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From: <al...@us...> - 2009-07-31 18:13:58
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Revision: 1911
http://obi.svn.sourceforge.net/obi/?rev=1911&view=rev
Author: alanr
Date: 2009-07-31 18:13:48 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
defined obi:spreadsheets;
Modified Paths:
--------------
trunk/src/tools/build/obi.asd
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From: <p_r...@us...> - 2009-07-31 15:24:47
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Revision: 1910
http://obi.svn.sourceforge.net/obi/?rev=1910&view=rev
Author: p_rocca_serra
Date: 2009-07-31 15:24:29 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
cleanup: setting restriction and objective
-laboratory animal (now defined class)
interesting results after classification
-fixing restriction on:
DNA sequence feature detection (replacement of double stranded DNA to deoxyribonucleic acid + assay objective added)
DNA sequence variation detection
(replacement of 'ribonucleic acid' with 'deoxyribo')
adding assay objective where needed
DNA sequence
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2009-07-31 14:01:16
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Revision: 1909
http://obi.svn.sourceforge.net/obi/?rev=1909&view=rev
Author: p_rocca_serra
Date: 2009-07-31 14:01:04 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
Process Branch review and clean-up:
adding assay objective to:
-Sequencing
-nucleic acid hyb
-nmr assay
-glucose tolerance test
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2009-07-31 11:06:12
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Revision: 1908
http://obi.svn.sourceforge.net/obi/?rev=1908&view=rev
Author: p_rocca_serra
Date: 2009-07-31 11:06:06 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
Process Branch review and clean-up:
fixing restrictions to the following classes:
-Sequencing:
(adding mass spectrometer so it is no longer only DNA sequencer as used to be'
+added objective
Classification show DNA sequencing (and subclasses) Edman Degradation
-RTPCR
-polymerase chain reaction
(adding realization of function and achieving of objective) -> a material amplification objective is most certainly needed
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <al...@us...> - 2009-07-31 02:13:19
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Revision: 1907
http://obi.svn.sourceforge.net/obi/?rev=1907&view=rev
Author: alanr
Date: 2009-07-31 02:13:04 +0000 (Fri, 31 Jul 2009)
Log Message:
-----------
some scripting on the way to importing select efo terms to obi
Added Paths:
-----------
trunk/src/ontology/spreadsheets/in/efo-2009-07-30.owl
trunk/src/ontology/spreadsheets/in/efo-extract.lisp
trunk/src/ontology/spreadsheets/in/efo-terms-cited.txt
trunk/src/ontology/spreadsheets/in/efo-terms.txt
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From: <al...@us...> - 2009-07-30 21:10:29
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Revision: 1906
http://obi.svn.sourceforge.net/obi/?rev=1906&view=rev
Author: alanr
Date: 2009-07-30 21:10:22 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
obofoundry->obolibrary
Modified Paths:
--------------
trunk/src/tools/build/add-assumed-individuals.lisp
trunk/src/tools/build/add-inferred-superclasses.lisp
trunk/src/tools/build/comment-ids-in-owl-file.lisp
trunk/src/tools/build/create-external-derived.lisp
trunk/src/tools/build/generate-obo.lisp
trunk/src/tools/build/normalize-namespaces.pl
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From: <al...@us...> - 2009-07-30 20:47:58
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Revision: 1905
http://obi.svn.sourceforge.net/obi/?rev=1905&view=rev
Author: alanr
Date: 2009-07-30 20:47:49 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
how did the uri http://purl.obolibrary.org/ob get in there?
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <al...@us...> - 2009-07-30 18:24:27
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Revision: 1904
http://obi.svn.sourceforge.net/obi/?rev=1904&view=rev
Author: alanr
Date: 2009-07-30 18:24:21 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
don't make disjoints to object, objectaggregate, fiatobjectpart
Modified Paths:
--------------
trunk/src/tools/build/add-disjoints.lisp
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From: <al...@us...> - 2009-07-30 18:23:51
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Revision: 1903
http://obi.svn.sourceforge.net/obi/?rev=1903&view=rev
Author: alanr
Date: 2009-07-30 18:23:43 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
Add organizationInstances
Modified Paths:
--------------
trunk/src/ontology/branches/obil.owl
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From: <al...@us...> - 2009-07-30 17:14:41
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Revision: 1902
http://obi.svn.sourceforge.net/obi/?rev=1902&view=rev
Author: alanr
Date: 2009-07-30 17:14:33 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
s/reference/refereced/
Modified Paths:
--------------
trunk/src/tools/build/add-assumed-individuals.lisp
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From: <mco...@us...> - 2009-07-30 17:14:05
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Revision: 1901
http://obi.svn.sourceforge.net/obi/?rev=1901&view=rev
Author: mcourtot
Date: 2009-07-30 17:13:58 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
updated restrictions on rodent care to be input and ouput Rodentia now that this term has been mireoted, as per Helen P.'s suggestion
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <al...@us...> - 2009-07-30 13:21:08
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Revision: 1900
http://obi.svn.sourceforge.net/obi/?rev=1900&view=rev
Author: alanr
Date: 2009-07-30 13:21:00 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
another obofoundry->obofoundry|obolibrary
Modified Paths:
--------------
trunk/src/tools/build/util.lisp
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From: <al...@us...> - 2009-07-30 13:14:10
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Revision: 1899
http://obi.svn.sourceforge.net/obi/?rev=1899&view=rev
Author: alanr
Date: 2009-07-30 13:14:03 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
obofoundry->obolibrary
Modified Paths:
--------------
trunk/src/tools/build/util.lisp
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From: <p_r...@us...> - 2009-07-30 09:03:43
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Revision: 1898
http://obi.svn.sourceforge.net/obi/?rev=1898&view=rev
Author: p_rocca_serra
Date: 2009-07-30 09:03:30 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
refining restrictions on glucose tolerance test
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <al...@us...> - 2009-07-30 07:41:55
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Revision: 1897
http://obi.svn.sourceforge.net/obi/?rev=1897&view=rev
Author: alanr
Date: 2009-07-30 07:41:49 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
;; for now only add individual where we know they make a difference -
;; specifically if class C mentioned individual I in it's class
;; expression, create an instance of C
Modified Paths:
--------------
trunk/src/tools/build/add-assumed-individuals.lisp
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From: <al...@us...> - 2009-07-30 06:12:36
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Revision: 1896
http://obi.svn.sourceforge.net/obi/?rev=1896&view=rev
Author: alanr
Date: 2009-07-30 06:12:27 +0000 (Thu, 30 Jul 2009)
Log Message:
-----------
replace obsolete_utilizes_reagent with has_specified_input
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <bjo...@us...> - 2009-07-29 16:48:26
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Revision: 1895
http://obi.svn.sourceforge.net/obi/?rev=1895&view=rev
Author: bjoernpeters
Date: 2009-07-29 16:48:15 +0000 (Wed, 29 Jul 2009)
Log Message:
-----------
updated the textual definitions of 'has_specified_input' + output + reverse to remove the use of roles (as discussed at the workshop. Also: Added again the 'has_specified participant relation (also discussed at the workshop). The latter seems to have negative impact on reasoning performance.
Modified Paths:
--------------
trunk/src/ontology/branches/Relations.owl
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From: <p_r...@us...> - 2009-07-29 16:43:52
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Revision: 1894
http://obi.svn.sourceforge.net/obi/?rev=1894&view=rev
Author: p_rocca_serra
Date: 2009-07-29 16:43:45 +0000 (Wed, 29 Jul 2009)
Log Message:
-----------
changes to restriction on glucose tolerance test (following early feedback from Bjoern)
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2009-07-29 16:11:00
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Revision: 1893
http://obi.svn.sourceforge.net/obi/?rev=1893&view=rev
Author: p_rocca_serra
Date: 2009-07-29 16:10:50 +0000 (Wed, 29 Jul 2009)
Log Message:
-----------
adding missing metadata to newly created class
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2009-07-29 15:29:13
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Revision: 1892
http://obi.svn.sourceforge.net/obi/?rev=1892&view=rev
Author: p_rocca_serra
Date: 2009-07-29 15:29:01 +0000 (Wed, 29 Jul 2009)
Log Message:
-----------
modeling glucose tolerance test:
uses analyte assay
uses administering substance in vivo
realizes time series design
and the specific output is about a disposition = insulin resistance (mireoted from HPO)
Note: OK HPO is not OBO foundry but to try it out
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2009-07-29 15:07:10
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Revision: 1891
http://obi.svn.sourceforge.net/obi/?rev=1891&view=rev
Author: p_rocca_serra
Date: 2009-07-29 15:07:03 +0000 (Wed, 29 Jul 2009)
Log Message:
-----------
adding insulin resistance from HPO and glucose metabolism from GO
Modified Paths:
--------------
trunk/src/ontology/branches/external.owl
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From: <al...@us...> - 2009-07-29 04:32:27
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Revision: 1890
http://obi.svn.sourceforge.net/obi/?rev=1890&view=rev
Author: alanr
Date: 2009-07-29 04:32:12 +0000 (Wed, 29 Jul 2009)
Log Message:
-----------
remove Helen's repository config oops
Removed Paths:
-------------
conf/
db/
hooks/
locks/
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From: <bjo...@us...> - 2009-07-29 02:30:43
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Revision: 1889
http://obi.svn.sourceforge.net/obi/?rev=1889&view=rev
Author: bjoernpeters
Date: 2009-07-29 02:30:27 +0000 (Wed, 29 Jul 2009)
Log Message:
-----------
updated genotyping definition as suggested by Chris Mungall
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <bjo...@us...> - 2009-07-29 02:10:32
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Revision: 1888
http://obi.svn.sourceforge.net/obi/?rev=1888&view=rev
Author: bjoernpeters
Date: 2009-07-29 02:10:24 +0000 (Wed, 29 Jul 2009)
Log Message:
-----------
Poster as presented at ICBO
Added Paths:
-----------
trunk/docs/posters/general_ICBO 2009/Poster.pdf
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From: <p_r...@us...> - 2009-07-28 21:40:46
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Revision: 1887
http://obi.svn.sourceforge.net/obi/?rev=1887&view=rev
Author: p_rocca_serra
Date: 2009-07-28 21:40:37 +0000 (Tue, 28 Jul 2009)
Log Message:
-----------
adding the following classes:
bisulfite sequencing
ChIP-SEQ assay
MeDIP-SEQ assay
immunoprecipitation
will need to fine tune the objectives
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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