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From: <jzh...@us...> - 2009-06-29 18:15:11
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Revision: 1762
http://obi.svn.sourceforge.net/obi/?rev=1762&view=rev
Author: jzheng24
Date: 2009-06-29 18:15:08 +0000 (Mon, 29 Jun 2009)
Log Message:
-----------
"xmlns:obi_rest=http://purl.obofoundry.org/obo/obi/TheRest.owl#" was removed since we don't use TheRest.owl anymore.
Consistency was check by Pellet 1.5.2 and is OK before and after removed this line.
Modified Paths:
--------------
trunk/src/ontology/branches/obi-quick-id.owl
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From: <jzh...@us...> - 2009-06-29 18:14:15
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Revision: 1761
http://obi.svn.sourceforge.net/obi/?rev=1761&view=rev
Author: jzheng24
Date: 2009-06-29 18:14:05 +0000 (Mon, 29 Jun 2009)
Log Message:
-----------
"xmlns:obi_rest=http://purl.obofoundry.org/obo/obi/TheRest.owl#" was removed since we don't use TheRest.owl anymore.
Consistency was check by Pellet 1.5.2 and is OK before and after removed this line.
Modified Paths:
--------------
trunk/src/ontology/branches/obi-owl-full.owl
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From: <jzh...@us...> - 2009-06-29 18:10:53
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Revision: 1760
http://obi.svn.sourceforge.net/obi/?rev=1760&view=rev
Author: jzheng24
Date: 2009-06-29 18:10:52 +0000 (Mon, 29 Jun 2009)
Log Message:
-----------
Because "TheRest.owl" has been deleted, no need to import TheRest.owl. The following line was removed.
<owl:imports> <owl:Ontology rdf:about="TheRest.owl"/></owl:imports>
Modified Paths:
--------------
trunk/src/ontology/branches/obi-lsw.owl.template
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From: <jzh...@us...> - 2009-06-29 18:09:41
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Revision: 1759
http://obi.svn.sourceforge.net/obi/?rev=1759&view=rev
Author: jzheng24
Date: 2009-06-29 18:09:40 +0000 (Mon, 29 Jun 2009)
Log Message:
-----------
"xmlns:obi_rest=http://purl.obofoundry.org/obo/obi/TheRest.owl#" was removed since we don't use TheRest.owl anymore.
Consistency was check by Pellet 1.5.2 and is OK before and after removed this line.
Modified Paths:
--------------
trunk/src/ontology/branches/externalDerived.owl
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From: <jzh...@us...> - 2009-06-29 18:08:14
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Revision: 1758
http://obi.svn.sourceforge.net/obi/?rev=1758&view=rev
Author: jzheng24
Date: 2009-06-29 18:08:11 +0000 (Mon, 29 Jun 2009)
Log Message:
-----------
"xmlns:obi_rest=http://purl.obofoundry.org/obo/obi/TheRest.owl#" was removed since we don't use TheRest.owl anymore.
Consistency was check by Pellet 1.5.2 and is OK before and after removed this line.
Modified Paths:
--------------
trunk/src/ontology/branches/external-byhand.owl
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From: <jzh...@us...> - 2009-06-29 18:07:18
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Revision: 1757
http://obi.svn.sourceforge.net/obi/?rev=1757&view=rev
Author: jzheng24
Date: 2009-06-29 18:07:16 +0000 (Mon, 29 Jun 2009)
Log Message:
-----------
"xmlns:obi_rest=http://purl.obofoundry.org/obo/obi/TheRest.owl#" was removed since we don't use TheRest.owl anymore.
Consistency was check by Pellet 1.5.2 and is OK before and after removed this line.
Modified Paths:
--------------
trunk/src/ontology/branches/external.owl
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From: <jzh...@us...> - 2009-06-29 18:05:23
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Revision: 1756
http://obi.svn.sourceforge.net/obi/?rev=1756&view=rev
Author: jzheng24
Date: 2009-06-29 18:05:17 +0000 (Mon, 29 Jun 2009)
Log Message:
-----------
"xmlns:obi_rest=http://purl.obofoundry.org/obo/obi/TheRest.owl#" was removed since we don't use TheRest.owl anymore.
Consistency was check by Pellet 1.5.2 and is OK before and after removed this line.
Modified Paths:
--------------
trunk/src/ontology/branches/dataTransformationInstances.owl
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From: <jzh...@us...> - 2009-06-29 18:04:02
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Revision: 1755
http://obi.svn.sourceforge.net/obi/?rev=1755&view=rev
Author: jzheng24
Date: 2009-06-29 18:03:53 +0000 (Mon, 29 Jun 2009)
Log Message:
-----------
"xmlns:obi_rest=http://purl.obofoundry.org/obo/obi/TheRest.owl#" was removed since we don't use TheRest.owl anymore.
Consistency was check by Pellet 1.5.2 and is OK before and after removed this line.
Modified Paths:
--------------
trunk/src/ontology/branches/AnnotationProperty.owl
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From: <jzh...@us...> - 2009-06-29 16:09:36
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Revision: 1754
http://obi.svn.sourceforge.net/obi/?rev=1754&view=rev
Author: jzheng24
Date: 2009-06-29 16:09:29 +0000 (Mon, 29 Jun 2009)
Log Message:
-----------
copied from instances folder, file modified by James,
version 1708
Added Paths:
-----------
trunk/src/ontology/branches/softwareInstances.owl
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From: <jzh...@us...> - 2009-06-29 16:08:51
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Revision: 1753
http://obi.svn.sourceforge.net/obi/?rev=1753&view=rev
Author: jzheng24
Date: 2009-06-29 16:08:49 +0000 (Mon, 29 Jun 2009)
Log Message:
-----------
copied from instances folder, file modified by James,
version 1708
Added Paths:
-----------
trunk/src/ontology/branches/dataTransformationInstances.owl
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From: <lso...@us...> - 2009-06-24 14:21:20
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Revision: 1751
http://obi.svn.sourceforge.net/obi/?rev=1751&view=rev
Author: lsoldatova
Date: 2009-06-24 13:46:21 +0000 (Wed, 24 Jun 2009)
Log Message:
-----------
the relations is_specified_input/ output_information_of is obsoleted
Modified Paths:
--------------
trunk/src/ontology/branches/Relations.owl
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From: <lso...@us...> - 2009-06-24 14:18:38
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Revision: 1752
http://obi.svn.sourceforge.net/obi/?rev=1752&view=rev
Author: lsoldatova
Date: 2009-06-24 14:09:24 +0000 (Wed, 24 Jun 2009)
Log Message:
-----------
obsoleted relations has_specified_input_information and relations has_specified_input_information
Modified Paths:
--------------
trunk/src/ontology/branches/AnnotationProperty.owl
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/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-owl-full.owl
trunk/src/ontology/branches/obi-quick-id.owl
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From: <jam...@us...> - 2009-06-24 09:44:23
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Revision: 1750
http://obi.svn.sourceforge.net/obi/?rev=1750&view=rev
Author: jamesmalone
Date: 2009-06-24 09:43:34 +0000 (Wed, 24 Jun 2009)
Log Message:
-----------
removal of references to has_specified_output_information from DT branch
Modified Paths:
--------------
trunk/src/ontology/branches/DataTransformation.owl
trunk/src/ontology/branches/DigitalEntityPlus.owl
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From: <lso...@us...> - 2009-06-23 14:12:19
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Revision: 1749
http://obi.svn.sourceforge.net/obi/?rev=1749&view=rev
Author: lsoldatova
Date: 2009-06-23 14:12:03 +0000 (Tue, 23 Jun 2009)
Log Message:
-----------
removed extra versions of the SIG paper
Removed Paths:
-------------
trunk/docs/papers/ISMB_2009/camera-ready-May13.doc
trunk/docs/papers/ISMB_2009/camera-ready.doc
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From: <lso...@us...> - 2009-06-23 14:05:57
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Revision: 1748
http://obi.svn.sourceforge.net/obi/?rev=1748&view=rev
Author: lsoldatova
Date: 2009-06-23 14:05:30 +0000 (Tue, 23 Jun 2009)
Log Message:
-----------
talk for Bio-ontologies SIG/ISMB
Added Paths:
-----------
trunk/docs/papers/ISMB_2009/OBI-SIG.ppt
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From: <jen...@us...> - 2009-06-22 15:10:37
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Revision: 1747
http://obi.svn.sourceforge.net/obi/?rev=1747&view=rev
Author: jenfostel
Date: 2009-06-22 15:10:35 +0000 (Mon, 22 Jun 2009)
Log Message:
-----------
added examples and def source for material sample role and editor note for specimen role
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <jam...@us...> - 2009-06-17 16:55:55
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Revision: 1746
http://obi.svn.sourceforge.net/obi/?rev=1746&view=rev
Author: jamesmalone
Date: 2009-06-17 16:55:51 +0000 (Wed, 17 Jun 2009)
Log Message:
-----------
starting work on action items from workshop being to replace has_specified_input/output_data to has_specified_input/output
Modified Paths:
--------------
trunk/src/ontology/branches/DataTransformation.owl
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From: <al...@us...> - 2009-06-12 18:14:22
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Revision: 1745
http://obi.svn.sourceforge.net/obi/?rev=1745&view=rev
Author: alanr
Date: 2009-06-12 18:14:19 +0000 (Fri, 12 Jun 2009)
Log Message:
-----------
Hopefull speed up reasoning. Change biological vector role to be a subclass of material to be added role, instead of saying it was realized in administering substance in vivo. Role back incorrect changes to Relations.owl. Add has_specified_output max 1 to administering substance in vivo also to speed up reasoning. On my machine, P3 is a dog, but p4 with fact++ is quite quick
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
trunk/src/ontology/branches/Relations.owl
trunk/src/ontology/branches/Role.owl
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From: <bjo...@us...> - 2009-06-12 16:42:33
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Revision: 1744
http://obi.svn.sourceforge.net/obi/?rev=1744&view=rev
Author: bjoernpeters
Date: 2009-06-12 16:30:47 +0000 (Fri, 12 Jun 2009)
Log Message:
-----------
Updated text for definitions from workshop notes.
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
trunk/src/ontology/branches/Role.owl
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From: <bjo...@us...> - 2009-06-12 15:38:17
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Revision: 1743
http://obi.svn.sourceforge.net/obi/?rev=1743&view=rev
Author: bjoernpeters
Date: 2009-06-12 15:38:15 +0000 (Fri, 12 Jun 2009)
Log Message:
-----------
Added new figure for James use case
Modified Paths:
--------------
trunk/docs/papers/release/Release-Manuscript-Master-shortened.doc
Added Paths:
-----------
trunk/docs/papers/release/Figures/GenePattern-Use-case-image.gif
trunk/docs/papers/release/Figures/assayManuscript.png
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From: <bjo...@us...> - 2009-06-12 13:22:27
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Revision: 1741
http://obi.svn.sourceforge.net/obi/?rev=1741&view=rev
Author: bjoernpeters
Date: 2009-06-12 12:19:09 +0000 (Fri, 12 Jun 2009)
Log Message:
-----------
Inserted updated Figure
Modified Paths:
--------------
trunk/docs/papers/release/Release-Manuscript-Master-shortened.doc
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From: <bjo...@us...> - 2009-06-12 13:22:12
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Revision: 1742
http://obi.svn.sourceforge.net/obi/?rev=1742&view=rev
Author: bjoernpeters
Date: 2009-06-12 12:28:22 +0000 (Fri, 12 Jun 2009)
Log Message:
-----------
Completed going through manuscript to check for presence of terms in OBI.
Modified Paths:
--------------
trunk/docs/papers/release/Release-Manuscript-Master-shortened.doc
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From: <al...@us...> - 2009-06-12 02:44:12
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Revision: 1740
http://obi.svn.sourceforge.net/obi/?rev=1740&view=rev
Author: alanr
Date: 2009-06-12 02:44:11 +0000 (Fri, 12 Jun 2009)
Log Message:
-----------
has_specified_participant is inverse functional. Speeds reasoning up x4. You can't be a specified participant of more than one process. (or can you?)
Modified Paths:
--------------
trunk/src/ontology/branches/Relations.owl
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From: <al...@us...> - 2009-06-11 21:51:15
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Revision: 1739
http://obi.svn.sourceforge.net/obi/?rev=1739&view=rev
Author: alanr
Date: 2009-06-11 21:51:13 +0000 (Thu, 11 Jun 2009)
Log Message:
-----------
iao.owl -> IAO.owl
Modified Paths:
--------------
trunk/src/ontology/branches/obil.owl
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From: <bjo...@us...> - 2009-06-11 17:10:51
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Revision: 1738
http://obi.svn.sourceforge.net/obi/?rev=1738&view=rev
Author: bjoernpeters
Date: 2009-06-11 17:10:50 +0000 (Thu, 11 Jun 2009)
Log Message:
-----------
Edits during workshop
Modified Paths:
--------------
trunk/docs/papers/release/Notes during workshop.docx
trunk/docs/papers/release/Release-Manuscript-Master-shortened.doc
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