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obi-svn-commit
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From: <cto...@us...> - 2010-05-12 22:00:58
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Revision: 2939
http://obi.svn.sourceforge.net/obi/?rev=2939&view=rev
Author: ctorniai
Date: 2010-05-12 22:00:52 +0000 (Wed, 12 May 2010)
Log Message:
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Added QTT files for eagle-i functions and devices
Added Paths:
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trunk/src/ontology/branches/QTT_ERO_function_device.owl
trunk/src/ontology/branches/QTT_ERO_function_device.pprj
trunk/src/ontology/branches/QTT_ERO_function_device.repository
trunk/src/ontology/spreadsheets/QTT_ERO_function_device.xls
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From: <jzh...@us...> - 2012-04-19 14:48:46
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Revision: 3519
http://obi.svn.sourceforge.net/obi/?rev=3519&view=rev
Author: jzheng24
Date: 2012-04-19 14:48:37 +0000 (Thu, 19 Apr 2012)
Log Message:
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obi core (13 terms)
Added Paths:
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trunk/src/ontology/obi-view/
trunk/src/ontology/obi-view/obi-core/
trunk/src/ontology/obi-view/obi-core/CORE_insubset.owl
trunk/src/ontology/obi-view/obi-core/OBI_terms_input.xlsx
trunk/src/ontology/obi-view/obi-core/investigation-core-OBI.jpg
trunk/src/ontology/obi-view/obi-core/obi_core.owl
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From: <jzh...@us...> - 2013-04-19 19:27:36
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Revision: 3751
http://obi.svn.sourceforge.net/obi/?rev=3751&view=rev
Author: jzheng24
Date: 2013-04-19 19:27:30 +0000 (Fri, 19 Apr 2013)
Log Message:
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OBI ids were assigned to newly added terms
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20130404.tab
trunk/src/ontology/spreadsheets/new_ids/newIDs_20130419.tab
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From: <jam...@us...> - 2013-06-01 18:17:43
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Revision: 3783
http://obi.svn.sourceforge.net/obi/?rev=3783&view=rev
Author: jamesaoverton
Date: 2013-06-01 18:17:37 +0000 (Sat, 01 Jun 2013)
Log Message:
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Assigning IDs to two new classes: 'conclusion based on data' (OBI_0001909), 'testable hypothesis' (OBI_0001908).
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20130601.tab
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From: <jzh...@us...> - 2013-06-11 18:25:52
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Revision: 3800
http://obi.svn.sourceforge.net/obi/?rev=3800&view=rev
Author: jzheng24
Date: 2013-06-11 18:25:44 +0000 (Tue, 11 Jun 2013)
Log Message:
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assign OBI ids to newly added terms for OBI/CLO alignment
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20130611.tab
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From: <jzh...@us...> - 2013-06-12 16:45:25
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Revision: 3802
http://sourceforge.net/p/obi/code/3802
Author: jzheng24
Date: 2013-06-12 16:45:23 +0000 (Wed, 12 Jun 2013)
Log Message:
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OBI ids were assigned to newly added terms
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20130612.tab
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From: <jzh...@us...> - 2013-08-12 18:16:40
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Revision: 3818
http://sourceforge.net/p/obi/code/3818
Author: jzheng24
Date: 2013-08-12 18:16:37 +0000 (Mon, 12 Aug 2013)
Log Message:
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Import terms from external resources using OntoFox tool
For NCBITaxon terms, only include OBI used organism + model organisms
Added Paths:
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trunk/src/ontology/importUsingOntofox/
trunk/src/ontology/importUsingOntofox/ChEBI_imports.owl
trunk/src/ontology/importUsingOntofox/GO_imports.owl
trunk/src/ontology/importUsingOntofox/NCBITaxon_imports.owl
trunk/src/ontology/importUsingOntofox/OBO_imports.owl
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/ChEBI_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/GO_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/NCBITaxon_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/OBO_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/PATO_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/UO_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/UO_input_instance.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/summary_externalTermsl.xlsx
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/~$summary_externalTermsl.xlsx
trunk/src/ontology/importUsingOntofox/PATO_imports.owl
trunk/src/ontology/importUsingOntofox/UO_imports.owl
trunk/src/ontology/importUsingOntofox/UO_instance_imports.owl
trunk/src/ontology/importUsingOntofox/catalog-v001.xml
trunk/src/ontology/importUsingOntofox/external-byhand.owl
trunk/src/ontology/importUsingOntofox/modelOrganism.txt
trunk/src/ontology/importUsingOntofox/obi.owl
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From: <jzh...@us...> - 2013-09-30 15:23:44
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Revision: 3837
http://sourceforge.net/p/obi/code/3837
Author: jzheng24
Date: 2013-09-30 15:23:42 +0000 (Mon, 30 Sep 2013)
Log Message:
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assign OBI id to newly added term 'molecular-labeled material'
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20130930.tab
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From: <jzh...@us...> - 2013-11-14 00:31:05
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Revision: 3901
http://sourceforge.net/p/obi/code/3901
Author: jzheng24
Date: 2013-11-14 00:31:04 +0000 (Thu, 14 Nov 2013)
Log Message:
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Added new devices for ENCODE group. Details of the terms see the tracker:
https://sourceforge.net/p/obi/obi-terms/683/
OBI ids were assigned to the newly added terms.
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20131113.tab
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From: <jzh...@us...> - 2013-12-02 22:35:10
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Revision: 3908
http://sourceforge.net/p/obi/code/3908
Author: jzheng24
Date: 2013-12-02 22:35:07 +0000 (Mon, 02 Dec 2013)
Log Message:
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OBI ids were assigned to newly added terms
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20131202.tab
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From: <p_r...@us...> - 2013-12-16 15:30:17
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Revision: 3912
http://sourceforge.net/p/obi/code/3912
Author: p_rocca_serra
Date: 2013-12-16 15:30:14 +0000 (Mon, 16 Dec 2013)
Log Message:
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edit to N50,genome coverage and sequence assembly process restrictions to clarify directionality
Modified Paths:
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trunk/src/ontology/branches/OntoFox_outputs/SO_imports.owl
trunk/src/ontology/branches/obi.owl
trunk/src/ontology/importUsingOntofox/catalog-v001.xml
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From: <jzh...@us...> - 2013-12-21 06:15:02
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Revision: 3915
http://sourceforge.net/p/obi/code/3915
Author: jzheng24
Date: 2013-12-21 06:14:59 +0000 (Sat, 21 Dec 2013)
Log Message:
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assign OBI ids to newly added terms
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20131221.tab
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From: <jzh...@us...> - 2014-02-04 18:35:30
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Revision: 3917
http://sourceforge.net/p/obi/code/3917
Author: jzheng24
Date: 2014-02-04 18:35:28 +0000 (Tue, 04 Feb 2014)
Log Message:
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Add 'freezing' and 'flash freezing' and update definition of 'freezing storage'
Details see tracker: https://sourceforge.net/p/obi/obi-terms/690/
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20140204.tab
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From: <jam...@us...> - 2014-08-18 18:08:14
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Revision: 3939
http://sourceforge.net/p/obi/code/3939
Author: jamesaoverton
Date: 2014-08-18 18:08:06 +0000 (Mon, 18 Aug 2014)
Log Message:
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Assigning IDs to new terms: 'ChIP assay', 'competitive binding reference ligand role', 'assay using chromatin immunoprecipitation'.
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20140818.tab
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From: <jam...@us...> - 2014-12-03 19:59:38
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Revision: 3953
http://sourceforge.net/p/obi/code/3953
Author: jamesaoverton
Date: 2014-12-03 19:59:30 +0000 (Wed, 03 Dec 2014)
Log Message:
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Assigning IDs to new terms; added a table of new terms since the 2014-08-18 release.
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20141203.tab
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From: <jam...@us...> - 2015-05-04 20:17:19
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Revision: 3985
http://sourceforge.net/p/obi/code/3985
Author: jamesaoverton
Date: 2015-05-04 20:17:18 +0000 (Mon, 04 May 2015)
Log Message:
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Updating 'Illumina HiSeq' terms
- updated existing HiSeq terms
- add number of flow cells and throughout to definition
- add 'Illumina' to primary label
- added OBI_0002048 'Illumina HiSeq 3000', fixes issue #758
- added OBI_0002049 'Illumina HiSeq 4000', fixes issue #759
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20150504.tab
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From: <jam...@us...> - 2015-09-15 14:26:30
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Revision: 4000
http://sourceforge.net/p/obi/code/4000
Author: jamesaoverton
Date: 2015-09-15 14:26:28 +0000 (Tue, 15 Sep 2015)
Log Message:
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Assign IDs for four new terms:
- OBI_0001971 Ion 316 Chip v2
- OBI_0001972 Ion 318 Chip v2
- OBI_0001973 ion semiconductor chip
- OBI_0001974 Ion 314 Chip v2
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20150915.tab
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From: <jam...@us...> - 2015-09-15 16:26:21
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Revision: 4002
http://sourceforge.net/p/obi/code/4002
Author: jamesaoverton
Date: 2015-09-15 16:26:19 +0000 (Tue, 15 Sep 2015)
Log Message:
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Added OBI_0001975 chromatin immunoprecipitation.
Closes: https://sourceforge.net/p/obi/obi-terms/768/
Modified Paths:
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trunk/src/ontology/branches/obi.owl
trunk/src/ontology/spreadsheets/new_ids/newIDs_20150915.tab
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From: <jam...@us...> - 2015-10-19 19:44:17
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Revision: 4007
http://sourceforge.net/p/obi/code/4007
Author: jamesaoverton
Date: 2015-10-19 19:44:16 +0000 (Mon, 19 Oct 2015)
Log Message:
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Adding assay templates from IEDB
- created `templates/` and `modules/` directories
- added `templates/obsolete.tsv` with obsolete IEDB assays
- added `templates/midlevel-assays.tsv`
- added `templates/epitope-assays.tsv`
- added OWL files for each template to `modules/`
- updated `catalog-v001.xml` to point to modules
- add `Makefile` for building modules from templates
- removed templated terms from `obi.owl`
- added import statements for each module to `obi.owl`
- added newID sheet listing 50 new terms
Modified Paths:
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trunk/src/ontology/branches/catalog-v001.xml
trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/branches/Makefile
trunk/src/ontology/branches/modules/
trunk/src/ontology/branches/modules/epitope-assays.owl
trunk/src/ontology/branches/modules/midlevel-assays.owl
trunk/src/ontology/branches/modules/obsolete.owl
trunk/src/ontology/branches/templates/
trunk/src/ontology/branches/templates/epitope-assays.tsv
trunk/src/ontology/branches/templates/midlevel-assays.tsv
trunk/src/ontology/branches/templates/obsolete.tsv
trunk/src/ontology/spreadsheets/new_ids/newIDs_20151019.tab
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From: <jam...@us...> - 2016-06-13 18:40:49
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Revision: 4063
http://sourceforge.net/p/obi/code/4063
Author: jamesaoverton
Date: 2016-06-13 18:40:47 +0000 (Mon, 13 Jun 2016)
Log Message:
-----------
Move biobank specimens to a new module
- add table of new IDs
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/branches/modules/biobank-specimens.owl
trunk/src/ontology/branches/templates/biobank-specimens.tsv
trunk/src/ontology/spreadsheets/new_ids/newIDs_20160608.tab
Removed Paths:
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trunk/src/ontology/branches/biobank_tissue_specimen.owl
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From: <jam...@us...> - 2016-06-14 15:51:58
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Revision: 4066
http://sourceforge.net/p/obi/code/4066
Author: jamesaoverton
Date: 2016-06-14 15:51:57 +0000 (Tue, 14 Jun 2016)
Log Message:
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Assign new ID and add newIDs sheet
Modified Paths:
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trunk/src/ontology/branches/obi.owl
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20160612.tab
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From: <jam...@us...> - 2016-06-14 15:54:27
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Revision: 4067
http://sourceforge.net/p/obi/code/4067
Author: jamesaoverton
Date: 2016-06-14 15:54:26 +0000 (Tue, 14 Jun 2016)
Log Message:
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Add 10 new assays for IEDB
Modified Paths:
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trunk/src/ontology/branches/modules/epitope-assays.owl
trunk/src/ontology/branches/modules/midlevel-assays.owl
trunk/src/ontology/branches/templates/epitope-assays.tsv
trunk/src/ontology/branches/templates/midlevel-assays.tsv
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20160613.tab
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From: <jam...@us...> - 2016-06-14 16:29:10
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Revision: 4068
http://sourceforge.net/p/obi/code/4068
Author: jamesaoverton
Date: 2016-06-14 16:29:09 +0000 (Tue, 14 Jun 2016)
Log Message:
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Fix bad ID assignment and updated newIDs tables
I assigned OBI:0002106 to 'Human 6x630K CGH Whole Genome Tiling Array'
but that ID was already taken, leading to logical errors.
That term now has ID OBI:0002109.
I updated the new terms lists with that correction
and some missing IDs that led to my mistake.
Modified Paths:
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trunk/src/ontology/branches/obi.owl
trunk/src/ontology/spreadsheets/new_ids/newIDs_20160612.tab
trunk/src/ontology/spreadsheets/new_ids/newIDs_20160613.tab
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From: <jam...@us...> - 2016-09-26 18:56:42
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Revision: 4078
http://sourceforge.net/p/obi/code/4078
Author: jamesaoverton
Date: 2016-09-26 18:56:40 +0000 (Mon, 26 Sep 2016)
Log Message:
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Add 8 new assays requested by ImmPort/IEDB, add new term ID list
Modified Paths:
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trunk/src/ontology/branches/modules/midlevel-assays.owl
trunk/src/ontology/branches/templates/midlevel-assays.tsv
Added Paths:
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trunk/src/ontology/spreadsheets/new_ids/newIDs_20160926.tab
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