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From: <al...@us...> - 2009-07-16 05:52:16
|
Revision: 1812
http://obi.svn.sourceforge.net/obi/?rev=1812&view=rev
Author: alanr
Date: 2009-07-16 05:52:11 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
A set of equivalences (obofoundry <-> oblibrary) for terms that were defined in the last official (pre) release
Added Paths:
-----------
trunk/src/ontology/january-prerelease-compat.owl
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From: <al...@us...> - 2009-07-16 05:48:51
|
Revision: 1811
http://obi.svn.sourceforge.net/obi/?rev=1811&view=rev
Author: alanr
Date: 2009-07-16 05:48:48 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
Change purl.obofoundry.org to purl.obolibrary.org. Use live dev version of IAO. Fix some usage of obsolete properties. Reasons and is consistent. See src/ontology/files-with-foundry-uris.txt for list of files that still have purl.obofoundry.org references and which should be changed
Modified Paths:
--------------
trunk/src/examples/development/OBIIrradiated/OBIIrradiated.owl
trunk/src/examples/development/alternate_concentration_bp/obi.owl
trunk/src/examples/development/concentration-alanr.owl
trunk/src/examples/development/concentration-demoed-vancouver-2009.owl
trunk/src/ontology/branches/AnnotationProperty.owl
trunk/src/ontology/branches/Biomaterial.owl
trunk/src/ontology/branches/DataFormatSpecification.owl
trunk/src/ontology/branches/DataTransformation.owl
trunk/src/ontology/branches/DigitalEntityPlus.owl
trunk/src/ontology/branches/InstrumentAndPart.owl
trunk/src/ontology/branches/OBI-Function.owl
trunk/src/ontology/branches/Obsolete.owl
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
trunk/src/ontology/branches/Quality.owl
trunk/src/ontology/branches/Relations.owl
trunk/src/ontology/branches/Role.owl
trunk/src/ontology/branches/external-byhand.owl
trunk/src/ontology/branches/external.owl
trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/instances/dataTransformationInstances.owl
trunk/src/ontology/branches/instances/softwareInstances.owl
trunk/src/ontology/branches/obi-lsw.owl.template
trunk/src/ontology/branches/obi-owl-full.owl
trunk/src/ontology/branches/obi-quick-id.owl
trunk/src/ontology/branches/obi.obo
trunk/src/ontology/branches/obi.pprj.template
trunk/src/ontology/branches/obid.owl
trunk/src/ontology/branches/obidi.owl
trunk/src/ontology/branches/obil.owl
trunk/src/tools/build/modify-uris.pl
trunk/src/tools/build/util.lisp
Added Paths:
-----------
trunk/src/ontology/files-with-foundry-uris.txt
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From: <al...@us...> - 2009-07-16 02:46:58
|
Revision: 1810
http://obi.svn.sourceforge.net/obi/?rev=1810&view=rev
Author: alanr
Date: 2009-07-16 02:46:56 +0000 (Thu, 16 Jul 2009)
Log Message:
-----------
use dev version of iao
Property Changed:
----------------
trunk/src/ontology/external/
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From: <bjo...@us...> - 2009-07-15 15:02:34
|
Revision: 1809
http://obi.svn.sourceforge.net/obi/?rev=1809&view=rev
Author: bjoernpeters
Date: 2009-07-15 15:02:33 +0000 (Wed, 15 Jul 2009)
Log Message:
-----------
removed split of document into sections
Removed Paths:
-------------
trunk/docs/papers/release/Acknowledgements.doc
trunk/docs/papers/release/Discussion.doc
trunk/docs/papers/release/Introduction.doc
trunk/docs/papers/release/Methodology.doc
trunk/docs/papers/release/Results.doc
trunk/docs/papers/release/Start.doc
trunk/docs/papers/release/combine-applescript.scpt
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From: <bjo...@us...> - 2009-07-15 14:59:58
|
Revision: 1808
http://obi.svn.sourceforge.net/obi/?rev=1808&view=rev
Author: bjoernpeters
Date: 2009-07-15 14:59:56 +0000 (Wed, 15 Jul 2009)
Log Message:
-----------
Extracted endnote library from document, and committed it as file.
Modified Paths:
--------------
trunk/docs/papers/release/Release-Manuscript-Master-shortened.doc
Added Paths:
-----------
trunk/docs/papers/release/release.Data/
trunk/docs/papers/release/release.Data/Trash/
trunk/docs/papers/release/release.Data/Trash/Trash.Data/
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/csort.MYD
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/csort.MYI
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/csort.frm
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/db.opt
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/jterms.MYD
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/jterms.MYI
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/jterms.frm
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/misc.MYD
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/misc.MYI
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/misc.frm
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/refs.MYD
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/refs.MYI
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/refs.frm
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/refs_ext.MYD
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/refs_ext.MYI
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/refs_ext.frm
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/terms.MYD
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/terms.MYI
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/terms.frm
trunk/docs/papers/release/release.Data/Trash/Trash.enl
trunk/docs/papers/release/release.Data/rdb/
trunk/docs/papers/release/release.Data/rdb/csort.MYD
trunk/docs/papers/release/release.Data/rdb/csort.MYI
trunk/docs/papers/release/release.Data/rdb/csort.frm
trunk/docs/papers/release/release.Data/rdb/db.opt
trunk/docs/papers/release/release.Data/rdb/jterms.MYD
trunk/docs/papers/release/release.Data/rdb/jterms.MYI
trunk/docs/papers/release/release.Data/rdb/jterms.frm
trunk/docs/papers/release/release.Data/rdb/misc.MYD
trunk/docs/papers/release/release.Data/rdb/misc.MYI
trunk/docs/papers/release/release.Data/rdb/misc.frm
trunk/docs/papers/release/release.Data/rdb/refs.MYD
trunk/docs/papers/release/release.Data/rdb/refs.MYI
trunk/docs/papers/release/release.Data/rdb/refs.frm
trunk/docs/papers/release/release.Data/rdb/refs_ext.MYD
trunk/docs/papers/release/release.Data/rdb/refs_ext.MYI
trunk/docs/papers/release/release.Data/rdb/refs_ext.frm
trunk/docs/papers/release/release.Data/rdb/terms.MYD
trunk/docs/papers/release/release.Data/rdb/terms.MYI
trunk/docs/papers/release/release.Data/rdb/terms.frm
trunk/docs/papers/release/release.enl
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From: <mco...@us...> - 2009-07-14 23:21:48
|
Revision: 1807
http://obi.svn.sourceforge.net/obi/?rev=1807&view=rev
Author: mcourtot
Date: 2009-07-14 23:21:46 +0000 (Tue, 14 Jul 2009)
Log Message:
-----------
as per AI from dev call 13th July 2009: obsoleted environmental matter, moved soil under material entity
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
trunk/src/ontology/branches/Obsolete.owl
trunk/src/ontology/branches/external.owl
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From: <jgr...@us...> - 2009-07-14 17:07:06
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Revision: 1806
http://obi.svn.sourceforge.net/obi/?rev=1806&view=rev
Author: jgreenbaum
Date: 2009-07-14 17:06:57 +0000 (Tue, 14 Jul 2009)
Log Message:
-----------
removed machine-specific line from template file
Modified Paths:
--------------
branches/ontie-dev/src/ontology/modules/ONTIE/obi-ontie.repository.template
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From: <bjo...@us...> - 2009-07-13 22:46:11
|
Revision: 1805
http://obi.svn.sourceforge.net/obi/?rev=1805&view=rev
Author: bjoernpeters
Date: 2009-07-13 22:46:10 +0000 (Mon, 13 Jul 2009)
Log Message:
-----------
Added editor note that sample role is 'relational', as discussed in todays call.
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <jgr...@us...> - 2009-07-13 21:43:45
|
Revision: 1804
http://obi.svn.sourceforge.net/obi/?rev=1804&view=rev
Author: jgreenbaum
Date: 2009-07-13 21:43:39 +0000 (Mon, 13 Jul 2009)
Log Message:
-----------
Replacing project-specific OWL files with 'templates'
Modified Paths:
--------------
branches/ontie-dev/src/ontology/modules/ONTIE/ONTIE.owl
Added Paths:
-----------
branches/ontie-dev/src/ontology/modules/ONTIE/obi-ontie.owl.template
branches/ontie-dev/src/ontology/modules/ONTIE/obi-ontie.pprj.template
branches/ontie-dev/src/ontology/modules/ONTIE/obi-ontie.repository.template
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.owl.template
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.pprj.template
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.repository.template
Removed Paths:
-------------
branches/ontie-dev/src/ontology/modules/ONTIE/obi-ontie.owl
branches/ontie-dev/src/ontology/modules/ONTIE/obi-ontie.pprj
branches/ontie-dev/src/ontology/modules/ONTIE/obi-ontie.repository
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.owl
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.pprj
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.repository
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From: <jgr...@us...> - 2009-07-13 21:15:21
|
Revision: 1803
http://obi.svn.sourceforge.net/obi/?rev=1803&view=rev
Author: jgreenbaum
Date: 2009-07-13 21:15:18 +0000 (Mon, 13 Jul 2009)
Log Message:
-----------
added obi-ontie files for viewing ONTIE alongside the full version of OBI
Modified Paths:
--------------
branches/ontie-dev/src/ontology/modules/ONTIE/ONTIE.owl
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-external.owl
Added Paths:
-----------
branches/ontie-dev/src/ontology/modules/ONTIE/obi-ontie.owl
branches/ontie-dev/src/ontology/modules/ONTIE/obi-ontie.pprj
branches/ontie-dev/src/ontology/modules/ONTIE/obi-ontie.repository
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From: <bjo...@us...> - 2009-07-13 17:11:56
|
Revision: 1802
http://obi.svn.sourceforge.net/obi/?rev=1802&view=rev
Author: bjoernpeters
Date: 2009-07-13 17:11:41 +0000 (Mon, 13 Jul 2009)
Log Message:
-----------
Call from 7/13/09: cleaned up use of 'specimen or reagent' roles, and added 'material entity' to those classes that were inferred only as 'independent continuant' or 'continuant, but were material entitites.
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
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From: <al...@us...> - 2009-07-11 07:05:20
|
Revision: 1801
http://obi.svn.sourceforge.net/obi/?rev=1801&view=rev
Author: alanr
Date: 2009-07-11 07:05:17 +0000 (Sat, 11 Jul 2009)
Log Message:
-----------
more parts, plus applescript to combine into one file. On pc use boiler macro from http://www.gmayor.com/Zips/boiler.zip
Added Paths:
-----------
trunk/docs/papers/release/Acknowledgements.doc
trunk/docs/papers/release/Start.doc
trunk/docs/papers/release/combine-applescript.scpt
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From: <al...@us...> - 2009-07-11 04:47:43
|
Revision: 1800
http://obi.svn.sourceforge.net/obi/?rev=1800&view=rev
Author: alanr
Date: 2009-07-11 04:47:40 +0000 (Sat, 11 Jul 2009)
Log Message:
-----------
splitting paper into sections for better distributed editing
Added Paths:
-----------
trunk/docs/papers/release/Discussion.doc
trunk/docs/papers/release/Introduction.doc
trunk/docs/papers/release/Methodology.doc
trunk/docs/papers/release/Results.doc
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From: <al...@us...> - 2009-07-11 04:31:27
|
Revision: 1799
http://obi.svn.sourceforge.net/obi/?rev=1799&view=rev
Author: alanr
Date: 2009-07-11 04:31:25 +0000 (Sat, 11 Jul 2009)
Log Message:
-----------
some edits by alan
Modified Paths:
--------------
trunk/docs/papers/release/Release-Manuscript-Master-shortened.doc
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From: <jgr...@us...> - 2009-07-10 23:55:59
|
Revision: 1798
http://obi.svn.sourceforge.net/obi/?rev=1798&view=rev
Author: jgreenbaum
Date: 2009-07-10 23:55:47 +0000 (Fri, 10 Jul 2009)
Log Message:
-----------
* ONTIE IDs changed to OBI_111XXXX
* URIs updated to 'purl.obolibrary.org' where appropriate
Modified Paths:
--------------
branches/ontie-dev/src/ontology/modules/ONTIE/ONTIE.owl
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-external.owl
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.owl
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.pprj
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.repository
Added Paths:
-----------
branches/ontie-dev/src/ontology/modules/ONTIE/README
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From: <jgr...@us...> - 2009-07-10 22:04:00
|
Revision: 1797
http://obi.svn.sourceforge.net/obi/?rev=1797&view=rev
Author: jgreenbaum
Date: 2009-07-10 22:03:56 +0000 (Fri, 10 Jul 2009)
Log Message:
-----------
Initial import of ONTIE
Added Paths:
-----------
branches/ontie-dev/src/ontology/modules/
branches/ontie-dev/src/ontology/modules/ONTIE/
branches/ontie-dev/src/ontology/modules/ONTIE/ONTIE.owl
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-external.owl
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.owl
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.pprj
branches/ontie-dev/src/ontology/modules/ONTIE/ontie-minimal.repository
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From: <jgr...@us...> - 2009-07-10 21:20:28
|
Revision: 1796
http://obi.svn.sourceforge.net/obi/?rev=1796&view=rev
Author: jgreenbaum
Date: 2009-07-10 21:20:25 +0000 (Fri, 10 Jul 2009)
Log Message:
-----------
Creating a branch for ONTIE development
Added Paths:
-----------
branches/ontie-dev/
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From: <mco...@us...> - 2009-07-10 21:02:55
|
Revision: 1795
http://obi.svn.sourceforge.net/obi/?rev=1795&view=rev
Author: mcourtot
Date: 2009-07-10 21:02:51 +0000 (Fri, 10 Jul 2009)
Log Message:
-----------
updated to use !oboinowl:ObsoleteClass instead of !obo:ObsoleteClass
Modified Paths:
--------------
trunk/src/tools/build/add-assumed-individuals.lisp
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From: <lso...@us...> - 2009-07-09 11:06:52
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Revision: 1794
http://obi.svn.sourceforge.net/obi/?rev=1794&view=rev
Author: lsoldatova
Date: 2009-07-09 11:06:44 +0000 (Thu, 09 Jul 2009)
Log Message:
-----------
the final slides
Modified Paths:
--------------
trunk/docs/papers/ISMB_2009/OBI-SIG.ppt
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From: <mco...@us...> - 2009-07-08 22:54:15
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Revision: 1793
http://obi.svn.sourceforge.net/obi/?rev=1793&view=rev
Author: mcourtot
Date: 2009-07-08 22:54:10 +0000 (Wed, 08 Jul 2009)
Log Message:
-----------
added instances path variable
Modified Paths:
--------------
trunk/src/tools/build/OBIrelease.sh
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From: <jzh...@us...> - 2009-07-08 22:04:03
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Revision: 1792
http://obi.svn.sourceforge.net/obi/?rev=1792&view=rev
Author: jzheng24
Date: 2009-07-08 22:04:02 +0000 (Wed, 08 Jul 2009)
Log Message:
-----------
remove line: xmlns:obi_rest="http://purl.obofoundry.org/obo/obi/TheRest.owl#"
Modified Paths:
--------------
trunk/src/ontology/branches/instances/softwareInstances.owl
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From: <jzh...@us...> - 2009-07-08 22:03:38
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Revision: 1791
http://obi.svn.sourceforge.net/obi/?rev=1791&view=rev
Author: jzheng24
Date: 2009-07-08 22:03:36 +0000 (Wed, 08 Jul 2009)
Log Message:
-----------
remove line: xmlns:obi_rest="http://purl.obofoundry.org/obo/obi/TheRest.owl#"
Modified Paths:
--------------
trunk/src/ontology/branches/instances/dataTransformationInstances.owl
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From: <mco...@us...> - 2009-07-08 21:42:45
|
Revision: 1790
http://obi.svn.sourceforge.net/obi/?rev=1790&view=rev
Author: mcourtot
Date: 2009-07-08 21:42:42 +0000 (Wed, 08 Jul 2009)
Log Message:
-----------
modified repository to reflect new location of instances directory
set force readOnly to true
Modified Paths:
--------------
trunk/src/ontology/branches/obi.repository.template
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From: <mco...@us...> - 2009-07-08 21:42:06
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Revision: 1789
http://obi.svn.sourceforge.net/obi/?rev=1789&view=rev
Author: mcourtot
Date: 2009-07-08 21:42:04 +0000 (Wed, 08 Jul 2009)
Log Message:
-----------
added instances directory under branches
Added Paths:
-----------
trunk/src/ontology/branches/instances/
trunk/src/ontology/branches/instances/dataTransformationInstances.owl
trunk/src/ontology/branches/instances/softwareInstances.owl
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From: <jzh...@us...> - 2009-07-08 16:16:21
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Revision: 1788
http://obi.svn.sourceforge.net/obi/?rev=1788&view=rev
Author: jzheng24
Date: 2009-07-08 16:16:20 +0000 (Wed, 08 Jul 2009)
Log Message:
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keep one copy under instances folder
Removed Paths:
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trunk/src/ontology/branches/softwareInstances.owl
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