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From: <jzh...@us...> - 2017-01-25 03:31:17
|
Revision: 4088
http://sourceforge.net/p/obi/code/4088
Author: jzheng24
Date: 2017-01-25 03:31:16 +0000 (Wed, 25 Jan 2017)
Log Message:
-----------
Edit 'cell specimen' and add 'single cell specimen (OBI_0002127). See tracker: https://sourceforge.net/p/obi/obi-terms/828/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <sto...@us...> - 2017-01-03 21:27:37
|
Revision: 4087
http://sourceforge.net/p/obi/code/4087
Author: stoeckert
Date: 2017-01-03 21:27:36 +0000 (Tue, 03 Jan 2017)
Log Message:
-----------
added stained slide specimens as per tracker #825
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_outputs/OBO_imports.owl
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From: <sto...@us...> - 2017-01-03 21:27:04
|
Revision: 4086
http://sourceforge.net/p/obi/code/4086
Author: stoeckert
Date: 2017-01-03 21:27:02 +0000 (Tue, 03 Jan 2017)
Log Message:
-----------
added stained slide specimens as per tracker #825
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/OBO_input.txt
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From: <sto...@us...> - 2017-01-03 21:25:54
|
Revision: 4085
http://sourceforge.net/p/obi/code/4085
Author: stoeckert
Date: 2017-01-03 21:25:52 +0000 (Tue, 03 Jan 2017)
Log Message:
-----------
added stained slide specimens as per tracker #825
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2016-10-13 14:19:20
|
Revision: 4084
http://sourceforge.net/p/obi/code/4084
Author: jamesaoverton
Date: 2016-10-13 14:19:18 +0000 (Thu, 13 Oct 2016)
Log Message:
-----------
Committing OBI release 2016-10-11
Added Paths:
-----------
releases/2016-10-11/
releases/2016-10-11/README.txt
releases/2016-10-11/branches/
releases/2016-10-11/branches/OntoFox_inputs/
releases/2016-10-11/branches/OntoFox_inputs/ChEBI_input.txt
releases/2016-10-11/branches/OntoFox_inputs/GO_input.txt
releases/2016-10-11/branches/OntoFox_inputs/NCBITaxon_input.txt
releases/2016-10-11/branches/OntoFox_inputs/OBO_input.txt
releases/2016-10-11/branches/OntoFox_inputs/PATO_input.txt
releases/2016-10-11/branches/OntoFox_inputs/SO_input.txt
releases/2016-10-11/branches/OntoFox_inputs/UO_input.txt
releases/2016-10-11/branches/OntoFox_inputs/UO_input_instance.txt
releases/2016-10-11/branches/OntoFox_inputs/readme.txt
releases/2016-10-11/branches/OntoFox_outputs/
releases/2016-10-11/branches/OntoFox_outputs/ChEBI_imports.owl
releases/2016-10-11/branches/OntoFox_outputs/GO_imports.owl
releases/2016-10-11/branches/OntoFox_outputs/NCBITaxon_imports.owl
releases/2016-10-11/branches/OntoFox_outputs/OBO_imports.owl
releases/2016-10-11/branches/OntoFox_outputs/PATO_imports.owl
releases/2016-10-11/branches/OntoFox_outputs/SO_imports.owl
releases/2016-10-11/branches/OntoFox_outputs/UO_imports.owl
releases/2016-10-11/branches/OntoFox_outputs/UO_instance_imports.owl
releases/2016-10-11/branches/catalog-v001.xml
releases/2016-10-11/branches/doap.template
releases/2016-10-11/branches/external-byhand.owl
releases/2016-10-11/branches/modules/
releases/2016-10-11/branches/modules/biobank-specimens.owl
releases/2016-10-11/branches/modules/epitope-assays.owl
releases/2016-10-11/branches/modules/midlevel-assays.owl
releases/2016-10-11/branches/modules/obsolete.owl
releases/2016-10-11/branches/obi.owl
releases/2016-10-11/branches/templates/
releases/2016-10-11/branches/templates/biobank-specimens.tsv
releases/2016-10-11/branches/templates/epitope-assays.tsv
releases/2016-10-11/branches/templates/midlevel-assays.tsv
releases/2016-10-11/branches/templates/obsolete.tsv
releases/2016-10-11/docs/
releases/2016-10-11/docs/obi.tsv
releases/2016-10-11/docs/obi.txt
releases/2016-10-11/docs/obi_core.tsv
releases/2016-10-11/docs/obi_core.txt
releases/2016-10-11/docs/obi_iedb.tsv
releases/2016-10-11/docs/obi_iedb.txt
releases/2016-10-11/docs/obi_isa.tsv
releases/2016-10-11/docs/obi_isa.txt
releases/2016-10-11/obi.owl
releases/2016-10-11/obi_core.owl
releases/2016-10-11/obi_iedb.owl
releases/2016-10-11/obi_isa.owl
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From: <jam...@us...> - 2016-10-11 17:21:29
|
Revision: 4083
http://sourceforge.net/p/obi/code/4083
Author: jamesaoverton
Date: 2016-10-11 17:21:27 +0000 (Tue, 11 Oct 2016)
Log Message:
-----------
Include a few more annotation properties
Modified Paths:
--------------
trunk/src/tools/build/core.txt
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From: <jam...@us...> - 2016-10-11 17:12:49
|
Revision: 4082
http://sourceforge.net/p/obi/code/4082
Author: jamesaoverton
Date: 2016-10-11 17:12:47 +0000 (Tue, 11 Oct 2016)
Log Message:
-----------
Include more annotation properties in core
Modified Paths:
--------------
trunk/src/tools/build/core.txt
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From: <jam...@us...> - 2016-10-11 17:05:11
|
Revision: 4081
http://sourceforge.net/p/obi/code/4081
Author: jamesaoverton
Date: 2016-10-11 17:05:10 +0000 (Tue, 11 Oct 2016)
Log Message:
-----------
Remove OBI_0002117 synonym 'WES'
Modified Paths:
--------------
trunk/src/ontology/branches/templates/midlevel-assays.tsv
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From: <jam...@us...> - 2016-10-11 16:59:51
|
Revision: 4080
http://sourceforge.net/p/obi/code/4080
Author: jamesaoverton
Date: 2016-10-11 16:59:50 +0000 (Tue, 11 Oct 2016)
Log Message:
-----------
Remove hyphen from 'in-situ', fixes #821
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2016-09-26 19:13:56
|
Revision: 4079
http://sourceforge.net/p/obi/code/4079
Author: jamesaoverton
Date: 2016-09-26 19:13:55 +0000 (Mon, 26 Sep 2016)
Log Message:
-----------
Remove NamedIndividual 'prostate gland', fix #822
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_outputs/OBO_imports.owl
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From: <jam...@us...> - 2016-09-26 18:56:42
|
Revision: 4078
http://sourceforge.net/p/obi/code/4078
Author: jamesaoverton
Date: 2016-09-26 18:56:40 +0000 (Mon, 26 Sep 2016)
Log Message:
-----------
Add 8 new assays requested by ImmPort/IEDB, add new term ID list
Modified Paths:
--------------
trunk/src/ontology/branches/modules/midlevel-assays.owl
trunk/src/ontology/branches/templates/midlevel-assays.tsv
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20160926.tab
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From: <jam...@us...> - 2016-09-26 18:22:33
|
Revision: 4077
http://sourceforge.net/p/obi/code/4077
Author: jamesaoverton
Date: 2016-09-26 18:22:31 +0000 (Mon, 26 Sep 2016)
Log Message:
-----------
Fix non-Unix line endings and bad character encodings
Modified Paths:
--------------
trunk/src/ontology/branches/modules/midlevel-assays.owl
trunk/src/ontology/branches/templates/midlevel-assays.tsv
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From: <jam...@us...> - 2016-09-26 15:18:06
|
Revision: 4076
http://sourceforge.net/p/obi/code/4076
Author: jamesaoverton
Date: 2016-09-26 15:18:04 +0000 (Mon, 26 Sep 2016)
Log Message:
-----------
Import 'rare earth metal atom' from ChEBI
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/ChEBI_input.txt
trunk/src/ontology/branches/OntoFox_outputs/ChEBI_imports.owl
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From: <mbr...@us...> - 2016-09-21 16:41:12
|
Revision: 4075
http://sourceforge.net/p/obi/code/4075
Author: mbrochhausen
Date: 2016-09-21 16:41:11 +0000 (Wed, 21 Sep 2016)
Log Message:
-----------
added term and edited 'mean calculation' according to tracker item 807
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <sto...@us...> - 2016-08-29 14:51:04
|
Revision: 4074
http://sourceforge.net/p/obi/code/4074
Author: stoeckert
Date: 2016-08-29 14:51:02 +0000 (Mon, 29 Aug 2016)
Log Message:
-----------
terms added for tracker items 799, 813, 814
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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|
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From: <jzh...@us...> - 2016-08-24 15:42:10
|
Revision: 4073
http://sourceforge.net/p/obi/code/4073
Author: jzheng24
Date: 2016-08-24 15:42:08 +0000 (Wed, 24 Aug 2016)
Log Message:
-----------
add new term DOI (ticket: 818) and edit PubMed ID (ticket: 819)
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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|
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From: <jam...@us...> - 2016-07-11 23:23:20
|
Revision: 4072
http://sourceforge.net/p/obi/code/4072
Author: jamesaoverton
Date: 2016-07-11 23:23:19 +0000 (Mon, 11 Jul 2016)
Log Message:
-----------
Add README for 2016-06-30 release
Added Paths:
-----------
releases/2016-06-30/README.txt
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From: <jam...@us...> - 2016-07-11 23:16:04
|
Revision: 4071
http://sourceforge.net/p/obi/code/4071
Author: jamesaoverton
Date: 2016-07-11 23:16:02 +0000 (Mon, 11 Jul 2016)
Log Message:
-----------
Committing OBI release 2016-06-30
Added Paths:
-----------
releases/2016-06-30/
releases/2016-06-30/branches/
releases/2016-06-30/branches/OntoFox_inputs/
releases/2016-06-30/branches/OntoFox_inputs/ChEBI_input.txt
releases/2016-06-30/branches/OntoFox_inputs/GO_input.txt
releases/2016-06-30/branches/OntoFox_inputs/NCBITaxon_input.txt
releases/2016-06-30/branches/OntoFox_inputs/OBO_input.txt
releases/2016-06-30/branches/OntoFox_inputs/PATO_input.txt
releases/2016-06-30/branches/OntoFox_inputs/SO_input.txt
releases/2016-06-30/branches/OntoFox_inputs/UO_input.txt
releases/2016-06-30/branches/OntoFox_inputs/UO_input_instance.txt
releases/2016-06-30/branches/OntoFox_inputs/readme.txt
releases/2016-06-30/branches/OntoFox_outputs/
releases/2016-06-30/branches/OntoFox_outputs/ChEBI_imports.owl
releases/2016-06-30/branches/OntoFox_outputs/GO_imports.owl
releases/2016-06-30/branches/OntoFox_outputs/NCBITaxon_imports.owl
releases/2016-06-30/branches/OntoFox_outputs/OBO_imports.owl
releases/2016-06-30/branches/OntoFox_outputs/PATO_imports.owl
releases/2016-06-30/branches/OntoFox_outputs/SO_imports.owl
releases/2016-06-30/branches/OntoFox_outputs/UO_imports.owl
releases/2016-06-30/branches/OntoFox_outputs/UO_instance_imports.owl
releases/2016-06-30/branches/catalog-v001.xml
releases/2016-06-30/branches/doap.template
releases/2016-06-30/branches/external-byhand.owl
releases/2016-06-30/branches/modules/
releases/2016-06-30/branches/modules/biobank-specimens.owl
releases/2016-06-30/branches/modules/epitope-assays.owl
releases/2016-06-30/branches/modules/midlevel-assays.owl
releases/2016-06-30/branches/modules/obsolete.owl
releases/2016-06-30/branches/obi.owl
releases/2016-06-30/branches/templates/
releases/2016-06-30/branches/templates/biobank-specimens.tsv
releases/2016-06-30/branches/templates/epitope-assays.tsv
releases/2016-06-30/branches/templates/midlevel-assays.tsv
releases/2016-06-30/branches/templates/obsolete.tsv
releases/2016-06-30/docs/
releases/2016-06-30/docs/obi.tsv
releases/2016-06-30/docs/obi.txt
releases/2016-06-30/docs/obi_core.tsv
releases/2016-06-30/docs/obi_core.txt
releases/2016-06-30/docs/obi_iedb.tsv
releases/2016-06-30/docs/obi_iedb.txt
releases/2016-06-30/docs/obi_isa.tsv
releases/2016-06-30/docs/obi_isa.txt
releases/2016-06-30/obi.owl
releases/2016-06-30/obi_core.owl
releases/2016-06-30/obi_iedb.owl
releases/2016-06-30/obi_isa.owl
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From: <jam...@us...> - 2016-06-30 20:07:45
|
Revision: 4070
http://sourceforge.net/p/obi/code/4070
Author: jamesaoverton
Date: 2016-06-30 20:07:43 +0000 (Thu, 30 Jun 2016)
Log Message:
-----------
Actually fix #803
- #803 'specimen from organism' uses 'derives from' some
('material anatomical entity' or 'anatomical cluster')
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2016-06-30 19:54:44
|
Revision: 4069
http://sourceforge.net/p/obi/code/4069
Author: jamesaoverton
Date: 2016-06-30 19:54:41 +0000 (Thu, 30 Jun 2016)
Log Message:
-----------
Replace CARO with UBERON: #803, #804, #805
- #805 replace five CARO terms with UBERON terms
- CARO_0000004 portion of organism substance -> UBERON_0000463
- CARO_0000043 portion of tissue -> UBERON_0000479
- CARO_0000055 multi-tissue structure -> UBERON_0000481
- CARO_0000066 epithelium -> UBERON_0000483
- CARO_0001008 gross anatomical part -> UBERON_0000465
- simplify OBO_input.txt
- update OBO_imports.owl
- #804 rename 'tissue specimen' to 'specimen from organism'
- #803 'specimen from organism' uses 'derives from' some
('material anatomical entity' or 'anatomical cluster')
Modified Paths:
--------------
trunk/src/ontology/branches/OntoFox_inputs/OBO_input.txt
trunk/src/ontology/branches/OntoFox_outputs/OBO_imports.owl
trunk/src/ontology/branches/external-byhand.owl
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2016-06-14 16:29:10
|
Revision: 4068
http://sourceforge.net/p/obi/code/4068
Author: jamesaoverton
Date: 2016-06-14 16:29:09 +0000 (Tue, 14 Jun 2016)
Log Message:
-----------
Fix bad ID assignment and updated newIDs tables
I assigned OBI:0002106 to 'Human 6x630K CGH Whole Genome Tiling Array'
but that ID was already taken, leading to logical errors.
That term now has ID OBI:0002109.
I updated the new terms lists with that correction
and some missing IDs that led to my mistake.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
trunk/src/ontology/spreadsheets/new_ids/newIDs_20160612.tab
trunk/src/ontology/spreadsheets/new_ids/newIDs_20160613.tab
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From: <jam...@us...> - 2016-06-14 15:54:27
|
Revision: 4067
http://sourceforge.net/p/obi/code/4067
Author: jamesaoverton
Date: 2016-06-14 15:54:26 +0000 (Tue, 14 Jun 2016)
Log Message:
-----------
Add 10 new assays for IEDB
Modified Paths:
--------------
trunk/src/ontology/branches/modules/epitope-assays.owl
trunk/src/ontology/branches/modules/midlevel-assays.owl
trunk/src/ontology/branches/templates/epitope-assays.tsv
trunk/src/ontology/branches/templates/midlevel-assays.tsv
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20160613.tab
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From: <jam...@us...> - 2016-06-14 15:51:58
|
Revision: 4066
http://sourceforge.net/p/obi/code/4066
Author: jamesaoverton
Date: 2016-06-14 15:51:57 +0000 (Tue, 14 Jun 2016)
Log Message:
-----------
Assign new ID and add newIDs sheet
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20160612.tab
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From: <jam...@us...> - 2016-06-14 15:42:45
|
Revision: 4065
http://sourceforge.net/p/obi/code/4065
Author: jamesaoverton
Date: 2016-06-14 15:42:43 +0000 (Tue, 14 Jun 2016)
Log Message:
-----------
Fix punning bug by declaring class BFO:0000003
Protege 5 complained about punning BFO:0000062 and BFO:0000063
as both ObjectProperty and AnnotationProperty.
The fix seems to be asserting that BFO:0000003 is an owl:Class
in external-by-hand.owl.
Otherwise BFO:0000003 is assumed to be an AnnotationProperty,
and since it is the domain and range of those relations
HermiT infers that the relations are AnnotationProperties.
(I think.)
Modified Paths:
--------------
trunk/src/ontology/branches/external-byhand.owl
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From: <jam...@us...> - 2016-06-13 18:41:52
|
Revision: 4064
http://sourceforge.net/p/obi/code/4064
Author: jamesaoverton
Date: 2016-06-13 18:41:51 +0000 (Mon, 13 Jun 2016)
Log Message:
-----------
Fix OntologyIRIs and line endings
Modified Paths:
--------------
trunk/src/ontology/branches/Makefile
trunk/src/ontology/branches/OntoFox_inputs/ChEBI_input.txt
trunk/src/ontology/branches/OntoFox_inputs/GO_input.txt
trunk/src/ontology/branches/OntoFox_inputs/NCBITaxon_input.txt
trunk/src/ontology/branches/OntoFox_inputs/OBO_input.txt
trunk/src/ontology/branches/OntoFox_inputs/PATO_input.txt
trunk/src/ontology/branches/OntoFox_inputs/SO_input.txt
trunk/src/ontology/branches/OntoFox_inputs/UO_input.txt
trunk/src/ontology/branches/OntoFox_inputs/UO_input_instance.txt
trunk/src/ontology/branches/OntoFox_outputs/ChEBI_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/GO_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/NCBITaxon_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/OBO_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/PATO_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/SO_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/UO_imports.owl
trunk/src/ontology/branches/OntoFox_outputs/UO_instance_imports.owl
trunk/src/ontology/branches/catalog-v001.xml
trunk/src/ontology/branches/modules/epitope-assays.owl
trunk/src/ontology/branches/modules/midlevel-assays.owl
trunk/src/ontology/branches/modules/obsolete.owl
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