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From: <jzh...@us...> - 2013-06-03 18:37:36
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Revision: 3789
http://obi.svn.sourceforge.net/obi/?rev=3789&view=rev
Author: jzheng24
Date: 2013-06-03 18:37:30 +0000 (Mon, 03 Jun 2013)
Log Message:
-----------
change logical axiom of 'planned process'
from plan specification and (has_part some objective specification)
to ?\226?\128?\152plan specification?\226?\128?\153
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-06-01 21:53:56
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Revision: 3788
http://obi.svn.sourceforge.net/obi/?rev=3788&view=rev
Author: jamesaoverton
Date: 2013-06-01 21:53:50 +0000 (Sat, 01 Jun 2013)
Log Message:
-----------
Added preliminary tools for reasoning and listing axioms as strings.
Modified Paths:
--------------
trunk/src/tools/build/build.xml
trunk/src/tools/build/config.properties
Added Paths:
-----------
trunk/src/tools/build/src/main/java/obi/Reasoner.java
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From: <jam...@us...> - 2013-06-01 21:46:31
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Revision: 3787
http://obi.svn.sourceforge.net/obi/?rev=3787&view=rev
Author: jamesaoverton
Date: 2013-06-01 21:46:19 +0000 (Sat, 01 Jun 2013)
Log Message:
-----------
Updated list of Core terms for the build tool.
Modified Paths:
--------------
trunk/src/tools/build/core.txt
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From: <jam...@us...> - 2013-06-01 21:29:20
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Revision: 3786
http://obi.svn.sourceforge.net/obi/?rev=3786&view=rev
Author: jamesaoverton
Date: 2013-06-01 21:29:14 +0000 (Sat, 01 Jun 2013)
Log Message:
-----------
Restrict 'evaluant role' to 'material entity' and update definitions and logical axioms for 'evaluant role', 'assay', 'assay objective'. I did my best to check inferred axioms before and after, and didn't notice any problems.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-06-01 21:01:14
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Revision: 3785
http://obi.svn.sourceforge.net/obi/?rev=3785&view=rev
Author: jamesaoverton
Date: 2013-06-01 21:01:08 +0000 (Sat, 01 Jun 2013)
Log Message:
-----------
Minor changes: replace some unnecessary Unicode characters.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-06-01 18:19:30
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Revision: 3784
http://obi.svn.sourceforge.net/obi/?rev=3784&view=rev
Author: jamesaoverton
Date: 2013-06-01 18:19:24 +0000 (Sat, 01 Jun 2013)
Log Message:
-----------
AMEND: Assigning IDs to two new classes: 'conclusion based on data' (OBI_0001909), 'testable hypothesis' (OBI_0001908).
Modified Paths:
--------------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20130601.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:
-----------
Assigning IDs to two new classes: 'conclusion based on data' (OBI_0001909), 'testable hypothesis' (OBI_0001908).
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20130601.tab
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From: <jam...@us...> - 2013-06-01 18:17:08
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Revision: 3782
http://obi.svn.sourceforge.net/obi/?rev=3782&view=rev
Author: jamesaoverton
Date: 2013-06-01 18:17:02 +0000 (Sat, 01 Jun 2013)
Log Message:
-----------
Revisions to the testing tool: added a 'release' task, distinct from the 'build' task, and updated the README.
Modified Paths:
--------------
trunk/src/tools/build/README.md
trunk/src/tools/build/build.xml
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From: <jam...@us...> - 2013-06-01 18:04:08
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Revision: 3781
http://obi.svn.sourceforge.net/obi/?rev=3781&view=rev
Author: jamesaoverton
Date: 2013-06-01 18:04:02 +0000 (Sat, 01 Jun 2013)
Log Message:
-----------
Adding table of new IDs created 2013-05-28: secondary_cell_culture_sample (OBI_0001905), cancer_cell_line (OBI_0001906), immortalizing_cell_line_transformation (OBI_0001907)
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20130528.tab
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From: <jam...@us...> - 2013-06-01 17:53:20
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Revision: 3780
http://obi.svn.sourceforge.net/obi/?rev=3780&view=rev
Author: jamesaoverton
Date: 2013-06-01 17:53:14 +0000 (Sat, 01 Jun 2013)
Log Message:
-----------
Update testing example to mention DataProperties.
Modified Paths:
--------------
trunk/src/tests/example.txt
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From: <jam...@us...> - 2013-06-01 17:51:28
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Revision: 3779
http://obi.svn.sourceforge.net/obi/?rev=3779&view=rev
Author: jamesaoverton
Date: 2013-06-01 17:51:22 +0000 (Sat, 01 Jun 2013)
Log Message:
-----------
Fixing a bug in the testing code: use HermiT instead of the structural reasoner.
Modified Paths:
--------------
trunk/src/tools/build/src/main/java/obi/Tester.java
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From: <jam...@us...> - 2013-06-01 17:50:16
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Revision: 3778
http://obi.svn.sourceforge.net/obi/?rev=3778&view=rev
Author: jamesaoverton
Date: 2013-06-01 17:50:09 +0000 (Sat, 01 Jun 2013)
Log Message:
-----------
Adding support for DataProperties to the testing tool, which requires an ugly hack around what I think is an OWLAPI bug.
Modified Paths:
--------------
trunk/src/tools/build/src/main/java/obi/Tester.java
trunk/src/tools/build/src/main/java/org/obolibrary/macro/ManchesterSyntaxTool.java
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From: <jam...@us...> - 2013-05-31 14:25:55
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Revision: 3777
http://obi.svn.sourceforge.net/obi/?rev=3777&view=rev
Author: jamesaoverton
Date: 2013-05-31 14:25:49 +0000 (Fri, 31 May 2013)
Log Message:
-----------
Philly2013: moved 'selection rule' and 'eligibility rule' to be direct children of 'directive information entity'.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-30 19:47:30
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Revision: 3776
http://obi.svn.sourceforge.net/obi/?rev=3776&view=rev
Author: jamesaoverton
Date: 2013-05-30 19:47:23 +0000 (Thu, 30 May 2013)
Log Message:
-----------
Small change to definition of 'planning'.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-30 19:02:57
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Revision: 3775
http://obi.svn.sourceforge.net/obi/?rev=3775&view=rev
Author: jamesaoverton
Date: 2013-05-30 19:02:51 +0000 (Thu, 30 May 2013)
Log Message:
-----------
Change definition of 'organization'.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-30 19:00:35
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Revision: 3774
http://obi.svn.sourceforge.net/obi/?rev=3774&view=rev
Author: jamesaoverton
Date: 2013-05-30 19:00:26 +0000 (Thu, 30 May 2013)
Log Message:
-----------
Changes to 'investigation agent role': revised definition, revised equivalent to, restrict to 'is realized by' some investigation, add editor note.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-30 18:37:25
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Revision: 3773
http://obi.svn.sourceforge.net/obi/?rev=3773&view=rev
Author: jamesaoverton
Date: 2013-05-30 18:37:19 +0000 (Thu, 30 May 2013)
Log Message:
-----------
Made 'investigation' subclass more specific: 'has part' some 'drawing a conclusion based on data'.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-30 18:26:17
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Revision: 3772
http://obi.svn.sourceforge.net/obi/?rev=3772&view=rev
Author: jamesaoverton
Date: 2013-05-30 18:26:11 +0000 (Thu, 30 May 2013)
Log Message:
-----------
Changes to definition of 'specimen role'; relabel 'specimen collection objective' and drop the axiom: 'is realized by' only investigation.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-30 16:52:07
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Revision: 3771
http://obi.svn.sourceforge.net/obi/?rev=3771&view=rev
Author: jamesaoverton
Date: 2013-05-30 16:52:00 +0000 (Thu, 30 May 2013)
Log Message:
-----------
Changes to 'specimen collection': adjusting definition, logical definition, and adding editor notes.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-30 15:45:43
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Revision: 3770
http://obi.svn.sourceforge.net/obi/?rev=3770&view=rev
Author: jamesaoverton
Date: 2013-05-30 15:45:37 +0000 (Thu, 30 May 2013)
Log Message:
-----------
Updating textual definition 'participant under investigation role'; updating textual definition and adding subclass axiom to 'informed consent process'.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-30 14:12:21
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Revision: 3769
http://obi.svn.sourceforge.net/obi/?rev=3769&view=rev
Author: jamesaoverton
Date: 2013-05-30 14:12:14 +0000 (Thu, 30 May 2013)
Log Message:
-----------
Updating 'information acquisition' and 'material acquisition'.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-30 13:31:19
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Revision: 3768
http://obi.svn.sourceforge.net/obi/?rev=3768&view=rev
Author: jamesaoverton
Date: 2013-05-30 13:31:12 +0000 (Thu, 30 May 2013)
Log Message:
-----------
Adjusted logical axioms of data transformation.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-05-29 21:57:32
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Revision: 3767
http://obi.svn.sourceforge.net/obi/?rev=3767&view=rev
Author: jzheng24
Date: 2013-05-29 21:57:23 +0000 (Wed, 29 May 2013)
Log Message:
-----------
Relabel some terms including independent, dependent, and controlled variable specification and make some minor changes of 'data transformation objective' definition. Details please see google doc: https://docs.google.com/document/d/1PpoBFt7zJc4AUbet3r_nVxBP8JNgui-Kof7Fr33CRlM/edit
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-05-29 20:58:40
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Revision: 3766
http://obi.svn.sourceforge.net/obi/?rev=3766&view=rev
Author: jzheng24
Date: 2013-05-29 20:58:33 +0000 (Wed, 29 May 2013)
Log Message:
-----------
workshop edits to core terms (James session, first part): hypothesis, conclusion, drawing a conclusion.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-05-29 14:54:37
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Revision: 3765
http://obi.svn.sourceforge.net/obi/?rev=3765&view=rev
Author: jamesaoverton
Date: 2013-05-29 14:54:30 +0000 (Wed, 29 May 2013)
Log Message:
-----------
Changes to 'measurement function' and 'measurement device'.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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