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From: <al...@us...> - 2008-10-21 20:09:01
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Revision: 1063
http://obi.svn.sourceforge.net/obi/?rev=1063&view=rev
Author: alanr
Date: 2008-10-21 20:08:52 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
Make Bjoern happy. Add measurement datum, measurment unit label, has measurement value, is about, is measurement of quality
Modified Paths:
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trunk/src/ontology/branches/external.owl
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From: <al...@us...> - 2008-10-21 20:06:54
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Revision: 1062
http://obi.svn.sourceforge.net/obi/?rev=1062&view=rev
Author: alanr
Date: 2008-10-21 20:06:51 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
one less unsatisfiable class. Injection still problematic
Modified Paths:
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trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2008-10-21 15:18:31
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Revision: 1061
http://obi.svn.sourceforge.net/obi/?rev=1061&view=rev
Author: p_rocca_serra
Date: 2008-10-21 15:18:29 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
Modifications:
addition of Restriction to:
-nucleic acid hybridization
-electrophoresis
-PCR-SSCP assay
Modified Paths:
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trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2008-10-21 15:08:48
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Revision: 1060
http://obi.svn.sourceforge.net/obi/?rev=1060&view=rev
Author: p_rocca_serra
Date: 2008-10-21 15:08:46 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
addition of agarose and polyacrylamide gel
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2008-10-21 15:00:28
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Revision: 1059
http://obi.svn.sourceforge.net/obi/?rev=1059&view=rev
Author: p_rocca_serra
Date: 2008-10-21 15:00:14 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
minor fixes
Modified Paths:
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trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2008-10-21 14:54:16
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Revision: 1058
http://obi.svn.sourceforge.net/obi/?rev=1058&view=rev
Author: p_rocca_serra
Date: 2008-10-21 14:54:09 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
Modifications:
metadata+restrictions on:
acclimatization down to radioactivity detection.
gaps in coverage are caused by need to import or create absent entities
Modified Paths:
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trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2008-10-21 13:19:05
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Revision: 1057
http://obi.svn.sourceforge.net/obi/?rev=1057&view=rev
Author: p_rocca_serra
Date: 2008-10-21 13:18:59 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
Modifications:
-metadata fixes (definitions, example, curation status)
-setting restriction (input, output, reagent) for the following classes:
-cell co-culturing
-cell fixation
-detection of label
-enrollment
-enzymatic amplification and children
-enzymatic cleavage and children
-enzymatic ligation
Modified Paths:
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trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2008-10-21 10:33:08
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Revision: 1056
http://obi.svn.sourceforge.net/obi/?rev=1056&view=rev
Author: p_rocca_serra
Date: 2008-10-21 10:32:57 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
Modifications:
-fix to restriction on eluate (only to some)
Note:
Classifier fails to classify eluate under 'artefact object'. This is down to 'elution' not having clear input and output. Material separation restrictions need to be modified to specify the nature of input and output not only their quantification
-> now moving to protocol branch
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2008-10-21 10:04:51
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Revision: 1055
http://obi.svn.sourceforge.net/obi/?rev=1055&view=rev
Author: p_rocca_serra
Date: 2008-10-21 10:04:38 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
Modifications:
-addition of metadata and restrictions to:
-organ section
-peptide construct
-xenograft
as for previous commits, restrictions indicate which protocol application produces such entities and when possible from what they derive from.
-metadata fixes consist in reviewing definitions, fixing those and adding pubmed based examples
-changes to hierarchy:
--pools of specimens is removed from 'population' children
--synthetic polypeptide is removed from 'entity of organismal origin' children
-addition of Blood: to be imported from FMA
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2008-10-21 09:18:07
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Revision: 1054
http://obi.svn.sourceforge.net/obi/?rev=1054&view=rev
Author: p_rocca_serra
Date: 2008-10-21 09:15:27 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
Modifications:
metadata addition + setting restrictions on:
cell pellet, collection and children, population and sample populations.
Note: pool of specimens needs to be moved
Note2: restrictions are set to indicate if the material entity is output of some process and if it has part, roles or qualities of some sort
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2008-10-21 08:33:15
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Revision: 1053
http://obi.svn.sourceforge.net/obi/?rev=1053&view=rev
Author: p_rocca_serra
Date: 2008-10-21 08:28:54 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2008-10-21 08:25:02
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Revision: 1052
http://obi.svn.sourceforge.net/obi/?rev=1052&view=rev
Author: p_rocca_serra
Date: 2008-10-21 08:22:20 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
Modifications:
-adding metadata and restrictions to the following classes:
--blood serum
--bronchial alveolar lavage
--cell culture + children
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2008-10-21 07:31:51
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Revision: 1051
http://obi.svn.sourceforge.net/obi/?rev=1051&view=rev
Author: p_rocca_serra
Date: 2008-10-21 07:31:41 +0000 (Tue, 21 Oct 2008)
Log Message:
-----------
modifications:
-addition of restrictions on extract, lysate, cell culture supernatant
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2008-10-20 21:55:12
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Revision: 1050
http://obi.svn.sourceforge.net/obi/?rev=1050&view=rev
Author: p_rocca_serra
Date: 2008-10-20 21:55:07 +0000 (Mon, 20 Oct 2008)
Log Message:
-----------
General Review of Branch: will spread over several commit
-Metadata addition for several classes
-Addition of restrictions
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2008-10-20 17:51:19
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Revision: 1049
http://obi.svn.sourceforge.net/obi/?rev=1049&view=rev
Author: p_rocca_serra
Date: 2008-10-20 17:51:12 +0000 (Mon, 20 Oct 2008)
Log Message:
-----------
modifications:
-fixes to curation status
-addition of metadata for syringe and needle
Modified Paths:
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trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <p_r...@us...> - 2008-10-20 17:39:28
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Revision: 1048
http://obi.svn.sourceforge.net/obi/?rev=1048&view=rev
Author: p_rocca_serra
Date: 2008-10-20 17:39:25 +0000 (Mon, 20 Oct 2008)
Log Message:
-----------
modification:
fixes to curation status for several entries
changed 'lethal injection' to 'intentional overdosing' in order to avoid multiple inheritance and be in line with killing parent class
adding metadata for classes added on friday
Modified Paths:
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trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2008-10-20 17:21:11
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Revision: 1047
http://obi.svn.sourceforge.net/obi/?rev=1047&view=rev
Author: p_rocca_serra
Date: 2008-10-20 17:21:07 +0000 (Mon, 20 Oct 2008)
Log Message:
-----------
modifications:
lysate: moved from 'entity of organismal origin' to 'material entity' change to definition
additions:
extract, precipitate, eluate with all metadata+restrictions
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2008-10-17 16:01:23
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Revision: 1046
http://obi.svn.sourceforge.net/obi/?rev=1046&view=rev
Author: p_rocca_serra
Date: 2008-10-17 16:01:13 +0000 (Fri, 17 Oct 2008)
Log Message:
-----------
addition to be discussed:
positional qualities .e.g intracardiac, dorsal, ventral...
metadata incomplete
Modified Paths:
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trunk/src/ontology/branches/Quality.owl
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From: <p_r...@us...> - 2008-10-17 15:59:20
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Revision: 1045
http://obi.svn.sourceforge.net/obi/?rev=1045&view=rev
Author: p_rocca_serra
Date: 2008-10-17 15:59:11 +0000 (Fri, 17 Oct 2008)
Log Message:
-----------
term addition:
syringe
needle
metadata incomplete
Modified Paths:
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trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <p_r...@us...> - 2008-10-17 15:58:16
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Revision: 1044
http://obi.svn.sourceforge.net/obi/?rev=1044&view=rev
Author: p_rocca_serra
Date: 2008-10-17 15:58:06 +0000 (Fri, 17 Oct 2008)
Log Message:
-----------
addition of:
transcription profiling
transcription factor binding site identification
genotyping
metabolite profiling
DNA sequence variation detection
DNA sequence feature detection
protein-protein interaction identication
curation status to be set, some metadata missing
Modified Paths:
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trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <mco...@us...> - 2008-10-16 21:47:59
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Revision: 1043
http://obi.svn.sourceforge.net/obi/?rev=1043&view=rev
Author: mcourtot
Date: 2008-10-16 21:47:55 +0000 (Thu, 16 Oct 2008)
Log Message:
-----------
added enzyme, DNA polymerase and reverse transcriptase
added obsolete_ prefix to all terms (easier to pick the right one when searching in protege)
Modified Paths:
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trunk/src/ontology/branches/Obsolete.owl
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From: <mco...@us...> - 2008-10-16 21:47:09
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Revision: 1042
http://obi.svn.sourceforge.net/obi/?rev=1042&view=rev
Author: mcourtot
Date: 2008-10-16 21:47:05 +0000 (Thu, 16 Oct 2008)
Log Message:
-----------
removed enzyme (replaced by defined class), DNA polymerase (replaced by import)
Modified Paths:
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trunk/src/ontology/branches/Biomaterial.owl
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From: <mco...@us...> - 2008-10-12 20:04:32
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Revision: 1041
http://obi.svn.sourceforge.net/obi/?rev=1041&view=rev
Author: mcourtot
Date: 2008-10-12 20:04:22 +0000 (Sun, 12 Oct 2008)
Log Message:
-----------
Alan corrected footnote for sparql neurocommons,slightly shrunk the image just above and then put in a couple of explicit page breaks.
this is the version that has been resubmitted.
Modified Paths:
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trunk/docs/papers/owled2008/owled2008eu_submission_38.pdf
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From: <mco...@us...> - 2008-10-11 17:15:40
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Revision: 1040
http://obi.svn.sourceforge.net/obi/?rev=1040&view=rev
Author: mcourtot
Date: 2008-10-11 17:15:33 +0000 (Sat, 11 Oct 2008)
Log Message:
-----------
latest version
Modified Paths:
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trunk/docs/papers/owled2008/owled2008eu_submission_38.pdf
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From: <al...@us...> - 2008-10-11 16:57:42
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Revision: 1039
http://obi.svn.sourceforge.net/obi/?rev=1039&view=rev
Author: alanr
Date: 2008-10-11 16:57:33 +0000 (Sat, 11 Oct 2008)
Log Message:
-----------
finished
Modified Paths:
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trunk/docs/papers/owled2008/owled2008eu_submission_38.docx
trunk/docs/papers/owled2008/owled2008eu_submission_38.pdf
Removed Paths:
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trunk/docs/papers/owled2008/owled2008eu_submission_38.doc
trunk/docs/papers/owled2008/owled2008eu_submission_38a.docx
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