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From: <jzh...@us...> - 2013-10-01 23:01:44
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Revision: 3838
http://sourceforge.net/p/obi/code/3838
Author: jzheng24
Date: 2013-10-01 23:01:41 +0000 (Tue, 01 Oct 2013)
Log Message:
-----------
modify axiom of 'molecular label' and 'molecular label role' by adding 'atom'
Modified Paths:
--------------
trunk/src/ontology/branches/external-byhand.owl
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-09-30 15:23:44
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Revision: 3837
http://sourceforge.net/p/obi/code/3837
Author: jzheng24
Date: 2013-09-30 15:23:42 +0000 (Mon, 30 Sep 2013)
Log Message:
-----------
assign OBI id to newly added term 'molecular-labeled material'
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20130930.tab
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From: <mb...@us...> - 2013-09-29 23:28:47
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Revision: 3836
http://sourceforge.net/p/obi/code/3836
Author: mbrush
Date: 2013-09-29 23:28:44 +0000 (Sun, 29 Sep 2013)
Log Message:
-----------
OBI:'detection of label' to be renamed 'detection of molecular label' and given updated definition/axioms based on developer consensus.?\194?\160
OBI:'labeling' to be renamed 'addition of molecular label' and given updated definition/axioms based on developer consensus.?\194?\160
ReO:?\226?\128?\152molecular label ?\194?\160imported from the Reagent Ontology?\194?\160
ReO:?\226?\128?\152molecular label role' ?\194?\160imported from the Reagent ontology to replace OBI:'label role' (which will be deprecated)?\194?\160
OBI:'molecular labeled material' ?\194?\160created as a new defined class (which upon reasoning will subsume several existing OBI classes such as 'labeled specimen' and 'labeled nucleic acid extract')
Modified Paths:
--------------
trunk/src/ontology/branches/external-byhand.owl
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-09-27 19:51:48
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Revision: 3835
http://sourceforge.net/p/obi/code/3835
Author: jzheng24
Date: 2013-09-27 19:51:44 +0000 (Fri, 27 Sep 2013)
Log Message:
-----------
add new terms needed from ChEBI and GO
add CLO terms (cell line cell related terms) needed to be imported and remove imported CL terms (cell line cell related terms) that deprecated in CL
Modified Paths:
--------------
trunk/src/ontology/importUsingOntofox/ChEBI_imports.owl
trunk/src/ontology/importUsingOntofox/GO_imports.owl
trunk/src/ontology/importUsingOntofox/OBO_imports.owl
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/ChEBI_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/OBO_input.txt
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From: <jzh...@us...> - 2013-09-27 19:49:47
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Revision: 3834
http://sourceforge.net/p/obi/code/3834
Author: jzheng24
Date: 2013-09-27 19:49:42 +0000 (Fri, 27 Sep 2013)
Log Message:
-----------
change metadata that imports ontoFox output owl files
remove 'editor preferred term' of imported terms which should be in the ontoFox output files
Modified Paths:
--------------
trunk/src/ontology/importUsingOntofox/obi.owl
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From: <jzh...@us...> - 2013-09-27 17:15:19
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Revision: 3833
http://sourceforge.net/p/obi/code/3833
Author: jzheng24
Date: 2013-09-27 17:15:17 +0000 (Fri, 27 Sep 2013)
Log Message:
-----------
add example of usage to 'processed specimen'
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-09-27 17:04:38
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Revision: 3832
http://sourceforge.net/p/obi/code/3832
Author: jzheng24
Date: 2013-09-27 17:04:35 +0000 (Fri, 27 Sep 2013)
Log Message:
-----------
removed 'obsolete_is_realized_by' property as annotationProperty (which was defined as objectProperty too) and removed its multiple rdfs:label and keep single label
removed double rdfs:label defined of some annotationProperties
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-09-27 16:43:02
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Revision: 3831
http://sourceforge.net/p/obi/code/3831
Author: jzheng24
Date: 2013-09-27 16:43:00 +0000 (Fri, 27 Sep 2013)
Log Message:
-----------
clean up annotationProperty statements
remove <IAO_0010000> with two rdfs:label 'axiom id' and 'has axiom label'
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-09-27 16:41:16
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Revision: 3830
http://sourceforge.net/p/obi/code/3830
Author: jzheng24
Date: 2013-09-27 16:41:12 +0000 (Fri, 27 Sep 2013)
Log Message:
-----------
'adjacent to' was defined as both annotation and object property
remove 'adjacent to' which defined as annotationProterty statements
Modified Paths:
--------------
trunk/src/ontology/branches/external-byhand.owl
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From: <jam...@us...> - 2013-09-27 13:23:17
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Revision: 3829
http://sourceforge.net/p/obi/code/3829
Author: jamesaoverton
Date: 2013-09-27 13:23:13 +0000 (Fri, 27 Sep 2013)
Log Message:
-----------
Moved terms with conflicting IRIs that were created for OBI out of IAO and into OBI's ID space: IAO_0000600 -> OBI_0001934; IAO_0000601 -> OBI_0001933; IAO_0000602 -> OBI_0001931; IAO_0000603 -> OBI_0001930; IAO_0000604 -> OBI_0001929; IAO_0000605 -> OBI_0001927; IAO_0000606 -> OBI_0001932; IAO_0000610 -> OBI_0001935; added table of new terms; updated data prototype.
Modified Paths:
--------------
trunk/src/examples/development/data-prototype.owl
trunk/src/examples/development/data-prototype.pdf
trunk/src/examples/development/data-prototype.txt
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20130926.tab
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From: <jam...@us...> - 2013-09-26 18:43:14
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Revision: 3828
http://sourceforge.net/p/obi/code/3828
Author: jamesaoverton
Date: 2013-09-26 18:43:12 +0000 (Thu, 26 Sep 2013)
Log Message:
-----------
Fixed IRI for 'has ID prefix'. See IAO issue 145.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-09-25 15:05:17
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Revision: 3827
http://sourceforge.net/p/obi/code/3827
Author: jamesaoverton
Date: 2013-09-25 15:05:15 +0000 (Wed, 25 Sep 2013)
Log Message:
-----------
Changes to data terms from OBI call 2013-09-09: 'measurement datum' removed disjunctive subClassOf axiom.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-09-25 14:18:21
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Revision: 3826
http://sourceforge.net/p/obi/code/3826
Author: jamesaoverton
Date: 2013-09-25 14:18:17 +0000 (Wed, 25 Sep 2013)
Log Message:
-----------
Belated change from OBI Philly 2013 workshop: 'measurement device' revised definition for clarity.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2013-09-25 13:13:24
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Revision: 3825
http://sourceforge.net/p/obi/code/3825
Author: jamesaoverton
Date: 2013-09-25 13:13:22 +0000 (Wed, 25 Sep 2013)
Log Message:
-----------
Following OBI call 2013-09-16: trimmed definition of 'human subject enrollment'; added example to 'processed specimen'.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-09-24 20:49:36
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Revision: 3824
http://sourceforge.net/p/obi/code/3824
Author: jzheng24
Date: 2013-09-24 20:49:34 +0000 (Tue, 24 Sep 2013)
Log Message:
-----------
make changes based on 2013-09-23 obi call discussion
details see 'Decision (2013-09-23)' part of google doc:
https://docs.google.com/document/d/1J3VjL6pbMY3q6GYZqsqqs4CbgEgIxnivMXcj_qcyznc/edit
Modified Paths:
--------------
trunk/src/ontology/branches/external-byhand.owl
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-09-19 21:27:43
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Revision: 3823
http://sourceforge.net/p/obi/code/3823
Author: jzheng24
Date: 2013-09-19 21:27:40 +0000 (Thu, 19 Sep 2013)
Log Message:
-----------
Made changes of PLAN related terms that were decided on Philly OBI workshop
Details see:
https://docs.google.com/document/d/1J3VjL6pbMY3q6GYZqsqqs4CbgEgIxnivMXcj_qcyznc/edit#
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <p_r...@us...> - 2013-09-12 10:01:58
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Revision: 3822
http://sourceforge.net/p/obi/code/3822
Author: p_rocca_serra
Date: 2013-09-12 10:01:56 +0000 (Thu, 12 Sep 2013)
Log Message:
-----------
implementing changes to selection rule, eligibility rule, as per action item. some of the discussion is capture under tracker item http://sourceforge.net/p/obi/obi-terms/678/, addition of selection class as a planned process, defined as realizing/concretizing a selection criterion. reasoning ok, acquisition and human subject enrollement being classified under selection
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-09-04 15:37:42
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Revision: 3821
http://sourceforge.net/p/obi/code/3821
Author: jzheng24
Date: 2013-09-04 15:37:38 +0000 (Wed, 04 Sep 2013)
Log Message:
-----------
Import 'Mammalia' from NCBITaxon as Bjoern suggested
Remove a temporary file
Modified Paths:
--------------
trunk/src/ontology/importUsingOntofox/NCBITaxon_imports.owl
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/NCBITaxon_input.txt
Removed Paths:
-------------
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/~$summary_externalTermsl.xlsx
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From: <jam...@us...> - 2013-08-16 19:39:16
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Revision: 3820
http://sourceforge.net/p/obi/code/3820
Author: jamesaoverton
Date: 2013-08-16 19:39:14 +0000 (Fri, 16 Aug 2013)
Log Message:
-----------
Updating data prototype with more conservative approach.
Modified Paths:
--------------
trunk/src/examples/development/data-prototype.owl
trunk/src/examples/development/data-prototype.pdf
trunk/src/examples/development/data-prototype.txt
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From: <jzh...@us...> - 2013-08-12 18:42:10
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Revision: 3819
http://sourceforge.net/p/obi/code/3819
Author: jzheng24
Date: 2013-08-12 18:42:08 +0000 (Mon, 12 Aug 2013)
Log Message:
-----------
fixed incorrect annotationProperty used in importing NCBITaxon terms (replace 'editor note' IAO_0000116 by 'alternative term' IAO:0000118)
Modified Paths:
--------------
trunk/src/ontology/importUsingOntofox/NCBITaxon_imports.owl
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/NCBITaxon_input.txt
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From: <jzh...@us...> - 2013-08-12 18:16:40
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Revision: 3818
http://sourceforge.net/p/obi/code/3818
Author: jzheng24
Date: 2013-08-12 18:16:37 +0000 (Mon, 12 Aug 2013)
Log Message:
-----------
Import terms from external resources using OntoFox tool
For NCBITaxon terms, only include OBI used organism + model organisms
Added Paths:
-----------
trunk/src/ontology/importUsingOntofox/
trunk/src/ontology/importUsingOntofox/ChEBI_imports.owl
trunk/src/ontology/importUsingOntofox/GO_imports.owl
trunk/src/ontology/importUsingOntofox/NCBITaxon_imports.owl
trunk/src/ontology/importUsingOntofox/OBO_imports.owl
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/ChEBI_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/GO_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/NCBITaxon_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/OBO_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/PATO_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/UO_input.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/UO_input_instance.txt
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/summary_externalTermsl.xlsx
trunk/src/ontology/importUsingOntofox/OntoFox_inputs/~$summary_externalTermsl.xlsx
trunk/src/ontology/importUsingOntofox/PATO_imports.owl
trunk/src/ontology/importUsingOntofox/UO_imports.owl
trunk/src/ontology/importUsingOntofox/UO_instance_imports.owl
trunk/src/ontology/importUsingOntofox/catalog-v001.xml
trunk/src/ontology/importUsingOntofox/external-byhand.owl
trunk/src/ontology/importUsingOntofox/modelOrganism.txt
trunk/src/ontology/importUsingOntofox/obi.owl
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From: <mb...@us...> - 2013-08-10 00:40:43
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Revision: 3817
http://sourceforge.net/p/obi/code/3817
Author: mbrush
Date: 2013-08-10 00:40:40 +0000 (Sat, 10 Aug 2013)
Log Message:
-----------
Final CLO alignment updates:
1. The existing class OBI_0100062 ('cell line', formerly called 'cell line culture'), was obsoleted and replaced by the new CLO:cell line class (CLO_0000031)
2. The existing class OBI_0100056 ('immortal cell line', formerly called 'immortalized cell line culture'), was obsoleted and replaced by a new CLO:immortal cell line class.
3. The existing class OBI 'mortal cell line' was obsoleted and replaced by a new CLO:mortal cell line class.
4. The CL:'cell line cell', CL:'mortal cell line cell', and CL:'immortal cell line cell' that are currently being imported from CL will be replaced by import of CLO classes with the same labels (since the CL classes were obsoleted and replaced by the CLO classes as well, which has already been vetted with CL folks)
Modified Paths:
--------------
trunk/src/ontology/branches/external.owl
trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-08-08 21:49:36
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Revision: 3816
http://sourceforge.net/p/obi/code/3816
Author: jzheng24
Date: 2013-08-08 21:49:33 +0000 (Thu, 08 Aug 2013)
Log Message:
-----------
Fix bugs reported by Alan and Mikhail, details see tracker:
https://sourceforge.net/p/obi/bugs/1/
IRI declared as both Annotation- and Object- properties (has_specified_input and has_specified_output)
https://sourceforge.net/p/obi/bugs/2/
CytoBuoy is a rdfs:label for two URIs
And remove multiple rdfs:label were assigned to some relations.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <mb...@us...> - 2013-08-07 00:22:28
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Revision: 3815
http://sourceforge.net/p/obi/code/3815
Author: mbrush
Date: 2013-08-07 00:22:26 +0000 (Wed, 07 Aug 2013)
Log Message:
-----------
minor change to 'addition of molecular tracer'
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2013-08-01 16:41:35
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Revision: 3814
http://sourceforge.net/p/obi/code/3814
Author: jzheng24
Date: 2013-08-01 16:41:26 +0000 (Thu, 01 Aug 2013)
Log Message:
-----------
remove unexpected import statement in the obi.owl
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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