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From: <p_r...@us...> - 2009-07-28 21:39:07
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Revision: 1886
http://obi.svn.sourceforge.net/obi/?rev=1886&view=rev
Author: p_rocca_serra
Date: 2009-07-28 21:38:48 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
adding bisulfite mireoted from chebi
Modified Paths:
--------------
trunk/src/ontology/branches/external.owl
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From: <p_r...@us...> - 2009-07-28 16:59:17
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Revision: 1885
http://obi.svn.sourceforge.net/obi/?rev=1885&view=rev
Author: p_rocca_serra
Date: 2009-07-28 16:59:09 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
adding luciferin and APS metadata
Modified Paths:
--------------
trunk/src/ontology/branches/externalDerived.owl
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From: <p_r...@us...> - 2009-07-28 16:57:29
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Revision: 1884
http://obi.svn.sourceforge.net/obi/?rev=1884&view=rev
Author: p_rocca_serra
Date: 2009-07-28 16:57:22 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
adding luciferin and APS
Modified Paths:
--------------
trunk/src/ontology/branches/external.owl
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From: <par...@us...> - 2009-07-28 16:04:56
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Revision: 1883
http://obi.svn.sourceforge.net/obi/?rev=1883&view=rev
Author: parkinso
Date: 2009-07-28 16:04:49 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
Added Paths:
-----------
README.txt
conf/
conf/authz
conf/passwd
conf/svnserve.conf
db/
db/current
db/format
db/fs-type
db/fsfs.conf
db/min-unpacked-rev
db/rep-cache.db
db/revprops/
db/revprops/0/
db/revprops/0/0
db/revs/
db/revs/0/
db/revs/0/0
db/transactions/
db/txn-current
db/txn-current-lock
db/txn-protorevs/
db/uuid
db/write-lock
format
hooks/
hooks/post-commit.tmpl
hooks/post-lock.tmpl
hooks/post-revprop-change.tmpl
hooks/post-unlock.tmpl
hooks/pre-commit.tmpl
hooks/pre-lock.tmpl
hooks/pre-revprop-change.tmpl
hooks/pre-unlock.tmpl
hooks/start-commit.tmpl
locks/
locks/db-logs.lock
locks/db.lock
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From: <p_r...@us...> - 2009-07-28 13:56:21
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Revision: 1882
http://obi.svn.sourceforge.net/obi/?rev=1882&view=rev
Author: p_rocca_serra
Date: 2009-07-28 13:56:10 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
fixing restriction for preceding step when dealing with Solexa and SOLiD sequencing (immobilization and amplification of a clone)
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <jam...@us...> - 2009-07-28 13:38:58
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Revision: 1881
http://obi.svn.sourceforge.net/obi/?rev=1881&view=rev
Author: jamesmalone
Date: 2009-07-28 13:38:36 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
changed restrictions so that dt and data visualizations classify under infor processing. Also added the only and some relations to speed up reasoning.
Modified Paths:
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trunk/src/ontology/branches/DataTransformation.owl
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From: <p_r...@us...> - 2009-07-28 13:33:05
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Revision: 1880
http://obi.svn.sourceforge.net/obi/?rev=1880&view=rev
Author: p_rocca_serra
Date: 2009-07-28 13:32:59 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
fixing is_manufactured_by to point to relevant instances of organization
(thx Alan/James)
Modified Paths:
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trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <p_r...@us...> - 2009-07-28 13:29:17
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Revision: 1879
http://obi.svn.sourceforge.net/obi/?rev=1879&view=rev
Author: p_rocca_serra
Date: 2009-07-28 13:29:09 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
adding Li-Cor and Roche as organization
Modified Paths:
--------------
trunk/src/ontology/branches/instances/organizationInstances.owl
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From: <p_r...@us...> - 2009-07-28 13:07:44
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Revision: 1878
http://obi.svn.sourceforge.net/obi/?rev=1878&view=rev
Author: p_rocca_serra
Date: 2009-07-28 13:07:36 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
newly added classes:
-library preparation
-Edman degradation
added all missing metadata and curation status to all recently added classes
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <jam...@us...> - 2009-07-28 12:59:06
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Revision: 1877
http://obi.svn.sourceforge.net/obi/?rev=1877&view=rev
Author: jamesmalone
Date: 2009-07-28 12:58:55 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
removed the restriction of data set or data item - data sets are data items so we can remove the former
Modified Paths:
--------------
trunk/src/ontology/branches/DataTransformation.owl
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From: Alan R. <ala...@gm...> - 2009-07-28 12:43:05
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On Tue, Jul 28, 2009 at 6:56 AM, <p_r...@us...> wrote: > Revision: 1874 > http://obi.svn.sourceforge.net/obi/?rev=1874&view=rev > Author: p_rocca_serra > Date: 2009-07-28 10:56:38 +0000 (Tue, 28 Jul 2009) > > Log Message: > ----------- > added another sequencer + set curation status and missing metadata > > I am still unable to set the 'is_manufactured_by' restriction to point to an instance of Organization. Does any body know how to do it in Protege? use restrictions like: is_manufactured_by has affy -Alan > > Modified Paths: > -------------- > trunk/src/ontology/branches/InstrumentAndPart.owl > > > This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. > > ------------------------------------------------------------------------------ > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day > trial. Simplify your report design, integration and deployment - and focus on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > Obi-svn-commit mailing list > Obi...@li... > https://lists.sourceforge.net/lists/listinfo/obi-svn-commit > |
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From: <jam...@us...> - 2009-07-28 12:15:57
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Revision: 1876
http://obi.svn.sourceforge.net/obi/?rev=1876&view=rev
Author: jamesmalone
Date: 2009-07-28 12:15:51 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
new output for SOM - topologically preserved clustered data set
Modified Paths:
--------------
trunk/src/ontology/branches/DataTransformation.owl
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From: <jam...@us...> - 2009-07-28 12:15:29
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Revision: 1875
http://obi.svn.sourceforge.net/obi/?rev=1875&view=rev
Author: jamesmalone
Date: 2009-07-28 12:15:20 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
addition of topologically preserved clustered data set
Modified Paths:
--------------
trunk/src/ontology/branches/DigitalEntityPlus.owl
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From: <p_r...@us...> - 2009-07-28 10:56:45
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Revision: 1874
http://obi.svn.sourceforge.net/obi/?rev=1874&view=rev
Author: p_rocca_serra
Date: 2009-07-28 10:56:38 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
added another sequencer + set curation status and missing metadata
I am still unable to set the 'is_manufactured_by' restriction to point to an instance of Organization. Does any body know how to do it in Protege?
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.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:
-----------
Adding 'paired-end library' and 'single fragment library'
need to add restrictions
metadata almost complete
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2009-07-28 07:22:30
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Revision: 1872
http://obi.svn.sourceforge.net/obi/?rev=1872&view=rev
Author: p_rocca_serra
Date: 2009-07-28 07:22:23 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
added restriction pointing to compatible instruments
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2009-07-28 07:21:38
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Revision: 1871
http://obi.svn.sourceforge.net/obi/?rev=1871&view=rev
Author: p_rocca_serra
Date: 2009-07-28 07:21:29 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
addition of Li-Cor instrument
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <p_r...@us...> - 2009-07-28 07:15:06
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Revision: 1869
http://obi.svn.sourceforge.net/obi/?rev=1869&view=rev
Author: p_rocca_serra
Date: 2009-07-28 06:13:56 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
Fixes to DNA sequencing related classes:
-addition of metadata (definition, source, example of usage, alternative terms...) still lacking curation status
-changes to restrictions:
has_agent replaced by 'has_specified_input' maybe revisited if necessary
addition of has_objective_specification as pointed by Alan
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2009-07-28 07:00:38
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Revision: 1870
http://obi.svn.sourceforge.net/obi/?rev=1870&view=rev
Author: p_rocca_serra
Date: 2009-07-28 07:00:27 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
adding 5 kind of DNA sequencers:
issue: how to specify the manufacturer (those are instances of Organization) . could not find a way to point to the correct instance for each DNA sequencer
I have supplied metadata except curation status
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <jgr...@us...> - 2009-07-27 23:11:45
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Revision: 1868
http://obi.svn.sourceforge.net/obi/?rev=1868&view=rev
Author: jgreenbaum
Date: 2009-07-27 23:11:39 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
corrected readonly status of iao in template file
Modified Paths:
--------------
branches/ontie-dev/src/ontology/modules/ONTIE/obi-ontie.repository.template
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From: <p_r...@us...> - 2009-07-27 21:52:53
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Revision: 1867
http://obi.svn.sourceforge.net/obi/?rev=1867&view=rev
Author: p_rocca_serra
Date: 2009-07-27 21:52:47 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
Modeling of DNA sequencing:
old DNA sequencing was incorrect
now declared as a defined class.
Classes added are:
-pyrosequencing
-chain termination sequencing
-Solid sequencing
-solexa sequencing
-helicos sequencing
defined classes added are
DNA sequencing by ligation
DNA sequencing by synthesis
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.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:
-----------
edit made during today's developer call - changed restriction on chemical solution to ensure correct reasoning
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
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From: <jam...@us...> - 2009-07-27 17:00:53
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Revision: 1865
http://obi.svn.sourceforge.net/obi/?rev=1865&view=rev
Author: jamesmalone
Date: 2009-07-27 17:00:46 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
edit made during today's developer call - added graph
Modified Paths:
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trunk/src/ontology/branches/DigitalEntityPlus.owl
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From: <al...@us...> - 2009-07-27 01:46:05
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Revision: 1864
http://obi.svn.sourceforge.net/obi/?rev=1864&view=rev
Author: alanr
Date: 2009-07-27 01:45:57 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
add iao/obsolete.owl
Modified Paths:
--------------
trunk/src/ontology/branches/obil.owl
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From: <al...@us...> - 2009-07-27 01:05:12
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Revision: 1863
http://obi.svn.sourceforge.net/obi/?rev=1863&view=rev
Author: alanr
Date: 2009-07-27 01:05:00 +0000 (Mon, 27 Jul 2009)
Log Message:
-----------
add annotation property declarations. Don't know why I have too.
Modified Paths:
--------------
trunk/src/ontology/external/bfo11.owl
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