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From: <p_r...@us...> - 2013-12-16 17:56:28
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Revision: 3913
http://sourceforge.net/p/obi/code/3913
Author: p_rocca_serra
Date: 2013-12-16 17:56:25 +0000 (Mon, 16 Dec 2013)
Log Message:
-----------
addition of has_performer relation between planned process and Homo sapiens/Organization/Device. Device used as placeholder to cover robot-scientist use case and only that"
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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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:
-----------
edit to N50,genome coverage and sequence assembly process restrictions to clarify directionality
Modified Paths:
--------------
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...> - 2013-12-16 00:11:41
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Revision: 3911
http://sourceforge.net/p/obi/code/3911
Author: jzheng24
Date: 2013-12-16 00:11:39 +0000 (Mon, 16 Dec 2013)
Log Message:
-----------
import two terms needed by NIAID GSC/BRC metadata
- http://purl.obolibrary.org/obo/PATO_0001995 organismal quality
- http://purl.obolibrary.org/obo/IDO_0000666 human pathogenicity disposition
moved all SO import into SO_input.txt
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/OBO_input.txt
trunk/src/ontology/branches/OntoFox_inputs/PATO_input.txt
trunk/src/ontology/branches/OntoFox_inputs/SO_input.txt
trunk/src/ontology/branches/OntoFox_outputs/PATO_imports.owl
trunk/src/ontology/branches/external-byhand.owl
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From: <jzh...@us...> - 2013-12-12 20:00:02
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Revision: 3910
http://sourceforge.net/p/obi/code/3910
Author: jzheng24
Date: 2013-12-12 19:59:58 +0000 (Thu, 12 Dec 2013)
Log Message:
-----------
Add some comments and make minor edits
Modified Paths:
--------------
trunk/docs/papers/release/Manuscript 2011.doc
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From: <cb...@us...> - 2013-12-08 14:32:32
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Revision: 3909
http://sourceforge.net/p/obi/code/3909
Author: cbosfn
Date: 2013-12-08 14:32:26 +0000 (Sun, 08 Dec 2013)
Log Message:
-----------
Added assay_design_patterns_CB.pdf as description of assay design patterns meeting basic requirements in the context of the VLN.
Added Paths:
-----------
trunk/docs/developer/assay/assay_design_patterns_CB.pdf
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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:
-----------
OBI ids were assigned to newly added terms
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20131202.tab
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From: <p_r...@us...> - 2013-12-02 20:40:57
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Revision: 3907
http://sourceforge.net/p/obi/code/3907
Author: p_rocca_serra
Date: 2013-12-02 20:40:54 +0000 (Mon, 02 Dec 2013)
Log Message:
-----------
adding SO import using Ontofox, adding N50,contigN50,scaffoldN50,genome coverage, computational run time, ram memory size as per use case described during OBI call
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_outputs/OBO_imports.owl
trunk/src/ontology/branches/catalog-v001.xml
trunk/src/ontology/branches/catalog.xml
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/branches/OntoFox_inputs/SO_input.txt
trunk/src/ontology/branches/OntoFox_outputs/SO_imports.owl
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From: <p_r...@us...> - 2013-12-02 20:37:42
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Revision: 3906
http://sourceforge.net/p/obi/code/3906
Author: p_rocca_serra
Date: 2013-12-02 20:37:40 +0000 (Mon, 02 Dec 2013)
Log Message:
-----------
adding ISA use cases presentation
Added Paths:
-----------
trunk/docs/developer/assay/ISA-use cases for OBI-Assays-December2013.pptx
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From: <jzh...@us...> - 2013-11-27 19:24:43
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Revision: 3905
http://sourceforge.net/p/obi/code/3905
Author: jzheng24
Date: 2013-11-27 19:24:41 +0000 (Wed, 27 Nov 2013)
Log Message:
-----------
4 BRC terms were added. Details see tracker:
https://sourceforge.net/p/obi/obi-terms/682/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-11-25 21:13:19
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Revision: 3904
http://sourceforge.net/p/obi/code/3904
Author: jzheng24
Date: 2013-11-25 21:13:16 +0000 (Mon, 25 Nov 2013)
Log Message:
-----------
All related documents related to assay discussion
Added Paths:
-----------
trunk/docs/developer/assay/
trunk/docs/developer/assay/20131125_Assay in OBI_jz.pptx
trunk/docs/developer/assay/20131125_assay_call.txt
trunk/docs/developer/assay/ENCODE_Assays.xlsx
trunk/docs/developer/assay/IEDB_MMExpressionsTcell.txt
trunk/docs/developer/assay/IEDB_TCellAssayExamples.xlsx
trunk/docs/developer/assay/LS_data scheme 3.pdf
trunk/docs/developer/assay/OBI assays.xlsx
trunk/docs/developer/assay/pattern-assay.jpg
trunk/docs/developer/assay/pattern-assay_analyte.jpg
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From: <jzh...@us...> - 2013-11-22 23:51:52
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Revision: 3903
http://sourceforge.net/p/obi/code/3903
Author: jzheng24
Date: 2013-11-22 23:51:50 +0000 (Fri, 22 Nov 2013)
Log Message:
-----------
obi FGED view which is a subset of OBI with FGED alternative terms generated by Ontodog using input file, OBI_FGED_v20131025.xlsx which marked FGED terms with FGED preferred labels if different from OBI labels
Added Paths:
-----------
releases/2013-10-25/OBI_FGED_v20131025.xlsx
releases/2013-10-25/obi_FGED.owl
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From: <jzh...@us...> - 2013-11-14 18:56:43
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Revision: 3902
http://sourceforge.net/p/obi/code/3902
Author: jzheng24
Date: 2013-11-14 18:56:38 +0000 (Thu, 14 Nov 2013)
Log Message:
-----------
modify devices added yesterday, see tracker:
https://sourceforge.net/p/obi/obi-terms/683/
Add 'LSRFortessa X-20' requested by anna maria masci, see tracker:
https://sourceforge.net/p/obi/obi-terms/684/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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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:
-----------
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:
--------------
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20131113.tab
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From: <jzh...@us...> - 2013-11-13 22:34:34
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Revision: 3900
http://sourceforge.net/p/obi/code/3900
Author: jzheng24
Date: 2013-11-13 22:34:32 +0000 (Wed, 13 Nov 2013)
Log Message:
-----------
Add some devices and manufacturer needed for adding ENCODE project requested devices
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-11-13 22:33:05
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Revision: 3899
http://sourceforge.net/p/obi/code/3899
Author: jzheng24
Date: 2013-11-13 22:33:03 +0000 (Wed, 13 Nov 2013)
Log Message:
-----------
import GO:DNA methylation
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: <jzh...@us...> - 2013-11-13 21:26:54
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Revision: 3898
http://sourceforge.net/p/obi/code/3898
Author: jzheng24
Date: 2013-11-13 21:26:52 +0000 (Wed, 13 Nov 2013)
Log Message:
-----------
fix errors of some UO classes declared as individuals
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_outputs/UO_instance_imports.owl
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From: <jzh...@us...> - 2013-11-13 21:01:40
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Revision: 3897
http://sourceforge.net/p/obi/code/3897
Author: jzheng24
Date: 2013-11-13 21:01:38 +0000 (Wed, 13 Nov 2013)
Log Message:
-----------
Added back 3 terms imported from ENVO which was missing after switching to OntoFox for MIROET
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/OBO_input.txt
trunk/src/ontology/branches/OntoFox_outputs/OBO_imports.owl
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From: <jzh...@us...> - 2013-11-13 19:22:17
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Revision: 3896
http://sourceforge.net/p/obi/code/3896
Author: jzheng24
Date: 2013-11-13 19:22:15 +0000 (Wed, 13 Nov 2013)
Log Message:
-----------
correct wrong format
Modified Paths:
--------------
releases/2013-10-25/docs/newIDs.tab
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From: <jam...@us...> - 2013-11-01 20:18:31
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Revision: 3895
http://sourceforge.net/p/obi/code/3895
Author: jamesaoverton
Date: 2013-11-01 20:18:28 +0000 (Fri, 01 Nov 2013)
Log Message:
-----------
Fixing SVN links in release checklist.
Modified Paths:
--------------
trunk/src/tools/build/README.md
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From: <jam...@us...> - 2013-11-01 20:04:07
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Revision: 3894
http://sourceforge.net/p/obi/code/3894
Author: jamesaoverton
Date: 2013-11-01 20:04:04 +0000 (Fri, 01 Nov 2013)
Log Message:
-----------
Added one more PURL to release checklist.
Modified Paths:
--------------
trunk/src/tools/build/README.md
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From: <jam...@us...> - 2013-11-01 19:58:25
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Revision: 3893
http://sourceforge.net/p/obi/code/3893
Author: jamesaoverton
Date: 2013-11-01 19:58:23 +0000 (Fri, 01 Nov 2013)
Log Message:
-----------
Revisions to OBI 2013-10-25 README.
Modified Paths:
--------------
releases/2013-10-25/README.txt
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From: <jam...@us...> - 2013-11-01 19:57:32
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Revision: 3892
http://sourceforge.net/p/obi/code/3892
Author: jamesaoverton
Date: 2013-11-01 19:57:30 +0000 (Fri, 01 Nov 2013)
Log Message:
-----------
Added release checklist to build tool README.
Modified Paths:
--------------
trunk/src/tools/build/README.md
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From: <jam...@us...> - 2013-11-01 19:18:44
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Revision: 3891
http://sourceforge.net/p/obi/code/3891
Author: jamesaoverton
Date: 2013-11-01 19:18:43 +0000 (Fri, 01 Nov 2013)
Log Message:
-----------
Updated README for 2013-10-25 release.
Modified Paths:
--------------
releases/2013-10-25/README.txt
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From: <jam...@us...> - 2013-11-01 19:17:56
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Revision: 3890
http://sourceforge.net/p/obi/code/3890
Author: jamesaoverton
Date: 2013-11-01 19:17:54 +0000 (Fri, 01 Nov 2013)
Log Message:
-----------
Minor changes to release candidate: revise 'glucose tolerance test' and update SVN revision.
Modified Paths:
--------------
releases/2013-10-25/obi.owl
releases/2013-10-25/obi_core.owl
releases/2013-10-25/obi_iedb.owl
releases/2013-10-25/obi_isa.owl
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From: <jam...@us...> - 2013-11-01 17:48:18
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Revision: 3889
http://sourceforge.net/p/obi/code/3889
Author: jamesaoverton
Date: 2013-11-01 17:48:16 +0000 (Fri, 01 Nov 2013)
Log Message:
-----------
The 'ant release' task now compares the new release to the previous release.
Modified Paths:
--------------
trunk/src/tools/build/build.xml
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