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From: <jam...@us...> - 2013-05-29 13:53:07
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Revision: 3764
http://obi.svn.sourceforge.net/obi/?rev=3764&view=rev
Author: jamesaoverton
Date: 2013-05-29 13:53:01 +0000 (Wed, 29 May 2013)
Log Message:
-----------
Assigning IDs to three new terms: secondary_cell_culture_sample (OBI_0001905), cancer_cell_line (OBI_0001906), immortalizing_cell_line_transformation (OBI_0001907).
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-29 01:20:44
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Revision: 3763
http://obi.svn.sourceforge.net/obi/?rev=3763&view=rev
Author: jamesaoverton
Date: 2013-05-29 01:20:38 +0000 (Wed, 29 May 2013)
Log Message:
-----------
Switching from Jena OntModel to Dataset, adding FROM, fixing Turtle matchers.
Modified Paths:
--------------
trunk/src/tests/example.txt
trunk/src/tools/build/src/main/java/obi/SPARQLTest.java
trunk/src/tools/build/src/main/java/obi/Tester.java
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From: <mb...@us...> - 2013-05-28 18:53:36
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Revision: 3762
http://obi.svn.sourceforge.net/obi/?rev=3762&view=rev
Author: mbrush
Date: 2013-05-28 18:53:27 +0000 (Tue, 28 May 2013)
Log Message:
-----------
updating reagent role definition and annotations
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-27 18:22:01
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Revision: 3761
http://obi.svn.sourceforge.net/obi/?rev=3761&view=rev
Author: jamesaoverton
Date: 2013-05-27 18:21:54 +0000 (Mon, 27 May 2013)
Log Message:
-----------
Cleaning up dependencies for testing tool.
Modified Paths:
--------------
trunk/src/tools/build/src/main/java/obi/DLTest.java
trunk/src/tools/build/src/main/java/obi/SPARQLTest.java
trunk/src/tools/build/src/main/java/obi/Test.java
trunk/src/tools/build/src/main/java/obi/Tester.java
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From: <jam...@us...> - 2013-05-27 18:17:34
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Revision: 3760
http://obi.svn.sourceforge.net/obi/?rev=3760&view=rev
Author: jamesaoverton
Date: 2013-05-27 18:17:26 +0000 (Mon, 27 May 2013)
Log Message:
-----------
Cleaning up automated testing code.
Modified Paths:
--------------
trunk/src/tools/build/src/main/java/obi/DLTest.java
trunk/src/tools/build/src/main/java/obi/SPARQLTest.java
trunk/src/tools/build/src/main/java/obi/Test.java
trunk/src/tools/build/src/main/java/obi/Tester.java
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From: <jam...@us...> - 2013-05-27 18:00:03
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Revision: 3759
http://obi.svn.sourceforge.net/obi/?rev=3759&view=rev
Author: jamesaoverton
Date: 2013-05-27 17:59:54 +0000 (Mon, 27 May 2013)
Log Message:
-----------
Fixed 'experiment' feature and added to README.
Modified Paths:
--------------
trunk/src/tools/build/README.md
trunk/src/tools/build/build.xml
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From: <jam...@us...> - 2013-05-27 17:54:04
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Revision: 3758
http://obi.svn.sourceforge.net/obi/?rev=3758&view=rev
Author: jamesaoverton
Date: 2013-05-27 17:53:54 +0000 (Mon, 27 May 2013)
Log Message:
-----------
Implemented Turtle and SPARQL for automated testing tool.
Modified Paths:
--------------
trunk/src/tests/example.txt
trunk/src/tools/build/README.md
trunk/src/tools/build/build.xml
trunk/src/tools/build/ivy.xml
trunk/src/tools/build/src/main/java/obi/Test.java
trunk/src/tools/build/src/main/java/obi/Tester.java
trunk/src/tools/build/src/main/resources/log4j.properties
Added Paths:
-----------
trunk/src/tools/build/src/main/java/obi/DLTest.java
trunk/src/tools/build/src/main/java/obi/SPARQLTest.java
Property Changed:
----------------
trunk/src/tools/build/
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From: <jam...@us...> - 2013-05-27 13:56:57
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Revision: 3757
http://obi.svn.sourceforge.net/obi/?rev=3757&view=rev
Author: jamesaoverton
Date: 2013-05-27 13:56:49 +0000 (Mon, 27 May 2013)
Log Message:
-----------
Changed tester to read indented code blocks (standard for Markdown format).
Modified Paths:
--------------
trunk/src/tests/example.txt
trunk/src/tools/build/src/main/java/obi/Tester.java
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From: <jam...@us...> - 2013-05-26 19:39:09
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Revision: 3756
http://obi.svn.sourceforge.net/obi/?rev=3756&view=rev
Author: jamesaoverton
Date: 2013-05-26 19:38:57 +0000 (Sun, 26 May 2013)
Log Message:
-----------
Initial implementation of automated testing for the build tool.
Modified Paths:
--------------
trunk/src/tools/build/README.md
trunk/src/tools/build/build.xml
trunk/src/tools/build/ivy.xml
Added Paths:
-----------
trunk/src/tests/
trunk/src/tests/example.txt
trunk/src/tools/build/ivysettings.xml
trunk/src/tools/build/src/main/java/obi/Test.java
trunk/src/tools/build/src/main/java/obi/Tester.java
trunk/src/tools/build/src/main/java/org/
trunk/src/tools/build/src/main/java/org/obolibrary/
trunk/src/tools/build/src/main/java/org/obolibrary/macro/
trunk/src/tools/build/src/main/java/org/obolibrary/macro/ManchesterSyntaxTool.java
trunk/src/tools/build/src/main/resources/
trunk/src/tools/build/src/main/resources/catalog-v001.xml
trunk/src/tools/build/src/main/resources/log4j.properties
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From: <jam...@us...> - 2013-05-20 21:18:30
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Revision: 3755
http://obi.svn.sourceforge.net/obi/?rev=3755&view=rev
Author: jamesaoverton
Date: 2013-05-20 21:18:24 +0000 (Mon, 20 May 2013)
Log Message:
-----------
Minor changes to README.
Modified Paths:
--------------
trunk/src/tools/build/README.md
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From: <jam...@us...> - 2013-05-20 21:07:32
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Revision: 3754
http://obi.svn.sourceforge.net/obi/?rev=3754&view=rev
Author: jamesaoverton
Date: 2013-05-20 21:07:25 +0000 (Mon, 20 May 2013)
Log Message:
-----------
Added code for assigning IDs and updated reporting code.
Modified Paths:
--------------
trunk/src/tools/build/README.md
trunk/src/tools/build/build.xml
trunk/src/tools/build/src/main/java/obi/Reporter.java
Added Paths:
-----------
trunk/src/tools/build/src/main/java/obi/Assigner.java
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From: <mb...@us...> - 2013-04-22 17:55:20
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Revision: 3753
http://obi.svn.sourceforge.net/obi/?rev=3753&view=rev
Author: mbrush
Date: 2013-04-22 17:55:13 +0000 (Mon, 22 Apr 2013)
Log Message:
-----------
adding slides from 4-22-13 developer call
Added Paths:
-----------
trunk/docs/developer/OBI Developer Call Presentations/4-22-13_OBI-CLO_CellCulture_Alignment.pptx
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From: <mb...@us...> - 2013-04-22 00:27:09
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Revision: 3752
http://obi.svn.sourceforge.net/obi/?rev=3752&view=rev
Author: mbrush
Date: 2013-04-22 00:27:02 +0000 (Mon, 22 Apr 2013)
Log Message:
-----------
- updated metadata on cell/culture classes
- added axiom to primary cultured cell: "not ('derives from' some ('cultured cell' and (is_specified_output_of some 'cell culture splitting')))"
- clarified definition and intended meaning of 'cell line immortalization', and created a new class 'immortalizing cell line genetic modification' that represents the genetic transformation part of 'cell line immortalilzation'
- updated definition of 'cell line immortalization' to clarify it as a type of 'establishing cell line' process
- created 'cancer cell line' class to use in defining 'establishing a cancer cell line'
- created 'immortalizing cell line transformation class' (part of a cell line imortalization process)
- created 'secondary cell culture sample' class: def = A cell culture sample comprised of a defined portion of a secondary cell culture that has been successively passaged together, and is output from a single cell culture splitting process (can be in active culture or stored in quiescence).
Modified Paths:
--------------
trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/obi.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:
-----------
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_20130404.tab
trunk/src/ontology/spreadsheets/new_ids/newIDs_20130419.tab
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From: <jzh...@us...> - 2013-04-19 19:15:29
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Revision: 3750
http://obi.svn.sourceforge.net/obi/?rev=3750&view=rev
Author: jzheng24
Date: 2013-04-19 19:15:19 +0000 (Fri, 19 Apr 2013)
Log Message:
-----------
Add NIAID GSCID-BRC requested terms, details see:
http://sourceforge.net/tracker/?func=detail&aid=3608207&group_id=177891&atid=886178
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <yon...@us...> - 2013-04-08 22:15:24
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Revision: 3749
http://obi.svn.sourceforge.net/obi/?rev=3749&view=rev
Author: yongqunh
Date: 2013-04-08 22:15:16 +0000 (Mon, 08 Apr 2013)
Log Message:
-----------
Updates on the obistat.owl, the Excel worksheet, and the PPT presentation after today's OBI conference call. Oliver He
Modified Paths:
--------------
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/OBIStat_new_terms_IDs-v2.xlsx
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/catalog-v001.xml
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/obistat.owl
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat_Apr82013.pptx
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From: <yon...@us...> - 2013-04-08 20:24:45
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Revision: 3748
http://obi.svn.sourceforge.net/obi/?rev=3748&view=rev
Author: yongqunh
Date: 2013-04-08 20:24:38 +0000 (Mon, 08 Apr 2013)
Log Message:
-----------
Original PPT slides that I presented this morning. Oliver He
Added Paths:
-----------
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat_Apr82013.pptx
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From: <yon...@us...> - 2013-04-08 00:03:02
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Revision: 3747
http://obi.svn.sourceforge.net/obi/?rev=3747&view=rev
Author: yongqunh
Date: 2013-04-08 00:02:48 +0000 (Mon, 08 Apr 2013)
Log Message:
-----------
More updates on OBIstat terms. Oliver
Modified Paths:
--------------
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/OBIStat_new_terms_IDs-v2.xlsx
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/catalog-v001.xml
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/obistat.owl
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From: <yon...@us...> - 2013-04-07 21:51:02
|
Revision: 3746
http://obi.svn.sourceforge.net/obi/?rev=3746&view=rev
Author: yongqunh
Date: 2013-04-07 21:50:52 +0000 (Sun, 07 Apr 2013)
Log Message:
-----------
Some updates. Oliver
Modified Paths:
--------------
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/OBIStat_new_terms_IDs-v2.xlsx
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/catalog-v001.xml
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/obistat.owl
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From: <yon...@us...> - 2013-04-07 12:01:06
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Revision: 3745
http://obi.svn.sourceforge.net/obi/?rev=3745&view=rev
Author: yongqunh
Date: 2013-04-07 12:00:55 +0000 (Sun, 07 Apr 2013)
Log Message:
-----------
Updated OBIstat source, which is the material that I will use for OBI statistics presentation on April 8, 2013. Oliver He
Added Paths:
-----------
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/OBIStat_new_terms_IDs-v2.xlsx
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/OBI_existing_stat_allAxioms.owl
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/OntoFox input/
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/OntoFox input/OBI_statisitics_OntoFox_import_input.txt
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/catalog-v001.xml
trunk/docs/presentations/OBI workshop May 2012 Ann Arbor/OBI Statistics/OBIstat source/obistat.owl
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From: <jam...@us...> - 2013-04-06 15:40:38
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Revision: 3744
http://obi.svn.sourceforge.net/obi/?rev=3744&view=rev
Author: jamesaoverton
Date: 2013-04-06 15:40:28 +0000 (Sat, 06 Apr 2013)
Log Message:
-----------
Added new OBI Core file.
Added Paths:
-----------
trunk/docs/presentations/OBI workshop May 2013 Philly - core review/core.owl
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From: <jam...@us...> - 2013-04-06 15:39:33
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Revision: 3743
http://obi.svn.sourceforge.net/obi/?rev=3743&view=rev
Author: jamesaoverton
Date: 2013-04-06 15:39:25 +0000 (Sat, 06 Apr 2013)
Log Message:
-----------
Tweaked build tool README.
Modified Paths:
--------------
trunk/src/tools/build/README.md
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From: <jam...@us...> - 2013-04-06 15:36:58
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Revision: 3742
http://obi.svn.sourceforge.net/obi/?rev=3742&view=rev
Author: jamesaoverton
Date: 2013-04-06 15:36:47 +0000 (Sat, 06 Apr 2013)
Log Message:
-----------
Tweaked the DOAP template.
Modified Paths:
--------------
trunk/src/ontology/branches/doap.template
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From: <jam...@us...> - 2013-04-06 15:30:11
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Revision: 3741
http://obi.svn.sourceforge.net/obi/?rev=3741&view=rev
Author: jamesaoverton
Date: 2013-04-06 15:30:00 +0000 (Sat, 06 Apr 2013)
Log Message:
-----------
Added new build tool.
Added Paths:
-----------
trunk/src/tools/build/README.md
trunk/src/tools/build/build.xml
trunk/src/tools/build/config.properties
trunk/src/tools/build/core.txt
trunk/src/tools/build/ivy.xml
trunk/src/tools/build/src/
trunk/src/tools/build/src/main/
trunk/src/tools/build/src/main/java/
trunk/src/tools/build/src/main/java/obi/
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/Metadator.java
trunk/src/tools/build/src/main/java/obi/Reporter.java
trunk/src/tools/build/src/main/java/owltools/
trunk/src/tools/build/src/main/java/owltools/io/
trunk/src/tools/build/src/main/java/owltools/io/CatalogXmlIRIMapper.java
trunk/src/tools/build/src/test/
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From: <jam...@us...> - 2013-04-06 15:29:09
|
Revision: 3740
http://obi.svn.sourceforge.net/obi/?rev=3740&view=rev
Author: jamesaoverton
Date: 2013-04-06 15:28:58 +0000 (Sat, 06 Apr 2013)
Log Message:
-----------
Add new build directory, and ignore props.
Added Paths:
-----------
trunk/src/tools/build/
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