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From: <fgi...@us...> - 2008-12-21 18:46:35
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Revision: 1288
http://obi.svn.sourceforge.net/obi/?rev=1288&view=rev
Author: fgibson_sf
Date: 2008-12-21 18:46:27 +0000 (Sun, 21 Dec 2008)
Log Message:
-----------
added class to obi-quick-id.owl for testing
Modified Paths:
--------------
trunk/src/ontology/branches/obi-quick-id.owl
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From: <fgi...@us...> - 2008-12-21 18:40:03
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Revision: 1287
http://obi.svn.sourceforge.net/obi/?rev=1287&view=rev
Author: fgibson_sf
Date: 2008-12-21 18:39:53 +0000 (Sun, 21 Dec 2008)
Log Message:
-----------
Addition of the quick-id.owl file and update of the template files accordingly
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl.template
trunk/src/ontology/branches/obi.repository.template
trunk/src/ontology/branches/obi.repository.template.pc
Added Paths:
-----------
trunk/src/ontology/branches/obi-quick-id.owl
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From: <mco...@us...> - 2008-12-19 22:25:43
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Revision: 1286
http://obi.svn.sourceforge.net/obi/?rev=1286&view=rev
Author: mcourtot
Date: 2008-12-19 22:25:40 +0000 (Fri, 19 Dec 2008)
Log Message:
-----------
removed extra import declaration added by Protege
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
trunk/src/ontology/branches/Quality.owl
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From: <mco...@us...> - 2008-12-19 20:33:48
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Revision: 1285
http://obi.svn.sourceforge.net/obi/?rev=1285&view=rev
Author: mcourtot
Date: 2008-12-19 20:33:45 +0000 (Fri, 19 Dec 2008)
Log Message:
-----------
added new pprj template, includes:
- curation widget
- label display
- set of preferred annotations to be used when creating new class
Added Paths:
-----------
trunk/src/ontology/branches/obi.pprj.annotations.templates
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From: <jen...@us...> - 2008-12-17 14:05:37
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Revision: 1284
http://obi.svn.sourceforge.net/obi/?rev=1284&view=rev
Author: jenfostel
Date: 2008-12-17 14:05:27 +0000 (Wed, 17 Dec 2008)
Log Message:
-----------
added restrictions to drug, protocol participant, reference and nutrient that these roles inhere in some material entity; do not have a reasoner access so i did not check consistency.
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <mco...@us...> - 2008-12-16 19:54:55
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Revision: 1283
http://obi.svn.sourceforge.net/obi/?rev=1283&view=rev
Author: mcourtot
Date: 2008-12-16 19:54:51 +0000 (Tue, 16 Dec 2008)
Log Message:
-----------
changed sparql endpoint from http://sparql.neurocommons.org/sparql/? to http://neurocommons.org:30322/sparql/
Modified Paths:
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trunk/src/tools/build/external-templates.txt
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From: <mco...@us...> - 2008-12-16 19:52:25
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Revision: 1282
http://obi.svn.sourceforge.net/obi/?rev=1282&view=rev
Author: mcourtot
Date: 2008-12-16 19:52:21 +0000 (Tue, 16 Dec 2008)
Log Message:
-----------
removed information about subclass of: this is already in external.owl, and creates duplicate and potential errors when modifying external.owl - when I move a class I need to update both files
Modified Paths:
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trunk/src/tools/build/create-external-derived.lisp
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From: <mco...@us...> - 2008-12-12 22:42:22
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Revision: 1281
http://obi.svn.sourceforge.net/obi/?rev=1281&view=rev
Author: mcourtot
Date: 2008-12-12 22:42:17 +0000 (Fri, 12 Dec 2008)
Log Message:
-----------
added editor note in obsolote_polypeptide to reflect the decision to use peptide only
Modified Paths:
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trunk/src/ontology/branches/Obsolete.owl
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From: <mco...@us...> - 2008-12-12 22:18:51
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Revision: 1280
http://obi.svn.sourceforge.net/obi/?rev=1280&view=rev
Author: mcourtot
Date: 2008-12-12 22:18:41 +0000 (Fri, 12 Dec 2008)
Log Message:
-----------
removed polypeptides (CHEBI_15841) and updated plan and biomaterial files accordingly
moved protein under peptides
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
trunk/src/ontology/branches/external.owl
trunk/src/ontology/branches/externalDerived.owl
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From: <bjo...@us...> - 2008-12-12 18:05:52
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Revision: 1279
http://obi.svn.sourceforge.net/obi/?rev=1279&view=rev
Author: bjoernpeters
Date: 2008-12-12 18:05:48 +0000 (Fri, 12 Dec 2008)
Log Message:
-----------
Biomaterial call (BP + MC). Cleaned up terms under molecular entity, primarily adding editor notes.
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <dan...@us...> - 2008-12-12 16:35:42
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Revision: 1278
http://obi.svn.sourceforge.net/obi/?rev=1278&view=rev
Author: daniel_schober
Date: 2008-12-12 16:35:32 +0000 (Fri, 12 Dec 2008)
Log Message:
-----------
Added Paths:
-----------
trunk/docs/developer/InstrumentBranchDocs/10MostImportantInstrumentClasses&Relations.doc
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From: <dan...@us...> - 2008-12-12 16:35:04
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Revision: 1277
http://obi.svn.sourceforge.net/obi/?rev=1277&view=rev
Author: daniel_schober
Date: 2008-12-12 16:34:54 +0000 (Fri, 12 Dec 2008)
Log Message:
-----------
added instrument 10 most wanted terms
Added Paths:
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trunk/docs/developer/InstrumentBranchDocs/
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From: <mco...@us...> - 2008-12-11 22:55:27
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Revision: 1276
http://obi.svn.sourceforge.net/obi/?rev=1276&view=rev
Author: mcourtot
Date: 2008-12-11 21:38:15 +0000 (Thu, 11 Dec 2008)
Log Message:
-----------
added missing contributors
Richard Bruskiewich
John Westbrook
Jay Greenbaum
Pierre Grenon
Chris Mungall
Matthew Pocock
Holger Stenzhorn
Modified Paths:
--------------
trunk/src/ontology/branches/TheRest.owl
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From: <bjo...@us...> - 2008-12-11 18:57:40
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Revision: 1275
http://obi.svn.sourceforge.net/obi/?rev=1275&view=rev
Author: bjoernpeters
Date: 2008-12-11 18:57:35 +0000 (Thu, 11 Dec 2008)
Log Message:
-----------
PlanAndPlannedProcess call. Material transformation was modified to artifact creation, manufacturing was added as a process, and corresponding definitions and objectives were created. Note: Currently nothing gets classified under artifact creation, and therefore materials are not correctly inferred as artifacts. We will need to update objectives of processes once we are happy to get this back.
In the Instrument branch, we only added an editor note to artifact object to note that we will have to incorporate byproducts as well.
Modified Paths:
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trunk/src/ontology/branches/InstrumentAndPart.owl
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <mco...@us...> - 2008-12-11 00:57:05
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Revision: 1274
http://obi.svn.sourceforge.net/obi/?rev=1274&view=rev
Author: mcourtot
Date: 2008-12-11 00:56:58 +0000 (Thu, 11 Dec 2008)
Log Message:
-----------
added preferred term, removed underscores and added curation status "example to be eventually removed" (waiting review from other consortium members)
Modified Paths:
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trunk/src/ontology/branches/Quality.owl
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From: <mco...@us...> - 2008-12-11 00:53:20
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Revision: 1273
http://obi.svn.sourceforge.net/obi/?rev=1273&view=rev
Author: mcourtot
Date: 2008-12-11 00:53:02 +0000 (Thu, 11 Dec 2008)
Log Message:
-----------
moved normalized_data_set from DT to Quality, as subclass of new bucket "_defined_output"
changed normalized_data_set to be a defined class
checked consistency and that b transfo and biexponential transfo still classify correctly
Modified Paths:
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trunk/src/ontology/branches/DataTransformation.owl
trunk/src/ontology/branches/Quality.owl
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From: <jam...@us...> - 2008-12-10 16:31:54
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Revision: 1272
http://obi.svn.sourceforge.net/obi/?rev=1272&view=rev
Author: jamesmalone
Date: 2008-12-10 16:31:51 +0000 (Wed, 10 Dec 2008)
Log Message:
-----------
Some extra axioms relating to output for normalization data transformations. The addition of outputs_specified_data some normalized_data_set allows us to say things about outputs of DTs and links us to the newly defined normalized_data_set
Modified Paths:
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trunk/src/ontology/branches/DataTransformation.owl
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From: <jam...@us...> - 2008-12-10 12:22:14
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Revision: 1271
http://obi.svn.sourceforge.net/obi/?rev=1271&view=rev
Author: jamesmalone
Date: 2008-12-10 11:30:59 +0000 (Wed, 10 Dec 2008)
Log Message:
-----------
addition of is_specified_output_data relation. This is the inverse of the outputs_specified_data relation and is needed to define the relation between the data and the process in which the data was produced.
Modified Paths:
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trunk/src/ontology/branches/Relations.owl
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From: <bjo...@us...> - 2008-12-09 23:04:18
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Revision: 1270
http://obi.svn.sourceforge.net/obi/?rev=1270&view=rev
Author: bjoernpeters
Date: 2008-12-09 23:04:12 +0000 (Tue, 09 Dec 2008)
Log Message:
-----------
Outcome of todays bonus PlanAndPlannedProcess call. We modified definitions of study design and protocol to differentiate them more clearly. Removed 'investigation planning'.
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <mco...@us...> - 2008-12-09 01:04:31
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Revision: 1269
http://obi.svn.sourceforge.net/obi/?rev=1269&view=rev
Author: mcourtot
Date: 2008-12-09 01:04:27 +0000 (Tue, 09 Dec 2008)
Log Message:
-----------
moved ilst-mode data file under binary digital entity as per Ryan's suggestion
Modified Paths:
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trunk/src/ontology/branches/DigitalEntityPlus.owl
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From: <jen...@us...> - 2008-12-08 17:07:52
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Revision: 1268
http://obi.svn.sourceforge.net/obi/?rev=1268&view=rev
Author: jenfostel
Date: 2008-12-08 17:07:18 +0000 (Mon, 08 Dec 2008)
Log Message:
-----------
Role branch call: moved specified input, specified output, nutrient roles out of protocol participant role into siblings of it.
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <fgi...@us...> - 2008-12-08 16:31:45
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Revision: 1267
http://obi.svn.sourceforge.net/obi/?rev=1267&view=rev
Author: fgibson_sf
Date: 2008-12-08 16:31:36 +0000 (Mon, 08 Dec 2008)
Log Message:
-----------
added missing curation status
Modified Paths:
--------------
trunk/src/ontology/branches/OBI-Function.owl
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From: <fgi...@us...> - 2008-12-08 15:15:59
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Revision: 1266
http://obi.svn.sourceforge.net/obi/?rev=1266&view=rev
Author: fgibson_sf
Date: 2008-12-08 15:15:50 +0000 (Mon, 08 Dec 2008)
Log Message:
-----------
added produce_data_function to some devices. Added the restrictions on information_processing_function has_part consume_data_function, has_part, produce_data_function
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
trunk/src/ontology/branches/OBI-Function.owl
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From: <mco...@us...> - 2008-12-06 02:22:12
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Revision: 1265
http://obi.svn.sourceforge.net/obi/?rev=1265&view=rev
Author: mcourtot
Date: 2008-12-06 01:37:13 +0000 (Sat, 06 Dec 2008)
Log Message:
-----------
added template file for obi repository for pc users - thanks Jennifer for pointing out this was missing
Added Paths:
-----------
trunk/src/ontology/branches/obi.repository.template.pc
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From: <mco...@us...> - 2008-12-05 20:28:02
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Revision: 1264
http://obi.svn.sourceforge.net/obi/?rev=1264&view=rev
Author: mcourtot
Date: 2008-12-05 20:27:58 +0000 (Fri, 05 Dec 2008)
Log Message:
-----------
oops - reverted to wrong version - now corrected, includes msi term with their msi IDs
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
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