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From: <mco...@us...> - 2008-11-19 23:20:19
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Revision: 1188
http://obi.svn.sourceforge.net/obi/?rev=1188&view=rev
Author: mcourtot
Date: 2008-11-19 23:20:16 +0000 (Wed, 19 Nov 2008)
Log Message:
-----------
added to regex for $localname
if the name contains OBI yes, but OBI must be at the beginning of the name, otherwise we accept things like inverse_of_OBI_0000298. This is then parsed and OBI ID extracted, and the normal property which had the OBI ID 0000298 gets flagged has duplicate and re IDed.
Modified Paths:
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trunk/src/tools/build/modify-uris.pl
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From: <mco...@us...> - 2008-11-19 22:07:33
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Revision: 1187
http://obi.svn.sourceforge.net/obi/?rev=1187&view=rev
Author: mcourtot
Date: 2008-11-19 22:07:28 +0000 (Wed, 19 Nov 2008)
Log Message:
-----------
corrected wrong curation status
replaced http://purl.obofoundry.org/obo/obi/OBI_0000328 by http://purl.obofoundry.org/obo/OBI_0000328
replaced http://purl.obofoundry.org/obo/obi/OBI_0000319 by http://purl.obofoundry.org/obo/OBI_0000319
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <jen...@us...> - 2008-11-19 16:49:53
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Revision: 1186
http://obi.svn.sourceforge.net/obi/?rev=1186&view=rev
Author: jenfostel
Date: 2008-11-19 16:49:43 +0000 (Wed, 19 Nov 2008)
Log Message:
-----------
added "specified" prefix to input and output roles
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <jen...@us...> - 2008-11-19 15:51:17
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Revision: 1185
http://obi.svn.sourceforge.net/obi/?rev=1185&view=rev
Author: jenfostel
Date: 2008-11-19 15:51:14 +0000 (Wed, 19 Nov 2008)
Log Message:
-----------
changed input, output, participant, drug and reagent definitions to refer only to "entity"
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <jen...@us...> - 2008-11-19 15:42:21
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Revision: 1184
http://obi.svn.sourceforge.net/obi/?rev=1184&view=rev
Author: jenfostel
Date: 2008-11-19 15:42:17 +0000 (Wed, 19 Nov 2008)
Log Message:
-----------
added definitions and examples for output role and reagent role
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <jen...@us...> - 2008-11-19 15:21:47
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Revision: 1183
http://obi.svn.sourceforge.net/obi/?rev=1183&view=rev
Author: jenfostel
Date: 2008-11-19 15:21:42 +0000 (Wed, 19 Nov 2008)
Log Message:
-----------
working on study participant, input role and evaluant role; added to definition; added notes and example.
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <jen...@us...> - 2008-11-19 15:07:15
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Revision: 1182
http://obi.svn.sourceforge.net/obi/?rev=1182&view=rev
Author: jenfostel
Date: 2008-11-19 15:07:08 +0000 (Wed, 19 Nov 2008)
Log Message:
-----------
added example of usage to study participant
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <mco...@us...> - 2008-11-19 05:14:23
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Revision: 1181
http://obi.svn.sourceforge.net/obi/?rev=1181&view=rev
Author: mcourtot
Date: 2008-11-19 05:14:15 +0000 (Wed, 19 Nov 2008)
Log Message:
-----------
re-added disjoints and inferred superclasses - cleaned-up
Modified Paths:
--------------
trunk/src/tools/build/OBITools/OBITools.jar
trunk/src/tools/build/OBITools/src/ca/bccrc/obi/OBIMerger.java
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From: <mco...@us...> - 2008-11-19 03:36:24
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Revision: 1180
http://obi.svn.sourceforge.net/obi/?rev=1180&view=rev
Author: mcourtot
Date: 2008-11-19 03:36:18 +0000 (Wed, 19 Nov 2008)
Log Message:
-----------
added imported from annotation where it was missing
Modified Paths:
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trunk/src/ontology/branches/external-byhand.owl
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From: <mco...@us...> - 2008-11-18 20:20:23
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Revision: 1179
http://obi.svn.sourceforge.net/obi/?rev=1179&view=rev
Author: mcourtot
Date: 2008-11-18 20:20:20 +0000 (Tue, 18 Nov 2008)
Log Message:
-----------
corrected has_part restriction to has_function on optical filter, obscuration bar and microarray wash station
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <dan...@us...> - 2008-11-18 17:48:35
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Revision: 1178
http://obi.svn.sourceforge.net/obi/?rev=1178&view=rev
Author: daniel_schober
Date: 2008-11-18 17:48:32 +0000 (Tue, 18 Nov 2008)
Log Message:
-----------
made instrument by virtue of part a helperclass/placeholder, since it has no metadata
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <fgi...@us...> - 2008-11-18 15:24:26
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Revision: 1177
http://obi.svn.sourceforge.net/obi/?rev=1177&view=rev
Author: fgibson_sf
Date: 2008-11-18 15:24:05 +0000 (Tue, 18 Nov 2008)
Log Message:
-----------
changed has_output to has_specified_output
Modified Paths:
--------------
trunk/src/ontology/branches/Relations.owl
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From: <fgi...@us...> - 2008-11-18 14:14:50
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Revision: 1176
http://obi.svn.sourceforge.net/obi/?rev=1176&view=rev
Author: fgibson_sf
Date: 2008-11-18 14:14:39 +0000 (Tue, 18 Nov 2008)
Log Message:
-----------
added inverse of inheres_in which is beaer_of, updated curation status for other relations
Modified Paths:
--------------
trunk/src/ontology/branches/Relations.owl
trunk/src/ontology/branches/external-byhand.owl
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From: <mco...@us...> - 2008-11-18 06:09:39
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Revision: 1175
http://obi.svn.sourceforge.net/obi/?rev=1175&view=rev
Author: mcourtot
Date: 2008-11-18 06:09:35 +0000 (Tue, 18 Nov 2008)
Log Message:
-----------
restored renatured that had been deleted
Modified Paths:
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trunk/src/ontology/branches/Quality.owl
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From: <mco...@us...> - 2008-11-18 00:26:58
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Revision: 1174
http://obi.svn.sourceforge.net/obi/?rev=1174&view=rev
Author: mcourtot
Date: 2008-11-18 00:26:56 +0000 (Tue, 18 Nov 2008)
Log Message:
-----------
moved hierarchy under conclusion (assessment and children) which were stored in the Role.owl file to the DigitalEntityPLus.owl file
Modified Paths:
--------------
trunk/src/ontology/branches/DigitalEntityPlus.owl
trunk/src/ontology/branches/Role.owl
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From: <mco...@us...> - 2008-11-17 23:24:11
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Revision: 1173
http://obi.svn.sourceforge.net/obi/?rev=1173&view=rev
Author: mcourtot
Date: 2008-11-17 23:24:03 +0000 (Mon, 17 Nov 2008)
Log Message:
-----------
added IAO as local import for OBI.
Note that this version has had its import of OBO_REL modified to not conflict with OBI's current import of http://purl.org/obo/owl/ro - need a decision on this
I would favor updating ro.owl and import http://purl.org/obo/owl/OBO_REL in OBI
Added Paths:
-----------
trunk/src/ontology/external/IAO.owl
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From: <mco...@us...> - 2008-11-17 20:37:09
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Revision: 1172
http://obi.svn.sourceforge.net/obi/?rev=1172&view=rev
Author: mcourtot
Date: 2008-11-17 20:37:05 +0000 (Mon, 17 Nov 2008)
Log Message:
-----------
moved the class specimen role to Obsolete.owl
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
trunk/src/ontology/branches/Role.owl
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From: <mco...@us...> - 2008-11-17 20:34:57
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Revision: 1171
http://obi.svn.sourceforge.net/obi/?rev=1171&view=rev
Author: mcourtot
Date: 2008-11-17 20:34:54 +0000 (Mon, 17 Nov 2008)
Log Message:
-----------
replaced specimen_role (OBI_0000254) with biological_specimen_role (OBI_0000112), preceeding deprecation of specimen role as discussed on Role call on 17 Nov 2008: both classes were deemed synonyms
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <mco...@us...> - 2008-11-17 17:41:29
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Revision: 1170
http://obi.svn.sourceforge.net/obi/?rev=1170&view=rev
Author: mcourtot
Date: 2008-11-17 17:41:25 +0000 (Mon, 17 Nov 2008)
Log Message:
-----------
obsoleted chromium_release_assay_effector_role
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
trunk/src/ontology/branches/Role.owl
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From: <mco...@us...> - 2008-11-17 17:38:49
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Revision: 1169
http://obi.svn.sourceforge.net/obi/?rev=1169&view=rev
Author: mcourtot
Date: 2008-11-17 17:38:47 +0000 (Mon, 17 Nov 2008)
Log Message:
-----------
- moved input and output roles as sibling of reagent role under study participant role
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <mco...@us...> - 2008-11-14 22:36:52
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Revision: 1168
http://obi.svn.sourceforge.net/obi/?rev=1168&view=rev
Author: mcourtot
Date: 2008-11-14 22:36:46 +0000 (Fri, 14 Nov 2008)
Log Message:
-----------
added domain and range of inheres_in relation
Modified Paths:
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trunk/src/ontology/branches/external-byhand.owl
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From: <mco...@us...> - 2008-11-14 20:20:09
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Revision: 1167
http://obi.svn.sourceforge.net/obi/?rev=1167&view=rev
Author: mcourtot
Date: 2008-11-14 20:19:59 +0000 (Fri, 14 Nov 2008)
Log Message:
-----------
removed extra instances of curation status
Modified Paths:
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trunk/src/ontology/branches/Relations.owl
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From: <fgi...@us...> - 2008-11-14 19:04:55
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Revision: 1166
http://obi.svn.sourceforge.net/obi/?rev=1166&view=rev
Author: fgibson_sf
Date: 2008-11-14 19:04:44 +0000 (Fri, 14 Nov 2008)
Log Message:
-----------
update of relations branch based on call action items
Modified Paths:
--------------
trunk/src/ontology/branches/Relations.owl
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From: <mco...@us...> - 2008-11-14 18:12:48
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Revision: 1165
http://obi.svn.sourceforge.net/obi/?rev=1165&view=rev
Author: mcourtot
Date: 2008-11-14 18:12:44 +0000 (Fri, 14 Nov 2008)
Log Message:
-----------
moved cellular component and cell under material entity
Modified Paths:
--------------
trunk/src/ontology/branches/external.owl
trunk/src/ontology/branches/externalDerived.owl
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From: <bjo...@us...> - 2008-11-14 18:08:09
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Revision: 1164
http://obi.svn.sourceforge.net/obi/?rev=1164&view=rev
Author: bjoernpeters
Date: 2008-11-14 18:08:07 +0000 (Fri, 14 Nov 2008)
Log Message:
-----------
biomaterial call; modified the organism part definition and subclasses to match
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
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