OBI

Revision: 2018
          http://obi.svn.sourceforge.net/obi/?rev=2018&view=rev
Author:   bjoernpeters
Date:     2009-08-19 16:49:10 +0000 (Wed, 19 Aug 2009)

Log Message:
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work on sequencing assays. split between those that determine the primary sequence of DNA / protein etc. vs. those like determine interaction sites, methylation sites. This is not completed but work in progress, and needs to be further aligned with Philippe's other classes.

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Revision: 2025
          http://obi.svn.sourceforge.net/obi/?rev=2025&view=rev
Author:   jzheng24
Date:     2009-08-24 15:57:07 +0000 (Mon, 24 Aug 2009)

Log Message:
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add label (and definition) for 4 imported terms

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Revision: 2027
          http://obi.svn.sourceforge.net/obi/?rev=2027&view=rev
Author:   jzheng24
Date:     2009-08-24 17:36:43 +0000 (Mon, 24 Aug 2009)

Log Message:
-----------
revert to version 2018

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Revision: 2032
          http://obi.svn.sourceforge.net/obi/?rev=2032&view=rev
Author:   bjoernpeters
Date:     2009-08-26 16:21:21 +0000 (Wed, 26 Aug 2009)

Log Message:
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modified 'taking sample from organism' to 'collecting specimen from organism', to take into account outcome of specimen<->sample discussion.

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Revision: 2033
          http://obi.svn.sourceforge.net/obi/?rev=2033&view=rev
Author:   bjoernpeters
Date:     2009-08-26 18:14:53 +0000 (Wed, 26 Aug 2009)

Log Message:
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Added instances of manufacturer roles to organization instances. Created defined manufacturer class. This addresses the manuscript concerns for now. 

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Revision: 2037
          http://obi.svn.sourceforge.net/obi/?rev=2037&view=rev
Author:   bjoernpeters
Date:     2009-08-27 02:31:08 +0000 (Thu, 27 Aug 2009)

Log Message:
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added glucometer

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Revision: 2038
          http://obi.svn.sourceforge.net/obi/?rev=2038&view=rev
Author:   bjoernpeters
Date:     2009-08-27 02:52:09 +0000 (Thu, 27 Aug 2009)

Log Message:
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obsoleted duplicate mass spectrometry term

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Revision: 2042
          http://obi.svn.sourceforge.net/obi/?rev=2042&view=rev
Author:   parkinso
Date:     2009-08-27 09:21:36 +0000 (Thu, 27 Aug 2009)

Log Message:
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added produce data function to glucometer, classified as instrument

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Revision: 2047
          http://obi.svn.sourceforge.net/obi/?rev=2047&view=rev
Author:   alanr
Date:     2009-08-28 04:41:36 +0000 (Fri, 28 Aug 2009)

Log Message:
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merge ontie

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Revision: 2051
          http://obi.svn.sourceforge.net/obi/?rev=2051&view=rev
Author:   alanr
Date:     2009-08-29 22:12:52 +0000 (Sat, 29 Aug 2009)

Log Message:
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fixed obsoleting of subclasses of obsolete_to_be_fixed

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Revision: 2055
          http://obi.svn.sourceforge.net/obi/?rev=2055&view=rev
Author:   jamesmalone
Date:     2009-09-01 12:21:46 +0000 (Tue, 01 Sep 2009)

Log Message:
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some obsolete roles moved

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Revision: 2058
          http://obi.svn.sourceforge.net/obi/?rev=2058&view=rev
Author:   bjoernpeters
Date:     2009-09-07 20:16:12 +0000 (Mon, 07 Sep 2009)

Log Message:
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removed 'has output' relation (introduced in ONTIE merge), and updated textual definitions 'is specified input / output' to be in sync with inverses.

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Revision: 2059
          http://obi.svn.sourceforge.net/obi/?rev=2059&view=rev
Author:   bjoernpeters
Date:     2009-09-07 22:25:37 +0000 (Mon, 07 Sep 2009)

Log Message:
-----------
removed ONTIE relations that are not necessary and (has process location, has output), renamed 'results from' to 'process is result of' to disambiguate with OBI relation of the same name. 

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Revision: 2060
          http://obi.svn.sourceforge.net/obi/?rev=2060&view=rev
Author:   bjoernpeters
Date:     2009-09-07 22:48:10 +0000 (Mon, 07 Sep 2009)

Log Message:
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merged 'disease' and 'disease iedb' into one term. 

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Revision: 2062
          http://obi.svn.sourceforge.net/obi/?rev=2062&view=rev
Author:   bjoernpeters
Date:     2009-09-07 23:36:53 +0000 (Mon, 07 Sep 2009)

Log Message:
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moved all PCR related terms under 'enzymatic amplification'. will need further cleanup, as some children are redundant. 

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Revision: 2063
          http://obi.svn.sourceforge.net/obi/?rev=2063&view=rev
Author:   bjoernpeters
Date:     2009-09-08 14:50:38 +0000 (Tue, 08 Sep 2009)

Log Message:
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fixed 'occurence of disease' which was still using the duplicate 'disease' term I obsoleted previously

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Revision: 2065
          http://obi.svn.sourceforge.net/obi/?rev=2065&view=rev
Author:   parkinso
Date:     2009-09-09 22:13:11 +0000 (Wed, 09 Sep 2009)

Log Message:
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Revision: 2068
          http://obi.svn.sourceforge.net/obi/?rev=2068&view=rev
Author:   parkinso
Date:     2009-09-14 10:04:05 +0000 (Mon, 14 Sep 2009)

Log Message:
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Obsoleted role of potential study participant based on email discussion. Existing child classes moved to _under discussion. 

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Revision: 2070
          http://obi.svn.sourceforge.net/obi/?rev=2070&view=rev
Author:   parkinso
Date:     2009-09-14 19:14:08 +0000 (Mon, 14 Sep 2009)

Log Message:
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1. edited drug role def. to make it more general
2. re-pointed obsolete class role of potential study participant to study subject
3. study participant role deprecated
4. excluded study participant role deprecated
5. study population role deprecated, child terms asserted under role

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Revision: 2072
          http://obi.svn.sourceforge.net/obi/?rev=2072&view=rev
Author:   parkinso
Date:     2009-09-15 13:23:51 +0000 (Tue, 15 Sep 2009)

Log Message:
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edited drug definition to conform to FG's proposal

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Revision: 2073
          http://obi.svn.sourceforge.net/obi/?rev=2073&view=rev
Author:   alanr
Date:     2009-09-15 21:17:29 +0000 (Tue, 15 Sep 2009)

Log Message:
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OBI_0000283 -> IAO_0000412

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Revision: 2077
          http://obi.svn.sourceforge.net/obi/?rev=2077&view=rev
Author:   mcourtot
Date:     2009-09-17 21:43:41 +0000 (Thu, 17 Sep 2009)

Log Message:
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added xmlns, corrected xml:base and added ontology URI

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Revision: 2080
          http://obi.svn.sourceforge.net/obi/?rev=2080&view=rev
Author:   parkinso
Date:     2009-09-23 20:02:12 +0000 (Wed, 23 Sep 2009)

Log Message:
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guar gum, fucoidan, antithrombin III added

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Revision: 2082
          http://obi.svn.sourceforge.net/obi/?rev=2082&view=rev
Author:   parkinso
Date:     2009-09-24 15:54:43 +0000 (Thu, 24 Sep 2009)

Log Message:
-----------


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Revision: 2084
          http://obi.svn.sourceforge.net/obi/?rev=2084&view=rev
Author:   parkinso
Date:     2009-09-24 16:14:22 +0000 (Thu, 24 Sep 2009)

Log Message:
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modified for clin trials use case

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Revision: 2085
          http://obi.svn.sourceforge.net/obi/?rev=2085&view=rev
Author:   alanr
Date:     2009-09-25 20:46:43 +0000 (Fri, 25 Sep 2009)

Log Message:
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how did the obi URL get to be obofoundry vs obolibrary? fixed.

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Revision: 2086
          http://obi.svn.sourceforge.net/obi/?rev=2086&view=rev
Author:   alanr
Date:     2009-09-25 20:53:35 +0000 (Fri, 25 Sep 2009)

Log Message:
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p4 bug. xml base confused as ontology uri. change to match.

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Revision: 2087
          http://obi.svn.sourceforge.net/obi/?rev=2087&view=rev
Author:   alanr
Date:     2009-09-25 21:26:28 +0000 (Fri, 25 Sep 2009)

Log Message:
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but the xml base back. mc said it hurts p3.

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Revision: 2096
          http://obi.svn.sourceforge.net/obi/?rev=2096&view=rev
Author:   bjoernpeters
Date:     2009-09-28 17:53:49 +0000 (Mon, 28 Sep 2009)

Log Message:
-----------
made ONTIE duplicates obsolete 

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Revision: 2099
          http://obi.svn.sourceforge.net/obi/?rev=2099&view=rev
Author:   bjoernpeters
Date:     2009-10-04 23:44:30 +0000 (Sun, 04 Oct 2009)

Log Message:
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modified epitope role to disposition, and updated affected relations

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Revision: 2102
          http://obi.svn.sourceforge.net/obi/?rev=2102&view=rev
Author:   bjoernpeters
Date:     2009-10-05 03:57:08 +0000 (Mon, 05 Oct 2009)

Log Message:
-----------
added more logical definition to PBS buffer. Specified hierarchy and reorganized conflicting test tube / collection tube / sample tube etc. 

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Revision: 2104
          http://obi.svn.sourceforge.net/obi/?rev=2104&view=rev
Author:   bjoernpeters
Date:     2009-10-05 17:59:58 +0000 (Mon, 05 Oct 2009)

Log Message:
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cleaned up ONTIE classes 

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Revision: 2112
          http://obi.svn.sourceforge.net/obi/?rev=2112&view=rev
Author:   bjoernpeters
Date:     2009-10-06 05:51:58 +0000 (Tue, 06 Oct 2009)

Log Message:
-----------
removed use of obsolete 'disease course' class. 

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Revision: 2120
          http://obi.svn.sourceforge.net/obi/?rev=2120&view=rev
Author:   alanr
Date:     2009-10-07 16:34:11 +0000 (Wed, 07 Oct 2009)

Log Message:
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fix curation status p4 lossage

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Revision: 2134
          http://obi.svn.sourceforge.net/obi/?rev=2134&view=rev
Author:   bjoernpeters
Date:     2009-10-09 21:30:41 +0000 (Fri, 09 Oct 2009)

Log Message:
-----------
several updates to infectious disease and related entities used in the IEDB export. 

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Revision: 2135
          http://obi.svn.sourceforge.net/obi/?rev=2135&view=rev
Author:   bjoernpeters
Date:     2009-10-09 22:12:44 +0000 (Fri, 09 Oct 2009)

Log Message:
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fixed inconsistent 'environmental exposure to infectious agent'

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Revision: 2136
          http://obi.svn.sourceforge.net/obi/?rev=2136&view=rev
Author:   bjoernpeters
Date:     2009-10-09 23:33:24 +0000 (Fri, 09 Oct 2009)

Log Message:
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removed multi asserted superclasses for processes; added MHC multimer for assay; changed label for 'disease stage' and 'spontaneous process' to be in line with definition

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Revision: 2138
          http://obi.svn.sourceforge.net/obi/?rev=2138&view=rev
Author:   bjoernpeters
Date:     2009-10-10 00:13:23 +0000 (Sat, 10 Oct 2009)

Log Message:
-----------


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Revision: 2142
          http://obi.svn.sourceforge.net/obi/?rev=2142&view=rev
Author:   parkinso
Date:     2009-10-11 23:28:32 +0000 (Sun, 11 Oct 2009)

Log Message:
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made multiple testing correction a defined class and added axions to existing child terms, and _unclassified terms asserted under data transformation. 

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Revision: 2152
          http://obi.svn.sourceforge.net/obi/?rev=2152&view=rev
Author:   bjoernpeters
Date:     2009-10-13 00:14:48 +0000 (Tue, 13 Oct 2009)

Log Message:
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changed effector and antigen presenting cell from role to function, and modified definitions accordingly. 

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Revision: 2155
          http://obi.svn.sourceforge.net/obi/?rev=2155&view=rev
Author:   alanr
Date:     2009-10-13 01:25:38 +0000 (Tue, 13 Oct 2009)

Log Message:
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fix morph of editor note to datatypeproperty

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Revision: 2160
          http://obi.svn.sourceforge.net/obi/?rev=2160&view=rev
Author:   parkinso
Date:     2009-10-13 04:02:43 +0000 (Tue, 13 Oct 2009)

Log Message:
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dt _unclassified terms moved to assert under dt and classify as model validation terms, defs added, curation complete

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Revision: 2164
          http://obi.svn.sourceforge.net/obi/?rev=2164&view=rev
Author:   jamesmalone
Date:     2009-10-13 11:03:29 +0000 (Tue, 13 Oct 2009)

Log Message:
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Additional GenePattern instance for data visualizations. Also some new data visualization classes and software instances corresponding to the DT visualization instances.

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Revision: 2179
          http://obi.svn.sourceforge.net/obi/?rev=2179&view=rev
Author:   bjoernpeters
Date:     2009-10-14 02:14:05 +0000 (Wed, 14 Oct 2009)

Log Message:
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Obsoleted the obi 'homo sapiens' / person term, to be replaced by the NCBI one, and updated usage throughout the file. 

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Revision: 2180
          http://obi.svn.sourceforge.net/obi/?rev=2180&view=rev
Author:   bjoernpeters
Date:     2009-10-14 02:25:26 +0000 (Wed, 14 Oct 2009)

Log Message:
-----------
Updated range of is_manufactured_by relation

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Revision: 2192
          http://obi.svn.sourceforge.net/obi/?rev=2192&view=rev
Author:   bjoernpeters
Date:     2009-10-14 18:36:38 +0000 (Wed, 14 Oct 2009)

Log Message:
-----------
added 'purification objective'

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Revision: 2193
          http://obi.svn.sourceforge.net/obi/?rev=2193&view=rev
Author:   bjoernpeters
Date:     2009-10-14 19:21:22 +0000 (Wed, 14 Oct 2009)

Log Message:
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modified label from extra cellular electrophysiology recording to extracellular ... 

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Revision: 2196
          http://obi.svn.sourceforge.net/obi/?rev=2196&view=rev
Author:   jzheng24
Date:     2009-10-14 22:35:20 +0000 (Wed, 14 Oct 2009)

Log Message:
-----------
add 'survival rate'
modify restrictions of 'survival assessment' and 'pathogen challenge'
move 'pathogen challenge' under 'administering substance in vivo'

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Revision: 2198
          http://obi.svn.sourceforge.net/obi/?rev=2198&view=rev
Author:   mcourtot
Date:     2009-10-14 23:19:35 +0000 (Wed, 14 Oct 2009)

Log Message:
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removed references to realizable information entity as per tracker item https://sourceforge.net/tracker/?func=detail&aid=2839101&group_id=177891&atid=886178
Note: I didn't update obsolete classes

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Revision: 2208
          http://obi.svn.sourceforge.net/obi/?rev=2208&view=rev
Author:   bjoernpeters
Date:     2009-10-15 16:34:25 +0000 (Thu, 15 Oct 2009)

Log Message:
-----------
changed instrument, device, platform, and ... recording device to be manufactured by some organization rather than some manufacturer

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Revision: 2209
          http://obi.svn.sourceforge.net/obi/?rev=2209&view=rev
Author:   parkinso
Date:     2009-10-15 22:21:43 +0000 (Thu, 15 Oct 2009)

Log Message:
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neuro use case classes added and existing one completed

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Revision: 2212
          http://obi.svn.sourceforge.net/obi/?rev=2212&view=rev
Author:   parkinso
Date:     2009-10-16 03:35:22 +0000 (Fri, 16 Oct 2009)

Log Message:
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mass measurement fixed, some typos and curation status. IEDB owe me.

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Revision: 2217
          http://obi.svn.sourceforge.net/obi/?rev=2217&view=rev
Author:   parkinso
Date:     2009-10-17 04:10:22 +0000 (Sat, 17 Oct 2009)

Log Message:
-----------
fixed more curation status. 

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Revision: 2218
          http://obi.svn.sourceforge.net/obi/?rev=2218&view=rev
Author:   parkinso
Date:     2009-10-17 04:28:00 +0000 (Sat, 17 Oct 2009)

Log Message:
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added unfolds in to measuring neural activity in caudate nucleus. improved def of micro electrode

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Revision: 2219
          http://obi.svn.sourceforge.net/obi/?rev=2219&view=rev
Author:   parkinso
Date:     2009-10-17 04:55:58 +0000 (Sat, 17 Oct 2009)

Log Message:
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more clean up, 2x yeast artificial chromosome, one obsoleted.

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Revision: 2224
          http://obi.svn.sourceforge.net/obi/?rev=2224&view=rev
Author:   alanr
Date:     2009-10-18 03:31:44 +0000 (Sun, 18 Oct 2009)

Log Message:
-----------
obsolete data, measured data, derived data item per tracker http://sourceforge.net/tracker/index.php?func=detail&aid=2581822&group_id=177891&atid=886178

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Revision: 2232
          http://obi.svn.sourceforge.net/obi/?rev=2232&view=rev
Author:   mcourtot
Date:     2009-10-18 19:21:04 +0000 (Sun, 18 Oct 2009)

Log Message:
-----------
specimen gathering -> specimen creation

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Revision: 2237
          http://obi.svn.sourceforge.net/obi/?rev=2237&view=rev
Author:   mcourtot
Date:     2009-10-18 22:00:46 +0000 (Sun, 18 Oct 2009)

Log Message:
-----------
retire measure function and use produce data function in its place and relabel produce data function as measure function - look at definition

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Revision: 2239
          http://obi.svn.sourceforge.net/obi/?rev=2239&view=rev
Author:   mcourtot
Date:     2009-10-18 22:04:36 +0000 (Sun, 18 Oct 2009)

Log Message:
-----------
obsoleted hypothesis

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Revision: 2242
          http://obi.svn.sourceforge.net/obi/?rev=2242&view=rev
Author:   mcourtot
Date:     2009-10-19 14:54:06 +0000 (Mon, 19 Oct 2009)

Log Message:
-----------
repaired strange grml commit grml :)

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Revision: 2243
          http://obi.svn.sourceforge.net/obi/?rev=2243&view=rev
Author:   mcourtot
Date:     2009-10-19 15:04:48 +0000 (Mon, 19 Oct 2009)

Log Message:
-----------
updated definition and example of usage of measure functionas per https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2845437&group_id=177891. Thanks Helen :)

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Revision: 2244
          http://obi.svn.sourceforge.net/obi/?rev=2244&view=rev
Author:   alanr
Date:     2009-10-19 15:57:40 +0000 (Mon, 19 Oct 2009)

Log Message:
-----------
add fucoidan classes

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Revision: 2249
          http://obi.svn.sourceforge.net/obi/?rev=2249&view=rev
Author:   mcourtot
Date:     2009-10-19 16:48:20 +0000 (Mon, 19 Oct 2009)

Log Message:
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- enrollement: restrictions should be put to organism
---- subclass human enrollment retsriction only homo sapiens
---- enrolled population role gets obsolete

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Revision: 2250
          http://obi.svn.sourceforge.net/obi/?rev=2250&view=rev
Author:   mcourtot
Date:     2009-10-19 16:54:30 +0000 (Mon, 19 Oct 2009)

Log Message:
-----------
https://sourceforge.net/tracker/index.php?func=detail&aid=2881843&group_id=177891&atid=886178 

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Revision: 2251
          http://obi.svn.sourceforge.net/obi/?rev=2251&view=rev
Author:   mcourtot
Date:     2009-10-19 16:57:47 +0000 (Mon, 19 Oct 2009)

Log Message:
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 take out restriction to data set output on error correction DT and multiple testing correction

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Revision: 2252
          http://obi.svn.sourceforge.net/obi/?rev=2252&view=rev
Author:   mcourtot
Date:     2009-10-19 17:11:39 +0000 (Mon, 19 Oct 2009)

Log Message:
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Survival analysis: survival analysis is a data transformation that involves the modeling of time to event data; the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables

http://en.wikipedia.org/wiki/Survival_analysis

Kaplan meier: a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored), Objective: survival analysis
http://en.wikipedia.org/wiki/Kaplan%E2%80%93Meier_estimator

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Revision: 2256
          http://obi.svn.sourceforge.net/obi/?rev=2256&view=rev
Author:   jamesmalone
Date:     2009-10-19 20:03:03 +0000 (Mon, 19 Oct 2009)

Log Message:
-----------
Clean up of some _unclassified in data transformation
Additional objectives and mass spec DT classes added

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Revision: 2257
          http://obi.svn.sourceforge.net/obi/?rev=2257&view=rev
Author:   jamesmalone
Date:     2009-10-19 20:20:08 +0000 (Mon, 19 Oct 2009)

Log Message:
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information processing obsolete
all DT unclassified now addressed - _unclassified removed from DT

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Revision: 2264
          http://obi.svn.sourceforge.net/obi/?rev=2264&view=rev
Author:   jamesmalone
Date:     2009-10-19 21:05:07 +0000 (Mon, 19 Oct 2009)

Log Message:
-----------
additional DT classes, some restriction fixes

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Revision: 2268
          http://obi.svn.sourceforge.net/obi/?rev=2268&view=rev
Author:   alanr
Date:     2009-10-20 13:55:12 +0000 (Tue, 20 Oct 2009)

Log Message:
-----------
some curation status for fucoidan

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Revision: 2269
          http://obi.svn.sourceforge.net/obi/?rev=2269&view=rev
Author:   bjoernpeters
Date:     2009-10-20 15:35:40 +0000 (Tue, 20 Oct 2009)

Log Message:
-----------


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Revision: 2272
          http://obi.svn.sourceforge.net/obi/?rev=2272&view=rev
Author:   bjoernpeters
Date:     2009-10-20 16:41:18 +0000 (Tue, 20 Oct 2009)

Log Message:
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done with calibration substance role (and dependent terms)

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Revision: 2273
          http://obi.svn.sourceforge.net/obi/?rev=2273&view=rev
Author:   bjoernpeters
Date:     2009-10-20 17:31:32 +0000 (Tue, 20 Oct 2009)

Log Message:
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retiring

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Revision: 2274
          http://obi.svn.sourceforge.net/obi/?rev=2274&view=rev
Author:   bjoernpeters
Date:     2009-10-20 17:48:56 +0000 (Tue, 20 Oct 2009)

Log Message:
-----------
finalized retiring uses of device, obsoleted class. 

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Revision: 2275
          http://obi.svn.sourceforge.net/obi/?rev=2275&view=rev
Author:   bjoernpeters
Date:     2009-10-20 18:17:07 +0000 (Tue, 20 Oct 2009)

Log Message:
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specimen and specimen role done

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Revision: 2277
          http://obi.svn.sourceforge.net/obi/?rev=2277&view=rev
Author:   bjoernpeters
Date:     2009-10-20 18:35:29 +0000 (Tue, 20 Oct 2009)

Log Message:
-----------
done with blood specimen

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Revision: 2279
          http://obi.svn.sourceforge.net/obi/?rev=2279&view=rev
Author:   bjoernpeters
Date:     2009-10-20 19:15:48 +0000 (Tue, 20 Oct 2009)

Log Message:
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done with patent

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Revision: 2283
          http://obi.svn.sourceforge.net/obi/?rev=2283&view=rev
Author:   parkinso
Date:     2009-10-20 22:13:25 +0000 (Tue, 20 Oct 2009)

Log Message:
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reviewing cur status for manuscript. up to assay. Note defered some to come back to tomorrow. Still probs with the processed material - if we remove these restrictions then reasons in real time p4. HP

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Revision: 2285
          http://obi.svn.sourceforge.net/obi/?rev=2285&view=rev
Author:   mcourtot
Date:     2009-10-20 22:21:58 +0000 (Tue, 20 Oct 2009)

Log Message:
-----------
updated definition of interpreting data as per Jennifer's update: "the process of evaluating the data gathered in an investigation in the context of literature knowledge with the objective to generate more general conclusions or to identify what additional data is necessary to draw conclusions"

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Revision: 2291
          http://obi.svn.sourceforge.net/obi/?rev=2291&view=rev
Author:   parkinso
Date:     2009-10-21 16:52:20 +0000 (Wed, 21 Oct 2009)

Log Message:
-----------
mapped paper terms to OBI.owl

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Revision: 2300
          http://obi.svn.sourceforge.net/obi/?rev=2300&view=rev
Author:   parkinso
Date:     2009-10-21 20:04:13 +0000 (Wed, 21 Oct 2009)

Log Message:
-----------
cleanup of _qualities, moving confered qualities to material entities, also fixed _dependent bearer child classes and obsoleted some unused terms

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Revision: 2304
          http://obi.svn.sourceforge.net/obi/?rev=2304&view=rev
Author:   parkinso
Date:     2009-10-21 20:21:49 +0000 (Wed, 21 Oct 2009)

Log Message:
-----------
fixed inconsistency

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Revision: 2305
          http://obi.svn.sourceforge.net/obi/?rev=2305&view=rev
Author:   parkinso
Date:     2009-10-21 20:39:55 +0000 (Wed, 21 Oct 2009)

Log Message:
-----------
clean up of more conferred qualities

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Revision: 2307
          http://obi.svn.sourceforge.net/obi/?rev=2307&view=rev
Author:   parkinso
Date:     2009-10-21 21:04:02 +0000 (Wed, 21 Oct 2009)

Log Message:
-----------
deprecated roles at JF's request, tracker items closed 

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Revision: 2310
          http://obi.svn.sourceforge.net/obi/?rev=2310&view=rev
Author:   parkinso
Date:     2009-10-21 21:29:47 +0000 (Wed, 21 Oct 2009)

Log Message:
-----------
instrument deprecated as agreed in workshop

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Revision: 2320
          http://obi.svn.sourceforge.net/obi/?rev=2320&view=rev
Author:   parkinso
Date:     2009-10-22 03:58:21 +0000 (Thu, 22 Oct 2009)

Log Message:
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deprecated _ prefi msi placeholder classes

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Revision: 2321
          http://obi.svn.sourceforge.net/obi/?rev=2321&view=rev
Author:   parkinso
Date:     2009-10-22 04:18:37 +0000 (Thu, 22 Oct 2009)

Log Message:
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removed _under discussion and asserted non deprecated classes under role. 

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Revision: 2322
          http://obi.svn.sourceforge.net/obi/?rev=2322&view=rev
Author:   parkinso
Date:     2009-10-22 05:23:07 +0000 (Thu, 22 Oct 2009)

Log Message:
-----------
workshop mandated cleanup of placeholders and other classes completed. HP

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Revision: 2328
          http://obi.svn.sourceforge.net/obi/?rev=2328&view=rev
Author:   mcourtot
Date:     2009-10-24 02:23:14 +0000 (Sat, 24 Oct 2009)

Log Message:
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removed annotation for IAO_0000184 that crept into OBI

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Revision: 2329
          http://obi.svn.sourceforge.net/obi/?rev=2329&view=rev
Author:   mcourtot
Date:     2009-10-24 02:29:26 +0000 (Sat, 24 Oct 2009)

Log Message:
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removed in branch annotation

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Revision: 2330
          http://obi.svn.sourceforge.net/obi/?rev=2330&view=rev
Author:   mcourtot
Date:     2009-10-24 02:50:39 +0000 (Sat, 24 Oct 2009)

Log Message:
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gene list visualization has output table (IAO_0000306) instead of report table
fix berichrom spelling - https://sourceforge.net/tracker/?func=detail&aid=2882587&group_id=177891&atid=886178

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Revision: 2331
          http://obi.svn.sourceforge.net/obi/?rev=2331&view=rev
Author:   mcourtot
Date:     2009-10-24 03:03:29 +0000 (Sat, 24 Oct 2009)

Log Message:
-----------
repaired obsolescence reason specification values set as string. those values have been copied to editor notes

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Revision: 2332
          http://obi.svn.sourceforge.net/obi/?rev=2332&view=rev
Author:   mcourtot
Date:     2009-10-24 03:18:29 +0000 (Sat, 24 Oct 2009)

Log Message:
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diagnosis -> diagnosis textual entity, moved from study interpretation to textual entity hierarchy as per workshop AI

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Revision: 2333
          http://obi.svn.sourceforge.net/obi/?rev=2333&view=rev
Author:   mcourtot
Date:     2009-10-24 03:25:19 +0000 (Sat, 24 Oct 2009)

Log Message:
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diagnosis take 2

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Revision: 2334
          http://obi.svn.sourceforge.net/obi/?rev=2334&view=rev
Author:   mcourtot
Date:     2009-10-24 13:50:14 +0000 (Sat, 24 Oct 2009)

Log Message:
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added variables specs
independent variable spec IAO_0000011 -> OBI_0000750 
 dependent variable spec IAO_0000014 -> OBI_0000751
controlled variable spec IAO_0000016 -> OBI_0000785

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Revision: 2336
          http://obi.svn.sourceforge.net/obi/?rev=2336&view=rev
Author:   alanr
Date:     2009-10-24 15:39:24 +0000 (Sat, 24 Oct 2009)

Log Message:
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newids

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Revision: 2338
          http://obi.svn.sourceforge.net/obi/?rev=2338&view=rev
Author:   alanr
Date:     2009-10-24 16:16:52 +0000 (Sat, 24 Oct 2009)

Log Message:
-----------
is-member-of

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Revision: 2344
          http://obi.svn.sourceforge.net/obi/?rev=2344&view=rev
Author:   mcourtot
Date:     2009-10-24 19:55:50 +0000 (Sat, 24 Oct 2009)

Log Message:
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corrected spelling of lighet emission function

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Revision: 2343
          http://obi.svn.sourceforge.net/obi/?rev=2343&view=rev
Author:   mcourtot
Date:     2009-10-24 19:52:54 +0000 (Sat, 24 Oct 2009)

Log Message:
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removed duplicate declaration of class conclusion textual entity

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Revision: 2342
          http://obi.svn.sourceforge.net/obi/?rev=2342&view=rev
Author:   mcourtot
Date:     2009-10-24 19:45:52 +0000 (Sat, 24 Oct 2009)

Log Message:
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obsoleted normalized which is now redundant with normalized data set OBI_0000451

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Revision: 2345
          http://obi.svn.sourceforge.net/obi/?rev=2345&view=rev
Author:   alanr
Date:     2009-10-25 02:42:58 +0000 (Sun, 25 Oct 2009)

Log Message:
-----------
TMPIAO_0000004

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Revision: 2346
          http://obi.svn.sourceforge.net/obi/?rev=2346&view=rev
Author:   bjoernpeters
Date:     2009-10-25 20:38:06 +0000 (Sun, 25 Oct 2009)

Log Message:
-----------
Added 'direct submission to IEDB' as a report. 

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Revision: 2371
          http://obi.svn.sourceforge.net/obi/?rev=2371&view=rev
Author:   alanr
Date:     2009-10-29 02:14:22 +0000 (Thu, 29 Oct 2009)

Log Message:
-----------
sorted editor notes. See http://obi-ontology.org/page/Releases/2009-11-06/Cleanup_log#What_was_done_to_editor_notes. Also decomposed classes at top level so they appear in tree. Also cleaned up some obsolete classes.

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Revision: 2374
          http://obi.svn.sourceforge.net/obi/?rev=2374&view=rev
Author:   bjoernpeters
Date:     2009-10-29 03:29:13 +0000 (Thu, 29 Oct 2009)

Log Message:
-----------
obsoleted 'antibody role' and reference to it. updated PBS buffer curation status to be in line with Table in manuscript.  

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Revision: 2375
          http://obi.svn.sourceforge.net/obi/?rev=2375&view=rev
Author:   mcourtot
Date:     2009-10-29 03:46:41 +0000 (Thu, 29 Oct 2009)

Log Message:
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we don't delete classes metadata just because there is a typo :) (light emission corrected)

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Revision: 2382
          http://obi.svn.sourceforge.net/obi/?rev=2382&view=rev
Author:   mcourtot
Date:     2009-11-01 00:09:37 +0000 (Sun, 01 Nov 2009)

Log Message:
-----------
flattened obsolete hierarchy

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Revision: 2389
          http://obi.svn.sourceforge.net/obi/?rev=2389&view=rev
Author:   mcourtot
Date:     2009-11-01 23:45:12 +0000 (Sun, 01 Nov 2009)

Log Message:
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image stream -> Amnis ImageStream, cf https://sourceforge.net/tracker/?func=detail&aid=2888037&group_id=177891&atid=886178

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Revision: 2390
          http://obi.svn.sourceforge.net/obi/?rev=2390&view=rev
Author:   mcourtot
Date:     2009-11-01 23:54:08 +0000 (Sun, 01 Nov 2009)

Log Message:
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example of usage to be added annotation property removed - cf https://sourceforge.net/tracker/?func=detail&aid=2887965&group_id=177891&atid=886178

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Revision: 2391
          http://obi.svn.sourceforge.net/obi/?rev=2391&view=rev
Author:   mcourtot
Date:     2009-11-02 00:02:52 +0000 (Mon, 02 Nov 2009)

Log Message:
-----------
removed source pending annotation property values - cf https://sourceforge.net/tracker/?func=detail&aid=2887928&group_id=177891&atid=886178

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Revision: 2392
          http://obi.svn.sourceforge.net/obi/?rev=2392&view=rev
Author:   mcourtot
Date:     2009-11-02 00:31:47 +0000 (Mon, 02 Nov 2009)

Log Message:
-----------
removed all empty annotation properties. nmr/chrom terms each add an     <obo:IAO_0000118 xml:lang="en"></obo:IAO_0000118> (alternative term) empty property...
https://sourceforge.net/tracker/?func=detail&aid=2887874&group_id=177891&atid=886178

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Revision: 2396
          http://obi.svn.sourceforge.net/obi/?rev=2396&view=rev
Author:   mcourtot
Date:     2009-11-02 02:47:30 +0000 (Mon, 02 Nov 2009)

Log Message:
-----------
added definition and editor note for protein-protein interaction detection assay. Thanks to Bjoern.

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Revision: 2397
          http://obi.svn.sourceforge.net/obi/?rev=2397&view=rev
Author:   alanr
Date:     2009-11-02 03:17:53 +0000 (Mon, 02 Nov 2009)

Log Message:
-----------
https://sourceforge.net/tracker/?func=detail&aid=2890524&group_id=177891&atid=886178

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Revision: 2417
          http://obi.svn.sourceforge.net/obi/?rev=2417&view=rev
Author:   mcourtot
Date:     2009-11-02 22:18:55 +0000 (Mon, 02 Nov 2009)

Log Message:
-----------
deprecated obsolete_hyphenated NMR platform. Subclasses were all Bruker manufactured and have been moved under Bruker NMR instrument (which should prbably be a defined class)

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Revision: 2421
          http://obi.svn.sourceforge.net/obi/?rev=2421&view=rev
Author:   mcourtot
Date:     2009-11-02 22:52:29 +0000 (Mon, 02 Nov 2009)

Log Message:
-----------
added injection function OBI_0005246

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Revision: 2437
          http://obi.svn.sourceforge.net/obi/?rev=2437&view=rev
Author:   alanr
Date:     2009-11-03 04:21:06 +0000 (Tue, 03 Nov 2009)

Log Message:
-----------
revision keyword

Property Changed:
----------------
    trunk/src/ontology/branches/obi.owl


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Revision: 2438
          http://obi.svn.sourceforge.net/obi/?rev=2438&view=rev
Author:   alanr
Date:     2009-11-03 04:21:39 +0000 (Tue, 03 Nov 2009)

Log Message:
-----------
revision keyword

Modified Paths:
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Revision: 2439
          http://obi.svn.sourceforge.net/obi/?rev=2439&view=rev
Author:   alanr
Date:     2009-11-03 05:13:08 +0000 (Tue, 03 Nov 2009)

Log Message:
-----------
metadata complete for guar gum, fucoidan

Modified Paths:
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Revision: 2442
          http://obi.svn.sourceforge.net/obi/?rev=2442&view=rev
Author:   alanr
Date:     2009-11-03 05:48:33 +0000 (Tue, 03 Nov 2009)

Log Message:
-----------
glucose molecules, resolving https://sourceforge.net/tracker/?func=detail&aid=2890830&group_id=177891&atid=886178

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Revision: 2464
          http://obi.svn.sourceforge.net/obi/?rev=2464&view=rev
Author:   mcourtot
Date:     2009-11-04 23:00:38 +0000 (Wed, 04 Nov 2009)

Log Message:
-----------
cleanup in progress

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Revision: 2466
          http://obi.svn.sourceforge.net/obi/?rev=2466&view=rev
Author:   mcourtot
Date:     2009-11-04 23:20:44 +0000 (Wed, 04 Nov 2009)

Log Message:
-----------
clean up of editor notes done

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Revision: 2469
          http://obi.svn.sourceforge.net/obi/?rev=2469&view=rev
Author:   mcourtot
Date:     2009-11-05 01:05:23 +0000 (Thu, 05 Nov 2009)

Log Message:
-----------
removed mention of entity of organismal origin which had been deprecated.
issue remaining for collection (of entities of organismal origin)

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Revision: 2473
          http://obi.svn.sourceforge.net/obi/?rev=2473&view=rev
Author:   mcourtot
Date:     2009-11-05 18:23:06 +0000 (Thu, 05 Nov 2009)

Log Message:
-----------
added editor note to collection (of entities of organismal origin) as per https://sourceforge.net/tracker/index.php?func=detail&aid=2888194&group_id=177891&atid=886178

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Revision: 2476
          http://obi.svn.sourceforge.net/obi/?rev=2476&view=rev
Author:   mcourtot
Date:     2009-11-06 04:07:32 +0000 (Fri, 06 Nov 2009)

Log Message:
-----------
removed rdfs:comment properties

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Revision: 2478
          http://obi.svn.sourceforge.net/obi/?rev=2478&view=rev
Author:   parkinso
Date:     2009-11-06 10:00:24 +0000 (Fri, 06 Nov 2009)

Log Message:
-----------
other cell obsoleted.

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Revision: 2486
          http://obi.svn.sourceforge.net/obi/?rev=2486&view=rev
Author:   alanr
Date:     2009-11-07 12:07:01 +0000 (Sat, 07 Nov 2009)

Log Message:
-----------
http://obi-ontology.org/page/Releases/2009-11-06/Cleanup_log#Preferred_labels

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Revision: 2487
          http://obi.svn.sourceforge.net/obi/?rev=2487&view=rev
Author:   alanr
Date:     2009-11-08 01:47:49 +0000 (Sun, 08 Nov 2009)

Log Message:
-----------
agreeing with and fixing issues in https://sourceforge.net/tracker/?func=detail&aid=2893997&group_id=177891&atid=886178

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Revision: 2489
          http://obi.svn.sourceforge.net/obi/?rev=2489&view=rev
Author:   alanr
Date:     2009-11-08 01:51:53 +0000 (Sun, 08 Nov 2009)

Log Message:
-----------
remove owl:versionInfo. It will be added by release script.

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Revision: 2495
          http://obi.svn.sourceforge.net/obi/?rev=2495&view=rev
Author:   alanr
Date:     2009-11-08 07:03:00 +0000 (Sun, 08 Nov 2009)

Log Message:
-----------
captialize Bernoulli

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Revision: 2504
          http://obi.svn.sourceforge.net/obi/?rev=2504&view=rev
Author:   alanr
Date:     2009-11-08 22:36:46 +0000 (Sun, 08 Nov 2009)

Log Message:
-----------
curator comment -> curator note

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Revision: 2513
          http://obi.svn.sourceforge.net/obi/?rev=2513&view=rev
Author:   alanr
Date:     2009-11-09 05:55:46 +0000 (Mon, 09 Nov 2009)

Log Message:
-----------
fixed spelling errors. See http://obi-ontology.org/page/Releases/2009-11-06/Cleanup_log#Spelling_corrections

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Revision: 2515
          http://obi.svn.sourceforge.net/obi/?rev=2515&view=rev
Author:   alanr
Date:     2009-11-09 05:59:11 +0000 (Mon, 09 Nov 2009)

Log Message:
-----------
missed hematopoeietic

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Revision: 2527
          http://obi.svn.sourceforge.net/obi/?rev=2527&view=rev
Author:   alanr
Date:     2009-11-10 19:07:13 +0000 (Tue, 10 Nov 2009)

Log Message:
-----------
add definitions from http://spreadsheets.google.com/ccc?key=0Aqgyu8cVTs1OdFhlS2l2dnM4cE9ESEhBcVhIcGx5SHc&hl=en

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Revision: 2553
          http://obi.svn.sourceforge.net/obi/?rev=2553&view=rev
Author:   alanr
Date:     2009-11-16 18:53:55 +0000 (Mon, 16 Nov 2009)

Log Message:
-----------
speciment -> specimen

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Revision: 2554
          http://obi.svn.sourceforge.net/obi/?rev=2554&view=rev
Author:   jzheng24
Date:     2009-11-16 20:56:05 +0000 (Mon, 16 Nov 2009)

Log Message:
-----------
Remove 'definition_source' in definitions (contain defprov) in following four terms
OBI_0000607 high resolution magicangle spin probe
OBI_0000480 Bruker high resolution probe
OBI_0000513 DISCOVERY console
OBI_0000590 Bruker 1mm MicroProbe

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Revision: 2565
          http://obi.svn.sourceforge.net/obi/?rev=2565&view=rev
Author:   parkinso
Date:     2009-11-18 10:19:45 +0000 (Wed, 18 Nov 2009)

Log Message:
-----------
clean up of inter-rater reliability and some dt terms defs improved - HP

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Revision: 2569
          http://obi.svn.sourceforge.net/obi/?rev=2569&view=rev
Author:   bjoernpeters
Date:     2009-11-23 18:18:25 +0000 (Mon, 23 Nov 2009)

Log Message:
-----------
obsoleted 'results from' and updated definition of 'artificially induced reverse transcription'

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Revision: 2570
          http://obi.svn.sourceforge.net/obi/?rev=2570&view=rev
Author:   parkinso
Date:     2009-11-23 20:15:32 +0000 (Mon, 23 Nov 2009)

Log Message:
-----------
various dt defs improved, couple of label changes as per priority 7 tracker items prior to release 1.0

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Revision: 2587
          http://obi.svn.sourceforge.net/obi/?rev=2587&view=rev
Author:   jamesmalone
Date:     2009-11-27 17:01:36 +0000 (Fri, 27 Nov 2009)

Log Message:
-----------
quick edit to address survival analysis DT

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Revision: 2595
          http://obi.svn.sourceforge.net/obi/?rev=2595&view=rev
Author:   parkinso
Date:     2009-11-30 18:11:21 +0000 (Mon, 30 Nov 2009)

Log Message:
-----------
added immortalized cell line culture and refactored child terms also added processes for these. HP.

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Revision: 2602
          http://obi.svn.sourceforge.net/obi/?rev=2602&view=rev
Author:   bjoernpeters
Date:     2009-12-02 19:44:39 +0000 (Wed, 02 Dec 2009)

Log Message:
-----------
added 'record of unknown sex' as ICE and 'postmortem / premortem specimen' as 'conveyed quality' as discussed on call regarding PATO imports for MO

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Revision: 2620
          http://obi.svn.sourceforge.net/obi/?rev=2620&view=rev
Author:   mcourtot
Date:     2009-12-04 22:29:27 +0000 (Fri, 04 Dec 2009)

Log Message:
-----------
added Monnie to list of creators as per Bjoern's email

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Revision: 2671
          http://obi.svn.sourceforge.net/obi/?rev=2671&view=rev
Author:   bjoernpeters
Date:     2009-12-16 17:12:14 +0000 (Wed, 16 Dec 2009)

Log Message:
-----------
added 'high molecular weight DNA extract'. 

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Revision: 2702
          http://obi.svn.sourceforge.net/obi/?rev=2702&view=rev
Author:   parkinso
Date:     2010-01-06 16:51:56 +0000 (Wed, 06 Jan 2010)

Log Message:
-----------
minor changes to document editing to make more generic, added inputs and outputs and change to definition. See tracker https://sourceforge.net/tracker/?func=detail&aid=2898827&group_id=177891&atid=886178

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Revision: 2712
          http://obi.svn.sourceforge.net/obi/?rev=2712&view=rev
Author:   alanr
Date:     2010-01-13 22:36:21 +0000 (Wed, 13 Jan 2010)

Log Message:
-----------
move documenting to IAO

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Revision: 2713
          http://obi.svn.sourceforge.net/obi/?rev=2713&view=rev
Author:   mcourtot
Date:     2010-01-13 23:22:13 +0000 (Wed, 13 Jan 2010)

Log Message:
-----------
added obsolescence reason specification to obsolete_documenting and term_replaced_by annotation (IAO_0000572)

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Revision: 2726
          http://obi.svn.sourceforge.net/obi/?rev=2726&view=rev
Author:   mcourtot
Date:     2010-01-20 23:18:19 +0000 (Wed, 20 Jan 2010)

Log Message:
-----------
moved survival curve in OBI as per http://code.google.com/p/information-artifact-ontology/issues/detail?id=19, as child of line graph
added restriction "is_about some survival rate"

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Revision: 2727
          http://obi.svn.sourceforge.net/obi/?rev=2727&view=rev
Author:   jzheng24
Date:     2010-01-21 20:28:28 +0000 (Thu, 21 Jan 2010)

Log Message:
-----------
Add deprecated term "survival assessment" back

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Revision: 2729
          http://obi.svn.sourceforge.net/obi/?rev=2729&view=rev
Author:   alanr
Date:     2010-01-26 07:13:58 +0000 (Tue, 26 Jan 2010)

Log Message:
-----------
fix bearer_of some ('objective specification... =>  ...bearer_of some (is_concretization_of some ('objective specification ... Thanks to MC for identifying the change that led to this - our clarification in IAO that inheres relates sdcs and ics

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Revision: 2731
          http://obi.svn.sourceforge.net/obi/?rev=2731&view=rev
Author:   jzheng24
Date:     2010-01-27 05:34:23 +0000 (Wed, 27 Jan 2010)

Log Message:
-----------
Add restriction 'has grain' some 'recombinant vector' to cDNA library and phage display library
https://sourceforge.net/tracker/?func=detail&aid=2894777&group_id=177891&atid=886178

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Revision: 2732
          http://obi.svn.sourceforge.net/obi/?rev=2732&view=rev
Author:   jzheng24
Date:     2010-01-27 07:07:00 +0000 (Wed, 27 Jan 2010)

Log Message:
-----------
5 RNA extractions and 6 RNA extracts related terms were added according to the spreadsheet
https://sourceforge.net/tracker/download.php?group_id=177891&atid=886178&file_id=360446&aid=2915152
Some restrictions were added to nucleic acid and RNA extraction.

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Revision: 2734
          http://obi.svn.sourceforge.net/obi/?rev=2734&view=rev
Author:   p_rocca_serra
Date:     2010-01-31 13:06:44 +0000 (Sun, 31 Jan 2010)

Log Message:
-----------
fixes to sequencing assays (now properly classified), fixes to rodent care so classifies under animal care, adding necessary placeholders for adding assays defined working with RNAO group, more work is needed, adding definition to validated information, corrections to logical constraints to curation information, for all adding or updating metadata

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Revision: 2735
          http://obi.svn.sourceforge.net/obi/?rev=2735&view=rev
Author:   p_rocca_serra
Date:     2010-01-31 19:51:24 +0000 (Sun, 31 Jan 2010)

Log Message:
-----------
added: northern,Southern,western blot analysis, random primed DNA labeling, labeled oligonucleotide, protein extract, asserted sequencing assay under assay. TODO add curation status to those classes

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Revision: 2736
          http://obi.svn.sourceforge.net/obi/?rev=2736&view=rev
Author:   bjoernpeters
Date:     2010-02-11 22:48:30 +0000 (Thu, 11 Feb 2010)

Log Message:
-----------
Added assays for the IEDB - cell mediated cell killing, detection of specific nucleic acids with complementary probes, cell proliferation, and cell culture analyte detection bioassays. Also reorganized affected sibling / parent / child classes. 

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Revision: 2737
          http://obi.svn.sourceforge.net/obi/?rev=2737&view=rev
Author:   jzheng24
Date:     2010-02-12 04:46:03 +0000 (Fri, 12 Feb 2010)

Log Message:
-----------
Fix typo. perturbe function -> perturb function

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Revision: 2738
          http://obi.svn.sourceforge.net/obi/?rev=2738&view=rev
Author:   jzheng24
Date:     2010-02-12 06:29:45 +0000 (Fri, 12 Feb 2010)

Log Message:
-----------
Deprecate class 'study result' according to the decision made on Dev call Jan 25, 2010

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Revision: 2743
          http://obi.svn.sourceforge.net/obi/?rev=2743&view=rev
Author:   jzheng24
Date:     2010-02-15 23:42:45 +0000 (Mon, 15 Feb 2010)

Log Message:
-----------
Remove 'nucleic acid' in obi.owl

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Revision: 2745
          http://obi.svn.sourceforge.net/obi/?rev=2745&view=rev
Author:   mcourtot
Date:     2010-02-17 21:15:20 +0000 (Wed, 17 Feb 2010)

Log Message:
-----------
added alternative term RT-PCR
added neutralization http://sourceforge.net/tracker/?func=detail&aid=2945555&group_id=177891&atid=886178 and microneutralization http://sourceforge.net/tracker/?func=detail&aid=2945556&group_id=177891&atid=886178
added real-time PCR http://sourceforge.net/tracker/?func=detail&aid=2945561&group_id=177891&atid=886178

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Revision: 2746
          http://obi.svn.sourceforge.net/obi/?rev=2746&view=rev
Author:   jzheng24
Date:     2010-02-17 23:27:45 +0000 (Wed, 17 Feb 2010)

Log Message:
-----------
assign IDs to new added terms

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Revision: 2747
          http://obi.svn.sourceforge.net/obi/?rev=2747&view=rev
Author:   mcourtot
Date:     2010-02-18 00:31:13 +0000 (Thu, 18 Feb 2010)

Log Message:
-----------
removed restriction to analyte assay on real time PCR

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Revision: 2749
          http://obi.svn.sourceforge.net/obi/?rev=2749&view=rev
Author:   bjoernpeters
Date:     2010-02-23 02:34:49 +0000 (Tue, 23 Feb 2010)

Log Message:
-----------
Modified header part of file; replaced with obi.owl from commit 2745 up until "<owl:Ontology rdf:about="">". This restores ability to reason and set active ontology when using obi-edit.pprj for BP. 

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Revision: 2750
          http://obi.svn.sourceforge.net/obi/?rev=2750&view=rev
Author:   alanr
Date:     2010-02-24 06:55:52 +0000 (Wed, 24 Feb 2010)

Log Message:
-----------
remove spurios instance of obsolescence reason specification

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Revision: 2765
          http://obi.svn.sourceforge.net/obi/?rev=2765&view=rev
Author:   bjoernpeters
Date:     2010-03-01 18:09:00 +0000 (Mon, 01 Mar 2010)

Log Message:
-----------
added 'labeled specimen' and subclasses 'labeled DNA specimen', labeled RNA specimen. Several open discussion items with these. 

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Revision: 2772
          http://obi.svn.sourceforge.net/obi/?rev=2772&view=rev
Author:   alanr
Date:     2010-03-03 17:16:32 +0000 (Wed, 03 Mar 2010)

Log Message:
-----------
Add freezing, fresh specimen, as worked on during meeting

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Revision: 2777
          http://obi.svn.sourceforge.net/obi/?rev=2777&view=rev
Author:   jamesmalone
Date:     2010-03-09 13:43:41 +0000 (Tue, 09 Mar 2010)

Log Message:
-----------
fix to data imputation objective

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Revision: 2785
          http://obi.svn.sourceforge.net/obi/?rev=2785&view=rev
Author:   bjoernpeters
Date:     2010-03-12 00:25:32 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
added assays (x-ray crystallography, surface plasmon resonance, promoter activity detection by reporter gene, radio immuno assay, cytometric bead array, intracellular material detection by flow). edited label of 'clinical diagnosis' to 'performing clinical diagnosis' to distinguish from ICE. 

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Revision: 2786
          http://obi.svn.sourceforge.net/obi/?rev=2786&view=rev
Author:   bjoernpeters
Date:     2010-03-12 01:28:54 +0000 (Fri, 12 Mar 2010)

Log Message:
-----------
Closed several tickets: Asserted that a lavage is a material separation, made 'columns' to children of chromotography columns as suggested by Melissa, removed N&S restrictions on platforms which made all corresponding instruments to platforms. 

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Revision: 2792
          http://obi.svn.sourceforge.net/obi/?rev=2792&view=rev
Author:   parkinso
Date:     2010-03-15 21:38:16 +0000 (Mon, 15 Mar 2010)

Log Message:
-----------
Added new child of killing. Tracker item https://sourceforge.net/tracker/index.php?func=detail&aid=2952718&group_id=177891&atid=886178

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Revision: 2793
          http://obi.svn.sourceforge.net/obi/?rev=2793&view=rev
Author:   parkinso
Date:     2010-03-15 21:49:57 +0000 (Mon, 15 Mar 2010)

Log Message:
-----------
supplies role updated https://sourceforge.net/tracker/index.php?func=detail&aid=2882555&group_id=177891&atid=886178

Modified Paths:
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Revision: 2796
          http://obi.svn.sourceforge.net/obi/?rev=2796&view=rev
Author:   bjoernpeters
Date:     2010-03-17 15:50:30 +0000 (Wed, 17 Mar 2010)

Log Message:
-----------
call edits ('easy tracker items'). Added DMEM, obsoleted 'collection of entities of organismal origin'. 

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Revision: 2797
          http://obi.svn.sourceforge.net/obi/?rev=2797&view=rev
Author:   parkinso
Date:     2010-03-17 18:34:31 +0000 (Wed, 17 Mar 2010)

Log Message:
-----------
added logical def to nucleic acid template role

https://sourceforge.net/tracker/?func=detail&aid=2906040&group_id=177891&atid=886178

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Revision: 2798
          http://obi.svn.sourceforge.net/obi/?rev=2798&view=rev
Author:   parkinso
Date:     2010-03-17 18:40:31 +0000 (Wed, 17 Mar 2010)

Log Message:
-----------
actioned https://sourceforge.net/tracker/?func=detail&aid=2906036&group_id=177891&atid=886178

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 2800
          http://obi.svn.sourceforge.net/obi/?rev=2800&view=rev
Author:   mcourtot
Date:     2010-03-17 23:45:46 +0000 (Wed, 17 Mar 2010)

Log Message:
-----------
added
- nasal swab http://sourceforge.net/tracker/?func=detail&aid=2946732&group_id=177891&atid=886178
- nasopharyngeal aspirate http://sourceforge.net/tracker/?func=detail&aid=2945564&group_id=177891&atid=886178
- cloacal sample: https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2971560&group_id=177891

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Revision: 2801
          http://obi.svn.sourceforge.net/obi/?rev=2801&view=rev
Author:   mcourtot
Date:     2010-03-17 23:47:24 +0000 (Wed, 17 Mar 2010)

Log Message:
-----------
cloacal sample: live birds -> organism as per HP's comment

Modified Paths:
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Revision: 2802
          http://obi.svn.sourceforge.net/obi/?rev=2802&view=rev
Author:   jzheng24
Date:     2010-03-18 14:27:36 +0000 (Thu, 18 Mar 2010)

Log Message:
-----------
Assign ids to new added terms 

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Revision: 2803
          http://obi.svn.sourceforge.net/obi/?rev=2803&view=rev
Author:   mcourtot
Date:     2010-03-18 17:20:47 +0000 (Thu, 18 Mar 2010)

Log Message:
-----------
modified header - see rev 2749 log

Revision Links:
--------------
    http://obi.svn.sourceforge.net/obi/?rev=2749&view=rev

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Revision: 2807
          http://obi.svn.sourceforge.net/obi/?rev=2807&view=rev
Author:   bjoernpeters
Date:     2010-03-18 22:56:15 +0000 (Thu, 18 Mar 2010)

Log Message:
-----------
added FACS assay for cell:cell conjugate detection, and several alternate terms. 

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Revision: 2815
          http://obi.svn.sourceforge.net/obi/?rev=2815&view=rev
Author:   bjoernpeters
Date:     2010-03-21 16:33:44 +0000 (Sun, 21 Mar 2010)

Log Message:
-----------
Added Eagle-i instrument requests, tracker 2921944. Also added 'container' as a defined class, and made modifications to restrictions to facilitate correct classification of 'device' terms. 

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Revision: 2816
          http://obi.svn.sourceforge.net/obi/?rev=2816&view=rev
Author:   bjoernpeters
Date:     2010-03-21 17:07:08 +0000 (Sun, 21 Mar 2010)

Log Message:
-----------
corrected logical definition of immunization (which classified as a material entity), and updated textual definition and example. 

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Revision: 2817
          http://obi.svn.sourceforge.net/obi/?rev=2817&view=rev
Author:   bjoernpeters
Date:     2010-03-21 17:39:24 +0000 (Sun, 21 Mar 2010)

Log Message:
-----------
Updated blood plasma to blood plasma specimen, and added editor note. 

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Revision: 2818
          http://obi.svn.sourceforge.net/obi/?rev=2818&view=rev
Author:   bjoernpeters
Date:     2010-03-21 18:08:28 +0000 (Sun, 21 Mar 2010)

Log Message:
-----------
Based on tracker 2892240, I made parthood relations between the 'artifically induced reverse transcription', reverse transcription PCR, and real time reverse transcription PCR assay. 

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Revision: 2819
          http://obi.svn.sourceforge.net/obi/?rev=2819&view=rev
Author:   bjoernpeters
Date:     2010-03-21 19:16:15 +0000 (Sun, 21 Mar 2010)

Log Message:
-----------
clarified the different uses of 'host' and 'host role' in the file, to distinguish the host of an immune response and the host of a symbiont. 

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Revision: 2820
          http://obi.svn.sourceforge.net/obi/?rev=2820&view=rev
Author:   bjoernpeters
Date:     2010-03-21 19:30:36 +0000 (Sun, 21 Mar 2010)

Log Message:
-----------
obsoleted 'sample population' as suggested in tracker 2822973. Notification to list was send out. Will revert if objections are made. 

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Revision: 2821
          http://obi.svn.sourceforge.net/obi/?rev=2821&view=rev
Author:   bjoernpeters
Date:     2010-03-21 19:53:46 +0000 (Sun, 21 Mar 2010)

Log Message:
-----------
deprecated 'fragment derived from protein' as announced on list. 

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Revision: 2822
          http://obi.svn.sourceforge.net/obi/?rev=2822&view=rev
Author:   bjoernpeters
Date:     2010-03-22 06:47:11 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
removed asserted owl:thing parents (protege artifact) from several classes

Modified Paths:
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Revision: 2823
          http://obi.svn.sourceforge.net/obi/?rev=2823&view=rev
Author:   bjoernpeters
Date:     2010-03-22 06:50:50 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
modified 'pool of specimen' to be a specimen itself. 

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Revision: 2824
          http://obi.svn.sourceforge.net/obi/?rev=2824&view=rev
Author:   bjoernpeters
Date:     2010-03-22 07:18:34 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
carrier role renamed to 'immune epitope carrier role' to be more specific as suggested in tracker. 
antigen role: set restriction to be 'only' but not 'some realized (tracker item from JF).  

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Revision: 2825
          http://obi.svn.sourceforge.net/obi/?rev=2825&view=rev
Author:   bjoernpeters
Date:     2010-03-22 07:30:08 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
modified label from 'pooling entities of organismal origin' to 'pooling specimens' based on Jie's concern and to be inline with the rest of OBI. 

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Revision: 2828
          http://obi.svn.sourceforge.net/obi/?rev=2828&view=rev
Author:   parkinso
Date:     2010-03-22 16:50:57 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
actioned role def cleanup https://sourceforge.net/tracker/?func=detail&aid=2906031&group_id=177891&atid=886178

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Revision: 2829
          http://obi.svn.sourceforge.net/obi/?rev=2829&view=rev
Author:   parkinso
Date:     2010-03-22 17:19:15 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
actioned https://sourceforge.net/tracker/?func=detail&aid=2906009&group_id=177891&atid=886178

Modified Paths:
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Revision: 2830
          http://obi.svn.sourceforge.net/obi/?rev=2830&view=rev
Author:   parkinso
Date:     2010-03-22 17:24:21 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
actioned https://sourceforge.net/tracker/?func=detail&aid=2902515&group_id=177891&atid=886178

Modified Paths:
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Revision: 2831
          http://obi.svn.sourceforge.net/obi/?rev=2831&view=rev
Author:   parkinso
Date:     2010-03-22 17:34:41 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
actioned https://sourceforge.net/tracker/?func=detail&aid=2906036&group_id=177891&atid=886178 and positive reference substance role

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Revision: 2832
          http://obi.svn.sourceforge.net/obi/?rev=2832&view=rev
Author:   parkinso
Date:     2010-03-22 17:57:34 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
actioned https://sourceforge.net/tracker/index.php?func=detail&aid=2906024&group_id=177891&atid=886178

Modified Paths:
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Revision: 2833
          http://obi.svn.sourceforge.net/obi/?rev=2833&view=rev
Author:   parkinso
Date:     2010-03-22 18:08:45 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
https://sourceforge.net/tracker/index.php?func=detail&aid=2902583&group_id=177891&atid=886178

Modified Paths:
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Revision: 2834
          http://obi.svn.sourceforge.net/obi/?rev=2834&view=rev
Author:   parkinso
Date:     2010-03-22 18:10:42 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
https://sourceforge.net/tracker/index.php?func=detail&aid=2902583&group_id=177891&atid=886178

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 2835
          http://obi.svn.sourceforge.net/obi/?rev=2835&view=rev
Author:   parkinso
Date:     2010-03-22 18:16:18 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
https://sourceforge.net/tracker/?func=detail&aid=2902564&group_id=177891&atid=886178

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 2836
          http://obi.svn.sourceforge.net/obi/?rev=2836&view=rev
Author:   parkinso
Date:     2010-03-22 18:35:14 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
https://sourceforge.net/tracker/?func=detail&aid=2902562&group_id=177891&atid=886178

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 2837
          http://obi.svn.sourceforge.net/obi/?rev=2837&view=rev
Author:   bjoernpeters
Date:     2010-03-22 20:38:33 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
partial implementation of 'services'. Need further work

Modified Paths:
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Revision: 2838
          http://obi.svn.sourceforge.net/obi/?rev=2838&view=rev
Author:   parkinso
Date:     2010-03-22 21:00:57 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2887909&group_id=177891 and https://sourceforge.net/tracker/index.php?func=detail&aid=2902524&group_id=177891&atid=886178

Modified Paths:
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Revision: 2839
          http://obi.svn.sourceforge.net/obi/?rev=2839&view=rev
Author:   parkinso
Date:     2010-03-22 21:18:24 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
roles fix

Modified Paths:
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Revision: 2844
          http://obi.svn.sourceforge.net/obi/?rev=2844&view=rev
Author:   parkinso
Date:     2010-03-22 23:09:54 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
https://sourceforge.net/tracker/?func=detail&aid=2906040&group_id=177891&atid=886178

Modified Paths:
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Revision: 2845
          http://obi.svn.sourceforge.net/obi/?rev=2845&view=rev
Author:   parkinso
Date:     2010-03-22 23:12:51 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
https://sourceforge.net/tracker/index.php?func=detail&aid=2906038&group_id=177891&atid=886178

Modified Paths:
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Revision: 2846
          http://obi.svn.sourceforge.net/obi/?rev=2846&view=rev
Author:   parkinso
Date:     2010-03-22 23:19:02 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
https://sourceforge.net/tracker/?func=detail&atid=886178&aid=2906019&group_id=177891

Modified Paths:
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Revision: 2847
          http://obi.svn.sourceforge.net/obi/?rev=2847&view=rev
Author:   parkinso
Date:     2010-03-22 23:22:13 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
https://sourceforge.net/tracker/index.php?func=detail&aid=2906015&group_id=177891&atid=886178

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 2848
          http://obi.svn.sourceforge.net/obi/?rev=2848&view=rev
Author:   parkinso
Date:     2010-03-22 23:31:18 +0000 (Mon, 22 Mar 2010)

Log Message:
-----------
https://sourceforge.net/tracker/?func=detail&aid=2906012&group_id=177891&atid=886178

Modified Paths:
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Revision: 2850
          http://obi.svn.sourceforge.net/obi/?rev=2850&view=rev
Author:   bjoernpeters
Date:     2010-03-23 17:03:14 +0000 (Tue, 23 Mar 2010)

Log Message:
-----------
Edingburgh handedness measurement datum on scoring scale

Modified Paths:
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Revision: 2857
          http://obi.svn.sourceforge.net/obi/?rev=2857&view=rev
Author:   bjoernpeters
Date:     2010-03-23 21:54:06 +0000 (Tue, 23 Mar 2010)

Log Message:
-----------
adding instrument functions; removing functions of parts. 

Modified Paths:
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Revision: 2858
          http://obi.svn.sourceforge.net/obi/?rev=2858&view=rev
Author:   mcourtot
Date:     2010-03-23 23:31:35 +0000 (Tue, 23 Mar 2010)

Log Message:
-----------
adding in intradermous injection, oral administration, intramuscular injection, intravenous injection and corresponding material entities to be replaced by FMA terms

Modified Paths:
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Revision: 2859
          http://obi.svn.sourceforge.net/obi/?rev=2859&view=rev
Author:   mcourtot
Date:     2010-03-23 23:58:45 +0000 (Tue, 23 Mar 2010)

Log Message:
-----------
added dose and dose specification as per VO use cases

Modified Paths:
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Revision: 2863
          http://obi.svn.sourceforge.net/obi/?rev=2863&view=rev
Author:   mcourtot
Date:     2010-03-24 00:19:18 +0000 (Wed, 24 Mar 2010)

Log Message:
-----------
replaced FMA terms hypodermis and dermis needed for VO use case

Modified Paths:
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Revision: 2865
          http://obi.svn.sourceforge.net/obi/?rev=2865&view=rev
Author:   mcourtot
Date:     2010-03-24 00:31:11 +0000 (Wed, 24 Mar 2010)

Log Message:
-----------
replaced vein by FMA vein

Modified Paths:
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Revision: 2866
          http://obi.svn.sourceforge.net/obi/?rev=2866&view=rev
Author:   mcourtot
Date:     2010-03-24 00:32:05 +0000 (Wed, 24 Mar 2010)

Log Message:
-----------
replaced last FMA term

Modified Paths:
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Revision: 2867
          http://obi.svn.sourceforge.net/obi/?rev=2867&view=rev
Author:   ctorniai
Date:     2010-03-24 05:23:59 +0000 (Wed, 24 Mar 2010)

Log Message:
-----------
Typo clean up form eagle-i terms

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Revision: 2869
          http://obi.svn.sourceforge.net/obi/?rev=2869&view=rev
Author:   parkinso
Date:     2010-03-24 22:50:06 +0000 (Wed, 24 Mar 2010)

Log Message:
-----------
incorrect equivalence on training fixed.

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Revision: 2870
          http://obi.svn.sourceforge.net/obi/?rev=2870&view=rev
Author:   bjoernpeters
Date:     2010-03-24 23:11:20 +0000 (Wed, 24 Mar 2010)

Log Message:
-----------


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Revision: 2872
          http://obi.svn.sourceforge.net/obi/?rev=2872&view=rev
Author:   bjoernpeters
Date:     2010-03-25 01:20:07 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
worked on study designs and attempted logical definitions

Modified Paths:
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Revision: 2873
          http://obi.svn.sourceforge.net/obi/?rev=2873&view=rev
Author:   parkinso
Date:     2010-03-25 17:14:50 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
roles review during meeting

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Revision: 2874
          http://obi.svn.sourceforge.net/obi/?rev=2874&view=rev
Author:   parkinso
Date:     2010-03-25 17:32:25 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
added logical def on trial statistician

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Revision: 2875
          http://obi.svn.sourceforge.net/obi/?rev=2875&view=rev
Author:   parkinso
Date:     2010-03-25 17:46:25 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
https://sourceforge.net/tracker/?func=detail&aid=2902514&group_id=177891&atid=886178

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Revision: 2876
          http://obi.svn.sourceforge.net/obi/?rev=2876&view=rev
Author:   parkinso
Date:     2010-03-25 18:09:44 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
deprecated blinded medication role.

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Revision: 2877
          http://obi.svn.sourceforge.net/obi/?rev=2877&view=rev
Author:   parkinso
Date:     2010-03-25 19:05:13 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
working through services and roles 

Modified Paths:
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Revision: 2878
          http://obi.svn.sourceforge.net/obi/?rev=2878&view=rev
Author:   parkinso
Date:     2010-03-25 19:26:05 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
still working through the services

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Revision: 2879
          http://obi.svn.sourceforge.net/obi/?rev=2879&view=rev
Author:   parkinso
Date:     2010-03-25 19:44:49 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
added defs to service provider roles

Modified Paths:
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Revision: 2880
          http://obi.svn.sourceforge.net/obi/?rev=2880&view=rev
Author:   parkinso
Date:     2010-03-25 19:48:14 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
added logical restriction to training role

Modified Paths:
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Revision: 2881
          http://obi.svn.sourceforge.net/obi/?rev=2881&view=rev
Author:   parkinso
Date:     2010-03-25 21:33:32 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
added usage examples for service provider roles

Modified Paths:
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Revision: 2882
          http://obi.svn.sourceforge.net/obi/?rev=2882&view=rev
Author:   parkinso
Date:     2010-03-25 21:41:15 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
deleted two temp device subclasses

Modified Paths:
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Revision: 2883
          http://obi.svn.sourceforge.net/obi/?rev=2883&view=rev
Author:   parkinso
Date:     2010-03-25 22:18:51 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
material sep device added

Modified Paths:
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Revision: 2884
          http://obi.svn.sourceforge.net/obi/?rev=2884&view=rev
Author:   parkinso
Date:     2010-03-25 23:20:10 +0000 (Thu, 25 Mar 2010)

Log Message:
-----------
asserted many processed materials under device and classify by function. yeay.

Modified Paths:
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Revision: 2885
          http://obi.svn.sourceforge.net/obi/?rev=2885&view=rev
Author:   mcourtot
Date:     2010-03-28 20:28:32 +0000 (Sun, 28 Mar 2010)

Log Message:
-----------
restored intradermous injection, oral administration, intramuscular injection, intravenous injection

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 2886
          http://obi.svn.sourceforge.net/obi/?rev=2886&view=rev
Author:   mcourtot
Date:     2010-03-29 17:24:33 +0000 (Mon, 29 Mar 2010)

Log Message:
-----------
restored intranasal administration, subcutaneous administration, dose, dose specification
classify in 582 sec in P3.4 and pellet 1.5.2

Modified Paths:
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Revision: 2889
          http://obi.svn.sourceforge.net/obi/?rev=2889&view=rev
Author:   jamesmalone
Date:     2010-03-30 10:45:14 +0000 (Tue, 30 Mar 2010)

Log Message:
-----------
fix to Edingburgh Handedness -> Edinburgh
completed tracker item 2961463 for specimen

Modified Paths:
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Revision: 2890
          http://obi.svn.sourceforge.net/obi/?rev=2890&view=rev
Author:   jamesmalone
Date:     2010-03-30 11:17:42 +0000 (Tue, 30 Mar 2010)

Log Message:
-----------
completed ticket for t-test
added anova - submitting f-value request to iao

Modified Paths:
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Revision: 2892
          http://obi.svn.sourceforge.net/obi/?rev=2892&view=rev
Author:   jzheng24
Date:     2010-03-30 18:11:44 +0000 (Tue, 30 Mar 2010)

Log Message:
-----------
Add restriction has role some 'label role' to some imported ChEBI terms. Details check 
https://sourceforge.net/tracker/?func=detail&aid=2955065&group_id=177891&atid=886178

Modified Paths:
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Revision: 2894
          http://obi.svn.sourceforge.net/obi/?rev=2894&view=rev
Author:   jzheng24
Date:     2010-03-30 22:49:05 +0000 (Tue, 30 Mar 2010)

Log Message:
-----------
add some storage processes and their related specimen requested by MO group. Details please check:
https://sourceforge.net/tracker/?func=detail&aid=2955131&group_id=177891&atid=886178

Modified Paths:
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Revision: 2895
          http://obi.svn.sourceforge.net/obi/?rev=2895&view=rev
Author:   jzheng24
Date:     2010-03-30 23:51:06 +0000 (Tue, 30 Mar 2010)

Log Message:
-----------
Assign IDs to new added classes

Modified Paths:
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Revision: 2897
          http://obi.svn.sourceforge.net/obi/?rev=2897&view=rev
Author:   jzheng24
Date:     2010-03-31 04:30:42 +0000 (Wed, 31 Mar 2010)

Log Message:
-----------
revision 2894 with instances added back

Revision Links:
--------------
    http://obi.svn.sourceforge.net/obi/?rev=2894&view=rev

Modified Paths:
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Revision: 2898
          http://obi.svn.sourceforge.net/obi/?rev=2898&view=rev
Author:   jzheng24
Date:     2010-03-31 04:57:28 +0000 (Wed, 31 Mar 2010)

Log Message:
-----------
new ids are assigned to new added classes

Modified Paths:
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Revision: 2899
          http://obi.svn.sourceforge.net/obi/?rev=2899&view=rev
Author:   alanr
Date:     2010-03-31 05:16:18 +0000 (Wed, 31 Mar 2010)

Log Message:
-----------
remove duplicate obiinowl namespace decl

Modified Paths:
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Revision: 2900
          http://obi.svn.sourceforge.net/obi/?rev=2900&view=rev
Author:   alanr
Date:     2010-03-31 05:26:51 +0000 (Wed, 31 Mar 2010)

Log Message:
-----------
what was I thinking

Modified Paths:
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Revision: 2901
          http://obi.svn.sourceforge.net/obi/?rev=2901&view=rev
Author:   alanr
Date:     2010-03-31 06:01:35 +0000 (Wed, 31 Mar 2010)

Log Message:
-----------
remove inverse of has category label

Modified Paths:
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Revision: 2906
          http://obi.svn.sourceforge.net/obi/?rev=2906&view=rev
Author:   alanr
Date:     2010-04-02 03:17:39 +0000 (Fri, 02 Apr 2010)

Log Message:
-----------
has coordinate unit label -> has category label in categorical measurement datum.

Modified Paths:
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Revision: 2909
          http://obi.svn.sourceforge.net/obi/?rev=2909&view=rev
Author:   alanr
Date:     2010-04-14 02:59:25 +0000 (Wed, 14 Apr 2010)

Log Message:
-----------
fix misused alternative term tags. remove the only two that were there, as property has been dropped

Modified Paths:
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Revision: 2911
          http://obi.svn.sourceforge.net/obi/?rev=2911&view=rev
Author:   alanr
Date:     2010-04-14 16:08:32 +0000 (Wed, 14 Apr 2010)

Log Message:
-----------
s/is member of/is member of organization/

Modified Paths:
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Revision: 2919
          http://obi.svn.sourceforge.net/obi/?rev=2919&view=rev
Author:   parkinso
Date:     2010-04-19 17:53:57 +0000 (Mon, 19 Apr 2010)

Log Message:
-----------
edits made in phone call, fix to equivalence on training process and sequencing training process, minor edit to devices clases, editor notes mainly

Modified Paths:
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Revision: 2922
          http://obi.svn.sourceforge.net/obi/?rev=2922&view=rev
Author:   parkinso
Date:     2010-04-21 17:13:47 +0000 (Wed, 21 Apr 2010)

Log Message:
-----------
commit after call, more work on device, logical def added, not nec+suf as additional processed materials classify under device in this case - need a better def of device, or modify some defs in proc. material

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Revision: 2923
          http://obi.svn.sourceforge.net/obi/?rev=2923&view=rev
Author:   jzheng24
Date:     2010-04-22 17:49:18 +0000 (Thu, 22 Apr 2010)

Log Message:
-----------
change restrictions of some specimen classes (fresh specimen, frozen specimen etc., storage process related terms), not assert them as a specimen

Modified Paths:
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Revision: 2924
          http://obi.svn.sourceforge.net/obi/?rev=2924&view=rev
Author:   parkinso
Date:     2010-04-23 12:51:39 +0000 (Fri, 23 Apr 2010)

Log Message:
-----------
Added device subclasses and made NMR parts parts-of NMT instrument and added reciprocal has-parts for NMR instrument.

Modified Paths:
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Revision: 2925
          http://obi.svn.sourceforge.net/obi/?rev=2925&view=rev
Author:   jzheng24
Date:     2010-04-26 17:18:17 +0000 (Mon, 26 Apr 2010)

Log Message:
-----------
edit polyacrylamide gel, details check tracker
https://sourceforge.net/tracker/index.php?func=detail&aid=2992356&group_id=177891&atid=886178
modify logical definition of 'NMR probe' and 'plate loader'

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Revision: 2928
          http://obi.svn.sourceforge.net/obi/?rev=2928&view=rev
Author:   ctorniai
Date:     2010-04-30 15:11:58 +0000 (Fri, 30 Apr 2010)

Log Message:
-----------
Corrected misspell in editor preferred term for:
gas laser and extra cellular electrophysiology

Modified Paths:
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Revision: 2929
          http://obi.svn.sourceforge.net/obi/?rev=2929&view=rev
Author:   jzheng24
Date:     2010-05-04 22:30:57 +0000 (Tue, 04 May 2010)

Log Message:
-----------
deprecate 'platform'
minor modification on textual definition of some terms

Modified Paths:
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Revision: 2953
          http://obi.svn.sourceforge.net/obi/?rev=2953&view=rev
Author:   parkinso
Date:     2010-05-19 20:34:33 +0000 (Wed, 19 May 2010)

Log Message:
-----------
added logical def to vibrotome

Modified Paths:
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Revision: 2954
          http://obi.svn.sourceforge.net/obi/?rev=2954&view=rev
Author:   parkinso
Date:     2010-05-24 16:58:51 +0000 (Mon, 24 May 2010)

Log Message:
-----------
added meta data to device and perturbational device

Modified Paths:
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Revision: 2958
          http://obi.svn.sourceforge.net/obi/?rev=2958&view=rev
Author:   parkinso
Date:     2010-05-26 15:53:44 +0000 (Wed, 26 May 2010)

Log Message:
-----------
added more functions to devices. not reasoned

Modified Paths:
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Revision: 2959
          http://obi.svn.sourceforge.net/obi/?rev=2959&view=rev
Author:   jzheng24
Date:     2010-05-27 00:02:39 +0000 (Thu, 27 May 2010)

Log Message:
-----------
Add three planned process classes. Details here
https://sourceforge.net/tracker/index.php?func=detail&aid=3007047&group_id=177891&atid=886178

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Revision: 2965
          http://obi.svn.sourceforge.net/obi/?rev=2965&view=rev
Author:   jzheng24
Date:     2010-05-31 00:11:22 +0000 (Mon, 31 May 2010)

Log Message:
-----------
add new term 'nucleic acid extract'

Modified Paths:
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Revision: 2971
          http://obi.svn.sourceforge.net/obi/?rev=2971&view=rev
Author:   p_rocca_serra
Date:     2010-06-05 09:44:37 +0000 (Sat, 05 Jun 2010)

Log Message:
-----------
creation of 21 assays for RNA + 2 defined classes to allow distinguishing assays by chemical probing and assays by enzymatic probing: need to review definition of bisulphite sequencing as it classifies under one of the those: obi.owl classifies under 250 sec before and after changes

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Revision: 2972
          http://obi.svn.sourceforge.net/obi/?rev=2972&view=rev
Author:   p_rocca_serra
Date:     2010-06-05 10:21:50 +0000 (Sat, 05 Jun 2010)

Log Message:
-----------
adding synonym to several SNRMA assays, fix to restriction so bisulphite sequencing no longer classifies under mapping structure assay using chemical probe, adding a placeholder for gene dosage test:OBI tracker ID: 3011558, reasoning OK

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Revision: 2974
          http://obi.svn.sourceforge.net/obi/?rev=2974&view=rev
Author:   p_rocca_serra
Date:     2010-06-07 07:20:20 +0000 (Mon, 07 Jun 2010)

Log Message:
-----------
minor fix to set restriction on right nuclease one of the newly added assays, reasoning OK

Modified Paths:
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Revision: 2975
          http://obi.svn.sourceforge.net/obi/?rev=2975&view=rev
Author:   jzheng24
Date:     2010-06-07 23:38:34 +0000 (Mon, 07 Jun 2010)

Log Message:
-----------
assign ids to new added terms

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Revision: 3000
          http://obi.svn.sourceforge.net/obi/?rev=3000&view=rev
Author:   p_rocca_serra
Date:     2010-06-13 14:20:19 +0000 (Sun, 13 Jun 2010)

Log Message:
-----------
adding inline probing and Ruthenium assay

Modified Paths:
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Revision: 3005
          http://obi.svn.sourceforge.net/obi/?rev=3005&view=rev
Author:   parkinso
Date:     2010-06-16 16:23:43 +0000 (Wed, 16 Jun 2010)

Log Message:
-----------
functions added for eagle-i instruments after call. HP

Modified Paths:
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Revision: 3007
          http://obi.svn.sourceforge.net/obi/?rev=3007&view=rev
Author:   alanr
Date:     2010-06-28 17:52:31 +0000 (Mon, 28 Jun 2010)

Log Message:
-----------
after dev call checkin see http://groups.google.com/group/obi-developer/browse_thread/thread/ca9f9ac5f81f36ad and http://groups.google.com/group/obi-developer/browse_thread/thread/587523af2cd04ad2

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Revision: 3009
          http://obi.svn.sourceforge.net/obi/?rev=3009&view=rev
Author:   jzheng24
Date:     2010-07-06 21:17:28 +0000 (Tue, 06 Jul 2010)

Log Message:
-----------
modify restrictions of some classes to fix inconsistency problem
Need to work on MeDIP-SEQ assay later. Issue posted on the page:
https://sourceforge.net/tracker/?func=detail&aid=3026017&group_id=177891&atid=886178

Modified Paths:
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Revision: 3010
          http://obi.svn.sourceforge.net/obi/?rev=3010&view=rev
Author:   jzheng24
Date:     2010-07-06 22:00:21 +0000 (Tue, 06 Jul 2010)

Log Message:
-----------
assign new ids

Modified Paths:
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Revision: 3012
          http://obi.svn.sourceforge.net/obi/?rev=3012&view=rev
Author:   jzheng24
Date:     2010-07-13 13:47:49 +0000 (Tue, 13 Jul 2010)

Log Message:
-----------
modify the restriction of 'chromatography'
add 'investigator' as alternative term of 'investigation agent role'

Modified Paths:
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Revision: 3016
          http://obi.svn.sourceforge.net/obi/?rev=3016&view=rev
Author:   jzheng24
Date:     2010-07-23 19:10:37 +0000 (Fri, 23 Jul 2010)

Log Message:
-----------
add alternative term to 'reporting party role'
move some storage process related specimen under _defined_material to avoid adding disjoint restrictions during release process. No change on 'fresh specimen' which defined as not specified output of storage process. need work out in the future 

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Revision: 3018
          http://obi.svn.sourceforge.net/obi/?rev=3018&view=rev
Author:   jzheng24
Date:     2010-07-26 17:10:58 +0000 (Mon, 26 Jul 2010)

Log Message:
-----------
Add value to 'has curation status' annotation property to the terms with property is empty

Modified Paths:
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Revision: 3024
          http://obi.svn.sourceforge.net/obi/?rev=3024&view=rev
Author:   jzheng24
Date:     2010-08-08 06:55:28 +0000 (Sun, 08 Aug 2010)

Log Message:
-----------
obsolete several terms
add curation status to OBI classes with empty curation status values 

Modified Paths:
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Revision: 3025
          http://obi.svn.sourceforge.net/obi/?rev=3025&view=rev
Author:   jzheng24
Date:     2010-08-09 22:26:50 +0000 (Mon, 09 Aug 2010)

Log Message:
-----------
Review the OBI classes with curation status which is uncurated and set to 'metadata complete' or 'metadata incomplete' status if possible

Uniform the definition format as BFO suggested if possible

Modified Paths:
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Revision: 3026
          http://obi.svn.sourceforge.net/obi/?rev=3026&view=rev
Author:   parkinso
Date:     2010-08-16 17:23:50 +0000 (Mon, 16 Aug 2010)

Log Message:
-----------
completed meta data for donor. def modified to remove ? and made more generic

Modified Paths:
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Revision: 3027
          http://obi.svn.sourceforge.net/obi/?rev=3027&view=rev
Author:   parkinso
Date:     2010-08-16 17:27:05 +0000 (Mon, 16 Aug 2010)

Log Message:
-----------
added meta data to environmental control device

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Revision: 3028
          http://obi.svn.sourceforge.net/obi/?rev=3028&view=rev
Author:   parkinso
Date:     2010-08-16 17:35:58 +0000 (Mon, 16 Aug 2010)

Log Message:
-----------
added meta data for handedness assay

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Revision: 3029
          http://obi.svn.sourceforge.net/obi/?rev=3029&view=rev
Author:   parkinso
Date:     2010-08-16 17:44:35 +0000 (Mon, 16 Aug 2010)

Log Message:
-----------
added meta data to material comb function

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Revision: 3030
          http://obi.svn.sourceforge.net/obi/?rev=3030&view=rev
Author:   parkinso
Date:     2010-08-16 17:52:27 +0000 (Mon, 16 Aug 2010)

Log Message:
-----------
training objective added meta data, service provision objective. same.

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Revision: 3031
          http://obi.svn.sourceforge.net/obi/?rev=3031&view=rev
Author:   parkinso
Date:     2010-08-16 17:56:10 +0000 (Mon, 16 Aug 2010)

Log Message:
-----------
vaccine prep added meta data

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Revision: 3033
          http://obi.svn.sourceforge.net/obi/?rev=3033&view=rev
Author:   jzheng24
Date:     2010-08-17 21:53:07 +0000 (Tue, 17 Aug 2010)

Log Message:
-----------
fix some terms with different label and editor preferred terms

Modified Paths:
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Revision: 3037
          http://obi.svn.sourceforge.net/obi/?rev=3037&view=rev
Author:   parkinso
Date:     2010-08-18 09:00:45 +0000 (Wed, 18 Aug 2010)

Log Message:
-----------
fixed pref term/label inconsistencies for 3 terms 'survival analysis objective '  'survival analysis'
blood plasma specimen'  'blood plasma'
centroid mass spectrum'  'centroid mass spectrum calculation'

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Revision: 3038
          http://obi.svn.sourceforge.net/obi/?rev=3038&view=rev
Author:   jzheng24
Date:     2010-08-18 15:05:44 +0000 (Wed, 18 Aug 2010)

Log Message:
-----------
merged device terms provided by eagle-i. 94 classes were added.

Modified Paths:
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Revision: 3039
          http://obi.svn.sourceforge.net/obi/?rev=3039&view=rev
Author:   alanr
Date:     2010-08-18 20:59:42 +0000 (Wed, 18 Aug 2010)

Log Message:
-----------
 -m "removed editor preferred labels that were blank by getting rid of lines
 
"<obo:IAO_0000111 rdf:datatype="http://www.w3.org/2001/XMLSchema#string"></obo:IAO_0000111>"

 and

 "<obo:IAO_0000111 xml:lang="en"></obo:IAO_0000111>".

 Then duplicated labels into editor preferred labels where the latter were by running (in lsw2)

 (with-ontology foo (:collecting t) 
	     ((loop for (term label) in (sparql '(:select (?term ?label ?preferred) () 
		   (:optional (?term !rdfs:label ?label))
		   (:optional (?term !obi:IAO_0000111 ?preferred))
		   (:filter
		    (and 
		     (regex (str ?term) "(?i).*obi.*")
		     (or (bound ?label) (bound ?preferred))
		     (or (equal (str ?label) "") (not (bound ?label))
			 (equal (str ?preferred) "") (not (bound ?preferred))))
		    ))
		 :kb kb :use-reasoner :none  :values t)
		   do (as `(annotation-assertion !obi:IAO_0000111 ,term ,label))))
	      (princ (to-owl-syntax foo :rdfxml)) 
	      nil)

and then pasting in the RDF other than the surrounding <RDF> tags.

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Revision: 3040
          http://obi.svn.sourceforge.net/obi/?rev=3040&view=rev
Author:   jzheng24
Date:     2010-08-19 16:07:04 +0000 (Thu, 19 Aug 2010)

Log Message:
-----------
Fix inconsistent label and editor preferred term, copy the value of preferred term to alternative term and label to preferred term

obo:OBI_0001015 "DMS structure mapping assay" "single nucleotide resolution mapping assay using DMS probe"
obo:OBI_0001030 "RNASE T1 structure mapping assay" "single nucleotide resolution mapping assay using RNAse T1"
obo:OBI_0001006 "CMCT structure mapping assay" "single nucleotide resolution mapping assay using CMCT probe"
obo:OBI_0001029 "OH-radical structure mapping assay" "single nucleotide resolution mapping assay using OH-radical probe"
obo:OBI_0001023 "Fe-BABE RNA structure mapping assay" "single nucleotide resolution mapping assay using Fe-BABE probe"
obo:OBI_0001018 "Rhodium DNA structure mapping assay" "single nucleotide resolution mapping assay using Rhodium probe"
obo:obi.owl#Class_53 "gel electrophoresis system" "electrophoresis system"
obo:OBI_0001027 "Terbium RNA structure mapping assay" "single nucleotide resolution mapping assay using Terbium probe"
obo:OBI_0001020 "Lead structure mapping assay" "single nucleotide resolution mapping assay using Lead probe"
obo:OBI_0001005 "RNASE CL3 structure mapping assay" "single nucleotide resolution mapping assay using RNAse CL3"
obo:OBI_0001026 "NMIA RNA structure mapping assay" "single nucleotide resolution mapping assay using NMIA probe"
obo:OBI_0001016 "DNASE 1 structure mapping assay" "single nucleotide resolution mapping assay using DNAse I"
obo:OBI_0000520 "clinical chemistry assay" "detection of analyte in blood sample"
obo:OBI_0001021 "RNASE T2 structure mapping assay" "single nucleotide resolution mapping assay using RNAse T2"
obo:OBI_0001011 "ENU structure mapping assay" "single nucleotide resolution mapping assay using ENU probe"
obo:OBI_0001035 "Nuclease S1 structure mapping assay" "single nucleotide resolution mapping assay using Nuclease S1"
obo:OBI_0001024 "RNASE U2 structure mapping assay" "single nucleotide resolution mapping assay using RNAse U2"
obo:OBI_0001008 "MPE-Fe(II) structure mapping assay" "single nucleotide resolution mapping assay using Fe-MP probe"
obo:OBI_0001019 "RNA ADA I RNA structure mapping assay" "single nucleotide resolution mapping assay using RNA adenosine deaminase I"
obo:OBI_0001012 "RNASE V1 structure mapping assay" "single nucleotide resolution mapping assay using RNAse V1"

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Revision: 3041
          http://obi.svn.sourceforge.net/obi/?rev=3041&view=rev
Author:   jzheng24
Date:     2010-08-19 16:33:55 +0000 (Thu, 19 Aug 2010)

Log Message:
-----------
Lost id of 'biological replicate role' when fixed the conflict of label and editor preferred term in revision 3033
Get the id back, http://purl.obolibrary.org/obo/OBI_0000198
rather than http://purl.obolibrary.org/obo/obi-edit/d

Revision Links:
--------------
    http://obi.svn.sourceforge.net/obi/?rev=3033&view=rev

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Revision: 3042
          http://obi.svn.sourceforge.net/obi/?rev=3042&view=rev
Author:   jzheng24
Date:     2010-08-19 17:15:22 +0000 (Thu, 19 Aug 2010)

Log Message:
-----------
assign IDs to the device terms (total of 94 classes)

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Revision: 3052
          http://obi.svn.sourceforge.net/obi/?rev=3052&view=rev
Author:   bjoernpeters
Date:     2010-09-16 22:57:07 +0000 (Thu, 16 Sep 2010)

Log Message:
-----------
added binding assay, children, and binding children. Very much work in progress, and some problems with working with Protege 4. 

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Revision: 3060
          http://obi.svn.sourceforge.net/obi/?rev=3060&view=rev
Author:   jzheng24
Date:     2010-10-13 16:09:04 +0000 (Wed, 13 Oct 2010)

Log Message:
-----------
Modify some/only used in the restrictions
- all 'is realized by' relations use 'only'
- all 'inheres_in' relations use 'some'

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Revision: 3061
          http://obi.svn.sourceforge.net/obi/?rev=3061&view=rev
Author:   jzheng24
Date:     2010-10-13 18:48:33 +0000 (Wed, 13 Oct 2010)

Log Message:
-----------
Deprecate OBI DNA ligase
Rename planned process OBI_0000907 supplies to supplying
Deleted the undefined and unused terms: OBI_1110121,OBI_0001009,OBI_0001025,OBI_0001051,OBI_0001069 

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Revision: 3062
          http://obi.svn.sourceforge.net/obi/?rev=3062&view=rev
Author:   jzheng24
Date:     2010-10-13 20:43:14 +0000 (Wed, 13 Oct 2010)

Log Message:
-----------
add/edit some labeled nucleic acid extract related OBI terms that requested by the MGED ontology

Modified Paths:
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Revision: 3064
          http://obi.svn.sourceforge.net/obi/?rev=3064&view=rev
Author:   jzheng24
Date:     2010-10-18 20:15:50 +0000 (Mon, 18 Oct 2010)

Log Message:
-----------
add 4 MO request terms (discussed on Oct 18, 2010 dev call):
individual organism identifier
array manufacturer role
dye swap quality control role
spike-in quality control role

add 'editor preferred term' and 'has curation status' property to 5 binding assay related terms for release

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Revision: 3066
          http://obi.svn.sourceforge.net/obi/?rev=3066&view=rev
Author:   jzheng24
Date:     2010-10-18 22:53:41 +0000 (Mon, 18 Oct 2010)

Log Message:
-----------
assign ids to new added terms
http://purl.obolibrary.org/obo/OBI_0001143  label: labeled nucleic acid extract
http://purl.obolibrary.org/obo/OBI_0001051  label: DNA extract
http://purl.obolibrary.org/obo/OBI_0001069  label: array manufacturer role
http://purl.obolibrary.org/obo/OBI_0001142  label: dye swap quality control role
http://purl.obolibrary.org/obo/OBI_0001140  label: spike-in quality control role
http://purl.obolibrary.org/obo/OBI_0001141  label: individual organism identifier
http://purl.obolibrary.org/obo/OBI_0001146  label: binding assay
http://purl.obolibrary.org/obo/OBI_0001009  label: binding detection assay
http://purl.obolibrary.org/obo/OBI_0001025  label: binding constant determination assay
http://purl.obolibrary.org/obo/OBI_0001145  label: binding characterization assay
http://purl.obolibrary.org/obo/OBI_0001144  label: binding constant

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Revision: 3070
          http://obi.svn.sourceforge.net/obi/?rev=3070&view=rev
Author:   jzheng24
Date:     2010-10-20 18:07:08 +0000 (Wed, 20 Oct 2010)

Log Message:
-----------
fix the restriction of 'array manufacturer role'

Modified Paths:
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Revision: 3072
          http://obi.svn.sourceforge.net/obi/?rev=3072&view=rev
Author:   jzheng24
Date:     2010-10-25 21:38:30 +0000 (Mon, 25 Oct 2010)

Log Message:
-----------
Add requested MO terms and their associated terms that discussed on Oct 25, 2010 dev call
cell culture expansion
gene knock in
gene knock out
induced mutation
chromosomal substitution
transfection
genetically modified material
genetic transformation objective

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Revision: 3073
          http://obi.svn.sourceforge.net/obi/?rev=3073&view=rev
Author:   jzheng24
Date:     2010-10-25 22:17:36 +0000 (Mon, 25 Oct 2010)

Log Message:
-----------
assigned ids to new added terms
http://purl.obolibrary.org/obo/OBI_0001147 label: cell culture expansion
http://purl.obolibrary.org/obo/OBI_0001149 label: gene knock in
http://purl.obolibrary.org/obo/OBI_0001148 label: gene knock out
http://purl.obolibrary.org/obo/OBI_0001150 label: chromosomal substitution
http://purl.obolibrary.org/obo/OBI_0001152 label: transfection
http://purl.obolibrary.org/obo/OBI_0001154 label: induced mutation
http://purl.obolibrary.org/obo/OBI_0001151 label: genetically modified material
http://purl.obolibrary.org/obo/OBI_0001153 label: genetic transformation objective

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Revision: 3074
          http://obi.svn.sourceforge.net/obi/?rev=3074&view=rev
Author:   jzheng24
Date:     2010-10-26 00:39:16 +0000 (Tue, 26 Oct 2010)

Log Message:
-----------
remove 290 obsolete OBI terms which were deprecated before Philly release (revision 2489)

Revision Links:
--------------
    http://obi.svn.sourceforge.net/obi/?rev=2489&view=rev

Modified Paths:
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Revision: 3075
          http://obi.svn.sourceforge.net/obi/?rev=3075&view=rev
Author:   jzheng24
Date:     2010-10-26 16:10:33 +0000 (Tue, 26 Oct 2010)

Log Message:
-----------
fix the noticed issue of fresh specimen and add needed disjoint restrictions of some specimens that added requested by MO

Modified Paths:
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Revision: 3080
          http://obi.svn.sourceforge.net/obi/?rev=3080&view=rev
Author:   bjoernpeters
Date:     2010-11-02 22:10:15 +0000 (Tue, 02 Nov 2010)

Log Message:
-----------
binding assays modeling - added definitions, added 3d structural coordinates as kind of output datum from crystallography. 

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Revision: 3081
          http://obi.svn.sourceforge.net/obi/?rev=3081&view=rev
Author:   jzheng24
Date:     2010-11-10 03:06:49 +0000 (Wed, 10 Nov 2010)

Log Message:
-----------
Four MO requested terms were added:
validation by real time PCR design
validation by reverse transcription PCR design
validation objective
reverse transcription polymerase chain reaction assay

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Revision: 3083
          http://obi.svn.sourceforge.net/obi/?rev=3083&view=rev
Author:   mcourtot
Date:     2010-11-18 19:22:05 +0000 (Thu, 18 Nov 2010)

Log Message:
-----------
added Melissa and Carlo as creators

Modified Paths:
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Revision: 3102
          http://obi.svn.sourceforge.net/obi/?rev=3102&view=rev
Author:   jzheng24
Date:     2010-12-07 00:51:13 +0000 (Tue, 07 Dec 2010)

Log Message:
-----------
Make modification according to the discussion on Nov 22, 2010 dev call
The changes are consistent to the 2010-10-26 Vancouver release RC2.

'activation'
- change status to uncurated,
- add editor note that this is too broad, and in GO scope anyway

'identification':
- Change status to uncurated;
- add editor note to say that specific identification objective should be used instead as necessary

'gene dosage assay'
 - add parent 'assay'

"image acquisition"
- remove 'digitized' from definition.
- Add examples: 'Taking a polaroid picture of a patients skin lesion'; 'Using a digital camera to take a picture of a gel'


'feature extraction'
- make child of data transformation'

"hemagglutination"
- change label to "induced hemagglutination",
- change definition to "The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances.",
- change parent to 'material processing'

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Revision: 3106
          http://obi.svn.sourceforge.net/obi/?rev=3106&view=rev
Author:   jzheng24
Date:     2010-12-10 21:28:17 +0000 (Fri, 10 Dec 2010)

Log Message:
-----------
Add 11 age measurement datum related terms (approved on Nov 15, 2010 dev call)

Modified Paths:
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Revision: 3107
          http://obi.svn.sourceforge.net/obi/?rev=3107&view=rev
Author:   jzheng24
Date:     2010-12-13 01:18:19 +0000 (Mon, 13 Dec 2010)

Log Message:
-----------
assign ids to the following terms
OBI_0001155  3D structural organization datum
OBI_0001156  age since planting measurement datum
OBI_0001157  age since hatching measurement datum
OBI_0001158  age measurement assay
OBI_0001159  age since egg laying measurement datum
OBI_0001160  assay validation objective
OBI_0001161  age since germination measurement datum
OBI_0001162  validation by reverse transcription PCR design
OBI_0001163  age since eclosion measurement datum
OBI_0001164  age since sowing measurement datum
OBI_0001165  age since coitus measurement datum
OBI_0001166  validation by real time PCR design
OBI_0001167  age measurement datum
OBI_0001168  age since fertilization measurement datum
OBI_0001169  age since birth measurement datum
OBI_0001170  reverse transcription polymerase chain reaction assay

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Revision: 3109
          http://obi.svn.sourceforge.net/obi/?rev=3109&view=rev
Author:   jzheng24
Date:     2010-12-13 18:53:27 +0000 (Mon, 13 Dec 2010)

Log Message:
-----------
add 'selectively maintained organism' and 'selective organism creation objective', discussed on Dec 13, 2010 dev call

Modified Paths:
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Revision: 3111
          http://obi.svn.sourceforge.net/obi/?rev=3111&view=rev
Author:   bjoernpeters
Date:     2010-12-21 22:10:46 +0000 (Tue, 21 Dec 2010)

Log Message:
-----------
Added binding datums, and the more general IC50, EC50, t1/2. Edited the incomplete 'prediction' term, which will need more discussion. 

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Revision: 3112
          http://obi.svn.sourceforge.net/obi/?rev=3112&view=rev
Author:   bjoernpeters
Date:     2010-12-22 02:03:37 +0000 (Wed, 22 Dec 2010)

Log Message:
-----------
implemented edits from call: added RNA sequencing; added alternative term for material supplier role, moved entries under 'spatial region' to 'site'. 

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Revision: 3118
          http://obi.svn.sourceforge.net/obi/?rev=3118&view=rev
Author:   bjoernpeters
Date:     2011-02-22 22:51:30 +0000 (Tue, 22 Feb 2011)

Log Message:
-----------
added 'infectous agent detection assay'

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Revision: 3130
          http://obi.svn.sourceforge.net/obi/?rev=3130&view=rev
Author:   bjoernpeters
Date:     2011-03-17 00:16:15 +0000 (Thu, 17 Mar 2011)

Log Message:
-----------
added individual epitope immunization and passive immunization. More to come and clean up. 

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Revision: 3131
          http://obi.svn.sourceforge.net/obi/?rev=3131&view=rev
Author:   bjoernpeters
Date:     2011-03-21 04:13:44 +0000 (Mon, 21 Mar 2011)

Log Message:
-----------
udpated passive immunization, epitope specific intervention

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Revision: 3132
          http://obi.svn.sourceforge.net/obi/?rev=3132&view=rev
Author:   bjoernpeters
Date:     2011-03-21 05:04:20 +0000 (Mon, 21 Mar 2011)

Log Message:
-----------
added epitope specific intervention assays

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Revision: 3133
          http://obi.svn.sourceforge.net/obi/?rev=3133&view=rev
Author:   bjoernpeters
Date:     2011-03-21 05:53:19 +0000 (Mon, 21 Mar 2011)

Log Message:
-----------
added restrictions to classify processes under 'material processing' if those were missing (vaccine preparation, cross linking, cell culture expansion) 

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Revision: 3134
          http://obi.svn.sourceforge.net/obi/?rev=3134&view=rev
Author:   bjoernpeters
Date:     2011-03-21 16:04:18 +0000 (Mon, 21 Mar 2011)

Log Message:
-----------
modified parents of processes to either biological process or planned process consistently, and made the two distinct. 

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Revision: 3135
          http://obi.svn.sourceforge.net/obi/?rev=3135&view=rev
Author:   bjoernpeters
Date:     2011-03-21 23:46:52 +0000 (Mon, 21 Mar 2011)

Log Message:
-----------


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Revision: 3143
          http://obi.svn.sourceforge.net/obi/?rev=3143&view=rev
Author:   jzheng24
Date:     2011-03-28 18:26:26 +0000 (Mon, 28 Mar 2011)

Log Message:
-----------
add one axiom to 'protein complex'

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Revision: 3146
          http://obi.svn.sourceforge.net/obi/?rev=3146&view=rev
Author:   jzheng24
Date:     2011-03-30 19:56:51 +0000 (Wed, 30 Mar 2011)

Log Message:
-----------
obsolete 3 service related roles, namely 
- 'material access provider role', OBI_0000936
- 'protocol service provider role', OBI_0000980
- 'training service provider role', OBI_0000929

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Revision: 3147
          http://obi.svn.sourceforge.net/obi/?rev=3147&view=rev
Author:   jzheng24
Date:     2011-03-30 20:15:00 +0000 (Wed, 30 Mar 2011)

Log Message:
-----------
22 terms were assigned with OBI ids:
http://purl.obolibrary.org/obo/OBI_0001171  label: half life datum (t 1/2)
http://purl.obolibrary.org/obo/OBI_0001172  label: dose response curve
http://purl.obolibrary.org/obo/OBI_0001173  label: service
http://purl.obolibrary.org/obo/OBI_0001174  label: passive immunization
http://purl.obolibrary.org/obo/OBI_0001175  label: selective organism creation objective
http://purl.obolibrary.org/obo/OBI_0001176  label: Individual epitope immunization in vivo
http://purl.obolibrary.org/obo/OBI_0001177  label: RNA sequencing
http://purl.obolibrary.org/obo/OBI_0001178  label: efficacy of epitope intervention experiment
http://purl.obolibrary.org/obo/OBI_0001179  label: epitope protection from infectious challenge experiment
http://purl.obolibrary.org/obo/OBI_0001180  label: half maximal effective concentration (EC50)
http://purl.obolibrary.org/obo/OBI_0001181  label: binding datum
http://purl.obolibrary.org/obo/OBI_0001182  label: negative binding datum
http://purl.obolibrary.org/obo/OBI_0001183  label: epitope protection from tumor challenge experiment
http://purl.obolibrary.org/obo/OBI_0001184  label: epitope protection experiment
http://purl.obolibrary.org/obo/OBI_0001185  label: selectively maintained organism
http://purl.obolibrary.org/obo/OBI_0001186  label: epitope protection from infectious challenge experiment based on pathogen burden
http://purl.obolibrary.org/obo/OBI_0001187  label: infectious agent detection assay
http://purl.obolibrary.org/obo/OBI_0001188  label: epitope disease excarbation experiment
http://purl.obolibrary.org/obo/OBI_0001189  label: epitope protection experiment based on survival
http://purl.obolibrary.org/obo/OBI_0001190  label: epitope treatment experiment
http://purl.obolibrary.org/obo/OBI_0001191  label: half maximal inhibitory concentration (IC50)
http://purl.obolibrary.org/obo/OBI_0001192  label: epitope specific immune intervention

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Revision: 3148
          http://obi.svn.sourceforge.net/obi/?rev=3148&view=rev
Author:   bjoernpeters
Date:     2011-03-31 14:30:37 +0000 (Thu, 31 Mar 2011)

Log Message:
-----------
updated preferred labels that were out of sync

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Revision: 3150
          http://obi.svn.sourceforge.net/obi/?rev=3150&view=rev
Author:   p_rocca_serra
Date:     2011-03-31 22:39:39 +0000 (Thu, 31 Mar 2011)

Log Message:
-----------
adding q-value, FWER adjusted p-value, modified several multiple testing correction method classes to specify p-value as input and respective adjusted p-values as output, fixed class label from Holm false discovery rate correction to Holm and Bonferroni family wise error rate correction method, modify restriction to allow correct classification

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Revision: 3156
          http://obi.svn.sourceforge.net/obi/?rev=3156&view=rev
Author:   jzheng24
Date:     2011-04-06 22:01:41 +0000 (Wed, 06 Apr 2011)

Log Message:
-----------
Modify some assay terms based on 2011/04/04 dev call
Modify definitions of most subclasses of data item in correct format

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Revision: 3158
          http://obi.svn.sourceforge.net/obi/?rev=3158&view=rev
Author:   bjoernpeters
Date:     2011-04-11 14:26:50 +0000 (Mon, 11 Apr 2011)

Log Message:
-----------
Added curation statuses and metadata to IEDB terms and general terms.  

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3159
          http://obi.svn.sourceforge.net/obi/?rev=3159&view=rev
Author:   bjoernpeters
Date:     2011-04-11 14:58:10 +0000 (Mon, 11 Apr 2011)

Log Message:
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Modified parentage for binding measurement related datum terms

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3160
          http://obi.svn.sourceforge.net/obi/?rev=3160&view=rev
Author:   bjoernpeters
Date:     2011-04-11 16:12:53 +0000 (Mon, 11 Apr 2011)

Log Message:
-----------


Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3161
          http://obi.svn.sourceforge.net/obi/?rev=3161&view=rev
Author:   jgreenbaum
Date:     2011-04-11 20:54:25 +0000 (Mon, 11 Apr 2011)

Log Message:
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added IEDB epitope-specific and T cell assay terms via MappingMaster

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3162
          http://obi.svn.sourceforge.net/obi/?rev=3162&view=rev
Author:   jgreenbaum
Date:     2011-04-11 23:21:04 +0000 (Mon, 11 Apr 2011)

Log Message:
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re-imported IEDB assays with revised definitions

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3165
          http://obi.svn.sourceforge.net/obi/?rev=3165&view=rev
Author:   jzheng24
Date:     2011-04-12 16:42:33 +0000 (Tue, 12 Apr 2011)

Log Message:
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merge study design related terms and genotype information related terms
fix some issues related to release, eg. curation status

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3166
          http://obi.svn.sourceforge.net/obi/?rev=3166&view=rev
Author:   jzheng24
Date:     2011-04-12 17:09:49 +0000 (Tue, 12 Apr 2011)

Log Message:
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merged the flow cytometers manufacturers provided by Karin Breuer (bccrc.ca), total 18 terms added as individuals of OBI:organization

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3168
          http://obi.svn.sourceforge.net/obi/?rev=3168&view=rev
Author:   jzheng24
Date:     2011-04-18 16:30:30 +0000 (Mon, 18 Apr 2011)

Log Message:
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Modify the ID of 'IEDB alternative term', replace 'IAO_0000118_1' with OBI_9991118

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3170
          http://obi.svn.sourceforge.net/obi/?rev=3170&view=rev
Author:   jzheng24
Date:     2011-04-18 17:15:27 +0000 (Mon, 18 Apr 2011)

Log Message:
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Fix the tags used for new added individuals of organization (Thing -> owl:Thing)

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3171
          http://obi.svn.sourceforge.net/obi/?rev=3171&view=rev
Author:   jzheng24
Date:     2011-04-18 17:37:13 +0000 (Mon, 18 Apr 2011)

Log Message:
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assigned IDs to 255 classes (classes mainly added by IEDB and Penn group) and 18 individuals of organization

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3172
          http://obi.svn.sourceforge.net/obi/?rev=3172&view=rev
Author:   ctorniai
Date:     2011-04-18 17:58:54 +0000 (Mon, 18 Apr 2011)

Log Message:
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Fixed service and DNA sequencing service:

Equivalent class:
'planned process'
 and ((realizes some 'service consumer role')
 and (realizes some 'service provider role'))

Superclasses:
has_part some 'planned process'

DNA sequencing service:
Superclasses:
        has_part some 'DNA sequencing'
        realizes some 'service consumer role'
        realizes some 'service provide role'

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    trunk/src/ontology/branches/obi.owl


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Revision: 3173
          http://obi.svn.sourceforge.net/obi/?rev=3173&view=rev
Author:   jzheng24
Date:     2011-04-19 15:38:17 +0000 (Tue, 19 Apr 2011)

Log Message:
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obsolete term 'DNA sequencing training service'
decision was made on 2011 San Diego workshop

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3203
          http://obi.svn.sourceforge.net/obi/?rev=3203&view=rev
Author:   jzheng24
Date:     2011-05-10 19:01:15 +0000 (Tue, 10 May 2011)

Log Message:
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add definition to two terms

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3211
          http://obi.svn.sourceforge.net/obi/?rev=3211&view=rev
Author:   jzheng24
Date:     2011-05-19 21:40:16 +0000 (Thu, 19 May 2011)

Log Message:
-----------
add/modify storage related terms

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3212
          http://obi.svn.sourceforge.net/obi/?rev=3212&view=rev
Author:   jzheng24
Date:     2011-05-23 23:20:22 +0000 (Mon, 23 May 2011)

Log Message:
-----------
add some terms for needs of functional genomics data annotation

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3213
          http://obi.svn.sourceforge.net/obi/?rev=3213&view=rev
Author:   jzheng24
Date:     2011-05-26 16:09:40 +0000 (Thu, 26 May 2011)

Log Message:
-----------
update definitions of terms added last time

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3214
          http://obi.svn.sourceforge.net/obi/?rev=3214&view=rev
Author:   bjoernpeters
Date:     2011-05-26 22:59:38 +0000 (Thu, 26 May 2011)

Log Message:
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added purified MHC molecule preparation. 
asserted that SPR assay is a binding assay

Modified Paths:
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    trunk/src/ontology/branches/obi.owl


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Revision: 3215
          http://obi.svn.sourceforge.net/obi/?rev=3215&view=rev
Author:   bjoernpeters
Date:     2011-06-09 22:38:05 +0000 (Thu, 09 Jun 2011)

Log Message:
-----------
added fluorescence detection in analogy to radioactivity detection; added restrictions to some existing assays to have them classify. Added assay for MHC binding by inhibiting T cells. 

Modified Paths:
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Revision: 3216
          http://obi.svn.sourceforge.net/obi/?rev=3216&view=rev
Author:   bjoernpeters
Date:     2011-06-14 21:53:33 +0000 (Tue, 14 Jun 2011)

Log Message:
-----------
The following classes were added to deal with MHC ligand identificatino assays in the IEDB: 
mass spectrometry of eluted MHC ligands
mass spectrometry of ligands eluted from soluble MHC
mass spectrometry of MHC ligands eluted from whole cells
T cell recognition of HPLC fractionated MHC ligand eluate compared to synthetic ligand
monospecific T cell recognition of eluted ligands 
Edman degradation of eluted MHC ligands
MHC protein complex ligand binding 

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