...> - 2009-01-15 18:23:30
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Revision: 1352
http://obi.svn.sourceforge.net/obi/?rev=1352&view=rev
Author: bjoernpeters
Date: 2009-01-15 18:23:19 +0000 (Thu, 15 Jan 2009)
Log Message:
-----------
PlanAndPlannedProcess call; some updates to administered substance process. More to follow.
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <jen...@us...> - 2009-01-15 15:59:13
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Revision: 1351
http://obi.svn.sourceforge.net/obi/?rev=1351&view=rev
Author: jenfostel
Date: 2009-01-15 15:59:03 +0000 (Thu, 15 Jan 2009)
Log Message:
-----------
added restrictions and improved definitions of study participant, study subject and study specimen. Ran into a problem when trying to allow an organism to bear study specimen role.
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <mco...@us...> - 2009-01-14 00:00:12
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Revision: 1350
http://obi.svn.sourceforge.net/obi/?rev=1350&view=rev
Author: mcourtot
Date: 2009-01-14 00:00:06 +0000 (Wed, 14 Jan 2009)
Log Message:
-----------
missing final parenthesis
Modified Paths:
--------------
trunk/src/tools/build/generate-obo.lisp
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From: <al...@us...> - 2009-01-13 23:03:17
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Revision: 1349
http://obi.svn.sourceforge.net/obi/?rev=1349&view=rev
Author: alanr
Date: 2009-01-13 23:03:10 +0000 (Tue, 13 Jan 2009)
Log Message:
-----------
properly quote quotes. combine multiple rdfs comments
Modified Paths:
--------------
trunk/src/tools/build/generate-obo.lisp
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From: <al...@us...> - 2009-01-13 22:59:21
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Revision: 1348
http://obi.svn.sourceforge.net/obi/?rev=1348&view=rev
Author: alanr
Date: 2009-01-13 22:59:18 +0000 (Tue, 13 Jan 2009)
Log Message:
-----------
combine multiple comments. Property quote quotes in definitions (?)
Modified Paths:
--------------
trunk/src/ontology/branches/obi.obo
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From: <mco...@us...> - 2009-01-13 18:38:22
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Revision: 1347
http://obi.svn.sourceforge.net/obi/?rev=1347&view=rev
Author: mcourtot
Date: 2009-01-13 18:38:10 +0000 (Tue, 13 Jan 2009)
Log Message:
-----------
removed unbalanced right parenthesis ;)
Modified Paths:
--------------
trunk/src/tools/build/generate-obo.lisp
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From: <al...@us...> - 2009-01-13 08:42:44
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Revision: 1346
http://obi.svn.sourceforge.net/obi/?rev=1346&view=rev
Author: alanr
Date: 2009-01-13 08:42:42 +0000 (Tue, 13 Jan 2009)
Log Message:
-----------
less protege noisage. Manual removal of spurios
is_a: oboInOwl:ObsoleteProperty ! ObsoleteProperty
Modified Paths:
--------------
trunk/src/ontology/branches/obi.obo
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From: <al...@us...> - 2009-01-13 08:42:17
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Revision: 1345
http://obi.svn.sourceforge.net/obi/?rev=1345&view=rev
Author: alanr
Date: 2009-01-13 08:42:05 +0000 (Tue, 13 Jan 2009)
Log Message:
-----------
yet more protege noisage
Modified Paths:
--------------
trunk/src/tools/build/generate-obo.lisp
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From: <al...@us...> - 2009-01-13 08:39:12
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Revision: 1344
http://obi.svn.sourceforge.net/obi/?rev=1344&view=rev
Author: alanr
Date: 2009-01-13 08:39:09 +0000 (Tue, 13 Jan 2009)
Log Message:
-----------
really get rid of protege noise
Modified Paths:
--------------
trunk/src/tools/build/generate-obo.lisp
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From: <al...@us...> - 2009-01-13 08:36:25
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Revision: 1343
http://obi.svn.sourceforge.net/obi/?rev=1343&view=rev
Author: alanr
Date: 2009-01-13 08:36:23 +0000 (Tue, 13 Jan 2009)
Log Message:
-----------
better?
Modified Paths:
--------------
trunk/src/ontology/branches/obi.obo
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From: <al...@us...> - 2009-01-13 07:37:39
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Revision: 1342
http://obi.svn.sourceforge.net/obi/?rev=1342&view=rev
Author: alanr
Date: 2009-01-13 07:37:29 +0000 (Tue, 13 Jan 2009)
Log Message:
-----------
don't use is_a: obo_rel:relationship
Modified Paths:
--------------
trunk/src/ontology/branches/obi.obo
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From: <al...@us...> - 2009-01-13 07:35:45
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Revision: 1341
http://obi.svn.sourceforge.net/obi/?rev=1341&view=rev
Author: alanr
Date: 2009-01-13 07:35:35 +0000 (Tue, 13 Jan 2009)
Log Message:
-----------
don't use is_a: obo_rel:relationship. Makes everyone happier. (everyone = obo edit 1 and 2)
Modified Paths:
--------------
trunk/src/tools/build/generate-obo.lisp
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From: <al...@us...> - 2009-01-13 07:13:48
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Revision: 1340
http://obi.svn.sourceforge.net/obi/?rev=1340&view=rev
Author: alanr
Date: 2009-01-13 07:13:39 +0000 (Tue, 13 Jan 2009)
Log Message:
-----------
don't make anything subproperty of obo_rel:relationship
Modified Paths:
--------------
trunk/src/ontology/branches/Relations.owl
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From: <al...@us...> - 2009-01-13 07:13:01
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Revision: 1339
http://obi.svn.sourceforge.net/obi/?rev=1339&view=rev
Author: alanr
Date: 2009-01-13 07:12:51 +0000 (Tue, 13 Jan 2009)
Log Message:
-----------
add some helper functions. status: tentative
Modified Paths:
--------------
trunk/src/tools/build/add-inferred-superclasses.lisp
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