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From: <al...@us...> - 2009-02-19 20:35:02
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Revision: 1513
http://obi.svn.sourceforge.net/obi/?rev=1513&view=rev
Author: alanr
Date: 2009-02-19 20:34:58 +0000 (Thu, 19 Feb 2009)
Log Message:
-----------
add xref_analog per http://groups.google.com/group/obi-developer/msg/98579f30abef93c6
Modified Paths:
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trunk/src/tools/build/generate-obo.lisp
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From: <al...@us...> - 2009-02-19 20:26:51
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Revision: 1512
http://obi.svn.sourceforge.net/obi/?rev=1512&view=rev
Author: alanr
Date: 2009-02-19 20:26:46 +0000 (Thu, 19 Feb 2009)
Log Message:
-----------
new draft with xref_analog
Modified Paths:
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trunk/src/ontology/branches/obi.obo
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From: <bjo...@us...> - 2009-02-19 18:03:14
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Revision: 1511
http://obi.svn.sourceforge.net/obi/?rev=1511&view=rev
Author: bjoernpeters
Date: 2009-02-19 18:03:10 +0000 (Thu, 19 Feb 2009)
Log Message:
-----------
Tightened logical definitions of 'analyte measurement assay' to point to the concentration etc.
Modified Paths:
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trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <jen...@us...> - 2009-02-19 17:07:26
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Revision: 1510
http://obi.svn.sourceforge.net/obi/?rev=1510&view=rev
Author: jenfostel
Date: 2009-02-19 17:07:21 +0000 (Thu, 19 Feb 2009)
Log Message:
-----------
worked on pellet and supernatant roles
Modified Paths:
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trunk/src/ontology/branches/Role.owl
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From: <jen...@us...> - 2009-02-19 16:44:21
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Revision: 1509
http://obi.svn.sourceforge.net/obi/?rev=1509&view=rev
Author: jenFostel
Date: 2009-02-19 16:44:16 +0000 (Thu, 19 Feb 2009)
Log Message:
-----------
updated biological vector and cloning insert.
Modified Paths:
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trunk/src/ontology/branches/Role.owl
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From: <bjo...@us...> - 2009-02-18 17:23:05
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Revision: 1508
http://obi.svn.sourceforge.net/obi/?rev=1508&view=rev
Author: bjoernpeters
Date: 2009-02-18 17:22:56 +0000 (Wed, 18 Feb 2009)
Log Message:
-----------
Added editor note to 'obsolete protocol application', explaining which alternative processes should be used after its obsoletion. No idea why this term is in the role.owl file.
Modified Paths:
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trunk/src/ontology/branches/Role.owl
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From: <jam...@us...> - 2009-02-18 12:41:12
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Revision: 1507
http://obi.svn.sourceforge.net/obi/?rev=1507&view=rev
Author: jamesmalone
Date: 2009-02-18 11:40:32 +0000 (Wed, 18 Feb 2009)
Log Message:
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This owl file was set up by James Malone to initially capture the GenePattern software instance required. The intention is all software instances will eventually live under this file. Note: the default Protege project and repository files in \trunk\src\ontology\branches do NOT point to this file and, hence, it is not imported automatically. You'll have to add this explicitly yourself.
Added Paths:
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trunk/src/ontology/instances/softwareInstances.owl
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From: <bjo...@us...> - 2009-02-18 03:51:25
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Revision: 1506
http://obi.svn.sourceforge.net/obi/?rev=1506&view=rev
Author: bjoernpeters
Date: 2009-02-18 03:51:21 +0000 (Wed, 18 Feb 2009)
Log Message:
-----------
reverted to revision 1444 to get rid of accidental previous commit (my new power point version touches all older files it opens, and marks them as 'modified' even if they are untouched)
Revision Links:
--------------
http://obi.svn.sourceforge.net/obi/?rev=1444&view=rev
Modified Paths:
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trunk/docs/developer/PlanAndPlannedProcessDocs/Plans_and_Planned_Processes.ppt
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From: <bjo...@us...> - 2009-02-18 03:23:05
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Revision: 1505
http://obi.svn.sourceforge.net/obi/?rev=1505&view=rev
Author: bjoernpeters
Date: 2009-02-18 01:50:25 +0000 (Wed, 18 Feb 2009)
Log Message:
-----------
Modified restriction on 'has_been_treated' to 'results from processing material' rather than 'results from protocol application', to be able to obsolete the latter process.
Modified Paths:
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trunk/src/ontology/branches/Quality.owl
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From: <bjo...@us...> - 2009-02-18 01:18:35
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Revision: 1504
http://obi.svn.sourceforge.net/obi/?rev=1504&view=rev
Author: bjoernpeters
Date: 2009-02-18 01:18:30 +0000 (Wed, 18 Feb 2009)
Log Message:
-----------
Modified Paths:
--------------
trunk/docs/developer/PlanAndPlannedProcessDocs/Plans_and_Planned_Processes.ppt
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From: <mco...@us...> - 2009-02-17 18:21:37
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Revision: 1503
http://obi.svn.sourceforge.net/obi/?rev=1503&view=rev
Author: mcourtot
Date: 2009-02-17 18:21:33 +0000 (Tue, 17 Feb 2009)
Log Message:
-----------
declared measured data item and derived data item as IAO data item
Modified Paths:
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trunk/src/ontology/branches/DigitalEntityPlus.owl
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From: <fgi...@us...> - 2009-02-16 12:17:55
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Revision: 1502
http://obi.svn.sourceforge.net/obi/?rev=1502&view=rev
Author: fgibson_sf
Date: 2009-02-16 11:56:53 +0000 (Mon, 16 Feb 2009)
Log Message:
-----------
reasoning error on study participant class. Should have been found before now as it is the SOP to reason over the ontology before checking in - No Reason, No check in!
Modified Paths:
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trunk/src/ontology/branches/Role.owl
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From: <jam...@us...> - 2009-02-16 11:12:49
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Revision: 1501
http://obi.svn.sourceforge.net/obi/?rev=1501&view=rev
Author: jamesmalone
Date: 2009-02-16 11:12:43 +0000 (Mon, 16 Feb 2009)
Log Message:
-----------
added output data to data vector reduction
Modified Paths:
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trunk/src/ontology/branches/DataTransformation.owl
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From: <jam...@us...> - 2009-02-16 10:40:21
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Revision: 1500
http://obi.svn.sourceforge.net/obi/?rev=1500&view=rev
Author: jamesmalone
Date: 2009-02-16 10:40:18 +0000 (Mon, 16 Feb 2009)
Log Message:
-----------
removed spurious imports my protege has added in (if I had a penny for every time I've done this...)
Modified Paths:
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trunk/src/ontology/branches/DigitalEntityPlus.owl
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From: <jam...@us...> - 2009-02-16 10:30:58
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Revision: 1499
http://obi.svn.sourceforge.net/obi/?rev=1499&view=rev
Author: jamesmalone
Date: 2009-02-16 10:30:54 +0000 (Mon, 16 Feb 2009)
Log Message:
-----------
change normalization objective -> data normalization objective to reflect specific (and different) uses of word normalization
Modified Paths:
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trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <jam...@us...> - 2009-02-16 10:28:38
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Revision: 1498
http://obi.svn.sourceforge.net/obi/?rev=1498&view=rev
Author: jamesmalone
Date: 2009-02-16 10:28:35 +0000 (Mon, 16 Feb 2009)
Log Message:
-----------
correction to imports
Modified Paths:
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trunk/src/ontology/branches/DataTransformation.owl
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From: <jam...@us...> - 2009-02-16 10:23:48
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Revision: 1497
http://obi.svn.sourceforge.net/obi/?rev=1497&view=rev
Author: jamesmalone
Date: 2009-02-16 10:23:39 +0000 (Mon, 16 Feb 2009)
Log Message:
-----------
new folder for storing instances. This is in preparation for me adding software instances (for GenePattern use case).
Added Paths:
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trunk/src/ontology/instances/
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From: <p_r...@us...> - 2009-02-15 13:25:29
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Revision: 1496
http://obi.svn.sourceforge.net/obi/?rev=1496&view=rev
Author: p_rocca_serra
Date: 2009-02-15 13:25:23 +0000 (Sun, 15 Feb 2009)
Log Message:
-----------
Changelog:
- material entity:
editor note added to mark the submission to BFO -> term to be imported.
- molecular entities:
AI for BP: log a request to CHEBI to use singular 'molecular entity' -> term to be imported.
-chemical entities in solution/mixture:
AI for Alan to implement
- anatomical entity (formerly macroscopic part of multicellular organism):
now a defined class: union of (multi-tissue structure, body substance, portion of tissue_
Label changed to anatomical entity as it was felt that 'macroscopic part of multicellular organism' introduce an impractical delineation.
editor note added: OBI 'anatomical entity' would essentially correspond to FMA 'material anatomical entity' rather than FMA 'physical anatomical entity'. OBI does not include 'immaterial anatomical entity' as it would clash with the parent class 'material entity'
There is also a documentation note:
DOCUMENTATION NOTE: OBI anatomical entity granularity level excludes cell and biological molecules.
- environmental matter:
left in place but branch core tag removed.
- entity of organismal origin
label changed to extracted entity of organismal origin during the call.
However I have the following questions:
entity of organismal origin:
Current definition= An entity of organismal origin is a biomaterial entity which is obtained from an organism.
alter definition to include the following:
An entity of organismal origin is a biomaterial entity which is obtained from an organism through a protocol application, a collection process
(this would be in agreement with slide 14 (8.EEOO) presented in '2009-02-BiomaterialCoreTerms-Vancouver.ppt')
Comment #1: Extracted seems to imply that a fraction/portion is collected from an organism
If we were to use 'derived entity of organismal origin', we might be able to cover bioengineered organism, should we wish to do. (e.g. we currently have transgenic organism asserted under EOO.the same entity asserted under extracted entity of organism origin would be odd).
Comment #2: Necessary and Sufficient conditions may need to be altered to reflect the changes.
-Organization:
stays where it is for now but feels odd to have it under material entity.
proposition to move if to BFO: possibly as a defined class.
The current editor notes capture the issues very well.
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <fgi...@us...> - 2009-02-13 10:38:34
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Revision: 1495
http://obi.svn.sourceforge.net/obi/?rev=1495&view=rev
Author: fgibson_sf
Date: 2009-02-13 10:38:23 +0000 (Fri, 13 Feb 2009)
Log Message:
-----------
Changed the N conditions to N&S conditions on study participant role
Modified Paths:
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trunk/src/ontology/branches/Role.owl
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From: <jam...@us...> - 2009-02-12 16:27:48
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Revision: 1494
http://obi.svn.sourceforge.net/obi/?rev=1494&view=rev
Author: jamesmalone
Date: 2009-02-12 16:27:41 +0000 (Thu, 12 Feb 2009)
Log Message:
-----------
changed measured and derived data to measured data item and derived data item labels
Modified Paths:
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trunk/src/ontology/branches/DigitalEntityPlus.owl
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From: <jen...@us...> - 2009-02-11 20:19:05
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Revision: 1493
http://obi.svn.sourceforge.net/obi/?rev=1493&view=rev
Author: jenfostel
Date: 2009-02-11 20:18:55 +0000 (Wed, 11 Feb 2009)
Log Message:
-----------
moved study participant to defined class; discovered that the reasoner refuses to connect
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <jam...@us...> - 2009-02-11 17:56:17
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Revision: 1492
http://obi.svn.sourceforge.net/obi/?rev=1492&view=rev
Author: jamesmalone
Date: 2009-02-11 17:56:14 +0000 (Wed, 11 Feb 2009)
Log Message:
-----------
added new definition of 'data' which is either derived data or measured data (which I also added) See definitions from workshop, core terms slides from DENRIE branch
Modified Paths:
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trunk/src/ontology/branches/DataTransformation.owl
trunk/src/ontology/branches/DigitalEntityPlus.owl
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From: <jam...@us...> - 2009-02-11 16:03:07
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Revision: 1491
http://obi.svn.sourceforge.net/obi/?rev=1491&view=rev
Author: jamesmalone
Date: 2009-02-11 16:03:04 +0000 (Wed, 11 Feb 2009)
Log Message:
-----------
added reduced dimension data set
Modified Paths:
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trunk/src/ontology/branches/DigitalEntityPlus.owl
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From: <mco...@us...> - 2009-02-11 15:47:25
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Revision: 1490
http://obi.svn.sourceforge.net/obi/?rev=1490&view=rev
Author: mcourtot
Date: 2009-02-11 15:47:18 +0000 (Wed, 11 Feb 2009)
Log Message:
-----------
updated some definition source
Modified Paths:
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trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <mco...@us...> - 2009-02-11 15:42:54
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Revision: 1489
http://obi.svn.sourceforge.net/obi/?rev=1489&view=rev
Author: mcourtot
Date: 2009-02-11 15:42:49 +0000 (Wed, 11 Feb 2009)
Log Message:
-----------
expanded definition source of instrument manually
Modified Paths:
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releases/2009-01-28/merged/OBI.owl
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