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From: <jzh...@us...> - 2015-02-06 20:26:45
|
Revision: 3964
http://sourceforge.net/p/obi/code/3964
Author: jzheng24
Date: 2015-02-06 20:26:43 +0000 (Fri, 06 Feb 2015)
Log Message:
-----------
Based on the SGD term request, https://sourceforge.net/p/obi/obi-terms/725/, following terms were added into obi.owl
OBI_0002032 parallel analysis of RNA structure
OBI_0002033 translation-associated transcript leader sequencing
OBI_0002034 transcript leader sequencing
OBI_0002035 peptide mass fingerprinting
OBI_0002036 array based nucleic acid structure mapping assay
OBI_0002037 micrococcal nuclease digestion followed by tiling array assay
and GO term: Mitochondrion
was imported
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/GO_input.txt
trunk/src/ontology/branches/OntoFox_outputs/GO_imports.owl
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2015-01-24 21:38:44
|
Revision: 3963
http://sourceforge.net/p/obi/code/3963
Author: jzheng24
Date: 2015-01-24 21:38:36 +0000 (Sat, 24 Jan 2015)
Log Message:
-----------
Add OBI NIAID-GSCID-BRC view into OBI SVN repository.
Added Paths:
-----------
releases/NIAID-GSCID-BRC-view/
releases/NIAID-GSCID-BRC-view/20131213/
releases/NIAID-GSCID-BRC-view/20131213/Ontodog-inputs.xlsx
releases/NIAID-GSCID-BRC-view/20131213/insubset.owl
releases/NIAID-GSCID-BRC-view/20131213/label.owl
releases/NIAID-GSCID-BRC-view/20131213/merged_obi.owl
releases/NIAID-GSCID-BRC-view/20131213/subset.owl
releases/NIAID-GSCID-BRC-view/20140105/
releases/NIAID-GSCID-BRC-view/20140105/NIAID-GSC-BRC.owl
releases/NIAID-GSCID-BRC-view/20140105/catalog-v001.xml
releases/NIAID-GSCID-BRC-view/20140105/ontoDog inputs/
releases/NIAID-GSCID-BRC-view/20140105/ontoDog inputs/Ontodog-inputs.xlsx
releases/NIAID-GSCID-BRC-view/20140105/ontoDog inputs/obi_merged.owl
releases/NIAID-GSCID-BRC-view/20140105/ontoDog outputs/
releases/NIAID-GSCID-BRC-view/20140105/ontoDog outputs/insubset.owl
releases/NIAID-GSCID-BRC-view/20140105/ontoDog outputs/label.owl
releases/NIAID-GSCID-BRC-view/20140105/ontoDog outputs/subset.owl
releases/NIAID-GSCID-BRC-view/20140105/subset_cleanAssertedParents.owl
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From: <jzh...@us...> - 2015-01-15 23:16:55
|
Revision: 3962
http://sourceforge.net/p/obi/code/3962
Author: jzheng24
Date: 2015-01-15 23:16:48 +0000 (Thu, 15 Jan 2015)
Log Message:
-----------
Four terms are added:
OBI_0002029 serial analysis of gene expression
OBI_0002030 genotyping by tiling array
OBI_0002031 genotyping by SNP array
OBI_0002028 SAGE ditag library preparation
Details see tracker: https://sourceforge.net/p/obi/obi-terms/720/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2015-01-03 00:40:41
|
Revision: 3960
http://sourceforge.net/p/obi/code/3960
Author: jzheng24
Date: 2015-01-03 00:40:27 +0000 (Sat, 03 Jan 2015)
Log Message:
-----------
Replaced OBI:disease by OGMS:disease, details see the tracker:
https://sourceforge.net/p/obi/obi-terms/732/
Move imported SO terms from OBO_imports.owl to SO_imports.owl manually (Notes: Import SO terms using OntoFox failed, need to check later)
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/OBO_input.txt
trunk/src/ontology/branches/OntoFox_outputs/OBO_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/SO_imports.owl
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2015-01-02 22:41:34
|
Revision: 3959
http://sourceforge.net/p/obi/code/3959
Author: jzheng24
Date: 2015-01-02 22:41:25 +0000 (Fri, 02 Jan 2015)
Log Message:
-----------
Added 7 new device terms requested by ENCODE group:
https://sourceforge.net/p/obi/obi-terms/729/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2015-01-02 22:38:57
|
Revision: 3958
http://sourceforge.net/p/obi/code/3958
Author: jzheng24
Date: 2015-01-02 22:38:50 +0000 (Fri, 02 Jan 2015)
Log Message:
-----------
Added new assay and device terms using ontoRat, input and output files of ontoRat
Added Paths:
-----------
trunk/src/ontology/branches/OntoRat/
trunk/src/ontology/branches/OntoRat/20141202_assay/
trunk/src/ontology/branches/OntoRat/20141202_assay/20141202_OBI_assay.owl
trunk/src/ontology/branches/OntoRat/20141202_assay/20141202_OBI_assay_input.xlsx
trunk/src/ontology/branches/OntoRat/20141202_assay/20141202_OBI_assay_ontoRat_setting.txt
trunk/src/ontology/branches/OntoRat/20141202_assay/20141202_OBI_assay_output.xlsx
trunk/src/ontology/branches/OntoRat/20150102_device/
trunk/src/ontology/branches/OntoRat/20150102_device/20150102_device.owl
trunk/src/ontology/branches/OntoRat/20150102_device/20150102_device_input.xlsx
trunk/src/ontology/branches/OntoRat/20150102_device/20150102_device_output.xlsx
trunk/src/ontology/branches/OntoRat/20150102_device/device_settings.txt
trunk/src/ontology/branches/OntoRat/20150102_device/readme.txt
trunk/src/ontology/branches/OntoRat/20150102_device/~$20150102_device_output.xlsx
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From: <jzh...@us...> - 2015-01-02 16:50:06
|
Revision: 3957
http://sourceforge.net/p/obi/code/3957
Author: jzheng24
Date: 2015-01-02 16:49:58 +0000 (Fri, 02 Jan 2015)
Log Message:
-----------
Made few changes requested by ENCODE group
- move SOLiD 3 Plus system as a child of AB SOLid System
- relabel term OBI_0000693
https://sourceforge.net/p/obi/obi-terms/728/
- add synonyms to term OBI_0001863
https://sourceforge.net/p/obi/obi-terms/727/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2014-12-16 18:08:30
|
Revision: 3956
http://sourceforge.net/p/obi/code/3956
Author: jamesaoverton
Date: 2014-12-16 18:08:19 +0000 (Tue, 16 Dec 2014)
Log Message:
-----------
Committing OBI release 2014-12-03
Added Paths:
-----------
releases/2014-12-03/
releases/2014-12-03/README.txt
releases/2014-12-03/branches/
releases/2014-12-03/branches/OntoFox_inputs/
releases/2014-12-03/branches/OntoFox_inputs/ChEBI_input.txt
releases/2014-12-03/branches/OntoFox_inputs/GO_input.txt
releases/2014-12-03/branches/OntoFox_inputs/NCBITaxon_input.txt
releases/2014-12-03/branches/OntoFox_inputs/OBO_input.txt
releases/2014-12-03/branches/OntoFox_inputs/PATO_input.txt
releases/2014-12-03/branches/OntoFox_inputs/SO_input.txt
releases/2014-12-03/branches/OntoFox_inputs/UO_input.txt
releases/2014-12-03/branches/OntoFox_inputs/UO_input_instance.txt
releases/2014-12-03/branches/OntoFox_inputs/readme.txt
releases/2014-12-03/branches/OntoFox_outputs/
releases/2014-12-03/branches/OntoFox_outputs/ChEBI_imports.owl
releases/2014-12-03/branches/OntoFox_outputs/GO_imports.owl
releases/2014-12-03/branches/OntoFox_outputs/NCBITaxon_imports.owl
releases/2014-12-03/branches/OntoFox_outputs/OBO_imports.owl
releases/2014-12-03/branches/OntoFox_outputs/PATO_imports.owl
releases/2014-12-03/branches/OntoFox_outputs/SO_imports.owl
releases/2014-12-03/branches/OntoFox_outputs/UO_imports.owl
releases/2014-12-03/branches/OntoFox_outputs/UO_instance_imports.owl
releases/2014-12-03/branches/catalog-v001.xml
releases/2014-12-03/branches/doap.template
releases/2014-12-03/branches/external-byhand.owl
releases/2014-12-03/branches/obi.owl
releases/2014-12-03/docs/
releases/2014-12-03/docs/newIDs.tab
releases/2014-12-03/docs/obi.tsv
releases/2014-12-03/docs/obi.txt
releases/2014-12-03/docs/obi_core.tsv
releases/2014-12-03/docs/obi_core.txt
releases/2014-12-03/docs/obi_iedb.tsv
releases/2014-12-03/docs/obi_iedb.txt
releases/2014-12-03/docs/obi_isa.tsv
releases/2014-12-03/docs/obi_isa.txt
releases/2014-12-03/external/
releases/2014-12-03/external/bfo2-alan/
releases/2014-12-03/external/bfo2-alan/README
releases/2014-12-03/external/bfo2-alan/bfo-relations.lisp
releases/2014-12-03/external/bfo2-alan/bfo1.1-to-2.lisp
releases/2014-12-03/external/bfo2-alan/ruttenberg-bfo2-all.owl
releases/2014-12-03/external/bfo2-alan/ruttenberg-bfo2-classes.obo
releases/2014-12-03/external/bfo2-alan/ruttenberg-bfo2-granularity.owl
releases/2014-12-03/external/bfo2-alan/ruttenberg-bfo2-regions.owl
releases/2014-12-03/external/bfo2-alan/ruttenberg-bfo2-relations.obo
releases/2014-12-03/external/bfo2-alan/ruttenberg-bfo2.owl
releases/2014-12-03/external/bfo2-alan/ruttenberg-classes.owl
releases/2014-12-03/external/bfo2-alan/ruttenberg-granularity.owl
releases/2014-12-03/external/bfo2-alan/ruttenberg-regions.owl
releases/2014-12-03/external/bfo2-alan/ruttenberg-relations-biotop-equiv.owl
releases/2014-12-03/external/bfo2-alan/ruttenberg-relations.owl
releases/2014-12-03/external/iao-bfo2/
releases/2014-12-03/external/iao-bfo2/IAO.owl
releases/2014-12-03/external/iao-bfo2/catalog-v001.xml
releases/2014-12-03/external/iao-bfo2/external.owl
releases/2014-12-03/external/iao-bfo2/externalByHand.owl
releases/2014-12-03/external/iao-bfo2/externalDerived.owl
releases/2014-12-03/external/iao-bfo2/iao-main.owl
releases/2014-12-03/external/iao-bfo2/obsolete.owl
releases/2014-12-03/external/iao-bfo2/ontology-metadata.owl
releases/2014-12-03/external/protege-dc.owl
releases/2014-12-03/obi.owl
releases/2014-12-03/obi_core.owl
releases/2014-12-03/obi_iedb.owl
releases/2014-12-03/obi_isa.owl
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From: <jam...@us...> - 2014-12-03 22:23:44
|
Revision: 3955
http://sourceforge.net/p/obi/code/3955
Author: jamesaoverton
Date: 2014-12-03 22:23:43 +0000 (Wed, 03 Dec 2014)
Log Message:
-----------
Importing CHEBI_29237 'deuterium atom' for use in revised IEDB assays; seems to be bringing with it some updated ChEBI annotations.
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/ChEBI_input.txt
trunk/src/ontology/branches/OntoFox_outputs/ChEBI_imports.owl
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From: <jam...@us...> - 2014-12-03 22:18:31
|
Revision: 3954
http://sourceforge.net/p/obi/code/3954
Author: jamesaoverton
Date: 2014-12-03 22:18:24 +0000 (Wed, 03 Dec 2014)
Log Message:
-----------
Importing three more terms from GO that will be used for revised IEDB assays: GO_0044809 GO_0044807 GO_0044808.
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/GO_input.txt
trunk/src/ontology/branches/OntoFox_outputs/GO_imports.owl
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From: <jam...@us...> - 2014-12-03 19:59:38
|
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:
-----------
Assigning IDs to new terms; added a table of new terms since the 2014-08-18 release.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20141203.tab
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From: <jam...@us...> - 2014-12-03 19:36:38
|
Revision: 3952
http://sourceforge.net/p/obi/code/3952
Author: jamesaoverton
Date: 2014-12-03 19:36:36 +0000 (Wed, 03 Dec 2014)
Log Message:
-----------
Added 'decision-theoretic analysis objective' and 'decision analysis study design' to close #714.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2014-12-03 19:02:44
|
Revision: 3951
http://sourceforge.net/p/obi/code/3951
Author: jamesaoverton
Date: 2014-12-03 19:02:42 +0000 (Wed, 03 Dec 2014)
Log Message:
-----------
Many fixes to broken Unicode characters in annotations. Editors: please be careful.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2014-12-03 17:17:38
|
Revision: 3950
http://sourceforge.net/p/obi/code/3950
Author: jzheng24
Date: 2014-12-03 17:17:31 +0000 (Wed, 03 Dec 2014)
Log Message:
-----------
Slides prepared by Chris and Jie that presented in FDA workshop on Nov 3, 2014
Added Paths:
-----------
trunk/docs/presentations/2014 FDA workshop/
trunk/docs/presentations/2014 FDA workshop/Biomedical Ontology in the Medical Informatics Workshop.pdf
trunk/docs/presentations/2014 FDA workshop/FDA_OBI.pdf
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From: <jzh...@us...> - 2014-12-03 00:24:02
|
Revision: 3949
http://sourceforge.net/p/obi/code/3949
Author: jzheng24
Date: 2014-12-03 00:23:50 +0000 (Wed, 03 Dec 2014)
Log Message:
-----------
OBI_0002014 DNA methylation profiling by ChIP-chip assay
Following assay terms were added in OBI
OBI_0002015 transcription profiling by MPSS assay
OBI_0002016 histone modification identification by ChIP-chip assay
OBI_0002017 histone modification identification by ChIP-Seq assay
OBI_0002018 transcription factor binding site identification by ChIP-chip assay
OBI_0002019 transcription factor binding site identification by ChIP-Seq assay
Detailed notes, please see tracker:
https://sourceforge.net/p/obi/obi-terms/721/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2014-12-03 00:22:30
|
Revision: 3948
http://sourceforge.net/p/obi/code/3948
Author: jzheng24
Date: 2014-12-03 00:22:28 +0000 (Wed, 03 Dec 2014)
Log Message:
-----------
Import one term from GO for defining OBI assay
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/GO_input.txt
trunk/src/ontology/branches/OntoFox_outputs/GO_imports.owl
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From: <p_r...@us...> - 2014-11-17 23:18:05
|
Revision: 3947
http://sourceforge.net/p/obi/code/3947
Author: p_rocca_serra
Date: 2014-11-17 23:17:53 +0000 (Mon, 17 Nov 2014)
Log Message:
-----------
adding targeted gene survey related classes following, closes #705
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2014-11-10 17:56:28
|
Revision: 3946
http://sourceforge.net/p/obi/code/3946
Author: jzheng24
Date: 2014-11-10 17:56:25 +0000 (Mon, 10 Nov 2014)
Log Message:
-----------
Add high-level structure hierarchy drawn by Jie
Modified Paths:
--------------
trunk/docs/papers/release/Figure 1.pptx
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From: <jzh...@us...> - 2014-11-10 17:51:30
|
Revision: 3945
http://sourceforge.net/p/obi/code/3945
Author: jzheng24
Date: 2014-11-10 17:51:29 +0000 (Mon, 10 Nov 2014)
Log Message:
-----------
Based on discussion on 11/10/2014 OBI call:
Remove the 'specimen role' inheres_in mouse and specify 'specimen role' inheres_in blood specimen is_realized_by 'analyte assay'
Modified Paths:
--------------
trunk/docs/papers/release/Figure 2.ppt
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From: <jzh...@us...> - 2014-10-27 16:31:34
|
Revision: 3944
http://sourceforge.net/p/obi/code/3944
Author: jzheng24
Date: 2014-10-27 16:31:30 +0000 (Mon, 27 Oct 2014)
Log Message:
-----------
'specimen collection' is changed to 'specimen collection process' on 10/27/2014, details see tracker:
http://sourceforge.net/p/obi/obi-terms/716/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2014-09-15 20:27:02
|
Revision: 3943
http://sourceforge.net/p/obi/code/3943
Author: jamesaoverton
Date: 2014-09-15 20:26:58 +0000 (Mon, 15 Sep 2014)
Log Message:
-----------
Added OBI_0001958 'systematic review study design'. Closes #715.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2014-09-02 14:30:08
|
Revision: 3942
http://sourceforge.net/p/obi/code/3942
Author: jzheng24
Date: 2014-09-02 14:29:58 +0000 (Tue, 02 Sep 2014)
Log Message:
-----------
Add 'hardware testing design' needed by annotation of Beta Cell Genomincs studies
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2014-08-25 19:16:32
|
Revision: 3941
http://sourceforge.net/p/obi/code/3941
Author: jamesaoverton
Date: 2014-08-25 19:16:30 +0000 (Mon, 25 Aug 2014)
Log Message:
-----------
Minor fixes to OBI release instructions.
Modified Paths:
--------------
trunk/src/tools/build/README.md
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From: <jam...@us...> - 2014-08-25 19:02:25
|
Revision: 3940
http://sourceforge.net/p/obi/code/3940
Author: jamesaoverton
Date: 2014-08-25 19:02:21 +0000 (Mon, 25 Aug 2014)
Log Message:
-----------
Committing OBI release 2014-08-18
Added Paths:
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releases/2014-08-18/
releases/2014-08-18/README.txt
releases/2014-08-18/branches/
releases/2014-08-18/branches/OntoFox_inputs/
releases/2014-08-18/branches/OntoFox_inputs/ChEBI_input.txt
releases/2014-08-18/branches/OntoFox_inputs/GO_input.txt
releases/2014-08-18/branches/OntoFox_inputs/NCBITaxon_input.txt
releases/2014-08-18/branches/OntoFox_inputs/OBO_input.txt
releases/2014-08-18/branches/OntoFox_inputs/PATO_input.txt
releases/2014-08-18/branches/OntoFox_inputs/SO_input.txt
releases/2014-08-18/branches/OntoFox_inputs/UO_input.txt
releases/2014-08-18/branches/OntoFox_inputs/UO_input_instance.txt
releases/2014-08-18/branches/OntoFox_inputs/readme.txt
releases/2014-08-18/branches/OntoFox_outputs/
releases/2014-08-18/branches/OntoFox_outputs/ChEBI_imports.owl
releases/2014-08-18/branches/OntoFox_outputs/GO_imports.owl
releases/2014-08-18/branches/OntoFox_outputs/NCBITaxon_imports.owl
releases/2014-08-18/branches/OntoFox_outputs/OBO_imports.owl
releases/2014-08-18/branches/OntoFox_outputs/PATO_imports.owl
releases/2014-08-18/branches/OntoFox_outputs/SO_imports.owl
releases/2014-08-18/branches/OntoFox_outputs/UO_imports.owl
releases/2014-08-18/branches/OntoFox_outputs/UO_instance_imports.owl
releases/2014-08-18/branches/catalog-v001.xml
releases/2014-08-18/branches/doap.template
releases/2014-08-18/branches/external-byhand.owl
releases/2014-08-18/branches/obi.owl
releases/2014-08-18/docs/
releases/2014-08-18/docs/newIDs.tab
releases/2014-08-18/docs/obi.tsv
releases/2014-08-18/docs/obi.txt
releases/2014-08-18/docs/obi_core.tsv
releases/2014-08-18/docs/obi_core.txt
releases/2014-08-18/docs/obi_iedb.tsv
releases/2014-08-18/docs/obi_iedb.txt
releases/2014-08-18/docs/obi_isa.tsv
releases/2014-08-18/docs/obi_isa.txt
releases/2014-08-18/external/
releases/2014-08-18/external/bfo2-alan/
releases/2014-08-18/external/bfo2-alan/README
releases/2014-08-18/external/bfo2-alan/bfo-relations.lisp
releases/2014-08-18/external/bfo2-alan/bfo1.1-to-2.lisp
releases/2014-08-18/external/bfo2-alan/ruttenberg-bfo2-all.owl
releases/2014-08-18/external/bfo2-alan/ruttenberg-bfo2-classes.obo
releases/2014-08-18/external/bfo2-alan/ruttenberg-bfo2-granularity.owl
releases/2014-08-18/external/bfo2-alan/ruttenberg-bfo2-regions.owl
releases/2014-08-18/external/bfo2-alan/ruttenberg-bfo2-relations.obo
releases/2014-08-18/external/bfo2-alan/ruttenberg-bfo2.owl
releases/2014-08-18/external/bfo2-alan/ruttenberg-classes.owl
releases/2014-08-18/external/bfo2-alan/ruttenberg-granularity.owl
releases/2014-08-18/external/bfo2-alan/ruttenberg-regions.owl
releases/2014-08-18/external/bfo2-alan/ruttenberg-relations-biotop-equiv.owl
releases/2014-08-18/external/bfo2-alan/ruttenberg-relations.owl
releases/2014-08-18/external/iao-bfo2/
releases/2014-08-18/external/iao-bfo2/IAO.owl
releases/2014-08-18/external/iao-bfo2/catalog-v001.xml
releases/2014-08-18/external/iao-bfo2/external.owl
releases/2014-08-18/external/iao-bfo2/externalByHand.owl
releases/2014-08-18/external/iao-bfo2/externalDerived.owl
releases/2014-08-18/external/iao-bfo2/iao-main.owl
releases/2014-08-18/external/iao-bfo2/obsolete.owl
releases/2014-08-18/external/iao-bfo2/ontology-metadata.owl
releases/2014-08-18/external/protege-dc.owl
releases/2014-08-18/obi.owl
releases/2014-08-18/obi_core.owl
releases/2014-08-18/obi_iedb.owl
releases/2014-08-18/obi_isa.owl
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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
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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