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From: <p_r...@us...> - 2008-11-08 08:17:37
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Revision: 1131
http://obi.svn.sourceforge.net/obi/?rev=1131&view=rev
Author: p_rocca_serra
Date: 2008-11-08 08:17:33 +0000 (Sat, 08 Nov 2008)
Log Message:
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Modification following BM call Nov, 7th 2008:
Preliminary commit 4
broncho alveolar lavage:
removing n&s condition (entity of organismal origin)
placed under material entity
classifies under 'artefactobject/entity of organism origin
as expected
no error from classifier
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2008-11-08 08:50:58
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Revision: 1132
http://obi.svn.sourceforge.net/obi/?rev=1132&view=rev
Author: p_rocca_serra
Date: 2008-11-08 08:50:53 +0000 (Sat, 08 Nov 2008)
Log Message:
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Modification following BM call Nov, 7th 2008:
Preliminary commit 5
setting restrictions on whole mount tissue
now classifies under AO/EOO
no error from classifier
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <bjo...@us...> - 2008-11-14 18:08:09
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Revision: 1164
http://obi.svn.sourceforge.net/obi/?rev=1164&view=rev
Author: bjoernpeters
Date: 2008-11-14 18:08:07 +0000 (Fri, 14 Nov 2008)
Log Message:
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biomaterial call; modified the organism part definition and subclasses to match
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <mco...@us...> - 2008-11-17 20:34:57
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Revision: 1171
http://obi.svn.sourceforge.net/obi/?rev=1171&view=rev
Author: mcourtot
Date: 2008-11-17 20:34:54 +0000 (Mon, 17 Nov 2008)
Log Message:
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replaced specimen_role (OBI_0000254) with biological_specimen_role (OBI_0000112), preceeding deprecation of specimen role as discussed on Role call on 17 Nov 2008: both classes were deemed synonyms
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.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:
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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: <mco...@us...> - 2008-12-22 21:29:44
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Revision: 1292
http://obi.svn.sourceforge.net/obi/?rev=1292&view=rev
Author: mcourtot
Date: 2008-12-22 21:29:42 +0000 (Mon, 22 Dec 2008)
Log Message:
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updated meatadate for newly created regulatory agency class
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <mco...@us...> - 2008-12-22 22:49:03
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Revision: 1295
http://obi.svn.sourceforge.net/obi/?rev=1295&view=rev
Author: mcourtot
Date: 2008-12-22 22:39:17 +0000 (Mon, 22 Dec 2008)
Log Message:
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the ones I missed :)
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <mco...@us...> - 2008-12-22 22:49:27
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Revision: 1294
http://obi.svn.sourceforge.net/obi/?rev=1294&view=rev
Author: mcourtot
Date: 2008-12-22 22:24:43 +0000 (Mon, 22 Dec 2008)
Log Message:
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updated- corrected all metadata
- one definition source per field
- one definition editor per field
- use of GROUP:, PERSON:, etc
- addition of preferred term (this is a required minimal metadata, and should be a copy of the label)
- addition/check of curation status
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <mco...@us...> - 2009-01-16 18:20:49
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Revision: 1356
http://obi.svn.sourceforge.net/obi/?rev=1356&view=rev
Author: mcourtot
Date: 2009-01-16 18:20:39 +0000 (Fri, 16 Jan 2009)
Log Message:
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added alt term source for homo sapiens
added in branch core annotation for core terms to test extraction
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <al...@us...> - 2009-01-23 22:55:18
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Revision: 1379
http://obi.svn.sourceforge.net/obi/?rev=1379&view=rev
Author: alanr
Date: 2009-01-23 22:55:14 +0000 (Fri, 23 Jan 2009)
Log Message:
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typo
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <al...@us...> - 2009-01-25 04:55:00
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Revision: 1386
http://obi.svn.sourceforge.net/obi/?rev=1386&view=rev
Author: alanr
Date: 2009-01-25 04:54:55 +0000 (Sun, 25 Jan 2009)
Log Message:
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and another annotation property
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <mco...@us...> - 2009-02-01 18:26:46
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Revision: 1437
http://obi.svn.sourceforge.net/obi/?rev=1437&view=rev
Author: mcourtot
Date: 2009-02-01 18:26:40 +0000 (Sun, 01 Feb 2009)
Log Message:
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added editor notes explaining:
- why enzyme doesn't classify under material entity
- interaction with envo
- position on fetus and parasites on macroscopic part of multicellular organism
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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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:
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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: <bjo...@us...> - 2009-02-20 17:39:37
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Revision: 1516
http://obi.svn.sourceforge.net/obi/?rev=1516&view=rev
Author: bjoernpeters
Date: 2009-02-20 17:39:32 +0000 (Fri, 20 Feb 2009)
Log Message:
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Biomat call. Work on the entity of organismal origin definition, and its subclasses. This is still work in progress to be continued in the next call.
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <mco...@us...> - 2009-03-06 17:34:56
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Revision: 1575
http://obi.svn.sourceforge.net/obi/?rev=1575&view=rev
Author: mcourtot
Date: 2009-03-06 17:34:40 +0000 (Fri, 06 Mar 2009)
Log Message:
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changed EOO to specimen during biomaterial call - see explanations in call notes
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <bjo...@us...> - 2009-03-13 16:36:15
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Revision: 1631
http://obi.svn.sourceforge.net/obi/?rev=1631&view=rev
Author: bjoernpeters
Date: 2009-03-13 16:36:06 +0000 (Fri, 13 Mar 2009)
Log Message:
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added the assertion 'cell culture' as a material entity
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <mco...@us...> - 2009-03-15 07:04:29
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Revision: 1638
http://obi.svn.sourceforge.net/obi/?rev=1638&view=rev
Author: mcourtot
Date: 2009-03-15 07:04:02 +0000 (Sun, 15 Mar 2009)
Log Message:
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asserted cell under material entity
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <jzh...@us...> - 2009-07-08 15:59:17
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Revision: 1776
http://obi.svn.sourceforge.net/obi/?rev=1776&view=rev
Author: jzheng24
Date: 2009-07-08 15:59:15 +0000 (Wed, 08 Jul 2009)
Log Message:
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remove line: xmlns:obi_rest="http://purl.obofoundry.org/obo/obi/TheRest.owl#"
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <bjo...@us...> - 2009-07-13 17:11:56
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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:
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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:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <jam...@us...> - 2009-07-27 17:03:37
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Revision: 1866
http://obi.svn.sourceforge.net/obi/?rev=1866&view=rev
Author: jamesmalone
Date: 2009-07-27 17:03:07 +0000 (Mon, 27 Jul 2009)
Log Message:
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edit made during today's developer call - changed restriction on chemical solution to ensure correct reasoning
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2009-07-28 10:40:36
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Revision: 1873
http://obi.svn.sourceforge.net/obi/?rev=1873&view=rev
Author: p_rocca_serra
Date: 2009-07-28 10:40:27 +0000 (Tue, 28 Jul 2009)
Log Message:
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Adding 'paired-end library' and 'single fragment library'
need to add restrictions
metadata almost complete
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <al...@us...> - 2009-07-31 20:50:41
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Revision: 1916
http://obi.svn.sourceforge.net/obi/?rev=1916&view=rev
Author: alanr
Date: 2009-07-31 20:50:25 +0000 (Fri, 31 Jul 2009)
Log Message:
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rdf:id cleanup consequences
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <al...@us...> - 2009-07-31 20:51:30
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Revision: 1917
http://obi.svn.sourceforge.net/obi/?rev=1917&view=rev
Author: alanr
Date: 2009-07-31 20:51:22 +0000 (Fri, 31 Jul 2009)
Log Message:
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rdf:id cleanup consequences
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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