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From: <agb...@us...> - 2013-10-23 10:27:51
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Revision: 3863
http://sourceforge.net/p/obi/code/3863
Author: agbeltran
Date: 2013-10-23 10:27:48 +0000 (Wed, 23 Oct 2013)
Log Message:
-----------
Adding TermAnnotator class to support adding annotations to ontologies
Added Paths:
-----------
trunk/src/tools/build/src/main/java/obi/TermAnnotator.java
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From: <jzh...@us...> - 2013-10-14 23:09:41
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Revision: 3862
http://sourceforge.net/p/obi/code/3862
Author: jzheng24
Date: 2013-10-14 23:09:36 +0000 (Mon, 14 Oct 2013)
Log Message:
-----------
Cannot retrieve definition of 'cell line cell' and 'cell line' from CLO using OntoFox, added manually
Modified Paths:
--------------
trunk/src/ontology/branches/external-byhand.owl
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From: <jzh...@us...> - 2013-10-11 20:02:33
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Revision: 3861
http://sourceforge.net/p/obi/code/3861
Author: jzheng24
Date: 2013-10-11 20:02:32 +0000 (Fri, 11 Oct 2013)
Log Message:
-----------
Read me file of how to generate import OWL file using OntoFox tool
Added Paths:
-----------
trunk/src/ontology/branches/OntoFox_inputs/readme.txt
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From: <jzh...@us...> - 2013-10-10 18:35:48
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Revision: 3860
http://sourceforge.net/p/obi/code/3860
Author: jzheng24
Date: 2013-10-10 18:35:44 +0000 (Thu, 10 Oct 2013)
Log Message:
-----------
edit annotations of deprecated terms, add 'replaced by term' URI to indicate term deprecated by importing which term in the external resources
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-10-10 13:20:29
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Revision: 3859
http://sourceforge.net/p/obi/code/3859
Author: jamesaoverton
Date: 2013-10-10 13:20:27 +0000 (Thu, 10 Oct 2013)
Log Message:
-----------
Fix an annoying warning in SVN revision getter.
Modified Paths:
--------------
trunk/src/tools/build/build.xml
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From: <jam...@us...> - 2013-10-10 13:19:50
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Revision: 3858
http://sourceforge.net/p/obi/code/3858
Author: jamesaoverton
Date: 2013-10-10 13:19:48 +0000 (Thu, 10 Oct 2013)
Log Message:
-----------
Allow comments for core list.
Modified Paths:
--------------
trunk/src/tools/build/core.txt
trunk/src/tools/build/src/main/java/obi/Extractor.java
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From: <jzh...@us...> - 2013-10-10 00:06:42
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Revision: 3857
http://sourceforge.net/p/obi/code/3857
Author: jzheng24
Date: 2013-10-10 00:06:40 +0000 (Thu, 10 Oct 2013)
Log Message:
-----------
include definitions of CL and CLO terms
cannot pull definition of 'cell line cell' using OntoFox, will fix it
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_outputs/OBO_imports.owl
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From: <jzh...@us...> - 2013-10-09 23:57:32
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Revision: 3856
http://sourceforge.net/p/obi/code/3856
Author: jzheng24
Date: 2013-10-09 23:57:29 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
remove 'editor preferred label' associated with imported terms since they will be generated using OntoFox tool
remove parent class asserted to the imported terms which should be defined in the OntoFox input file
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-10-09 22:54:17
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Revision: 3855
http://sourceforge.net/p/obi/code/3855
Author: jzheng24
Date: 2013-10-09 22:54:15 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
import UBERON:life cycle stage as subclaas of GO:biological_process rather than BFO:process since it is asserted as GO:biological_process in obi.owl file
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/OBO_input.txt
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From: <jzh...@us...> - 2013-10-09 22:34:22
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Revision: 3854
http://sourceforge.net/p/obi/code/3854
Author: jzheng24
Date: 2013-10-09 22:34:18 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Pull definitions of terms from CL/CLO (forget in the previous version)
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/OBO_input.txt
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From: <jam...@us...> - 2013-10-09 15:38:16
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Revision: 3853
http://sourceforge.net/p/obi/code/3853
Author: jamesaoverton
Date: 2013-10-09 15:38:14 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Bugfix for Metadator; make sure DOAP goes back in after reasoning.
Modified Paths:
--------------
trunk/src/tools/build/build.xml
trunk/src/tools/build/src/main/java/obi/Metadator.java
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From: <jam...@us...> - 2013-10-09 15:12:54
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Revision: 3852
http://sourceforge.net/p/obi/code/3852
Author: jamesaoverton
Date: 2013-10-09 15:12:52 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Even better SVN revision getter in build.xml.
Modified Paths:
--------------
trunk/src/tools/build/build.xml
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From: <jam...@us...> - 2013-10-09 15:10:22
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Revision: 3851
http://sourceforge.net/p/obi/code/3851
Author: jamesaoverton
Date: 2013-10-09 15:10:21 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Better SVN revision getter in build.xml.
Modified Paths:
--------------
trunk/src/tools/build/build.xml
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From: <jam...@us...> - 2013-10-09 15:04:59
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Revision: 3850
http://sourceforge.net/p/obi/code/3850
Author: jamesaoverton
Date: 2013-10-09 15:04:58 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Various small fixes based on feedback from Jie.
Modified Paths:
--------------
trunk/src/tools/build/build.xml
trunk/src/tools/build/config.properties
trunk/src/tools/build/core.txt
trunk/src/tools/build/src/main/java/obi/Metadator.java
trunk/src/tools/build/src/main/java/obi/TermUpdater.java
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From: <jam...@us...> - 2013-10-09 15:04:35
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Revision: 3849
http://sourceforge.net/p/obi/code/3849
Author: jamesaoverton
Date: 2013-10-09 15:04:33 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Remove unnecessary asserted subClassAxioms.
Modified Paths:
--------------
trunk/src/tools/build/src/main/java/obi/Reasoner.java
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From: <jam...@us...> - 2013-10-09 14:46:58
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Revision: 3848
http://sourceforge.net/p/obi/code/3848
Author: jamesaoverton
Date: 2013-10-09 14:46:55 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
Updated DOAP template to insert current SVN revision of the release (as opposed to the template itself).
Modified Paths:
--------------
trunk/src/ontology/branches/doap.template
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From: <jzh...@us...> - 2013-10-09 05:32:45
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Revision: 3847
http://sourceforge.net/p/obi/code/3847
Author: jzheng24
Date: 2013-10-09 05:32:43 +0000 (Wed, 09 Oct 2013)
Log Message:
-----------
change all reviewed OBI terms (inner core + related terms) with curation status 'ready for release'
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-10-08 23:48:09
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Revision: 3846
http://sourceforge.net/p/obi/code/3846
Author: jzheng24
Date: 2013-10-08 23:48:07 +0000 (Tue, 08 Oct 2013)
Log Message:
-----------
add annotation properties (mainly 'curation status') to some classes identified by release tool developed by James
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-10-08 16:21:10
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Revision: 3845
http://sourceforge.net/p/obi/code/3845
Author: jamesaoverton
Date: 2013-10-08 16:21:08 +0000 (Tue, 08 Oct 2013)
Log Message:
-----------
Added curation status to entity reports.
Modified Paths:
--------------
trunk/src/tools/build/src/main/java/obi/Reporter.java
trunk/src/tools/build/src/main/java/obi/TermUpdater.java
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From: <jam...@us...> - 2013-10-08 15:59:21
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Revision: 3844
http://sourceforge.net/p/obi/code/3844
Author: jamesaoverton
Date: 2013-10-08 15:59:19 +0000 (Tue, 08 Oct 2013)
Log Message:
-----------
Tweaked release task in build file, updated README.
Modified Paths:
--------------
trunk/src/tools/build/README.md
trunk/src/tools/build/build.xml
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From: <jam...@us...> - 2013-10-08 15:38:14
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Revision: 3843
http://sourceforge.net/p/obi/code/3843
Author: jamesaoverton
Date: 2013-10-08 15:38:11 +0000 (Tue, 08 Oct 2013)
Log Message:
-----------
Updated Ivy and removed ivysettings.xml; fixed reasoner; better reporter with summary counts; updated build.xml.
Modified Paths:
--------------
trunk/src/tools/build/build.xml
trunk/src/tools/build/ivy.xml
trunk/src/tools/build/src/main/java/obi/Builder.java
trunk/src/tools/build/src/main/java/obi/Reasoner.java
trunk/src/tools/build/src/main/java/obi/Reporter.java
trunk/src/tools/build/src/main/java/obi/TermUpdater.java
Removed Paths:
-------------
trunk/src/tools/build/ivysettings.xml
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From: <jzh...@us...> - 2013-10-08 05:19:02
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Revision: 3842
http://sourceforge.net/p/obi/code/3842
Author: jzheng24
Date: 2013-10-08 05:19:00 +0000 (Tue, 08 Oct 2013)
Log Message:
-----------
Import terms from external resources using OntoFox
Modified Paths:
--------------
trunk/src/ontology/branches/catalog-v001.xml
trunk/src/ontology/branches/external-byhand.owl
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/branches/OntoFox_inputs/
trunk/src/ontology/branches/OntoFox_inputs/ChEBI_input.txt
trunk/src/ontology/branches/OntoFox_inputs/GO_input.txt
trunk/src/ontology/branches/OntoFox_inputs/NCBITaxon_input.txt
trunk/src/ontology/branches/OntoFox_inputs/OBO_input.txt
trunk/src/ontology/branches/OntoFox_inputs/PATO_input.txt
trunk/src/ontology/branches/OntoFox_inputs/UO_input.txt
trunk/src/ontology/branches/OntoFox_inputs/UO_input_instance.txt
trunk/src/ontology/branches/OntoFox_outputs/
trunk/src/ontology/branches/OntoFox_outputs/ChEBI_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/GO_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/NCBITaxon_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/OBO_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/PATO_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/UO_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/UO_instance_imports.owl
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From: <jam...@us...> - 2013-10-05 15:24:31
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Revision: 3841
http://sourceforge.net/p/obi/code/3841
Author: jamesaoverton
Date: 2013-10-05 15:24:30 +0000 (Sat, 05 Oct 2013)
Log Message:
-----------
Merge duplicate definitions in TermUpdater; updated README.
Modified Paths:
--------------
trunk/src/tools/build/README.md
trunk/src/tools/build/src/main/java/obi/TermUpdater.java
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From: <jam...@us...> - 2013-10-05 13:57:55
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Revision: 3840
http://sourceforge.net/p/obi/code/3840
Author: jamesaoverton
Date: 2013-10-05 13:57:51 +0000 (Sat, 05 Oct 2013)
Log Message:
-----------
Updating build tool with TermUpdater and ViewMaker classes and a 'release' Ant task.
Modified Paths:
--------------
trunk/src/tools/build/build.xml
trunk/src/tools/build/config.properties
trunk/src/tools/build/src/main/java/obi/Builder.java
trunk/src/tools/build/src/main/java/obi/Extractor.java
trunk/src/tools/build/src/main/java/obi/Reporter.java
Added Paths:
-----------
trunk/src/tools/build/src/main/java/obi/TermUpdater.java
trunk/src/tools/build/src/main/java/obi/ViewMaker.java
Property Changed:
----------------
trunk/src/tools/build/
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From: <mb...@us...> - 2013-10-04 22:02:50
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Revision: 3839
http://sourceforge.net/p/obi/code/3839
Author: mbrush
Date: 2013-10-04 22:02:48 +0000 (Fri, 04 Oct 2013)
Log Message:
-----------
updated label and classification of lymph node cell and splenocyte to reflect definitions of these classes (ie labeled as specimens and classified under cell specimen)
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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