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From: <al...@us...> - 2008-06-22 10:51:53
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Revision: 761
http://obi.svn.sourceforge.net/obi/?rev=761&view=rev
Author: alanr
Date: 2008-06-21 20:48:01 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
perl add-to-external.pl child parent [path to external.owl]
e.g.
perl add-to-external.pl PRO:000000001 CHEBI:23091
adds, to external.owl:
<owl:Class rdf:about="http://purl.org/obo/owl/PRO#PRO_000000001">
<rdfs:subClassOf rdf:resource="http://purl.org/obo/owl/CHEBI#CHEBI_23091"/>
<OBI_0000283 rdf:resource="http://purl.org/obo/owl/PRO"/>
</owl:Class>
One can use the ids as above, or the URIs
perl add-to-external.pl http://purl.org/obo/owl/PRO#PRO_000000001 CHEBI:23091
would do the same thing.
There is some validation.
- Checks that the child isn't already in external.owl
- Checks that the parent *is* in external.owl, or is an OBI term.
- Verifies that the external term is from an ontology that we sanction. Adjust
@valid_externals, currently qw(PATO PRO FMA CHEBI GO CL NCBITaxon ENVO) to add more.
It does not validate that the actual id is correct. Future work. Be careful.
Added Paths:
-----------
trunk/src/tools/add-to-external.pl
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From: <p_r...@us...> - 2008-06-22 10:36:06
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Revision: 757
http://obi.svn.sourceforge.net/obi/?rev=757&view=rev
Author: p_rocca_serra
Date: 2008-06-21 11:00:32 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
PRS:210608: addition of test relation Results_from allowing association between quality and Process
Modified Paths:
--------------
trunk/src/ontology/branches/Relations.owl
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From: <p_r...@us...> - 2008-06-22 08:39:09
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Revision: 748
http://obi.svn.sourceforge.net/obi/?rev=748&view=rev
Author: p_rocca_serra
Date: 2008-06-21 02:41:25 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
PRS: ongoing work: adding qualities(states) / protocol application and relations. will add metadata+ further restrictions later today
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
trunk/src/ontology/branches/Quality.owl
trunk/src/ontology/branches/Relations.owl
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From: <p_r...@us...> - 2008-06-22 08:16:22
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Revision: 755
http://obi.svn.sourceforge.net/obi/?rev=755&view=rev
Author: p_rocca_serra
Date: 2008-06-21 10:57:32 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
PRS: monomer moved under role and polymer under quality. both to be discussed in role branch
Modified Paths:
--------------
trunk/src/ontology/branches/Quality.owl
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From: <al...@us...> - 2008-06-22 08:03:49
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Revision: 762
http://obi.svn.sourceforge.net/obi/?rev=762&view=rev
Author: alanr
Date: 2008-06-21 20:49:57 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
remove stray comments
Modified Paths:
--------------
trunk/src/tools/add-to-external.pl
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From: <p_r...@us...> - 2008-06-22 02:22:35
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Revision: 758
http://obi.svn.sourceforge.net/obi/?rev=758&view=rev
Author: p_rocca_serra
Date: 2008-06-21 11:02:30 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
PRS:210608: addition of monomer under role
Modified Paths:
--------------
trunk/src/ontology/branches/Role.owl
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From: <p_r...@us...> - 2008-06-21 20:49:22
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Revision: 751
http://obi.svn.sourceforge.net/obi/?rev=751&view=rev
Author: p_rocca_serra
Date: 2008-06-21 10:36:22 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
PRS: adding more restrictions (input/output, reagent/device) when possible -> identification of gaps in coverage in instrument branch and also role branch. Need to "import" more terms from OBO Foundry ontologies.
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2008-06-21 20:48:21
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Revision: 752
http://obi.svn.sourceforge.net/obi/?rev=752&view=rev
Author: p_rocca_serra
Date: 2008-06-21 10:53:07 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
PRS: obsoletion of biomolecule (from biomaterial)
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
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From: <p_r...@us...> - 2008-06-21 20:48:21
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Revision: 753
http://obi.svn.sourceforge.net/obi/?rev=753&view=rev
Author: p_rocca_serra
Date: 2008-06-21 10:54:11 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
PRS: adding more restrictions (input/output, reagent/device) when possible -> identification of gaps in coverage in instrument branch and also role branch. Need to "import" more terms from OBO Foundry ontologies.
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2008-06-21 20:46:55
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Revision: 754
http://obi.svn.sourceforge.net/obi/?rev=754&view=rev
Author: p_rocca_serra
Date: 2008-06-21 10:54:49 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/src/ontology/branches/Quality.owl
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From: <p_r...@us...> - 2008-06-21 18:49:01
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Revision: 760
http://obi.svn.sourceforge.net/obi/?rev=760&view=rev
Author: p_rocca_serra
Date: 2008-06-21 11:04:31 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <p_r...@us...> - 2008-06-21 16:18:58
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Revision: 749
http://obi.svn.sourceforge.net/obi/?rev=749&view=rev
Author: p_rocca_serra
Date: 2008-06-21 08:30:36 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
PRS: metadata added to all new PA terms added (+26 classes)
Modified Paths:
--------------
trunk/src/ontology/branches/PlanAndPlannedProcess.owl
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From: <p_r...@us...> - 2008-06-21 16:18:52
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Revision: 750
http://obi.svn.sourceforge.net/obi/?rev=750&view=rev
Author: p_rocca_serra
Date: 2008-06-21 08:59:14 -0700 (Sat, 21 Jun 2008)
Log Message:
-----------
PRS: addition of 51 quality/state -> set restriction pointed to Associated Process or Protocol Application. Curation status set to uncurated. Note Definition could be automatically generated. Example_of_usage might not be required here due to restrictions used to define the class.
Modified Paths:
--------------
trunk/src/ontology/branches/Quality.owl
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From: <jam...@us...> - 2008-06-20 13:05:44
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Revision: 747
http://obi.svn.sourceforge.net/obi/?rev=747&view=rev
Author: jamesmalone
Date: 2008-06-20 06:05:52 -0700 (Fri, 20 Jun 2008)
Log Message:
-----------
'Software' class restored under obsolete.owl (previously deleted from file accidentally)
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
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From: <p_r...@us...> - 2008-06-20 12:22:57
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Revision: 746
http://obi.svn.sourceforge.net/obi/?rev=746&view=rev
Author: p_rocca_serra
Date: 2008-06-20 05:23:05 -0700 (Fri, 20 Jun 2008)
Log Message:
-----------
PRS: obseletion of biomaterial defined class (not restriction has_role (specimen_role or biological_role) has been removed
Modified Paths:
--------------
trunk/src/ontology/branches/Obsolete.owl
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From: <p_r...@us...> - 2008-06-20 12:22:06
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Revision: 745
http://obi.svn.sourceforge.net/obi/?rev=745&view=rev
Author: p_rocca_serra
Date: 2008-06-20 05:22:15 -0700 (Fri, 20 Jun 2008)
Log Message:
-----------
PRS: deprecating biomaterial and subclassing person under eukaryotes
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
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From: <p_r...@us...> - 2008-06-20 12:20:52
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Revision: 744
http://obi.svn.sourceforge.net/obi/?rev=744&view=rev
Author: p_rocca_serra
Date: 2008-06-20 05:20:57 -0700 (Fri, 20 Jun 2008)
Log Message:
-----------
PRS: removing underscore in label /preferedterm
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
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From: <man...@us...> - 2008-06-19 17:09:23
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Revision: 743
http://obi.svn.sourceforge.net/obi/?rev=743&view=rev
Author: manduchi
Date: 2008-06-19 10:09:31 -0700 (Thu, 19 Jun 2008)
Log Message:
-----------
modifications reflecting decisions of DT conference call on June 19, 2008
Modified Paths:
--------------
trunk/docs/developer/DT/EM_BkgCorrection_TimeSeries.xls
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From: <man...@us...> - 2008-06-19 13:06:57
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Revision: 742
http://obi.svn.sourceforge.net/obi/?rev=742&view=rev
Author: manduchi
Date: 2008-06-19 06:06:56 -0700 (Thu, 19 Jun 2008)
Log Message:
-----------
Proposed definitions for background correction and time series analysis, together with comments on issues
Added Paths:
-----------
trunk/docs/developer/DT/EM_BkgCorrection_TimeSeries.xls
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From: <al...@us...> - 2008-06-19 01:48:02
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Revision: 741
http://obi.svn.sourceforge.net/obi/?rev=741&view=rev
Author: alanr
Date: 2008-06-18 18:48:09 -0700 (Wed, 18 Jun 2008)
Log Message:
-----------
factor out (path-of-last-released-obi) from (lost-terms)
(path-of-released-obi) depends on the logical pathname "obi:releases;"
being defined, which is done when loading obi.asd, and assumes that
the releases directory is a sibling to the trunk.
If you want to be explicit in the kbs being compared in lost-terms,
instead of relying on (path-of-last-released-obi) use
(lost-terms :current kb1 :previous kb2)
Modified Paths:
--------------
trunk/src/tools/build/qc-queries.lisp
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From: <mco...@us...> - 2008-06-18 21:42:41
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Revision: 740
http://obi.svn.sourceforge.net/obi/?rev=740&view=rev
Author: mcourtot
Date: 2008-06-18 14:42:04 -0700 (Wed, 18 Jun 2008)
Log Message:
-----------
added wget for the OBI-ProtegeFriendly.pprj file, to get all the architecture ready for easy SVN commit
Modified Paths:
--------------
trunk/src/tools/build/OBIrelease.sh
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From: <mco...@us...> - 2008-06-18 21:00:36
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Revision: 739
http://obi.svn.sourceforge.net/obi/?rev=739&view=rev
Author: mcourtot
Date: 2008-06-18 13:59:32 -0700 (Wed, 18 Jun 2008)
Log Message:
-----------
added funding info from Chris S.
Modified Paths:
--------------
trunk/docs/developer/posters/obi_ismb_poster_v2.ppt
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From: <mco...@us...> - 2008-06-17 23:50:19
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Revision: 738
http://obi.svn.sourceforge.net/obi/?rev=738&view=rev
Author: mcourtot
Date: 2008-06-17 16:50:23 -0700 (Tue, 17 Jun 2008)
Log Message:
-----------
reorganization of resource page as approved during dev call
Modified Paths:
--------------
web/trunk/htdocs/resources/index.php
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From: <mco...@us...> - 2008-06-17 23:48:33
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Revision: 737
http://obi.svn.sourceforge.net/obi/?rev=737&view=rev
Author: mcourtot
Date: 2008-06-17 16:48:38 -0700 (Tue, 17 Jun 2008)
Log Message:
-----------
added new document page on sf website as approved during dev calle
Added Paths:
-----------
web/trunk/htdocs/resources/documents.php
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From: <mco...@us...> - 2008-06-17 23:13:40
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Revision: 736
http://obi.svn.sourceforge.net/obi/?rev=736&view=rev
Author: mcourtot
Date: 2008-06-17 16:13:47 -0700 (Tue, 17 Jun 2008)
Log Message:
-----------
added qc-queries:
# preforms some check on the file
# currently:
# --- is there any rdfs:Class (instead of owl:Class)
# --- list of terms missing a curation status instance
# --- list of terms with extra curation instance (only one allowed per term)
# --- list of (OBI) terms with non OBI IDs
# --- list of terms missing a label
# --- list of classes that are asserted under a defined class
# writes the result of the queries in the merged directory, in the file qc-queries-report.txt
# TODO: add lost-terms
Modified Paths:
--------------
trunk/src/tools/build/OBIrelease.sh
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