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From: <jam...@us...> - 2014-08-18 17:30:46
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Revision: 3938
http://sourceforge.net/p/obi/code/3938
Author: jamesaoverton
Date: 2014-08-18 17:30:43 +0000 (Mon, 18 Aug 2014)
Log Message:
-----------
Added 'competitive binding reference ligand role' from ticket #709.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <p_r...@us...> - 2014-06-09 22:06:31
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Revision: 3937
http://sourceforge.net/p/obi/code/3937
Author: p_rocca_serra
Date: 2014-06-09 22:06:24 +0000 (Mon, 09 Jun 2014)
Log Message:
-----------
adding ChIP assay and parent class as per request my plloyd, closes issue #707
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <mco...@us...> - 2014-06-05 18:07:19
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Revision: 3936
http://sourceforge.net/p/obi/code/3936
Author: mcourtot
Date: 2014-06-05 18:07:14 +0000 (Thu, 05 Jun 2014)
Log Message:
-----------
addressed https://sourceforge.net/p/obi/obi-terms/708/ by adding rdfs comment with attribution
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <al...@us...> - 2014-05-28 14:54:38
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Revision: 3935
http://sourceforge.net/p/obi/code/3935
Author: alanr
Date: 2014-05-28 14:54:36 +0000 (Wed, 28 May 2014)
Log Message:
-----------
Summary: update purl
Modified Paths:
--------------
trunk/src/ontology/branches/crux-staging.owl
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From: <al...@us...> - 2014-05-28 14:53:36
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Revision: 3934
http://sourceforge.net/p/obi/code/3934
Author: alanr
Date: 2014-05-28 14:53:35 +0000 (Wed, 28 May 2014)
Log Message:
-----------
update to latest obi
Modified Paths:
--------------
trunk/src/ontology/branches/crux-staging.owl
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From: <jam...@us...> - 2014-04-14 19:37:32
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Revision: 3933
http://sourceforge.net/p/obi/code/3933
Author: jamesaoverton
Date: 2014-04-14 19:37:28 +0000 (Mon, 14 Apr 2014)
Log Message:
-----------
Bjoern's revisions to the manuscript.
Modified Paths:
--------------
trunk/docs/papers/release/Manuscript 2014.doc
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From: <jam...@us...> - 2014-04-01 16:05:28
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Revision: 3932
http://sourceforge.net/p/obi/code/3932
Author: jamesaoverton
Date: 2014-04-01 16:05:24 +0000 (Tue, 01 Apr 2014)
Log Message:
-----------
Committing OBI release 2014-03-29
Added Paths:
-----------
releases/2014-03-29/
releases/2014-03-29/README.txt
releases/2014-03-29/branches/
releases/2014-03-29/branches/OntoFox_inputs/
releases/2014-03-29/branches/OntoFox_inputs/ChEBI_input.txt
releases/2014-03-29/branches/OntoFox_inputs/GO_input.txt
releases/2014-03-29/branches/OntoFox_inputs/NCBITaxon_input.txt
releases/2014-03-29/branches/OntoFox_inputs/OBO_input.txt
releases/2014-03-29/branches/OntoFox_inputs/PATO_input.txt
releases/2014-03-29/branches/OntoFox_inputs/SO_input.txt
releases/2014-03-29/branches/OntoFox_inputs/UO_input.txt
releases/2014-03-29/branches/OntoFox_inputs/UO_input_instance.txt
releases/2014-03-29/branches/OntoFox_inputs/readme.txt
releases/2014-03-29/branches/OntoFox_outputs/
releases/2014-03-29/branches/OntoFox_outputs/ChEBI_imports.owl
releases/2014-03-29/branches/OntoFox_outputs/GO_imports.owl
releases/2014-03-29/branches/OntoFox_outputs/NCBITaxon_imports.owl
releases/2014-03-29/branches/OntoFox_outputs/OBO_imports.owl
releases/2014-03-29/branches/OntoFox_outputs/PATO_imports.owl
releases/2014-03-29/branches/OntoFox_outputs/SO_imports.owl
releases/2014-03-29/branches/OntoFox_outputs/UO_imports.owl
releases/2014-03-29/branches/OntoFox_outputs/UO_instance_imports.owl
releases/2014-03-29/branches/catalog-v001.xml
releases/2014-03-29/branches/doap.template
releases/2014-03-29/branches/external-byhand.owl
releases/2014-03-29/branches/obi.owl
releases/2014-03-29/docs/
releases/2014-03-29/docs/newIDs.tab
releases/2014-03-29/docs/obi.tsv
releases/2014-03-29/docs/obi.txt
releases/2014-03-29/docs/obi_core.tsv
releases/2014-03-29/docs/obi_core.txt
releases/2014-03-29/docs/obi_iedb.tsv
releases/2014-03-29/docs/obi_iedb.txt
releases/2014-03-29/docs/obi_isa.tsv
releases/2014-03-29/docs/obi_isa.txt
releases/2014-03-29/external/
releases/2014-03-29/external/bfo2-alan/
releases/2014-03-29/external/bfo2-alan/README
releases/2014-03-29/external/bfo2-alan/bfo-relations.lisp
releases/2014-03-29/external/bfo2-alan/bfo1.1-to-2.lisp
releases/2014-03-29/external/bfo2-alan/ruttenberg-bfo2-all.owl
releases/2014-03-29/external/bfo2-alan/ruttenberg-bfo2-classes.obo
releases/2014-03-29/external/bfo2-alan/ruttenberg-bfo2-granularity.owl
releases/2014-03-29/external/bfo2-alan/ruttenberg-bfo2-regions.owl
releases/2014-03-29/external/bfo2-alan/ruttenberg-bfo2-relations.obo
releases/2014-03-29/external/bfo2-alan/ruttenberg-bfo2.owl
releases/2014-03-29/external/bfo2-alan/ruttenberg-classes.owl
releases/2014-03-29/external/bfo2-alan/ruttenberg-granularity.owl
releases/2014-03-29/external/bfo2-alan/ruttenberg-regions.owl
releases/2014-03-29/external/bfo2-alan/ruttenberg-relations-biotop-equiv.owl
releases/2014-03-29/external/bfo2-alan/ruttenberg-relations.owl
releases/2014-03-29/external/iao-bfo2/
releases/2014-03-29/external/iao-bfo2/IAO.owl
releases/2014-03-29/external/iao-bfo2/catalog-v001.xml
releases/2014-03-29/external/iao-bfo2/external.owl
releases/2014-03-29/external/iao-bfo2/externalByHand.owl
releases/2014-03-29/external/iao-bfo2/externalDerived.owl
releases/2014-03-29/external/iao-bfo2/iao-main.owl
releases/2014-03-29/external/iao-bfo2/obsolete.owl
releases/2014-03-29/external/iao-bfo2/ontology-metadata.owl
releases/2014-03-29/external/protege-dc.owl
releases/2014-03-29/obi.owl
releases/2014-03-29/obi_core.owl
releases/2014-03-29/obi_iedb.owl
releases/2014-03-29/obi_isa.owl
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From: <jam...@us...> - 2014-03-29 23:09:50
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Revision: 3931
http://sourceforge.net/p/obi/code/3931
Author: jamesaoverton
Date: 2014-03-29 23:09:46 +0000 (Sat, 29 Mar 2014)
Log Message:
-----------
Minor changes to labels of 'forward PCR primer' and 'reverse PCR primer'; minor changes to textual definitions of 'number of errors', 'genome coverage', 'sequence annotation provider', and 'sequence annotation provider role'; added textual definitions for 'NanoString Technologies', 'Nimblegen', 'Pacific Biosciences'.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <p_r...@us...> - 2014-03-29 15:26:28
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Revision: 3930
http://sourceforge.net/p/obi/code/3930
Author: p_rocca_serra
Date: 2014-03-29 15:26:25 +0000 (Sat, 29 Mar 2014)
Log Message:
-----------
adding definition and all metadata to pcr primer, dropping axiom leading to classification of primer as information entity, change axiom of number of errors class now set to process instead of genome assembly process, change to definition of genome coverage so no need to change label
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2014-03-17 20:46:52
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Revision: 3929
http://sourceforge.net/p/obi/code/3929
Author: jamesaoverton
Date: 2014-03-17 20:46:49 +0000 (Mon, 17 Mar 2014)
Log Message:
-----------
Build tool fix: use Builder.loadLocalOntology method in Assigner.java.
Modified Paths:
--------------
trunk/src/tools/build/src/main/java/obi/Assigner.java
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From: <jam...@us...> - 2014-03-14 23:59:06
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Revision: 3928
http://sourceforge.net/p/obi/code/3928
Author: jamesaoverton
Date: 2014-03-14 23:59:03 +0000 (Fri, 14 Mar 2014)
Log Message:
-----------
Minor changes to build tool.
Modified Paths:
--------------
trunk/src/tools/build/README.md
trunk/src/tools/build/build.xml
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From: <jzh...@us...> - 2014-03-12 23:24:00
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Revision: 3927
http://sourceforge.net/p/obi/code/3927
Author: jzheng24
Date: 2014-03-12 23:23:55 +0000 (Wed, 12 Mar 2014)
Log Message:
-----------
'freezing' and 'flash freezing' with OBI ids assigned on Feb 4, 2014
Modified Paths:
--------------
trunk/src/ontology/branches/obi_dev_merged.owl
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From: <jzh...@us...> - 2014-03-12 22:40:12
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Revision: 3926
http://sourceforge.net/p/obi/code/3926
Author: jzheng24
Date: 2014-03-12 22:40:10 +0000 (Wed, 12 Mar 2014)
Log Message:
-----------
'flash freezing' and 'freezing' with OBI ids assigned on Feb 4, 2014
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <yon...@us...> - 2014-03-12 21:58:49
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Revision: 3925
http://sourceforge.net/p/obi/code/3925
Author: yongqunh
Date: 2014-03-12 21:58:46 +0000 (Wed, 12 Mar 2014)
Log Message:
-----------
I generated a file called "obi_dev_merged.owl" that merged all latest OBI-related OWL files into one merged owl file. I will test how I can display the latest OBI development version using Ontobee.
-- Oliver He
Added Paths:
-----------
trunk/src/ontology/branches/obi_dev_merged.owl
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From: <jzh...@us...> - 2014-03-10 21:09:07
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Revision: 3924
http://sourceforge.net/p/obi/code/3924
Author: jzheng24
Date: 2014-03-10 21:09:04 +0000 (Mon, 10 Mar 2014)
Log Message:
-----------
add license information to the OWL files:
<dc:license rdf:resource="http://creativecommons.org/licenses/by/3.0/"/>
Modified Paths:
--------------
releases/2013-10-25/obi.owl
releases/2013-10-25/obi_FGED.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: <jzh...@us...> - 2014-03-10 21:08:31
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Revision: 3923
http://sourceforge.net/p/obi/code/3923
Author: jzheng24
Date: 2014-03-10 21:08:27 +0000 (Mon, 10 Mar 2014)
Log Message:
-----------
Add CC-by 3.0 license information:
<dc:license rdf:resource="http://creativecommons.org/licenses/by/3.0/"/>
Fix synonym of OBI_0001853, to be DNase-Seq to DNase-seq, see tracker: http://sourceforge.net/p/obi/obi-terms/693/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2014-03-04 22:16:20
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Revision: 3922
http://sourceforge.net/p/obi/code/3922
Author: jzheng24
Date: 2014-03-04 22:16:17 +0000 (Tue, 04 Mar 2014)
Log Message:
-----------
Gave more meaningful IRI to BFO_classes.owl
Modified Paths:
--------------
trunk/docs/developer/BFO 2 slim/BFO_classes.owl
trunk/docs/developer/BFO 2 slim/OntoFox_classes_input.txt
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From: <jzh...@us...> - 2014-03-04 16:16:33
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Revision: 3921
http://sourceforge.net/p/obi/code/3921
Author: jzheng24
Date: 2014-03-04 16:16:26 +0000 (Tue, 04 Mar 2014)
Log Message:
-----------
BFO subset only contains BFO classes and the OntoFox input file that used to generate the subset
Added Paths:
-----------
trunk/docs/developer/BFO 2 slim/BFO_classes.owl
trunk/docs/developer/BFO 2 slim/OntoFox_classes_input.txt
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From: <jzh...@us...> - 2014-03-03 20:27:03
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Revision: 3920
http://sourceforge.net/p/obi/code/3920
Author: jzheng24
Date: 2014-03-03 20:26:57 +0000 (Mon, 03 Mar 2014)
Log Message:
-----------
Subset of BFO 2 (Graz release) contains only BFO classes and 4 commonly used atemporal relations generated using OntoFox and the OntoFox input file
Added Paths:
-----------
trunk/docs/developer/BFO 2 slim/
trunk/docs/developer/BFO 2 slim/BFO_classes_aTemporalRelations.owl
trunk/docs/developer/BFO 2 slim/OntoFox_input.txt
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From: <bjo...@us...> - 2014-02-24 17:53:22
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Revision: 3919
http://sourceforge.net/p/obi/code/3919
Author: bjoernpeters
Date: 2014-02-24 17:53:20 +0000 (Mon, 24 Feb 2014)
Log Message:
-----------
added synonym for bisulfite-seq
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2014-02-14 16:26:06
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Revision: 3918
http://sourceforge.net/p/obi/code/3918
Author: jamesaoverton
Date: 2014-02-14 16:26:04 +0000 (Fri, 14 Feb 2014)
Log Message:
-----------
Created a new version of the OBI release manuscript by accepting most revisions to the 2011 version, cleaning up comments, then adding my own revisions and comments; updated completed action items; updated Figure 1.jpg from pptx.
Modified Paths:
--------------
trunk/docs/papers/release/Action Iterms.xls
trunk/docs/papers/release/Figure 1.jpg
Added Paths:
-----------
trunk/docs/papers/release/Manuscript 2014.doc
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From: <jzh...@us...> - 2014-02-04 18:35:30
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Revision: 3917
http://sourceforge.net/p/obi/code/3917
Author: jzheng24
Date: 2014-02-04 18:35:28 +0000 (Tue, 04 Feb 2014)
Log Message:
-----------
Add 'freezing' and 'flash freezing' and update definition of 'freezing storage'
Details see tracker: https://sourceforge.net/p/obi/obi-terms/690/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20140204.tab
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From: <jzh...@us...> - 2014-01-06 20:04:44
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Revision: 3916
http://sourceforge.net/p/obi/code/3916
Author: jzheng24
Date: 2014-01-06 20:04:42 +0000 (Mon, 06 Jan 2014)
Log Message:
-----------
OBI-core: semantic representation of investigations (both clinical and biological investigations) using all OBI core terms
obi-investigation: semantic representation of all kinds scientific investigations using some of OBI core terms
Added Paths:
-----------
trunk/docs/papers/release/OBI-core.cmap
trunk/docs/papers/release/OBI-core.jpg
trunk/docs/papers/release/obi-investigation.cmap
trunk/docs/papers/release/obi-investigation.jpg
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From: <jzh...@us...> - 2013-12-21 06:15:02
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Revision: 3915
http://sourceforge.net/p/obi/code/3915
Author: jzheng24
Date: 2013-12-21 06:14:59 +0000 (Sat, 21 Dec 2013)
Log Message:
-----------
assign OBI ids to newly added terms
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20131221.tab
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From: <jzh...@us...> - 2013-12-21 06:01:53
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Revision: 3914
http://sourceforge.net/p/obi/code/3914
Author: jzheng24
Date: 2013-12-21 06:01:49 +0000 (Sat, 21 Dec 2013)
Log Message:
-----------
add 3 terms needed for NIAID GSC-BRC metadata, see tracker:
https://sourceforge.net/p/obi/obi-terms/688/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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