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From: <jam...@us...> - 2013-04-06 15:25:19
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Revision: 3739
http://obi.svn.sourceforge.net/obi/?rev=3739&view=rev
Author: jamesaoverton
Date: 2013-04-06 15:25:11 +0000 (Sat, 06 Apr 2013)
Log Message:
-----------
Moving old build tools.
Added Paths:
-----------
trunk/src/tools/old-build/
Removed Paths:
-------------
trunk/src/tools/build/
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From: <jzh...@us...> - 2013-04-05 17:51:57
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Revision: 3738
http://obi.svn.sourceforge.net/obi/?rev=3738&view=rev
Author: jzheng24
Date: 2013-04-05 17:51:44 +0000 (Fri, 05 Apr 2013)
Log Message:
-----------
Add folder to hold all documents for 2013 Philly Workshop focusing on OBI core terms review
Added Paths:
-----------
trunk/docs/presentations/OBI workshop May 2013 Philly - core review/
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From: <jzh...@us...> - 2013-04-04 22:42:48
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Revision: 3737
http://obi.svn.sourceforge.net/obi/?rev=3737&view=rev
Author: jzheng24
Date: 2013-04-04 22:42:40 +0000 (Thu, 04 Apr 2013)
Log Message:
-----------
Add 'reagent' in OBI. Copied the metadata from REO and assigned OBI id: OBI_0001879
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-04-01 18:31:57
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Revision: 3736
http://obi.svn.sourceforge.net/obi/?rev=3736&view=rev
Author: jzheng24
Date: 2013-04-01 18:31:47 +0000 (Mon, 01 Apr 2013)
Log Message:
-----------
update ID of 'secondary cultured cell'
Modified Paths:
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trunk/src/ontology/branches/external.owl
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From: <jzh...@us...> - 2013-03-28 21:28:33
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Revision: 3735
http://obi.svn.sourceforge.net/obi/?rev=3735&view=rev
Author: jzheng24
Date: 2013-03-28 21:28:26 +0000 (Thu, 28 Mar 2013)
Log Message:
-----------
List of newly added OBI terms with their OBI ids
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20130328.tab
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From: <jzh...@us...> - 2013-03-28 21:27:34
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Revision: 3734
http://obi.svn.sourceforge.net/obi/?rev=3734&view=rev
Author: jzheng24
Date: 2013-03-28 21:27:28 +0000 (Thu, 28 Mar 2013)
Log Message:
-----------
Assign OBI ids to newly added terms
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-03-28 20:55:39
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Revision: 3733
http://obi.svn.sourceforge.net/obi/?rev=3733&view=rev
Author: jzheng24
Date: 2013-03-28 20:55:31 +0000 (Thu, 28 Mar 2013)
Log Message:
-----------
removed unwanted objectProperty 'paticipates_in_at__all_times'
Modified Paths:
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trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-03-28 20:33:34
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Revision: 3732
http://obi.svn.sourceforge.net/obi/?rev=3732&view=rev
Author: jzheng24
Date: 2013-03-28 20:33:27 +0000 (Thu, 28 Mar 2013)
Log Message:
-----------
Add ENCODE people submitted assay terms:
https://sourceforge.net/tracker/?func=detail&aid=3609025&group_id=177891&atid=886178
Modified Paths:
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trunk/src/ontology/branches/obi.owl
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From: <mb...@us...> - 2013-03-27 19:59:36
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Revision: 3731
http://obi.svn.sourceforge.net/obi/?rev=3731&view=rev
Author: mbrush
Date: 2013-03-27 19:59:26 +0000 (Wed, 27 Mar 2013)
Log Message:
-----------
- updated cell/culture terms based on recent CLO alignment work (mostly annotation/metadata updates)
- fixed URIs of establishing cell culture and establishing primary cell culture
- added alt term and comment to 'cell culture splitting, and axioms to reference active cell culture samples as input/output
- added maintaining cell culture subclasses to align with CLO classes
Modified Paths:
--------------
trunk/src/ontology/branches/external.owl
trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-03-27 00:54:52
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Revision: 3730
http://obi.svn.sourceforge.net/obi/?rev=3730&view=rev
Author: jzheng24
Date: 2013-03-27 00:54:44 +0000 (Wed, 27 Mar 2013)
Log Message:
-----------
Terms requested by ENCODE people has been added. Details see:
https://sourceforge.net/tracker/?func=detail&aid=3609025&group_id=177891&atid=886178
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-03-25 17:50:48
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Revision: 3729
http://obi.svn.sourceforge.net/obi/?rev=3729&view=rev
Author: jzheng24
Date: 2013-03-25 17:50:42 +0000 (Mon, 25 Mar 2013)
Log Message:
-----------
PCO ontology presented by Ramona Walls on March 25, 2013 OBI dev call.
Added Paths:
-----------
trunk/docs/presentations/PCO_Mar2013.pdf
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From: <mb...@us...> - 2013-03-22 23:15:14
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Revision: 3728
http://obi.svn.sourceforge.net/obi/?rev=3728&view=rev
Author: mbrush
Date: 2013-03-22 23:15:07 +0000 (Fri, 22 Mar 2013)
Log Message:
-----------
pres edits
Modified Paths:
--------------
trunk/docs/presentations/OBI-CLO-CL March 2013 Alignment/3-21-13_CLO-OBI_cell_culture_alignment.pptx
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From: <mb...@us...> - 2013-03-22 19:07:32
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Revision: 3727
http://obi.svn.sourceforge.net/obi/?rev=3727&view=rev
Author: mbrush
Date: 2013-03-22 19:07:24 +0000 (Fri, 22 Mar 2013)
Log Message:
-----------
minor updates
Modified Paths:
--------------
trunk/docs/presentations/OBI-CLO-CL March 2013 Alignment/3-21-13_CLO-OBI_cell_culture_alignment.pptx
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From: <mb...@us...> - 2013-03-22 19:03:57
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Revision: 3726
http://obi.svn.sourceforge.net/obi/?rev=3726&view=rev
Author: mbrush
Date: 2013-03-22 19:03:50 +0000 (Fri, 22 Mar 2013)
Log Message:
-----------
implemented 'genetic material' class according to decisions on dev calls
included the axiom: 'is part of' some (cell or Viruses)
Modified Paths:
--------------
trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/obi.owl
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From: <mb...@us...> - 2013-03-21 21:19:13
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Revision: 3725
http://obi.svn.sourceforge.net/obi/?rev=3725&view=rev
Author: mbrush
Date: 2013-03-21 21:19:05 +0000 (Thu, 21 Mar 2013)
Log Message:
-----------
adding docs for OBI-CLO alignment work
Added Paths:
-----------
trunk/docs/presentations/OBI-CLO-CL March 2013 Alignment/
trunk/docs/presentations/OBI-CLO-CL March 2013 Alignment/3-21-13_CLO-OBI_cell_culture_alignment.pptx
trunk/docs/presentations/OBI-CLO-CL March 2013 Alignment/obi_cell_line_3-21-13.owl
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From: <mb...@us...> - 2013-03-20 16:37:27
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Revision: 3724
http://obi.svn.sourceforge.net/obi/?rev=3724&view=rev
Author: mbrush
Date: 2013-03-20 16:37:13 +0000 (Wed, 20 Mar 2013)
Log Message:
-----------
- general editing of annotations on cell line/culture classes
- made estab cell culture a child of material processing
- made cultured cell a defined class
Modified Paths:
--------------
trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-03-15 22:38:31
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Revision: 3723
http://obi.svn.sourceforge.net/obi/?rev=3723&view=rev
Author: jzheng24
Date: 2013-03-15 22:38:24 +0000 (Fri, 15 Mar 2013)
Log Message:
-----------
Fixed issues reported by Venkat
Trackers:
https://sourceforge.net/tracker/?func=detail&aid=3607908&group_id=177891&atid=886178
https://sourceforge.net/tracker/?func=detail&aid=3607906&group_id=177891&atid=886178
https://sourceforge.net/tracker/?func=detail&aid=3607911&group_id=177891&atid=886178
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <mb...@us...> - 2013-03-08 20:19:10
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Revision: 3722
http://obi.svn.sourceforge.net/obi/?rev=3722&view=rev
Author: mbrush
Date: 2013-03-08 20:19:03 +0000 (Fri, 08 Mar 2013)
Log Message:
-----------
- axiom on cell culture sample: is_specified_output_of some 'material portioning'
- updated documentation on cell/culture classes
Modified Paths:
--------------
trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/obi.owl
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From: <mb...@us...> - 2013-03-07 20:12:58
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Revision: 3721
http://obi.svn.sourceforge.net/obi/?rev=3721&view=rev
Author: mbrush
Date: 2013-03-07 20:12:52 +0000 (Thu, 07 Mar 2013)
Log Message:
-----------
added def to establishing cell culture
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <mb...@us...> - 2013-03-07 20:09:38
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Revision: 3720
http://obi.svn.sourceforge.net/obi/?rev=3720&view=rev
Author: mbrush
Date: 2013-03-07 20:09:30 +0000 (Thu, 07 Mar 2013)
Log Message:
-----------
cell/culture modeling edits:
- replaced imported 'exp modified cell in vitro' class form CL with 'cell in vitro' class from CL
- MIREOTED in native cell from CL
- changed editor note on cell line cell
- updated axiom on estab primary cell culture to has spec output soem primary cell culture, and has spec input some native cell
- changed all axioms on sultures and culture sampels from has grain min 2 cell to has grain some cell
- changed labels of culture sampels to be culture portions (kep sampel as alternative term)
- created exploratory immortal cell line and mortal cell line classes
- merged existing 'cell culture' class and its subtypes with new cell culture sample classes (kept original URI, and any metadata that was still relevant, but relabeled classes and updated definitions for many)
Modified Paths:
--------------
trunk/src/ontology/branches/external.owl
trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/obi.owl
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From: <mb...@us...> - 2013-03-06 22:56:58
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Revision: 3719
http://obi.svn.sourceforge.net/obi/?rev=3719&view=rev
Author: mbrush
Date: 2013-03-06 22:56:51 +0000 (Wed, 06 Mar 2013)
Log Message:
-----------
- updated definitions and comments on cell culture sample, cell line sample, and primary cell culture sample, and cell line
- created new cell culture (exploratory) class as placeholder - added definition, comment, editor note, and axioms
- similarly, created new primary cell culture (exploratory) class as placeholder - added definition, comment, editor note, and axioms
- renamed 'estab cell culture' as 'establishing primary cell culture'
- created new establishing cell culture class - replaced some of old usages with this new class
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <mb...@us...> - 2013-03-05 23:48:44
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Revision: 3718
http://obi.svn.sourceforge.net/obi/?rev=3718&view=rev
Author: mbrush
Date: 2013-03-05 23:48:36 +0000 (Tue, 05 Mar 2013)
Log Message:
-----------
minor edits to cell/culture model
- moved cell line immortaliz and estab cancer cell line to be children of 'estab cell line'
- removed axiom from cell culture sample about being output of some establishment of cell culture
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <mb...@us...> - 2013-03-05 15:24:16
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Revision: 3717
http://obi.svn.sourceforge.net/obi/?rev=3717&view=rev
Author: mbrush
Date: 2013-03-05 15:24:10 +0000 (Tue, 05 Mar 2013)
Log Message:
-----------
fixed minor errors
Modified Paths:
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trunk/docs/developer/OBI Developer Call Presentations/3-4-13_OBI_GeneticMateiral.pptx
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From: <mb...@us...> - 2013-03-04 18:48:08
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Revision: 3716
http://obi.svn.sourceforge.net/obi/?rev=3716&view=rev
Author: mbrush
Date: 2013-03-04 18:48:02 +0000 (Mon, 04 Mar 2013)
Log Message:
-----------
uploaded 3-4-13 dev call presentation on 'genetic material'
Added Paths:
-----------
trunk/docs/developer/OBI Developer Call Presentations/3-4-13_OBI_GeneticMateiral.pptx
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From: <mb...@us...> - 2013-03-01 23:08:32
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Revision: 3715
http://obi.svn.sourceforge.net/obi/?rev=3715&view=rev
Author: mbrush
Date: 2013-03-01 23:08:25 +0000 (Fri, 01 Mar 2013)
Log Message:
-----------
cell/culture modeling refinement
- removed temp class participates in at all times, and replaced its usage in axioms on actively cultured cell, and active cell culture with 'participates in'
- cleaned up definitions/comments/notes on cell culture classes
- created class 'establishing cell line' as child of 'establishing cell culture'
- moved cell line to be child of cell culture, gave axioms formerly inherited from cell line sample, and gave axiom spec output of some establishing cell line
- changed curation status on cell line culture and immortal cell line culture to 'requires discussion'
- added editor note to cell culture and primary cell culture indicating their proposed future definition and use - vet with OBI before changing
- changed axiom on cell line cell to is_specified_output_of some 'establishing cell line'
- changed axioms on cell culture cell and cell line cell to (is_specified_output_of some 'establishing cell culture/line') or ('derives from' some (is_specified_output_of some 'establishing cell culture line'))
Modified Paths:
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trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/obi.owl
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