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From: <al...@us...> - 2008-03-02 08:33:33
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Revision: 360
http://obi.svn.sourceforge.net/obi/?rev=360&view=rev
Author: alanr
Date: 2008-03-02 00:33:33 -0800 (Sun, 02 Mar 2008)
Log Message:
-----------
replace namespace declarations in all the files
Added Paths:
-----------
branchDevelopment/trunk/sourcecodes/normalize-namespaces.pl
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From: <al...@us...> - 2008-03-02 08:32:49
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Revision: 359
http://obi.svn.sourceforge.net/obi/?rev=359&view=rev
Author: alanr
Date: 2008-03-02 00:32:50 -0800 (Sun, 02 Mar 2008)
Log Message:
-----------
normalize the namespace declarations across all the files, arranged so
that protege doesn't make up any of it's own namespace prefixes
Modified Paths:
--------------
branchDevelopment/trunk/AnnotationProperty.owl
branchDevelopment/trunk/Biomaterial.owl
branchDevelopment/trunk/DataTransformation.owl
branchDevelopment/trunk/DigitalEntityPlus.owl
branchDevelopment/trunk/InstrumentAndPart.owl
branchDevelopment/trunk/OBI-Function.owl
branchDevelopment/trunk/Obsolete.owl
branchDevelopment/trunk/PlanAndPlannedProcess.owl
branchDevelopment/trunk/Quality.owl
branchDevelopment/trunk/Relations.owl
branchDevelopment/trunk/Role.owl
branchDevelopment/trunk/TheRest.owl
branchDevelopment/trunk/external.owl
branchDevelopment/trunk/externalDerived.owl
branchDevelopment/trunk/gather-class-uris.pl
branchDevelopment/trunk/obi-owl-full.owl
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From: <al...@us...> - 2008-03-02 04:04:56
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Revision: 358
http://obi.svn.sourceforge.net/obi/?rev=358&view=rev
Author: alanr
Date: 2008-03-01 20:05:00 -0800 (Sat, 01 Mar 2008)
Log Message:
-----------
Addressing tracker item 1905051 http://sourceforge.net/tracker/index.php?func=detail&aid=1905051&group_id=177891&atid=886178
Modified Paths:
--------------
branchDevelopment/trunk/PlanAndPlannedProcess.owl
branchDevelopment/trunk/external.owl
branchDevelopment/trunk/externalDerived.owl
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From: <bb...@us...> - 2008-03-01 23:27:51
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Revision: 357
http://obi.svn.sourceforge.net/obi/?rev=357&view=rev
Author: bbug
Date: 2008-03-01 15:27:56 -0800 (Sat, 01 Mar 2008)
Log Message:
-----------
dropped the Version tag. Its not a value svn:keyword and therefore cannot be substituted.
Modified Paths:
--------------
branchDevelopment/trunk/obi.owl.template
Property Changed:
----------------
branchDevelopment/trunk/obi.owl.template
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From: <bb...@us...> - 2008-03-01 23:20:03
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Revision: 356
http://obi.svn.sourceforge.net/obi/?rev=356&view=rev
Author: bbug
Date: 2008-03-01 15:20:03 -0800 (Sat, 01 Mar 2008)
Log Message:
-----------
trying to add a version number keyword to be substituted.
Modified Paths:
--------------
branchDevelopment/trunk/obi.owl.template
Property Changed:
----------------
branchDevelopment/trunk/obi.owl.template
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From: <bb...@us...> - 2008-03-01 22:06:31
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Revision: 355
http://obi.svn.sourceforge.net/obi/?rev=355&view=rev
Author: bbug
Date: 2008-03-01 14:05:47 -0800 (Sat, 01 Mar 2008)
Log Message:
-----------
trying a second time to fix the revision keyword.
Modified Paths:
--------------
branchDevelopment/trunk/obi.owl.template
Property Changed:
----------------
branchDevelopment/trunk/obi.owl.template
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From: <bb...@us...> - 2008-03-01 22:00:59
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Revision: 354
http://obi.svn.sourceforge.net/obi/?rev=354&view=rev
Author: bbug
Date: 2008-03-01 14:00:44 -0800 (Sat, 01 Mar 2008)
Log Message:
-----------
repaired the revision keyword in this file.
Modified Paths:
--------------
branchDevelopment/trunk/obi.owl.template
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From: <bb...@us...> - 2008-02-29 21:42:23
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Revision: 353
http://obi.svn.sourceforge.net/obi/?rev=353&view=rev
Author: bbug
Date: 2008-02-29 13:42:26 -0800 (Fri, 29 Feb 2008)
Log Message:
-----------
added Annotation Property EnumerationClass constraints and removed the direct import of protege-dc.owl
Modified Paths:
--------------
branchDevelopment/trunk/AnnotationProperty.owl
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From: <jen...@us...> - 2008-02-29 19:20:42
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Revision: 352
http://obi.svn.sourceforge.net/obi/?rev=352&view=rev
Author: jenfostel
Date: 2008-02-29 11:20:45 -0800 (Fri, 29 Feb 2008)
Log Message:
-----------
changed underscores to spaces in RF label
Modified Paths:
--------------
branchDevelopment/trunk/Role.owl
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From: <jen...@us...> - 2008-02-29 17:09:13
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Revision: 351
http://obi.svn.sourceforge.net/obi/?rev=351&view=rev
Author: jenfostel
Date: 2008-02-29 09:09:02 -0800 (Fri, 29 Feb 2008)
Log Message:
-----------
Completed the _role tags, fixed redundant reagent terms, added biological specimen terms from tracker
Modified Paths:
--------------
branchDevelopment/trunk/Role.owl
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From: <al...@us...> - 2008-02-29 16:45:43
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Revision: 350
http://obi.svn.sourceforge.net/obi/?rev=350&view=rev
Author: alanr
Date: 2008-02-29 08:45:48 -0800 (Fri, 29 Feb 2008)
Log Message:
-----------
oops - OBI_900003 -> OBI_303. Deleted wrong one
Modified Paths:
--------------
branchDevelopment/trunk/InstrumentAndPart.owl
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From: <al...@us...> - 2008-02-29 15:04:26
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Revision: 349
http://obi.svn.sourceforge.net/obi/?rev=349&view=rev
Author: alanr
Date: 2008-02-29 07:04:30 -0800 (Fri, 29 Feb 2008)
Log Message:
-----------
OBI_264 fix, OBI_900004 fix.
Modified Paths:
--------------
branchDevelopment/trunk/Biomaterial.owl
branchDevelopment/trunk/InstrumentAndPart.owl
branchDevelopment/trunk/TheRest.owl
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From: <bjo...@us...> - 2008-02-29 00:01:52
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Revision: 348
http://obi.svn.sourceforge.net/obi/?rev=348&view=rev
Author: bjoernpeters
Date: 2008-02-28 16:01:48 -0800 (Thu, 28 Feb 2008)
Log Message:
-----------
After todays PlanAndPlannedProcess, implements reorganization of top level plan hierarchy. Needs to be further coordinated with DENRIE branch. See todays emails for further clarification
Modified Paths:
--------------
branchDevelopment/trunk/PlanAndPlannedProcess.owl
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From: <mco...@us...> - 2008-02-28 18:58:01
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Revision: 347
http://obi.svn.sourceforge.net/obi/?rev=347&view=rev
Author: mcourtot
Date: 2008-02-28 10:57:57 -0800 (Thu, 28 Feb 2008)
Log Message:
-----------
added notes from developers call 20080227
Added Paths:
-----------
web/trunk/htdocs/notes/developers/2008/20080227.txt
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From: <bb...@us...> - 2008-02-28 00:02:25
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Revision: 346
http://obi.svn.sourceforge.net/obi/?rev=346&view=rev
Author: bbug
Date: 2008-02-27 16:02:30 -0800 (Wed, 27 Feb 2008)
Log Message:
-----------
Curation status enumeration class instances added to the AnnotationProperties file. Also added an import for protege-dc, since it defines DC RDF properties as owl:AnnotationProperties. Without protege-dc, the file is not OWL DL unless the DC properties used are explicitly declared as owl:AnnotationProperties.
Modified Paths:
--------------
branchDevelopment/trunk/AnnotationProperty.owl
branchDevelopment/trunk/OBI-Function.owl
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From: <jen...@us...> - 2008-02-27 16:29:52
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Revision: 345
http://obi.svn.sourceforge.net/obi/?rev=345&view=rev
Author: jenfostel
Date: 2008-02-27 08:29:55 -0800 (Wed, 27 Feb 2008)
Log Message:
-----------
organized role branch so that new terms are in class called "move to uses"; waiting for this branch to be defined
Modified Paths:
--------------
branchDevelopment/trunk/Role.owl
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From: <jen...@us...> - 2008-02-27 16:04:13
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Revision: 344
http://obi.svn.sourceforge.net/obi/?rev=344&view=rev
Author: jenfostel
Date: 2008-02-27 08:04:12 -0800 (Wed, 27 Feb 2008)
Log Message:
-----------
added _role to terms
Modified Paths:
--------------
branchDevelopment/trunk/Role.owl
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From: <al...@us...> - 2008-02-26 19:29:40
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Revision: 343
http://obi.svn.sourceforge.net/obi/?rev=343&view=rev
Author: alanr
Date: 2008-02-26 11:29:13 -0800 (Tue, 26 Feb 2008)
Log Message:
-----------
removed spurious Axiom_1 (protege)
Modified Paths:
--------------
branchDevelopment/trunk/InstrumentAndPart.owl
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From: <al...@us...> - 2008-02-26 19:23:02
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Revision: 342
http://obi.svn.sourceforge.net/obi/?rev=342&view=rev
Author: alanr
Date: 2008-02-26 11:21:36 -0800 (Tue, 26 Feb 2008)
Log Message:
-----------
more spurious import statements - protege?
Modified Paths:
--------------
branchDevelopment/trunk/Biomaterial.owl
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From: <mco...@us...> - 2008-02-25 22:25:35
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Revision: 341
http://obi.svn.sourceforge.net/obi/?rev=341&view=rev
Author: mcourtot
Date: 2008-02-25 14:24:49 -0800 (Mon, 25 Feb 2008)
Log Message:
-----------
corrected restrictions on test_synthetic peptide
Modified Paths:
--------------
branchDevelopment/trunk/Biomaterial.owl
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From: <dan...@us...> - 2008-02-25 15:02:32
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Revision: 340
http://obi.svn.sourceforge.net/obi/?rev=340&view=rev
Author: daniel_schober
Date: 2008-02-25 07:02:34 -0800 (Mon, 25 Feb 2008)
Log Message:
-----------
moved sex_effect under _to_be_fixed helper class and indicated _GO_Molecular_Function as helper class.
Modified Paths:
--------------
branchDevelopment/trunk/TheRest.owl
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From: <dan...@us...> - 2008-02-25 14:55:28
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Revision: 339
http://obi.svn.sourceforge.net/obi/?rev=339&view=rev
Author: daniel_schober
Date: 2008-02-25 06:55:15 -0800 (Mon, 25 Feb 2008)
Log Message:
-----------
made '_PATO_quality' follow naming convention for helper classes
Modified Paths:
--------------
branchDevelopment/trunk/TheRest.owl
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From: <dan...@us...> - 2008-02-25 14:46:09
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Revision: 338
http://obi.svn.sourceforge.net/obi/?rev=338&view=rev
Author: daniel_schober
Date: 2008-02-25 06:46:15 -0800 (Mon, 25 Feb 2008)
Log Message:
-----------
fixed '_to_be_fixed' to follow helper class naming convention (underscore prefix added)
Modified Paths:
--------------
branchDevelopment/trunk/TheRest.owl
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From: <dan...@us...> - 2008-02-25 14:27:50
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Revision: 337
http://obi.svn.sourceforge.net/obi/?rev=337&view=rev
Author: daniel_schober
Date: 2008-02-25 06:27:55 -0800 (Mon, 25 Feb 2008)
Log Message:
-----------
updated label of 'software' and made it subclass of 'to_be_fixed'helper class.
Modified Paths:
--------------
branchDevelopment/trunk/InstrumentAndPart.owl
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From: <p_r...@us...> - 2008-02-24 22:42:12
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Revision: 336
http://obi.svn.sourceforge.net/obi/?rev=336&view=rev
Author: p_rocca_serra
Date: 2008-02-24 14:42:07 -0800 (Sun, 24 Feb 2008)
Log Message:
-----------
changes to BM file:
creation of _CHEBI_object import placeholder class
-moved from 'unclassified with its childern
-moved biomolecule class with its children under _CHEBI_object
creation of a class Collection (metadata to be added)
-moved Population class as a child of collection
-moved Sample-population as a child of population
-moved cDNA library, Phage display library as children of Collection
PRS: 22-02-2008: screening library (from previously unclassified) was temporarily placed there but
while working on definition of cDNA library and looking at example of usage for screening library, a screening library should be a defined class -> any material library which has input_role in a screening protocol application
Under biomaterial
creation of helper class _move to role?
creation of helper class _move to protocol application?
-moved genetic_modification
note: need to check/submit to PATO 'genetically modified' as a quality
creation of helper class _move to information_content_entity? -> submission to tracker Item 1899832
-moved Genotype
-moved strain
-moved serotype
-moved genetic information content
creation of helper class _move to site?
-moved in_vivo biomaterial
-need to add in-vitro biomaterial (this is following discussion during Vancouver Meeting)
creation of helper class, "?a defined class is needed" where we put
-moved natural and artificial material
-moved ecotype
NOTE1: post call during file review,by the same line of reasoning, decided to move class 'experimental biomaterial entity' and children there
OK with everyone ?
NOTE2: For all classes placed underneath, I have created an editor note with a possible statement for creating the defined class.
I have based the statement on the proposal made by Bjoern.
I have also created a google spreadsheet similar to that used by DT and fill in the blancks
I have to update to add objectives and constraints
creation of helper class "move to quality"
-moved 'immortal cell' from cell and submit 'immortal' to PATO
addition of role to the following classes
-cell entity
-blood plasma
-blood serum
-virus
-viroid
-cultivar
-molecular mixture
-entity of organismal origin
-xenograft
-cDNA library
-phage display library
-screening library (but pay attention to point made earlier)
NOTE3:
I have not added anything to biomolecule as more work is required (monomer is not necessarily a biomolecule)
QUESTIONS:
under chemical entity we have 'peptide and polypeptide'
under unclassified we have 'fragment derived from protein'
under experimental biomaterial entity we have 'synthetic polypeptide'
I believe the last 2 could be defined classes
synthetic peptide = a peptide with output_role during chemical synthesis protocol application
I have created a test defined class with a 'has_role some (has_role some output_role)' restriction but I don't how to capture protocol_application = chemical synthesis (which by the way is absent from PA)
On the same line, need from members of BM-branch to review the Material Transformation spreadsheet
During the creation of the spreadsheet,I have noted we were missing organs and tissues
I have therefore created placeholders under multicellular entity of organismal origin (OBI_100057) with a mapping to 2 CARO entries.
(This is to help keep track of the things we may need to import/slurp using the procedure outlined by Alan and documented by Melanie.)
Modified Paths:
--------------
branchDevelopment/trunk/Biomaterial.owl
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