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From: <mco...@us...> - 2008-05-30 19:58:00
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Revision: 685
http://obi.svn.sourceforge.net/obi/?rev=685&view=rev
Author: mcourtot
Date: 2008-05-30 12:58:07 -0700 (Fri, 30 May 2008)
Log Message:
-----------
release
Added Paths:
-----------
tags/releases/2008-05-30/build/
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From: <mco...@us...> - 2008-05-30 19:53:50
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Revision: 684
http://obi.svn.sourceforge.net/obi/?rev=684&view=rev
Author: mcourtot
Date: 2008-05-30 12:53:59 -0700 (Fri, 30 May 2008)
Log Message:
-----------
files corrected for release
Modified Paths:
--------------
trunk/src/ontology/branches/AnnotationProperty.owl
trunk/src/ontology/branches/Biomaterial.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/TheRest.owl
trunk/src/ontology/branches/disjoints.owl
trunk/src/ontology/branches/external.owl
trunk/src/ontology/branches/externalDerived.owl
Added Paths:
-----------
trunk/src/ontology/branches/inferred-superclasses.owl
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From: <mco...@us...> - 2008-05-30 19:40:50
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Revision: 683
http://obi.svn.sourceforge.net/obi/?rev=683&view=rev
Author: mcourtot
Date: 2008-05-30 12:40:46 -0700 (Fri, 30 May 2008)
Log Message:
-----------
creates new obid.owl including inferred-superclasses.owl and protege frendly
added new checkpoint after creation of disjoints and superclasses
generates comments for the OBI.owl file
Modified Paths:
--------------
trunk/src/tools/build/OBIrelease.sh
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From: <bjo...@us...> - 2008-05-30 17:09:08
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Revision: 682
http://obi.svn.sourceforge.net/obi/?rev=682&view=rev
Author: bjoernpeters
Date: 2008-05-30 10:09:11 -0700 (Fri, 30 May 2008)
Log Message:
-----------
Modified Paths:
--------------
branches/bpbranch/branches/Biomaterial.owl
branches/bpbranch/branches/PlanAndPlannedProcess.owl
branches/bpbranch/branches/biomat-changes.txt
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From: <bjo...@us...> - 2008-05-30 15:30:08
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Revision: 681
http://obi.svn.sourceforge.net/obi/?rev=681&view=rev
Author: bjoernpeters
Date: 2008-05-30 08:30:16 -0700 (Fri, 30 May 2008)
Log Message:
-----------
moved out cells from organism parts
Modified Paths:
--------------
branches/bpbranch/branches/Biomaterial.owl
branches/bpbranch/branches/DigitalEntityPlus.owl
branches/bpbranch/branches/InstrumentAndPart.owl
branches/bpbranch/branches/PlanAndPlannedProcess.owl
branches/bpbranch/branches/Role.owl
branches/bpbranch/branches/TheRest.owl
branches/bpbranch/branches/external.owl
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From: <jam...@us...> - 2008-05-30 09:37:02
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Revision: 680
http://obi.svn.sourceforge.net/obi/?rev=680&view=rev
Author: jamesmalone
Date: 2008-05-30 02:37:04 -0700 (Fri, 30 May 2008)
Log Message:
-----------
Minor fixes
Modified Paths:
--------------
trunk/src/ontology/branches/DataTransformation.owl
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From: <bjo...@us...> - 2008-05-30 08:24:31
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Revision: 679
http://obi.svn.sourceforge.net/obi/?rev=679&view=rev
Author: bjoernpeters
Date: 2008-05-30 01:24:37 -0700 (Fri, 30 May 2008)
Log Message:
-----------
Modified Paths:
--------------
branches/bpbranch/branches/Biomaterial.owl
branches/bpbranch/branches/DigitalEntityPlus.owl
branches/bpbranch/branches/InstrumentAndPart.owl
branches/bpbranch/branches/PlanAndPlannedProcess.owl
branches/bpbranch/branches/Role.owl
branches/bpbranch/branches/TheRest.owl
branches/bpbranch/branches/external.owl
Added Paths:
-----------
branches/bpbranch/branches/biomat-changes.txt
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From: <al...@us...> - 2008-05-30 03:02:26
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Revision: 678
http://obi.svn.sourceforge.net/obi/?rev=678&view=rev
Author: alanr
Date: 2008-05-29 20:02:34 -0700 (Thu, 29 May 2008)
Log Message:
-----------
add comment to file
Modified Paths:
--------------
trunk/src/tools/build/comment-ids-in-owl-file.lisp
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From: <al...@us...> - 2008-05-30 03:01:00
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Revision: 677
http://obi.svn.sourceforge.net/obi/?rev=677&view=rev
Author: alanr
Date: 2008-05-29 20:01:04 -0700 (Thu, 29 May 2008)
Log Message:
-----------
(comment-ids-in-owl-file in out kb)
Using the labels in kb, reads input file, and puts an xml comment with
the propertly label before properties that use an OBI id, and an xml
comment with the label after the use of any other entity.
Comment's won't persis after editing the file and saving in protege,
so this is something to run on release, or when you need an annotated
copy to do some text editing of the OWL files.
e.g.
<owl:Class rdf:about="http://purl.obofoundry.org/obo/OBI_0000219"><!-- cellular_feature_identification_objective -->
<!-- definition --><OBI_0000291 xml:lang="en">Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.</OBI_0000291>
<!-- definition source --><OBI_0000279 xml:lang="en">source pending</OBI_0000279>
<!-- definition editor --><OBI_0000274 xml:lang="en">Jennifer Fostel</OBI_0000274>
<!-- example of usage --><OBI_0000287 xml:lang="en">example_of_usage to be added</OBI_0000287>
<!-- preferred term --><OBI_0000288 xml:lang="en">cellular_feature_identification_objective</OBI_0000288>
<rdfs:subClassOf>
<owl:Class rdf:about="http://purl.obofoundry.org/obo/OBI_0000015"/><!-- biological_feature_identification_objective -->
</rdfs:subClassOf>
<!-- curation status --><OBI_0000281 rdf:resource="http://purl.obofoundry.org/obo/OBI_0000319"/><!-- metadata complete -->
<rdfs:label xml:lang="en">cellular_feature_identification_objective</rdfs:label>
</owl:Class>
Added Paths:
-----------
trunk/src/tools/build/comment-ids-in-owl-file.lisp
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From: <al...@us...> - 2008-05-30 02:26:24
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Revision: 676
http://obi.svn.sourceforge.net/obi/?rev=676&view=rev
Author: alanr
Date: 2008-05-29 19:26:32 -0700 (Thu, 29 May 2008)
Log Message:
-----------
correct xml:base
Modified Paths:
--------------
trunk/src/tools/build/add-inferred-superclasses.lisp
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From: <mco...@us...> - 2008-05-30 02:01:11
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Revision: 675
http://obi.svn.sourceforge.net/obi/?rev=675&view=rev
Author: mcourtot
Date: 2008-05-29 19:01:19 -0700 (Thu, 29 May 2008)
Log Message:
-----------
new jar following addition of inferred-superclasses to merger script
Modified Paths:
--------------
trunk/src/tools/build/OBITools/OBITools.jar
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From: <mco...@us...> - 2008-05-30 02:00:22
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Revision: 674
http://obi.svn.sourceforge.net/obi/?rev=674&view=rev
Author: mcourtot
Date: 2008-05-29 19:00:30 -0700 (Thu, 29 May 2008)
Log Message:
-----------
added inferred-superclasses to the list of branches to merge
Modified Paths:
--------------
trunk/src/tools/build/OBITools/src/ca/bccrc/obi/OBIMerger.java
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From: <mco...@us...> - 2008-05-29 23:16:39
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Revision: 673
http://obi.svn.sourceforge.net/obi/?rev=673&view=rev
Author: mcourtot
Date: 2008-05-29 16:16:47 -0700 (Thu, 29 May 2008)
Log Message:
-----------
uncommented generation doc
Modified Paths:
--------------
trunk/src/tools/build/OBIrelease.sh
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From: <mco...@us...> - 2008-05-29 23:04:45
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Revision: 672
http://obi.svn.sourceforge.net/obi/?rev=672&view=rev
Author: mcourtot
Date: 2008-05-29 16:04:49 -0700 (Thu, 29 May 2008)
Log Message:
-----------
added SVN logs generation
Modified Paths:
--------------
trunk/src/tools/build/OBIrelease.sh
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From: <al...@us...> - 2008-05-29 22:36:33
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Revision: 671
http://obi.svn.sourceforge.net/obi/?rev=671&view=rev
Author: alanr
Date: 2008-05-29 15:36:40 -0700 (Thu, 29 May 2008)
Log Message:
-----------
bugfix
Modified Paths:
--------------
trunk/src/tools/build/write-purls.lisp
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From: <mco...@us...> - 2008-05-29 22:32:22
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Revision: 670
http://obi.svn.sourceforge.net/obi/?rev=670&view=rev
Author: mcourtot
Date: 2008-05-29 15:32:23 -0700 (Thu, 29 May 2008)
Log Message:
-----------
added inferred superclasses generation, and grouped some lisp calls to decrease execution time.
Modified Paths:
--------------
trunk/src/tools/build/OBIrelease.sh
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From: <mco...@us...> - 2008-05-29 20:29:34
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Revision: 669
http://obi.svn.sourceforge.net/obi/?rev=669&view=rev
Author: mcourtot
Date: 2008-05-29 13:29:39 -0700 (Thu, 29 May 2008)
Log Message:
-----------
new jar following modifications to the merger script
Modified Paths:
--------------
trunk/src/tools/build/OBITools/OBITools.jar
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From: <mco...@us...> - 2008-05-29 20:29:04
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Revision: 668
http://obi.svn.sourceforge.net/obi/?rev=668&view=rev
Author: mcourtot
Date: 2008-05-29 13:29:11 -0700 (Thu, 29 May 2008)
Log Message:
-----------
modified xml:base to http://purl.obofoundry.org/obo/obi.owl to improve tool support
modified Jena writer to use absolute URIs (e.g. rdf:about="http://purl.obofoundry.org/obo/OBI_0000086") instead of relatives
Modified Paths:
--------------
trunk/src/tools/build/OBITools/src/ca/bccrc/obi/OBIMerger.java
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From: <mco...@us...> - 2008-05-29 20:27:01
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Revision: 667
http://obi.svn.sourceforge.net/obi/?rev=667&view=rev
Author: mcourtot
Date: 2008-05-29 13:27:08 -0700 (Thu, 29 May 2008)
Log Message:
-----------
modified to compile only the designated files instead of everything in src. at the moment includes only the OBIMerger.java
Modified Paths:
--------------
trunk/src/tools/build/OBITools/buildJar.xml
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From: <mco...@us...> - 2008-05-29 19:19:49
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Revision: 666
http://obi.svn.sourceforge.net/obi/?rev=666&view=rev
Author: mcourtot
Date: 2008-05-29 12:19:57 -0700 (Thu, 29 May 2008)
Log Message:
-----------
moved obsolete role classes to obsolete file, removed extra axioms
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
trunk/src/ontology/branches/Role.owl
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From: <mco...@us...> - 2008-05-29 19:03:19
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Revision: 665
http://obi.svn.sourceforge.net/obi/?rev=665&view=rev
Author: mcourtot
Date: 2008-05-29 12:03:18 -0700 (Thu, 29 May 2008)
Log Message:
-----------
moved PA roles and Hypothesis under discussion
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <mco...@us...> - 2008-05-29 18:20:22
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Revision: 664
http://obi.svn.sourceforge.net/obi/?rev=664&view=rev
Author: mcourtot
Date: 2008-05-29 11:20:29 -0700 (Thu, 29 May 2008)
Log Message:
-----------
replaced all metadata incomplete curation status by metadata complete (via direct edit of the file, 138 replaced) as per JF request
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <mco...@us...> - 2008-05-29 18:09:31
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Revision: 663
http://obi.svn.sourceforge.net/obi/?rev=663&view=rev
Author: mcourtot
Date: 2008-05-29 11:09:38 -0700 (Thu, 29 May 2008)
Log Message:
-----------
moved obsolete classes investigation site role (and trial site role, its child)
precipitate role
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
trunk/src/ontology/branches/Role.owl
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From: <jen...@us...> - 2008-05-29 17:52:43
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Revision: 662
http://obi.svn.sourceforge.net/obi/?rev=662&view=rev
Author: jenfostel
Date: 2008-05-29 10:52:44 -0700 (Thu, 29 May 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <dan...@us...> - 2008-05-29 12:21:59
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Revision: 661
http://obi.svn.sourceforge.net/obi/?rev=661&view=rev
Author: daniel_schober
Date: 2008-05-29 05:22:06 -0700 (Thu, 29 May 2008)
Log Message:
-----------
Re-set curation status for alternative term, alternative term citation and alternative term tag to 'pending final vetting' (due to pending encoding issue)
Modified Paths:
--------------
trunk/src/ontology/branches/AnnotationProperty.owl
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