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From: <dan...@us...> - 2008-05-29 11:17:31
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Revision: 660
http://obi.svn.sourceforge.net/obi/?rev=660&view=rev
Author: daniel_schober
Date: 2008-05-29 04:17:39 -0700 (Thu, 29 May 2008)
Log Message:
-----------
Added curation status values to all metadata annotation properties and 'curation status' class. Some definitions were updated, e.g. the 'curation status' class def now reflects the updated enumerated instance list.
Experimental annotation properties that were added without group approval were added the curation status 'uncurated'.
Modified Paths:
--------------
trunk/src/ontology/branches/AnnotationProperty.owl
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From: <dan...@us...> - 2008-05-29 10:19:27
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Revision: 659
http://obi.svn.sourceforge.net/obi/?rev=659&view=rev
Author: daniel_schober
Date: 2008-05-29 03:19:35 -0700 (Thu, 29 May 2008)
Log Message:
-----------
a preferred term was added to all agreed upon OBI metadata tags/annotation properties
Modified Paths:
--------------
trunk/src/ontology/branches/AnnotationProperty.owl
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From: <dan...@us...> - 2008-05-29 09:46:13
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Revision: 658
http://obi.svn.sourceforge.net/obi/?rev=658&view=rev
Author: daniel_schober
Date: 2008-05-29 02:46:20 -0700 (Thu, 29 May 2008)
Log Message:
-----------
I added missing metadata to our metadata: definition source and definition editor were set as follows for all annotation properties (and the curation status class) that were agreed upon by the group. Alans new, experimental ones were not touched.
<OBI_0000279 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GROUP:OBI:http://obi.sourceforge.net</OBI_0000279>
<OBI_0000274 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">PERSON:Daniel Schober</OBI_0000274>
Modified Paths:
--------------
trunk/src/ontology/branches/AnnotationProperty.owl
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From: <al...@us...> - 2008-05-29 03:51:25
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Revision: 657
http://obi.svn.sourceforge.net/obi/?rev=657&view=rev
Author: alanr
Date: 2008-05-28 20:51:33 -0700 (Wed, 28 May 2008)
Log Message:
-----------
preparing for release
Added Paths:
-----------
tags/releases/2008-05-30/
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From: <p_r...@us...> - 2008-05-28 23:06:47
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Revision: 656
http://obi.svn.sourceforge.net/obi/?rev=656&view=rev
Author: p_rocca_serra
Date: 2008-05-28 16:06:55 -0700 (Wed, 28 May 2008)
Log Message:
-----------
PRS: Modification of restriction on biomaterial class in order to reflect change from specimen_role to biological specimen role
-restriction modified also at level of entity of organism original
-cell culture supernatant and whole mount tissue removed from asserted hierarchy under entity of organismal origin and placed under material.
for both class, restriction added such that both have 'has_role some (reagent role or biological specimen role)
for cell culture supernant, restriction added is 'is output of some isolation of cell culture supernatant (process)
for whole mount tissue, restriction added is 'is output of some histological preparation
Running Pellet classifier does not report pb (except centrifuge being inconsistent)
Entity of organism origin is classified under biomaterial as expected
cell culture supernatnat is classified under Entity of organism origin as expected just like whole mount tissue.
Need to do the same of all other asserted class. Process is painfull due to protege bug which add additional (not wanted) statements to restrictions .
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
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From: <mco...@us...> - 2008-05-28 21:48:17
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Revision: 655
http://obi.svn.sourceforge.net/obi/?rev=655&view=rev
Author: mcourtot
Date: 2008-05-28 14:48:25 -0700 (Wed, 28 May 2008)
Log Message:
-----------
reorganized directories, created merged directory to ease SVN commit
Modified Paths:
--------------
trunk/src/tools/build/OBIrelease.sh
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From: <mco...@us...> - 2008-05-28 21:20:59
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Revision: 654
http://obi.svn.sourceforge.net/obi/?rev=654&view=rev
Author: mcourtot
Date: 2008-05-28 14:21:05 -0700 (Wed, 28 May 2008)
Log Message:
-----------
corrected uri of experimental biomaterial entity and its curation status
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
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From: <bjo...@us...> - 2008-05-28 14:17:19
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Revision: 653
http://obi.svn.sourceforge.net/obi/?rev=653&view=rev
Author: bjoernpeters
Date: 2008-05-28 07:17:26 -0700 (Wed, 28 May 2008)
Log Message:
-----------
Modified Paths:
--------------
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
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From: <bjo...@us...> - 2008-05-28 13:51:21
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Revision: 652
http://obi.svn.sourceforge.net/obi/?rev=652&view=rev
Author: bjoernpeters
Date: 2008-05-28 06:51:19 -0700 (Wed, 28 May 2008)
Log Message:
-----------
Modified Paths:
--------------
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
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From: <jam...@us...> - 2008-05-28 08:49:03
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Revision: 651
http://obi.svn.sourceforge.net/obi/?rev=651&view=rev
Author: jamesmalone
Date: 2008-05-28 01:49:11 -0700 (Wed, 28 May 2008)
Log Message:
-----------
First draft outline of OBI poster for ISMB main session
Added Paths:
-----------
trunk/docs/developer/posters/obi_ismb_poster.ppt
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From: <jam...@us...> - 2008-05-28 08:45:37
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Revision: 650
http://obi.svn.sourceforge.net/obi/?rev=650&view=rev
Author: jamesmalone
Date: 2008-05-28 01:45:44 -0700 (Wed, 28 May 2008)
Log Message:
-----------
new folder for storing posters
Added Paths:
-----------
trunk/docs/developer/posters/
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From: <mco...@us...> - 2008-05-27 22:38:39
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Revision: 649
http://obi.svn.sourceforge.net/obi/?rev=649&view=rev
Author: mcourtot
Date: 2008-05-27 15:38:25 -0700 (Tue, 27 May 2008)
Log Message:
-----------
added logo of OBI as provided by Jennifer
Added Paths:
-----------
web/trunk/htdocs/images/obilogo.jpg
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From: <bjo...@us...> - 2008-05-27 02:44:22
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Revision: 648
http://obi.svn.sourceforge.net/obi/?rev=648&view=rev
Author: bjoernpeters
Date: 2008-05-26 19:44:27 -0700 (Mon, 26 May 2008)
Log Message:
-----------
Modified Paths:
--------------
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
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From: <bjo...@us...> - 2008-05-24 04:47:05
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Revision: 647
http://obi.svn.sourceforge.net/obi/?rev=647&view=rev
Author: bjoernpeters
Date: 2008-05-23 21:47:08 -0700 (Fri, 23 May 2008)
Log Message:
-----------
Modified Paths:
--------------
branches/bpbranch/branches/DigitalEntityPlus.owl
branches/bpbranch/branches/InstrumentAndPart.owl
branches/bpbranch/branches/PlanAndPlannedProcess.owl
branches/bpbranch/branches/TheRest.owl
Added Paths:
-----------
branches/bpbranch/branches/changes.txt
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From: <bjo...@us...> - 2008-05-24 02:09:17
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Revision: 646
http://obi.svn.sourceforge.net/obi/?rev=646&view=rev
Author: bjoernpeters
Date: 2008-05-23 19:09:24 -0700 (Fri, 23 May 2008)
Log Message:
-----------
made a copy
Added Paths:
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branches/bpbranch/
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From: <mco...@us...> - 2008-05-22 22:55:18
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Revision: 645
http://obi.svn.sourceforge.net/obi/?rev=645&view=rev
Author: mcourtot
Date: 2008-05-22 15:55:26 -0700 (Thu, 22 May 2008)
Log Message:
-----------
corrected metadata of cell: removed definition editors and sources, and curation status as this term is imported from Cell Ontology
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
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From: <mco...@us...> - 2008-05-22 21:17:52
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Revision: 644
http://obi.svn.sourceforge.net/obi/?rev=644&view=rev
Author: mcourtot
Date: 2008-05-22 14:17:20 -0700 (Thu, 22 May 2008)
Log Message:
-----------
notes from dev call 20080521
Added Paths:
-----------
web/trunk/htdocs/notes/developers/2008/20080521.txt
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From: <bjo...@us...> - 2008-05-22 16:46:38
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Revision: 643
http://obi.svn.sourceforge.net/obi/?rev=643&view=rev
Author: bjoernpeters
Date: 2008-05-22 08:48:19 -0700 (Thu, 22 May 2008)
Log Message:
-----------
investigation definition and associated reorganization of process branch
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <man...@us...> - 2008-05-22 15:38:52
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Revision: 642
http://obi.svn.sourceforge.net/obi/?rev=642&view=rev
Author: manduchi
Date: 2008-05-22 08:38:32 -0700 (Thu, 22 May 2008)
Log Message:
-----------
includes comments from conference all on 05/22/08, file review completed
Modified Paths:
--------------
trunk/docs/developer/DT/GenePatternUseCases.xls
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From: <p_r...@us...> - 2008-05-22 07:35:22
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Revision: 641
http://obi.svn.sourceforge.net/obi/?rev=641&view=rev
Author: p_rocca_serra
Date: 2008-05-22 00:35:28 -0700 (Thu, 22 May 2008)
Log Message:
-----------
PRS: retrofit of :
<owl:Class rdf:about="OBI_0100059">
<rdfs:subClassOf>
<owl:Class rdf:about="OBI_0302712"/>
</rdfs:subClassOf>
<OBI_0000287 xml:lang="en">example_of_usage to be added</ OBI_0000287>
<OBI_0000288 xml:lang="en">experimental biomateral entity</ OBI_0000288>
<OBI_0000281 rdf:resource="OBI_0000320"/>
<OBI_0000275 xml:lang="en">DS: what is this? Does the 'experimental' here refer to the biomaterials role in an experiment? Or does this refer to the metadata level, e.g. indicating this class' experimental status?</OBI_0000275>
<rdfs:label xml:lang="en">experimental biomateral entity</ rdfs:label>
</owl:Class>
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
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From: <bjo...@us...> - 2008-05-22 04:14:33
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Revision: 640
http://obi.svn.sourceforge.net/obi/?rev=640&view=rev
Author: bjoernpeters
Date: 2008-05-21 21:14:40 -0700 (Wed, 21 May 2008)
Log Message:
-----------
first half of the investigation re-definition
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <bjo...@us...> - 2008-05-22 03:16:15
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Revision: 639
http://obi.svn.sourceforge.net/obi/?rev=639&view=rev
Author: bjoernpeters
Date: 2008-05-21 20:16:23 -0700 (Wed, 21 May 2008)
Log Message:
-----------
Update to PC specific instructions
Modified Paths:
--------------
trunk/docs/developer/instructions-svn-local.txt
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From: <p_r...@us...> - 2008-05-21 20:21:03
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Revision: 638
http://obi.svn.sourceforge.net/obi/?rev=638&view=rev
Author: p_rocca_serra
Date: 2008-05-21 13:20:25 -0700 (Wed, 21 May 2008)
Log Message:
-----------
PRS: 'restoring' deleted classes from Biomaterial to Obsolete.owl and flatening obsoleted structures coming from biomaterial
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
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From: <p_r...@us...> - 2008-05-21 20:17:38
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Revision: 637
http://obi.svn.sourceforge.net/obi/?rev=637&view=rev
Author: p_rocca_serra
Date: 2008-05-21 13:16:57 -0700 (Wed, 21 May 2008)
Log Message:
-----------
PRS: restoring deleting classes to obsolote.owl
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
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From: <jam...@us...> - 2008-05-21 08:37:46
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Revision: 636
http://obi.svn.sourceforge.net/obi/?rev=636&view=rev
Author: jamesmalone
Date: 2008-05-21 01:37:30 -0700 (Wed, 21 May 2008)
Log Message:
-----------
Fix to PLS-DA, DT and submatrix extraction classes.
Modified Paths:
--------------
trunk/src/ontology/branches/DataTransformation.owl
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