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From: <al...@us...> - 2007-10-11 07:25:08
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Revision: 160
http://obi.svn.sourceforge.net/obi/?rev=160&view=rev
Author: alanr
Date: 2007-10-11 00:25:07 -0700 (Thu, 11 Oct 2007)
Log Message:
-----------
just notes. Need to script this
Added Paths:
-----------
branchDevelopment/trunk/sourcecodes/loading-obi-into-neurocommons.txt
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From: <bjo...@us...> - 2007-10-04 17:06:08
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Revision: 159
http://obi.svn.sourceforge.net/obi/?rev=159&view=rev
Author: bjoernpeters
Date: 2007-10-04 10:06:03 -0700 (Thu, 04 Oct 2007)
Log Message:
-----------
Modified Paths:
--------------
branchDevelopment/trunk/ProtocolApplication.owl
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From: <dan...@us...> - 2007-10-04 16:02:40
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Revision: 158
http://obi.svn.sourceforge.net/obi/?rev=158&view=rev
Author: daniel_schober
Date: 2007-10-04 09:02:41 -0700 (Thu, 04 Oct 2007)
Log Message:
-----------
this is the file for the autoid plugin, indicating the last used class ID.
Added Paths:
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branchDevelopment/trunk/lastac_autoID/default.properties.biomaterial
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From: <dan...@us...> - 2007-10-04 15:59:23
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Revision: 157
http://obi.svn.sourceforge.net/obi/?rev=157&view=rev
Author: daniel_schober
Date: 2007-10-04 08:58:49 -0700 (Thu, 04 Oct 2007)
Log Message:
-----------
The following terms as submitted by the PA branch were added.
"General comments on the biomaterial branch: Many classes do not have label and preferred_label both set. Some , especially the helper classes are without IDs. I marked questionable classes with a '?', and put my issues in the editor note annotation property."
Comment Schober parent_term / where does it go preferred_term definition example editor_note source branch / community
put under cell culture biomaterial primary cell culture cells put directly into culture from a tissue source spleen cells put directly into culture Protocol App Branch
put under cell culture biomaterial cell line culture long term culture of cells that are replicating continuosly. The cell population is homogenous but not clonal HeLa cells Protocol App Branch
put under cell culture biomaterial clonal cell culture "cell culture in which all cells can be assumed to be identical, tracking back to a single ancestor cell" cell cut KPC
"Put under cell component, but may be alternative term for that." biomaterial cellular compartment part of a cell enlosed by a membrane cytosol KPC
Put under enzyme Biomaterial / Reagent DNA polymerase An enzyme which facilitates the copying of DNA. Taq polymerase is a commonly used DNA polymerase to copy DNA templates in PCR reactions. KPC
Put under biological_macromolecule biomaterial / reagent enzyme A protein which mediates a defined chemical reaction to one or more target molecules A protease is an enzyme which catalyses the breakdown of proteins into smaller peptides. KPC
Probably pass to roles branch biomaterial / reagent Bead A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations. KPC
Pass to Instruments/labware branch biomaterial / reagent dialysis membrane a semi permeable membrance with known pore size A dialysis membrane of pore size 1000 Da MWCO is used to separate molecules of greater than 1000 Da MWCO from those which are less than 1000 Da MWCO. KPC
Put under artificially_engineered_biomaterial biomaterial / reagent cloning vector "a autonomous replicating vehicle, such as a plasmid or virus vector, which can be modified by the insertion of foreign DNA and when introduced into recipient cells does not alter the viability of those cells" The DNA expressing the protein of interest was inserted within pM13 which was then transfected into a cell line to facilitate expression of the protein. KPC
Put under experimental biomaterial. Probably a role? biomaterial / reagent dye A substance capable of staining or coloring defined targets Acridine orange is a nucleic acid selective dye. KPC
Put under enzyme biomaterial / reagent reverse transcriptase "an enzyme that faciliatates the conversion of RNA to DNA. May be natural, recombinant or modified" Avian reverse transcriptase transcribes RNA into complementary DNA. KPC
Modified Paths:
--------------
branchDevelopment/trunk/Biomaterial.owl
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From: <dan...@us...> - 2007-10-04 08:49:55
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Revision: 156
http://obi.svn.sourceforge.net/obi/?rev=156&view=rev
Author: daniel_schober
Date: 2007-10-04 01:49:58 -0700 (Thu, 04 Oct 2007)
Log Message:
-----------
minor orthographic correction
Modified Paths:
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branchDevelopment/trunk/AnnotationProperty.owl
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From: <all...@us...> - 2007-10-03 16:09:49
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Revision: 155
http://obi.svn.sourceforge.net/obi/?rev=155&view=rev
Author: allysonlister
Date: 2007-10-03 09:09:40 -0700 (Wed, 03 Oct 2007)
Log Message:
-----------
October 3 developer's telecon
Added Paths:
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web/trunk/htdocs/notes/developers/200710/
web/trunk/htdocs/notes/developers/200710/20071003.txt
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From: <all...@us...> - 2007-10-02 13:53:37
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Revision: 154
http://obi.svn.sourceforge.net/obi/?rev=154&view=rev
Author: allysonlister
Date: 2007-10-02 06:53:31 -0700 (Tue, 02 Oct 2007)
Log Message:
-----------
Developer notes for 26 September
Added Paths:
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web/trunk/htdocs/notes/developers/200709/20070926.txt
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From: <bjo...@us...> - 2007-10-01 14:16:25
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Revision: 153
http://obi.svn.sourceforge.net/obi/?rev=153&view=rev
Author: bjoernpeters
Date: 2007-10-01 07:16:29 -0700 (Mon, 01 Oct 2007)
Log Message:
-----------
Removed Paths:
-------------
branchDevelopment/trunk/test-bp.txt
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From: <bjo...@us...> - 2007-10-01 14:16:08
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Revision: 152
http://obi.svn.sourceforge.net/obi/?rev=152&view=rev
Author: bjoernpeters
Date: 2007-10-01 07:16:07 -0700 (Mon, 01 Oct 2007)
Log Message:
-----------
Added Paths:
-----------
branchDevelopment/trunk/test-bp.txt
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From: <dan...@us...> - 2007-09-25 11:33:17
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Revision: 151
http://obi.svn.sourceforge.net/obi/?rev=151&view=rev
Author: daniel_schober
Date: 2007-09-25 04:33:21 -0700 (Tue, 25 Sep 2007)
Log Message:
-----------
Three new terms submitted from PA Branch were included and their definitions refined.
Modified Paths:
--------------
branchDevelopment/trunk/InstrumentAndPart.owl
branchDevelopment/trunk/lastac_autoID/default.properties.InstrumentAndPart
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From: <al...@us...> - 2007-09-21 15:45:16
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Revision: 150
http://obi.svn.sourceforge.net/obi/?rev=150&view=rev
Author: alanr
Date: 2007-09-21 08:45:15 -0700 (Fri, 21 Sep 2007)
Log Message:
-----------
added is_manufactured_by relation from TC today with Liju
Modified Paths:
--------------
branchDevelopment/trunk/Relations.owl
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From: <jgr...@us...> - 2007-09-20 18:23:39
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Revision: 149
http://obi.svn.sourceforge.net/obi/?rev=149&view=rev
Author: jgreenbaum
Date: 2007-09-20 11:23:42 -0700 (Thu, 20 Sep 2007)
Log Message:
-----------
* created planned_process - needs to be incorporated into obi.owl file
* cleaned up one level below protocol_application
* created defined_protocol_application
Modified Paths:
--------------
branchDevelopment/trunk/ProtocolApplication.owl
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From: <all...@us...> - 2007-09-20 08:11:00
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Revision: 148
http://obi.svn.sourceforge.net/obi/?rev=148&view=rev
Author: allysonlister
Date: 2007-09-20 01:10:53 -0700 (Thu, 20 Sep 2007)
Log Message:
-----------
moved denrie notes to correct month (August), added developers notes
Added Paths:
-----------
web/trunk/htdocs/notes/developers/200708/20070829-denrie.txt
web/trunk/htdocs/notes/developers/200709/20070919.txt
Removed Paths:
-------------
web/trunk/htdocs/notes/developers/200709/20070929-denrie.txt
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From: <al...@us...> - 2007-09-18 06:23:19
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Revision: 147
http://obi.svn.sourceforge.net/obi/?rev=147&view=rev
Author: alanr
Date: 2007-09-17 23:23:18 -0700 (Mon, 17 Sep 2007)
Log Message:
-----------
removed use of intersection-of LSW artifact.
Modified Paths:
--------------
branchDevelopment/trunk/ProtocolApplication.owl
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From: <al...@us...> - 2007-09-16 09:20:28
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Revision: 146
http://obi.svn.sourceforge.net/obi/?rev=146&view=rev
Author: alanr
Date: 2007-09-16 02:20:30 -0700 (Sun, 16 Sep 2007)
Log Message:
-----------
Hacky code for importing pa spreadsheet using lsw
Added Paths:
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branchDevelopment/trunk/sourcecodes/sheet-importer.lisp
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From: <al...@us...> - 2007-09-16 09:15:47
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Revision: 145
http://obi.svn.sourceforge.net/obi/?rev=145&view=rev
Author: alanr
Date: 2007-09-16 02:15:50 -0700 (Sun, 16 Sep 2007)
Log Message:
-----------
>From spreadsheet
Modified Paths:
--------------
branchDevelopment/trunk/ProtocolApplication.owl
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From: <all...@us...> - 2007-09-13 10:59:27
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Revision: 144
http://obi.svn.sourceforge.net/obi/?rev=144&view=rev
Author: allysonlister
Date: 2007-09-13 03:59:20 -0700 (Thu, 13 Sep 2007)
Log Message:
-----------
New notes from a few different meetings.
Added Paths:
-----------
web/trunk/htdocs/notes/coordinators/20070815.txt
web/trunk/htdocs/notes/coordinators/20070912.txt
web/trunk/htdocs/notes/developers/200709/
web/trunk/htdocs/notes/developers/200709/20070929-denrie.txt
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From: <al...@us...> - 2007-09-08 06:14:42
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Revision: 143
http://obi.svn.sourceforge.net/obi/?rev=143&view=rev
Author: alanr
Date: 2007-09-07 23:14:40 -0700 (Fri, 07 Sep 2007)
Log Message:
-----------
Add files related to discussion of object hierarchy. Collectivity demo from Rector, NoCollectivity from Bjoern, and petri-dish from Alan
Added Paths:
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branchDevelopment/trunk/development-examples/NoCollectiveConstitutes.owl
branchDevelopment/trunk/development-examples/collectivity-demo.owl
branchDevelopment/trunk/development-examples/petri-dish.owl
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From: <jgr...@us...> - 2007-08-30 17:35:40
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Revision: 142
http://obi.svn.sourceforge.net/obi/?rev=142&view=rev
Author: jgreenbaum
Date: 2007-08-30 10:35:39 -0700 (Thu, 30 Aug 2007)
Log Message:
-----------
* cleaned up ProtocolApplication.owl
* removed "PA_to_be_reviewed" class & distributed subclasses accordingly
* removed classes without proper definitions
* renamed classes according to naming conventions
Modified Paths:
--------------
branchDevelopment/trunk/ProtocolApplication.owl
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From: <all...@us...> - 2007-08-30 10:13:29
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Revision: 141
http://obi.svn.sourceforge.net/obi/?rev=141&view=rev
Author: allysonlister
Date: 2007-08-30 03:12:47 -0700 (Thu, 30 Aug 2007)
Log Message:
-----------
Moved development-examples out of the top-level dirs, and into trunk where it belongs. See SVN docs for information on best-practice directory structure for subversion projects.
Removed Paths:
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branchDevelopment/development-examples/
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From: <all...@us...> - 2007-08-30 10:12:19
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Revision: 140
http://obi.svn.sourceforge.net/obi/?rev=140&view=rev
Author: allysonlister
Date: 2007-08-30 03:11:55 -0700 (Thu, 30 Aug 2007)
Log Message:
-----------
Moved development-examples out of the top-level dirs, and into trunk where it belongs. See SVN docs for information on best-practice directory structure for subversion projects.
Added Paths:
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branchDevelopment/trunk/development-examples/
branchDevelopment/trunk/development-examples/TheOntologyOfObjects/
branchDevelopment/trunk/development-examples/TheOntologyOfObjects/Object.owl
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From: <all...@us...> - 2007-08-30 09:32:30
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Revision: 139
http://obi.svn.sourceforge.net/obi/?rev=139&view=rev
Author: allysonlister
Date: 2007-08-30 02:32:11 -0700 (Thu, 30 Aug 2007)
Log Message:
-----------
Added minutes from 22 and 29 August.
Added Paths:
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web/trunk/htdocs/notes/developers/200708/
web/trunk/htdocs/notes/developers/200708/20070822.txt
web/trunk/htdocs/notes/developers/200708/20070829.txt
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From: <fgi...@us...> - 2007-08-22 15:41:26
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Revision: 138
http://obi.svn.sourceforge.net/obi/?rev=138&view=rev
Author: fgibson_sf
Date: 2007-08-22 08:41:20 -0700 (Wed, 22 Aug 2007)
Log Message:
-----------
updated the hierarchy by removing heterogenous_portion and homogenous_portion
Modified Paths:
--------------
branchDevelopment/development-examples/TheOntologyOfObjects/Object.owl
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From: <fgi...@us...> - 2007-08-21 13:07:23
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Revision: 137
http://obi.svn.sourceforge.net/obi/?rev=137&view=rev
Author: fgibson_sf
Date: 2007-08-21 06:07:18 -0700 (Tue, 21 Aug 2007)
Log Message:
-----------
-Added new version on Object.owl
-Deleted all media files for the video as they do not work
Modified Paths:
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branchDevelopment/development-examples/TheOntologyOfObjects/Object.owl
Removed Paths:
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branchDevelopment/development-examples/TheOntologyOfObjects/TheOntologyOfObjects.html
branchDevelopment/development-examples/TheOntologyOfObjects/TheOntologyOfObjects_media/
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From: <dan...@us...> - 2007-08-17 16:45:59
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Revision: 136
http://obi.svn.sourceforge.net/obi/?rev=136&view=rev
Author: daniel_schober
Date: 2007-08-17 09:46:00 -0700 (Fri, 17 Aug 2007)
Log Message:
-----------
DS: I have put the Perl sources into a corresponding folder. An instructions file how to use these should be generated in there too.
Modified Paths:
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branchDevelopment/trunk/Biomaterial.owl
branchDevelopment/trunk/InstrumentAndPart.owl
Added Paths:
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branchDevelopment/trunk/sourcecodes/
branchDevelopment/trunk/sourcecodes/join-branches.pl
branchDevelopment/trunk/sourcecodes/make-all-in-one.pl
Removed Paths:
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branchDevelopment/trunk/join-branches.pl
branchDevelopment/trunk/make-all-in-one.pl
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