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From: <al...@us...> - 2009-08-06 05:57:57
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Revision: 1936
http://obi.svn.sourceforge.net/obi/?rev=1936&view=rev
Author: alanr
Date: 2009-08-06 05:57:48 +0000 (Thu, 06 Aug 2009)
Log Message:
-----------
add obsolete-report.lisp
Modified Paths:
--------------
trunk/src/tools/build/obi.asd
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From: <al...@us...> - 2009-08-06 05:48:47
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Revision: 1935
http://obi.svn.sourceforge.net/obi/?rev=1935&view=rev
Author: alanr
Date: 2009-08-06 05:48:37 +0000 (Thu, 06 Aug 2009)
Log Message:
-----------
(report-users-of-obsolete kb)
->
patent content(OBI_0000028) uses obsolete_narrative object
metabolite profiling(OBI_0000366) uses obsolete_environmental matter
electronic case report form(OBI_0000167) uses obsolete_digital document
electronic case report tabulation(OBI_0000083) uses obsolete_digital document
eSource document(OBI_0000158) uses obsolete_digital document
eMedical record(OBI_0000078) uses obsolete_digital document
gene list visualization(OBI_0200191) uses obsolete_report table
cloning insert role(OBI_0000416) uses obsolete_recombinant plasmid construction
list-mode data file(OBI_0000021) uses obsolete_binary digital entity
investigation results report(OBI_0000218) uses obsolete_report
journal article content(IAO_0000013) uses obsolete_report
obsolete_report element(IAO_0000091) uses obsolete_report
analytical cytology data file(OBI_0000210) uses obsolete_digital entity
Added Paths:
-----------
trunk/src/tools/build/obsolete-report.lisp
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From: <al...@us...> - 2009-08-05 06:10:17
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Revision: 1934
http://obi.svn.sourceforge.net/obi/?rev=1934&view=rev
Author: alanr
Date: 2009-08-05 06:10:09 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
minor fixes to annotation properties found during qc checks for release
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
trunk/src/ontology/branches/InstrumentAndPart.owl
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <al...@us...> - 2009-08-05 06:05:41
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Revision: 1933
http://obi.svn.sourceforge.net/obi/?rev=1933&view=rev
Author: alanr
Date: 2009-08-05 06:05:33 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
Another IAO_0000117->IAO_0000116 fix
Multiline value for (definition editor)(!obi:IAO_0000117) on (liquid handler)(!obi:OBI_0400112):
-----
DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses.
TW: This is required by MO.
FG & DS: Capture as function.
All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class.
The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation.
-----
Modified Paths:
--------------
releases/2009-07-31/branches/InstrumentAndPart.owl
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From: <al...@us...> - 2009-08-05 06:03:11
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Revision: 1932
http://obi.svn.sourceforge.net/obi/?rev=1932&view=rev
Author: alanr
Date: 2009-08-05 06:03:03 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
Used IAO_0000117 instead of IAO_0000116 - fixed
CL-USER> (malformed-metadata kb)
Multiline value for (definition editor)(!obi:IAO_0000117) on (organism)(!obo:OBI_0100026):
-----
13-02-2009:
OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.
This issue is outside the scope of OBI.
-----
Modified Paths:
--------------
releases/2009-07-31/branches/Biomaterial.owl
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From: <al...@us...> - 2009-08-05 05:32:28
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Revision: 1931
http://obi.svn.sourceforge.net/obi/?rev=1931&view=rev
Author: alanr
Date: 2009-08-05 05:32:17 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
missing-curation qc-query: don't show obsolete classes
Modified Paths:
--------------
trunk/src/tools/build/qc-queries.lisp
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From: <al...@us...> - 2009-08-05 05:28:25
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Revision: 1930
http://obi.svn.sourceforge.net/obi/?rev=1930&view=rev
Author: alanr
Date: 2009-08-05 05:28:15 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
accidental use of owl:versioninfo instead of IAO_O000115 (definition)
Modified Paths:
--------------
releases/2009-07-31/branches/PlanAndPlannedProcess.owl
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From: <al...@us...> - 2009-08-05 05:04:27
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Revision: 1929
http://obi.svn.sourceforge.net/obi/?rev=1929&view=rev
Author: alanr
Date: 2009-08-05 05:04:21 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
add
Added Paths:
-----------
releases/2009-07-31/external/
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From: <mco...@us...> - 2009-08-05 01:09:19
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Revision: 1928
http://obi.svn.sourceforge.net/obi/?rev=1928&view=rev
Author: mcourtot
Date: 2009-08-05 01:09:11 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
repaired IDs for has_specified_participant
Modified Paths:
--------------
releases/2009-07-31/branches/Relations.owl
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From: <mco...@us...> - 2009-08-05 01:08:06
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Revision: 1927
http://obi.svn.sourceforge.net/obi/?rev=1927&view=rev
Author: mcourtot
Date: 2009-08-05 01:07:54 +0000 (Wed, 05 Aug 2009)
Log Message:
-----------
repaired IDs for has_specified_participant
Modified Paths:
--------------
trunk/src/ontology/branches/Relations.owl
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From: <al...@us...> - 2009-08-04 01:19:43
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Revision: 1926
http://obi.svn.sourceforge.net/obi/?rev=1926&view=rev
Author: alanr
Date: 2009-08-04 01:19:35 +0000 (Tue, 04 Aug 2009)
Log Message:
-----------
fix setting of xml:base when rewriting. good catch mc.
Modified Paths:
--------------
trunk/src/tools/build/rewrite-instances.lisp
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From: <mco...@us...> - 2009-08-03 16:51:28
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Revision: 1925
http://obi.svn.sourceforge.net/obi/?rev=1925&view=rev
Author: mcourtot
Date: 2009-08-03 16:51:16 +0000 (Mon, 03 Aug 2009)
Log Message:
-----------
added correct xml:base
Modified Paths:
--------------
trunk/src/ontology/branches/instances/dataTransformationInstances.owl
trunk/src/ontology/branches/instances/organizationInstances.owl
trunk/src/ontology/branches/instances/softwareInstances.owl
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From: <al...@us...> - 2009-08-02 10:22:17
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Revision: 1924
http://obi.svn.sourceforge.net/obi/?rev=1924&view=rev
Author: alanr
Date: 2009-08-02 10:22:04 +0000 (Sun, 02 Aug 2009)
Log Message:
-----------
review CHEBI terms from EFO
Added Paths:
-----------
trunk/src/ontology/spreadsheets/in/check-efo-chebi.lisp
trunk/src/ontology/spreadsheets/in/efo-chebi.txt
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From: <jzh...@us...> - 2009-07-31 23:45:41
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Revision: 1923
http://obi.svn.sourceforge.net/obi/?rev=1923&view=rev
Author: jzheng24
Date: 2009-07-31 23:45:27 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
rewrite instances uri
Added Paths:
-----------
releases/2009-07-31/uri-rewrites.txt
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From: <jzh...@us...> - 2009-07-31 23:44:43
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Revision: 1922
http://obi.svn.sourceforge.net/obi/?rev=1922&view=rev
Author: jzheng24
Date: 2009-07-31 23:44:37 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
File about uri generated during OBI release process
Added Paths:
-----------
releases/2009-07-31/uri-report.txt
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From: <jzh...@us...> - 2009-07-31 23:32:31
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Revision: 1921
http://obi.svn.sourceforge.net/obi/?rev=1921&view=rev
Author: jzheng24
Date: 2009-07-31 23:32:23 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
Copy files with assigned ids in Branches directory to releases directory for 2009-07-31 release
Added Paths:
-----------
releases/2009-07-31/branches/
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From: <jzh...@us...> - 2009-07-31 23:06:57
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Revision: 1920
http://obi.svn.sourceforge.net/obi/?rev=1920&view=rev
Author: jzheng24
Date: 2009-07-31 23:06:51 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
update files with new assigned ids
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/instances/dataTransformationInstances.owl
trunk/src/ontology/branches/instances/organizationInstances.owl
trunk/src/ontology/branches/instances/softwareInstances.owl
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From: <mco...@us...> - 2009-07-31 21:25:56
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Revision: 1919
http://obi.svn.sourceforge.net/obi/?rev=1919&view=rev
Author: mcourtot
Date: 2009-07-31 21:25:47 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
added iao/obsolete.owl
Modified Paths:
--------------
trunk/src/tools/build/OBIrelease.sh
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From: <mco...@us...> - 2009-07-31 21:05:10
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Revision: 1918
http://obi.svn.sourceforge.net/obi/?rev=1918&view=rev
Author: mcourtot
Date: 2009-07-31 21:04:56 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
updated
Modified Paths:
--------------
trunk/src/tools/build/OBIrelease.sh
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From: <al...@us...> - 2009-07-31 20:51:30
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Revision: 1917
http://obi.svn.sourceforge.net/obi/?rev=1917&view=rev
Author: alanr
Date: 2009-07-31 20:51:22 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
rdf:id cleanup consequences
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
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From: <al...@us...> - 2009-07-31 20:50:41
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Revision: 1916
http://obi.svn.sourceforge.net/obi/?rev=1916&view=rev
Author: alanr
Date: 2009-07-31 20:50:25 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
rdf:id cleanup consequences
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
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From: <al...@us...> - 2009-07-31 20:45:26
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Revision: 1915
http://obi.svn.sourceforge.net/obi/?rev=1915&view=rev
Author: alanr
Date: 2009-07-31 20:45:20 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
rdf:id evil
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <al...@us...> - 2009-07-31 20:43:09
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Revision: 1914
http://obi.svn.sourceforge.net/obi/?rev=1914&view=rev
Author: alanr
Date: 2009-07-31 20:42:49 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
rdf:ID = evil
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <al...@us...> - 2009-07-31 20:40:07
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Revision: 1913
http://obi.svn.sourceforge.net/obi/?rev=1913&view=rev
Author: alanr
Date: 2009-07-31 20:39:56 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
remove spurios imports!
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <jzh...@us...> - 2009-07-31 19:35:50
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Revision: 1912
http://obi.svn.sourceforge.net/obi/?rev=1912&view=rev
Author: jzheng24
Date: 2009-07-31 19:35:43 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
releases on 2009-07-31
Added Paths:
-----------
releases/2009-07-31/
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