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From: <jzh...@us...> - 2013-02-27 23:39:19
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Revision: 3714
http://obi.svn.sourceforge.net/obi/?rev=3714&view=rev
Author: jzheng24
Date: 2013-02-27 23:39:13 +0000 (Wed, 27 Feb 2013)
Log Message:
-----------
correct wrong mapping recorded in the editor notes
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-02-27 23:34:43
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Revision: 3713
http://obi.svn.sourceforge.net/obi/?rev=3713&view=rev
Author: jzheng24
Date: 2013-02-27 23:34:29 +0000 (Wed, 27 Feb 2013)
Log Message:
-----------
correct wrong mapping recorded in the file
Modified Paths:
--------------
releases/2012-01-18/doc/BFO-RO-terms.xls
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From: <jzh...@us...> - 2013-02-27 23:18:11
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Revision: 3712
http://obi.svn.sourceforge.net/obi/?rev=3712&view=rev
Author: jzheng24
Date: 2013-02-27 23:18:05 +0000 (Wed, 27 Feb 2013)
Log Message:
-----------
correct wrong mapping recorded in the file
Modified Paths:
--------------
releases/2012-01-18/doc/BFO-RO-terms.txt
releases/2012-01-18/doc/BFO-RO-terms.xls
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From: <jzh...@us...> - 2013-02-19 18:09:20
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Revision: 3711
http://obi.svn.sourceforge.net/obi/?rev=3711&view=rev
Author: jzheng24
Date: 2013-02-19 18:09:13 +0000 (Tue, 19 Feb 2013)
Log Message:
-----------
Added 'ISA alternative term' requested by Alejandra Gonzalez-Beltran
https://sourceforge.net/tracker/?func=detail&aid=3603413&group_id=177891&atid=886178
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-02-08 17:18:10
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Revision: 3710
http://obi.svn.sourceforge.net/obi/?rev=3710&view=rev
Author: jzheng24
Date: 2013-02-08 17:18:03 +0000 (Fri, 08 Feb 2013)
Log Message:
-----------
correct ID for 'disease course' which should be OGMS_0000063 not OGMS_0000022
Modified Paths:
--------------
trunk/src/ontology/branches/external-byhand.owl
trunk/src/ontology/branches/external.owl
trunk/src/ontology/branches/obi.owl
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From: <bjo...@us...> - 2013-01-28 18:14:00
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Revision: 3709
http://obi.svn.sourceforge.net/obi/?rev=3709&view=rev
Author: bjoernpeters
Date: 2013-01-28 18:13:51 +0000 (Mon, 28 Jan 2013)
Log Message:
-----------
On the call, edited human subject enrollment, and participant under investigation role. Some edits still needed (in particular adding a 'enrolled human subject population', which uncomplicates the logical definitions, and clarifies that members of the population should also be considered 'under investigation'.
Modified Paths:
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trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-01-08 20:22:05
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Revision: 3708
http://obi.svn.sourceforge.net/obi/?rev=3708&view=rev
Author: jzheng24
Date: 2013-01-08 20:21:59 +0000 (Tue, 08 Jan 2013)
Log Message:
-----------
update the OWL files to working BFO1.2 compatible version
Modified Paths:
--------------
releases/2011-07-20-BFO1.2/branches/external-byhand.owl
releases/2011-07-20-BFO1.2/branches/external.owl
releases/2011-07-20-BFO1.2/branches/externalDerived.owl
releases/2011-07-20-BFO1.2/branches/obi.owl
releases/2011-07-20-BFO1.2/external/iao/IAO.owl
releases/2011-07-20-BFO1.2/external/iao/external.owl
releases/2011-07-20-BFO1.2/external/iao/externalByHand.owl
releases/2011-07-20-BFO1.2/external/iao/externalDerived.owl
releases/2011-07-20-BFO1.2/external/iao/iao-dev.owl
releases/2011-07-20-BFO1.2/external/iao/iao-main.owl
releases/2011-07-20-BFO1.2/external/iao/obsolete.owl
releases/2011-07-20-BFO1.2/external/iao/ontology-metadata.owl
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From: <mb...@us...> - 2013-01-07 19:35:20
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Revision: 3707
http://obi.svn.sourceforge.net/obi/?rev=3707&view=rev
Author: mbrush
Date: 2013-01-07 19:35:14 +0000 (Mon, 07 Jan 2013)
Log Message:
-----------
- implemented participates in at all times object property as placeholder for BFO2:participates in at all times (http://purl.obolibrary.org/obo/BFO_0000166) . . . needed to create logical definition for 'active cell culture' and 'actively cultured cell' classes.
- added required metadata to new cell/culture/line classes
- replaced usage of 'has granular part' with 'has grain'
- updated textual def of cultured cell (to reflect update in CL-edit.owl)
Modified Paths:
--------------
trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/obi.owl
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From: <mb...@us...> - 2013-01-06 17:59:58
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Revision: 3706
http://obi.svn.sourceforge.net/obi/?rev=3706&view=rev
Author: mbrush
Date: 2013-01-06 17:59:52 +0000 (Sun, 06 Jan 2013)
Log Message:
-----------
added 'actively cultured cell' and 'active cell culture sample' classes, updated metadata for new cell/culture sample classes
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <mb...@us...> - 2013-01-04 21:58:16
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Revision: 3705
http://obi.svn.sourceforge.net/obi/?rev=3705&view=rev
Author: mbrush
Date: 2013-01-04 21:58:10 +0000 (Fri, 04 Jan 2013)
Log Message:
-----------
- mireoted from CL: experimentally modified cell in vitro, cultured cell, primary cultured cell, cell line cell, mortal cell line cell, immortal cell line cell
- added axioms to primary cultured cell and cell line cell, mortal cell line cell
- obsoleted immortal cell (replaced by 'CL:immortal cell line cell'), and cell line cell (replaced by CL:cell line cell)
- added a cell culture sample hierarcy comprised of new OBI classes: cell culture sample, cell line sample, immortal cell line sample, mortal cell line sample, primary cell culture sample, cell line
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...> - 2013-01-04 00:12:59
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Revision: 3704
http://obi.svn.sourceforge.net/obi/?rev=3704&view=rev
Author: jzheng24
Date: 2013-01-04 00:12:40 +0000 (Fri, 04 Jan 2013)
Log Message:
-----------
testing BFO version converter tool developed by He group by updating OBI and IAO to BFO 1.2 version
Added Paths:
-----------
releases/2011-07-20-BFO1.2/
releases/2011-07-20-BFO1.2/branches/
releases/2011-07-20-BFO1.2/branches/catalog-v001.xml
releases/2011-07-20-BFO1.2/branches/external-byhand.owl
releases/2011-07-20-BFO1.2/branches/external.owl
releases/2011-07-20-BFO1.2/branches/externalDerived.owl
releases/2011-07-20-BFO1.2/branches/obi.owl
releases/2011-07-20-BFO1.2/doc/
releases/2011-07-20-BFO1.2/doc/OBIrelease-SVN-disjoint.sh
releases/2011-07-20-BFO1.2/doc/OBIrelease-qualityCheck.txt
releases/2011-07-20-BFO1.2/doc/PruneSubClasses.java
releases/2011-07-20-BFO1.2/doc/readme.txt
releases/2011-07-20-BFO1.2/doc/uncurated-terms.txt
releases/2011-07-20-BFO1.2/external/
releases/2011-07-20-BFO1.2/external/bfo.owl
releases/2011-07-20-BFO1.2/external/bfo11.owl
releases/2011-07-20-BFO1.2/external/iao/
releases/2011-07-20-BFO1.2/external/iao/IAO.owl
releases/2011-07-20-BFO1.2/external/iao/external.owl
releases/2011-07-20-BFO1.2/external/iao/externalByHand.owl
releases/2011-07-20-BFO1.2/external/iao/externalDerived.owl
releases/2011-07-20-BFO1.2/external/iao/iao-dev.owl
releases/2011-07-20-BFO1.2/external/iao/iao-main.owl
releases/2011-07-20-BFO1.2/external/iao/obsolete.owl
releases/2011-07-20-BFO1.2/external/iao/ontology-metadata.owl
releases/2011-07-20-BFO1.2/external/protege-dc.owl
releases/2011-07-20-BFO1.2/external/protege.owl
releases/2011-07-20-BFO1.2/external/ro.owl
releases/2011-07-20-BFO1.2/external/ro_bfo_bridge11.owl
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From: <jzh...@us...> - 2013-01-02 18:24:17
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Revision: 3703
http://obi.svn.sourceforge.net/obi/?rev=3703&view=rev
Author: jzheng24
Date: 2013-01-02 18:24:11 +0000 (Wed, 02 Jan 2013)
Log Message:
-----------
details of OBI IDs assigned to newly added terms
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/
trunk/src/ontology/spreadsheets/new_ids/newIDs_20130102.tab
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From: <jzh...@us...> - 2013-01-02 18:23:41
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Revision: 3702
http://obi.svn.sourceforge.net/obi/?rev=3702&view=rev
Author: jzheng24
Date: 2013-01-02 18:23:31 +0000 (Wed, 02 Jan 2013)
Log Message:
-----------
assign OBI ids to 104 newly added terms
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-01-02 17:01:41
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Revision: 3701
http://obi.svn.sourceforge.net/obi/?rev=3701&view=rev
Author: jzheng24
Date: 2013-01-02 17:01:34 +0000 (Wed, 02 Jan 2013)
Log Message:
-----------
Add new term 'specimen collector role'
Add Christian Bolling and Matthew Brush as creators
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2012-12-18 16:31:00
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Revision: 3700
http://obi.svn.sourceforge.net/obi/?rev=3700&view=rev
Author: jamesaoverton
Date: 2012-12-18 16:30:53 +0000 (Tue, 18 Dec 2012)
Log Message:
-----------
OBI Core review changes to: device, acquisition, material acquisition, information acquisition.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2012-12-10 18:23:09
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Revision: 3699
http://obi.svn.sourceforge.net/obi/?rev=3699&view=rev
Author: jamesaoverton
Date: 2012-12-10 18:22:57 +0000 (Mon, 10 Dec 2012)
Log Message:
-----------
Updating dependent, independent, and controlled variable specification terms based on developer's call 2012-12-10.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2012-12-03 18:31:40
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Revision: 3698
http://obi.svn.sourceforge.net/obi/?rev=3698&view=rev
Author: jamesaoverton
Date: 2012-12-03 18:31:34 +0000 (Mon, 03 Dec 2012)
Log Message:
-----------
Based on 2012-11-26 OBI call, renaming 'study subject role', adding editor note, and revising examples.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2012-12-03 18:29:37
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Revision: 3697
http://obi.svn.sourceforge.net/obi/?rev=3697&view=rev
Author: jamesaoverton
Date: 2012-12-03 18:29:26 +0000 (Mon, 03 Dec 2012)
Log Message:
-----------
Based on 2012-12-03 OBI call, slight modification to textual definition of assay (added 'physical examination to distinguish from prediction) and to logical definition of data transformation (refer to 'algorithm' rather than just 'plan specification').
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <rv...@us...> - 2012-11-29 00:51:53
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Revision: 3696
http://obi.svn.sourceforge.net/obi/?rev=3696&view=rev
Author: rvita
Date: 2012-11-29 00:51:47 +0000 (Thu, 29 Nov 2012)
Log Message:
-----------
edited iedb alternative terms for existing T cell assays to make chemokine nomenclature consistent
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <p_r...@us...> - 2012-11-27 11:45:53
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Revision: 3695
http://obi.svn.sourceforge.net/obi/?rev=3695&view=rev
Author: p_rocca_serra
Date: 2012-11-27 11:45:43 +0000 (Tue, 27 Nov 2012)
Log Message:
-----------
creation of selection_rule class, adding restriction to acquisition , adding realises/concretizes eligility rule to human subject enrollement class, fixing typos in definitions of acquisition related classes (posession/possession)
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <p_r...@us...> - 2012-11-27 10:17:02
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Revision: 3694
http://obi.svn.sourceforge.net/obi/?rev=3694&view=rev
Author: p_rocca_serra
Date: 2012-11-27 10:16:51 +0000 (Tue, 27 Nov 2012)
Log Message:
-----------
adding editor notes capturing resolution of core class review investigation and study subject role
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2012-11-19 19:51:33
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Revision: 3693
http://obi.svn.sourceforge.net/obi/?rev=3693&view=rev
Author: jamesaoverton
Date: 2012-11-19 19:51:26 +0000 (Mon, 19 Nov 2012)
Log Message:
-----------
Made changes discussed on the 2012-11-12 OBI development call.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <rv...@us...> - 2012-11-17 02:38:15
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Revision: 3692
http://obi.svn.sourceforge.net/obi/?rev=3692&view=rev
Author: rvita
Date: 2012-11-17 02:38:09 +0000 (Sat, 17 Nov 2012)
Log Message:
-----------
added new IEDB T cell cytokine assays via mapping master, following same pattern as previous assays
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <rv...@us...> - 2012-11-12 23:51:49
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Revision: 3691
http://obi.svn.sourceforge.net/obi/?rev=3691&view=rev
Author: rvita
Date: 2012-11-12 23:51:43 +0000 (Mon, 12 Nov 2012)
Log Message:
-----------
imported GO chemokine production terms for IEDB T cell assays
Modified Paths:
--------------
trunk/src/ontology/branches/external-byhand.owl
trunk/src/ontology/branches/external.owl
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From: <cb...@us...> - 2012-10-29 15:28:16
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Revision: 3690
http://obi.svn.sourceforge.net/obi/?rev=3690&view=rev
Author: cbosfn
Date: 2012-10-29 15:28:07 +0000 (Mon, 29 Oct 2012)
Log Message:
-----------
Implemented review related changes.
Added axiom obi:investigation subClassOf has_part some obi:drawing a conclusion
Removed axiom obi:investigation subClassOf has specified output iao:conclusion textual entity.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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