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From: <al...@us...> - 2008-06-06 05:47:15
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Revision: 710
http://obi.svn.sourceforge.net/obi/?rev=710&view=rev
Author: alanr
Date: 2008-06-05 22:47:22 -0700 (Thu, 05 Jun 2008)
Log Message:
-----------
functions to interacting with purl.org
Added Paths:
-----------
trunk/src/tools/build/purl.lisp
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From: <bjo...@us...> - 2008-06-05 16:04:38
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Revision: 709
http://obi.svn.sourceforge.net/obi/?rev=709&view=rev
Author: bjoernpeters
Date: 2008-06-05 09:03:40 -0700 (Thu, 05 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
branches/bpbranch/branches/Biomaterial.owl
branches/bpbranch/branches/DigitalEntityPlus.owl
branches/bpbranch/branches/InstrumentAndPart.owl
branches/bpbranch/branches/PlanAndPlannedProcess.owl
branches/bpbranch/branches/Role.owl
branches/bpbranch/branches/TheRest.owl
branches/bpbranch/branches/external.owl
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From: <man...@us...> - 2008-06-05 15:57:29
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Revision: 708
http://obi.svn.sourceforge.net/obi/?rev=708&view=rev
Author: manduchi
Date: 2008-06-05 08:57:33 -0700 (Thu, 05 Jun 2008)
Log Message:
-----------
updated according to discussion at conference call on 06/05/08
Modified Paths:
--------------
trunk/docs/developer/DT/EM_ClusteringTerms.xls
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From: <jam...@us...> - 2008-06-05 13:56:19
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Revision: 707
http://obi.svn.sourceforge.net/obi/?rev=707&view=rev
Author: jamesmalone
Date: 2008-06-05 06:56:26 -0700 (Thu, 05 Jun 2008)
Log Message:
-----------
dev notes from 5th june 2008
Added Paths:
-----------
web/trunk/htdocs/notes/developers/2008/20080605.txt
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From: <jam...@us...> - 2008-06-05 09:56:25
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Revision: 706
http://obi.svn.sourceforge.net/obi/?rev=706&view=rev
Author: jamesmalone
Date: 2008-06-05 02:56:31 -0700 (Thu, 05 Jun 2008)
Log Message:
-----------
Complete clean up of TheRest.owl. moved physical_document to material and subclass axiom for platform transferred to instrument owl file
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
trunk/src/ontology/branches/InstrumentAndPart.owl
trunk/src/ontology/branches/TheRest.owl
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From: <man...@us...> - 2008-06-04 21:50:47
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Revision: 705
http://obi.svn.sourceforge.net/obi/?rev=705&view=rev
Author: manduchi
Date: 2008-06-04 13:43:35 -0700 (Wed, 04 Jun 2008)
Log Message:
-----------
Proposal for updates to the current terms under cluster method
Added Paths:
-----------
trunk/docs/developer/DT/EM_ClusteringTerms.xls
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From: <jam...@us...> - 2008-06-04 09:16:49
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Revision: 704
http://obi.svn.sourceforge.net/obi/?rev=704&view=rev
Author: jamesmalone
Date: 2008-06-04 02:16:50 -0700 (Wed, 04 Jun 2008)
Log Message:
-----------
Tidying up of therest.owl: movement of classes to appropriate branch files and obsolescence of some classes
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
trunk/src/ontology/branches/TheRest.owl
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From: <p_r...@us...> - 2008-06-04 09:01:40
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Revision: 703
http://obi.svn.sourceforge.net/obi/?rev=703&view=rev
Author: p_rocca_serra
Date: 2008-06-04 02:01:39 -0700 (Wed, 04 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
branches/prsbranch/external/bfo11.owl
branches/prsbranch/external/protege-dc.owl
branches/prsbranch/external/ro.owl
branches/prsbranch/external/ro_bfo1-1_bridge.owl
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From: <p_r...@us...> - 2008-06-04 09:01:08
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Revision: 702
http://obi.svn.sourceforge.net/obi/?rev=702&view=rev
Author: p_rocca_serra
Date: 2008-06-04 02:01:11 -0700 (Wed, 04 Jun 2008)
Log Message:
-----------
representing with restrictions
Modified Paths:
--------------
branches/prsbranch/branches/Biomaterial.owl
branches/prsbranch/branches/PlanAndPlannedProcess.owl
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From: <al...@us...> - 2008-06-03 16:53:11
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Revision: 701
http://obi.svn.sourceforge.net/obi/?rev=701&view=rev
Author: alanr
Date: 2008-06-03 09:53:14 -0700 (Tue, 03 Jun 2008)
Log Message:
-----------
usage: perl obi-lisp-eval.pl '(+ 1 2)' . Evaluates argument in lisp. Starts up a new lisp in background if one isn't already there. To quit backround lisp: perl obi-lisp-eval.pl '(quit)'
Added Paths:
-----------
trunk/bin/obi-lisp-eval.pl
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From: <fgi...@us...> - 2008-06-03 16:22:52
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Revision: 700
http://obi.svn.sourceforge.net/obi/?rev=700&view=rev
Author: fgibson_sf
Date: 2008-06-03 09:22:38 -0700 (Tue, 03 Jun 2008)
Log Message:
-----------
Completion of long overdue action on my part. Added the following
Mass spectrometer
has_part ion_source
has_part mass_analyzer
has_part ion_detector
Ion_source: An ion source is a device that is part of a mass
spectrometer that ionizes the material under analysis. The ions are
then transported by magnetic or electric fields to the mass analyzer.
Techniques for ionization have been key to determining what types of
samples can be analyzed by mass spectrometry. Electron ionization and
chemical ionization are used for gases and vapors. In chemical
ionization sources, the materila is ionized by chemical ion-molecule
reactions during collisions in the source. Two techniques often used
with liquid and solid biological samples include electrospray
ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser
desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp
(Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson
(Editor) (ISBN 0-941901-31-9))).
http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source
Mass_analyzer: A Mass analyzer is a device that separates ions
according to their mass-to-charge ratio. All mass spectrometers are
based on dynamics of charged particles in electric and magnetic fields
in vacuum where the following two laws of Lorentz force law and
Newton's second law of motion apply
http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer
Ion_detector: An ion detector is a device that measures and records
the charge induced or current produced when an ion passes by or hits a
surface. In a scanning instrument the signal produced in the detector
during the course of the scan versus where the instrument is in the
scan (at what m/Q) will produce a mass spectrum, a record of ions as a
function of m/Q.
http://en.wikipedia.org/wiki/Mass_spectrometry#Detector
-Ontology is consistent
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <p_r...@us...> - 2008-06-02 22:19:04
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Revision: 699
http://obi.svn.sourceforge.net/obi/?rev=699&view=rev
Author: p_rocca_serra
Date: 2008-06-02 15:19:04 -0700 (Mon, 02 Jun 2008)
Log Message:
-----------
setting a bunch of restrictions on Materials, ProtocolApplications
Adding class to protocolapplicaiton and Biomaterials where needed
Added Paths:
-----------
branches/prsbranch/
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From: <mco...@us...> - 2008-06-02 22:03:33
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Revision: 698
http://obi.svn.sourceforge.net/obi/?rev=698&view=rev
Author: mcourtot
Date: 2008-06-02 15:03:40 -0700 (Mon, 02 Jun 2008)
Log Message:
-----------
added notes dev call 28th may 2008
Added Paths:
-----------
web/trunk/htdocs/notes/developers/2008/20080528.txt
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From: <mco...@us...> - 2008-06-02 21:11:43
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Revision: 697
http://obi.svn.sourceforge.net/obi/?rev=697&view=rev
Author: mcourtot
Date: 2008-06-02 14:11:45 -0700 (Mon, 02 Jun 2008)
Log Message:
-----------
added some text - very early draft!
Modified Paths:
--------------
trunk/docs/developer/posters/obi_ismb_poster.ppt
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From: <jam...@us...> - 2008-06-02 16:48:05
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Revision: 696
http://obi.svn.sourceforge.net/obi/?rev=696&view=rev
Author: jamesmalone
Date: 2008-06-02 09:48:14 -0700 (Mon, 02 Jun 2008)
Log Message:
-----------
Tidying up of therest.owl : movement of states, now obsolete due to work in biomaterial and sex effect
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
trunk/src/ontology/branches/TheRest.owl
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From: <jam...@us...> - 2008-06-02 15:10:47
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Revision: 695
http://obi.svn.sourceforge.net/obi/?rev=695&view=rev
Author: jamesmalone
Date: 2008-06-02 08:10:32 -0700 (Mon, 02 Jun 2008)
Log Message:
-----------
Tidying up of therest.owl : movement of disease (needs discussing on quality branch as per editor notes)
Modified Paths:
--------------
trunk/src/ontology/branches/Quality.owl
trunk/src/ontology/branches/TheRest.owl
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From: <dan...@us...> - 2008-06-02 09:52:50
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Revision: 694
http://obi.svn.sourceforge.net/obi/?rev=694&view=rev
Author: daniel_schober
Date: 2008-06-02 02:52:58 -0700 (Mon, 02 Jun 2008)
Log Message:
-----------
Added definittion source value according to BNF GROUP using escaped < and >, e.g. < and >
Modified Paths:
--------------
trunk/src/ontology/branches/AnnotationProperty.owl
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From: <al...@us...> - 2008-05-30 22:12:21
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Revision: 693
http://obi.svn.sourceforge.net/obi/?rev=693&view=rev
Author: alanr
Date: 2008-05-30 15:12:25 -0700 (Fri, 30 May 2008)
Log Message:
-----------
new qc query (lost-terms &key current)
Modified Paths:
--------------
trunk/src/tools/build/qc-queries.lisp
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From: <mco...@us...> - 2008-05-30 20:47:59
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Revision: 692
http://obi.svn.sourceforge.net/obi/?rev=692&view=rev
Author: mcourtot
Date: 2008-05-30 13:48:06 -0700 (Fri, 30 May 2008)
Log Message:
-----------
and removed the links that I always forget...
Modified Paths:
--------------
trunk/docs/user/release_notes.html
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From: <mco...@us...> - 2008-05-30 20:45:40
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Revision: 691
http://obi.svn.sourceforge.net/obi/?rev=691&view=rev
Author: mcourtot
Date: 2008-05-30 13:45:48 -0700 (Fri, 30 May 2008)
Log Message:
-----------
added mising XML comments info
Modified Paths:
--------------
trunk/docs/user/release_notes.html
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From: <mco...@us...> - 2008-05-30 20:44:45
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Revision: 690
http://obi.svn.sourceforge.net/obi/?rev=690&view=rev
Author: mcourtot
Date: 2008-05-30 13:44:46 -0700 (Fri, 30 May 2008)
Log Message:
-----------
added release notes 2008-05-30 release
Modified Paths:
--------------
trunk/docs/user/release_notes.html
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From: <mco...@us...> - 2008-05-30 20:28:03
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Revision: 689
http://obi.svn.sourceforge.net/obi/?rev=689&view=rev
Author: mcourtot
Date: 2008-05-30 13:28:08 -0700 (Fri, 30 May 2008)
Log Message:
-----------
html report new release
Added Paths:
-----------
tags/releases/2008-05-30/obi-lsw-report.html
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From: <mco...@us...> - 2008-05-30 20:01:32
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Revision: 688
http://obi.svn.sourceforge.net/obi/?rev=688&view=rev
Author: mcourtot
Date: 2008-05-30 13:01:40 -0700 (Fri, 30 May 2008)
Log Message:
-----------
the release
Added Paths:
-----------
tags/releases/2008-05-30/merged/
tags/releases/2008-05-30/merged/OBI.owl
tags/releases/2008-05-30/merged/SVNlogs.txt
tags/releases/2008-05-30/merged/list-purls.xml
tags/releases/2008-05-30/merged/md5.txt
tags/releases/2008-05-30/merged/protege/
tags/releases/2008-05-30/merged/protege/OBI-ProtegeFriendly.owl
tags/releases/2008-05-30/merged/protege/OBI-ProtegeFriendly.pprj
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From: <mco...@us...> - 2008-05-30 19:58:57
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Revision: 687
http://obi.svn.sourceforge.net/obi/?rev=687&view=rev
Author: mcourtot
Date: 2008-05-30 12:59:03 -0700 (Fri, 30 May 2008)
Log Message:
-----------
release
Added Paths:
-----------
tags/releases/2008-05-30/branches/
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From: <mco...@us...> - 2008-05-30 19:58:41
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Revision: 686
http://obi.svn.sourceforge.net/obi/?rev=686&view=rev
Author: mcourtot
Date: 2008-05-30 12:58:44 -0700 (Fri, 30 May 2008)
Log Message:
-----------
release
Added Paths:
-----------
tags/releases/2008-05-30/external/
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