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From: <bjo...@us...> - 2015-11-18 00:57:12
|
Revision: 4013
http://sourceforge.net/p/obi/code/4013
Author: bjoernpeters
Date: 2015-11-18 00:57:11 +0000 (Wed, 18 Nov 2015)
Log Message:
-----------
Manuscript version sent out for review 11/17. This version has all changes accepted, the previous one has all changes still in.
Modified Paths:
--------------
trunk/docs/papers/release/2015 PLoS ONE submission/Manuscript 2015.doc
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
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From: <bjo...@us...> - 2015-11-18 00:51:43
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Revision: 4012
http://sourceforge.net/p/obi/code/4012
Author: bjoernpeters
Date: 2015-11-18 00:51:41 +0000 (Wed, 18 Nov 2015)
Log Message:
-----------
Modified Paths:
--------------
trunk/docs/papers/release/2015 PLoS ONE submission/Manuscript 2015.doc
Added Paths:
-----------
trunk/docs/papers/release/2015 PLoS ONE submission/Supplemental Table 1.xlsx
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From: <sto...@us...> - 2015-11-17 22:24:04
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Revision: 4011
http://sourceforge.net/p/obi/code/4011
Author: stoeckert
Date: 2015-11-17 22:24:02 +0000 (Tue, 17 Nov 2015)
Log Message:
-----------
added biobank terms #778
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <bjo...@us...> - 2015-11-11 04:21:09
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Revision: 4010
http://sourceforge.net/p/obi/code/4010
Author: bjoernpeters
Date: 2015-11-11 04:21:07 +0000 (Wed, 11 Nov 2015)
Log Message:
-----------
Added Paths:
-----------
trunk/docs/papers/release/2015 PLoS ONE submission/
trunk/docs/papers/release/2015 PLoS ONE submission/Figure 1.jpg
trunk/docs/papers/release/2015 PLoS ONE submission/Figure 1.pptx
trunk/docs/papers/release/2015 PLoS ONE submission/Figure 2.pdf
trunk/docs/papers/release/2015 PLoS ONE submission/Figure 2.ppt
trunk/docs/papers/release/2015 PLoS ONE submission/Figure 2.tif
trunk/docs/papers/release/2015 PLoS ONE submission/Figure 3.pptx
trunk/docs/papers/release/2015 PLoS ONE submission/Manuscript 2015.doc
trunk/docs/papers/release/2015 PLoS ONE submission/Supplemental Table 2.xls
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From: <jam...@us...> - 2015-11-04 16:04:52
|
Revision: 4009
http://sourceforge.net/p/obi/code/4009
Author: jamesaoverton
Date: 2015-11-04 16:04:50 +0000 (Wed, 04 Nov 2015)
Log Message:
-----------
Committing OBI release 2015-10-20
Added Paths:
-----------
releases/2015-10-20/
releases/2015-10-20/README.txt
releases/2015-10-20/branches/
releases/2015-10-20/branches/OntoFox_inputs/
releases/2015-10-20/branches/OntoFox_inputs/ChEBI_input.txt
releases/2015-10-20/branches/OntoFox_inputs/GO_input.txt
releases/2015-10-20/branches/OntoFox_inputs/NCBITaxon_input.txt
releases/2015-10-20/branches/OntoFox_inputs/OBO_input.txt
releases/2015-10-20/branches/OntoFox_inputs/PATO_input.txt
releases/2015-10-20/branches/OntoFox_inputs/SO_input.txt
releases/2015-10-20/branches/OntoFox_inputs/UO_input.txt
releases/2015-10-20/branches/OntoFox_inputs/UO_input_instance.txt
releases/2015-10-20/branches/OntoFox_inputs/readme.txt
releases/2015-10-20/branches/OntoFox_outputs/
releases/2015-10-20/branches/OntoFox_outputs/ChEBI_imports.owl
releases/2015-10-20/branches/OntoFox_outputs/GO_imports.owl
releases/2015-10-20/branches/OntoFox_outputs/NCBITaxon_imports.owl
releases/2015-10-20/branches/OntoFox_outputs/OBO_imports.owl
releases/2015-10-20/branches/OntoFox_outputs/PATO_imports.owl
releases/2015-10-20/branches/OntoFox_outputs/SO_imports.owl
releases/2015-10-20/branches/OntoFox_outputs/UO_imports.owl
releases/2015-10-20/branches/OntoFox_outputs/UO_instance_imports.owl
releases/2015-10-20/branches/catalog-v001.xml
releases/2015-10-20/branches/doap.template
releases/2015-10-20/branches/external-byhand.owl
releases/2015-10-20/branches/modules/
releases/2015-10-20/branches/modules/epitope-assays.owl
releases/2015-10-20/branches/modules/midlevel-assays.owl
releases/2015-10-20/branches/modules/obsolete.owl
releases/2015-10-20/branches/obi.owl
releases/2015-10-20/branches/templates/
releases/2015-10-20/branches/templates/epitope-assays.tsv
releases/2015-10-20/branches/templates/midlevel-assays.tsv
releases/2015-10-20/branches/templates/obsolete.tsv
releases/2015-10-20/docs/
releases/2015-10-20/docs/obi.tsv
releases/2015-10-20/docs/obi.txt
releases/2015-10-20/docs/obi_core.tsv
releases/2015-10-20/docs/obi_core.txt
releases/2015-10-20/docs/obi_iedb.tsv
releases/2015-10-20/docs/obi_iedb.txt
releases/2015-10-20/docs/obi_isa.tsv
releases/2015-10-20/docs/obi_isa.txt
releases/2015-10-20/obi.owl
releases/2015-10-20/obi_core.owl
releases/2015-10-20/obi_iedb.owl
releases/2015-10-20/obi_isa.owl
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From: <jam...@us...> - 2015-10-20 14:59:23
|
Revision: 4008
http://sourceforge.net/p/obi/code/4008
Author: jamesaoverton
Date: 2015-10-20 14:59:21 +0000 (Tue, 20 Oct 2015)
Log Message:
-----------
Add new source directories to release
Modified Paths:
--------------
trunk/src/tools/build/build.xml
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From: <jam...@us...> - 2015-10-19 19:44:17
|
Revision: 4007
http://sourceforge.net/p/obi/code/4007
Author: jamesaoverton
Date: 2015-10-19 19:44:16 +0000 (Mon, 19 Oct 2015)
Log Message:
-----------
Adding assay templates from IEDB
- created `templates/` and `modules/` directories
- added `templates/obsolete.tsv` with obsolete IEDB assays
- added `templates/midlevel-assays.tsv`
- added `templates/epitope-assays.tsv`
- added OWL files for each template to `modules/`
- updated `catalog-v001.xml` to point to modules
- add `Makefile` for building modules from templates
- removed templated terms from `obi.owl`
- added import statements for each module to `obi.owl`
- added newID sheet listing 50 new terms
Modified Paths:
--------------
trunk/src/ontology/branches/catalog-v001.xml
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/branches/Makefile
trunk/src/ontology/branches/modules/
trunk/src/ontology/branches/modules/epitope-assays.owl
trunk/src/ontology/branches/modules/midlevel-assays.owl
trunk/src/ontology/branches/modules/obsolete.owl
trunk/src/ontology/branches/templates/
trunk/src/ontology/branches/templates/epitope-assays.tsv
trunk/src/ontology/branches/templates/midlevel-assays.tsv
trunk/src/ontology/branches/templates/obsolete.tsv
trunk/src/ontology/spreadsheets/new_ids/newIDs_20151019.tab
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From: <jam...@us...> - 2015-10-19 19:22:17
|
Revision: 4006
http://sourceforge.net/p/obi/code/4006
Author: jamesaoverton
Date: 2015-10-19 19:22:16 +0000 (Mon, 19 Oct 2015)
Log Message:
-----------
Update to RO release 2015-10-07
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2015-09-30 22:05:17
|
Revision: 4005
http://sourceforge.net/p/obi/code/4005
Author: jamesaoverton
Date: 2015-09-30 22:05:16 +0000 (Wed, 30 Sep 2015)
Log Message:
-----------
Fix README for 2015-09-15 release
Modified Paths:
--------------
releases/2015-09-15/README.txt
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From: <jzh...@us...> - 2015-09-29 14:06:42
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Revision: 4004
http://sourceforge.net/p/obi/code/4004
Author: jzheng24
Date: 2015-09-29 14:06:40 +0000 (Tue, 29 Sep 2015)
Log Message:
-----------
OBI_0600012
- change label to "environmental material collection process"
- add SubClassOf: 'has specified input' some 'environmental material'
Details see tracker: https://sourceforge.net/p/obi/obi-terms/779/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2015-09-25 18:00:46
|
Revision: 4003
http://sourceforge.net/p/obi/code/4003
Author: jamesaoverton
Date: 2015-09-25 18:00:45 +0000 (Fri, 25 Sep 2015)
Log Message:
-----------
Committing OBI release 2015-09-15
Added Paths:
-----------
releases/2015-09-15/
releases/2015-09-15/README.txt
releases/2015-09-15/branches/
releases/2015-09-15/branches/OntoFox_inputs/
releases/2015-09-15/branches/OntoFox_inputs/ChEBI_input.txt
releases/2015-09-15/branches/OntoFox_inputs/GO_input.txt
releases/2015-09-15/branches/OntoFox_inputs/NCBITaxon_input.txt
releases/2015-09-15/branches/OntoFox_inputs/OBO_input.txt
releases/2015-09-15/branches/OntoFox_inputs/PATO_input.txt
releases/2015-09-15/branches/OntoFox_inputs/SO_input.txt
releases/2015-09-15/branches/OntoFox_inputs/UO_input.txt
releases/2015-09-15/branches/OntoFox_inputs/UO_input_instance.txt
releases/2015-09-15/branches/OntoFox_inputs/readme.txt
releases/2015-09-15/branches/OntoFox_outputs/
releases/2015-09-15/branches/OntoFox_outputs/ChEBI_imports.owl
releases/2015-09-15/branches/OntoFox_outputs/GO_imports.owl
releases/2015-09-15/branches/OntoFox_outputs/NCBITaxon_imports.owl
releases/2015-09-15/branches/OntoFox_outputs/OBO_imports.owl
releases/2015-09-15/branches/OntoFox_outputs/PATO_imports.owl
releases/2015-09-15/branches/OntoFox_outputs/SO_imports.owl
releases/2015-09-15/branches/OntoFox_outputs/UO_imports.owl
releases/2015-09-15/branches/OntoFox_outputs/UO_instance_imports.owl
releases/2015-09-15/branches/catalog-v001.xml
releases/2015-09-15/branches/doap.template
releases/2015-09-15/branches/external-byhand.owl
releases/2015-09-15/branches/obi.owl
releases/2015-09-15/docs/
releases/2015-09-15/docs/obi.tsv
releases/2015-09-15/docs/obi.txt
releases/2015-09-15/docs/obi_core.tsv
releases/2015-09-15/docs/obi_core.txt
releases/2015-09-15/docs/obi_iedb.tsv
releases/2015-09-15/docs/obi_iedb.txt
releases/2015-09-15/docs/obi_isa.tsv
releases/2015-09-15/docs/obi_isa.txt
releases/2015-09-15/obi.owl
releases/2015-09-15/obi_core.owl
releases/2015-09-15/obi_iedb.owl
releases/2015-09-15/obi_isa.owl
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From: <jam...@us...> - 2015-09-15 16:26:21
|
Revision: 4002
http://sourceforge.net/p/obi/code/4002
Author: jamesaoverton
Date: 2015-09-15 16:26:19 +0000 (Tue, 15 Sep 2015)
Log Message:
-----------
Added OBI_0001975 chromatin immunoprecipitation.
Closes: https://sourceforge.net/p/obi/obi-terms/768/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
trunk/src/ontology/spreadsheets/new_ids/newIDs_20150915.tab
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From: <jam...@us...> - 2015-09-15 16:10:24
|
Revision: 4001
http://sourceforge.net/p/obi/code/4001
Author: jamesaoverton
Date: 2015-09-15 16:10:23 +0000 (Tue, 15 Sep 2015)
Log Message:
-----------
Add alternative terms for:
- OBI_0001971 Ion 316 Chip v2
- OBI_0001972 Ion 318 Chip v2
- OBI_0001973 ion semiconductor chip
- OBI_0001974 Ion 314 Chip v2
Fix datatypes.
Closes tracker items: 766, 773, 774, 775
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2015-09-15 14:26:30
|
Revision: 4000
http://sourceforge.net/p/obi/code/4000
Author: jamesaoverton
Date: 2015-09-15 14:26:28 +0000 (Tue, 15 Sep 2015)
Log Message:
-----------
Assign IDs for four new terms:
- OBI_0001971 Ion 316 Chip v2
- OBI_0001972 Ion 318 Chip v2
- OBI_0001973 ion semiconductor chip
- OBI_0001974 Ion 314 Chip v2
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20150915.tab
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From: <jam...@us...> - 2015-09-14 16:01:46
|
Revision: 3999
http://sourceforge.net/p/obi/code/3999
Author: jamesaoverton
Date: 2015-09-14 16:01:45 +0000 (Mon, 14 Sep 2015)
Log Message:
-----------
Update references, use PDF version of Figure 2
Modified Paths:
--------------
trunk/docs/papers/release/Manuscript 2014.doc
Added Paths:
-----------
trunk/docs/papers/release/Figure 2.pdf
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From: <jai...@us...> - 2015-09-14 00:07:44
|
Revision: 3998
http://sourceforge.net/p/obi/code/3998
Author: jainwave
Date: 2015-09-14 00:07:42 +0000 (Mon, 14 Sep 2015)
Log Message:
-----------
adding ion chips
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jam...@us...> - 2015-08-31 14:31:05
|
Revision: 3997
http://sourceforge.net/p/obi/code/3997
Author: jamesaoverton
Date: 2015-08-31 14:31:04 +0000 (Mon, 31 Aug 2015)
Log Message:
-----------
Update figure to use "1.2 mg/ml"
Modified Paths:
--------------
trunk/docs/papers/release/Figure 2.jpg
trunk/docs/papers/release/Figure 2.ppt
trunk/docs/papers/release/Figure 2.tif
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From: <p_r...@us...> - 2015-08-27 17:47:11
|
Revision: 3996
http://sourceforge.net/p/obi/code/3996
Author: p_rocca_serra
Date: 2015-08-27 17:47:09 +0000 (Thu, 27 Aug 2015)
Log Message:
-----------
reinstantiating updates to ISA section in OBI manuscript
Modified Paths:
--------------
trunk/docs/papers/release/Manuscript 2014.doc
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From: <jam...@us...> - 2015-08-22 13:19:54
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Revision: 3995
http://sourceforge.net/p/obi/code/3995
Author: jamesaoverton
Date: 2015-08-22 13:19:52 +0000 (Sat, 22 Aug 2015)
Log Message:
-----------
Update manuscript Figure 2
- change 'contained in' to 'located in'
- change '100 mg/dl' to '1000 mg/ml'
Modified Paths:
--------------
trunk/docs/papers/release/Figure 2.jpg
trunk/docs/papers/release/Figure 2.ppt
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From: <sto...@us...> - 2015-08-13 14:13:51
|
Revision: 3994
http://sourceforge.net/p/obi/code/3994
Author: stoeckert
Date: 2015-08-13 14:13:50 +0000 (Thu, 13 Aug 2015)
Log Message:
-----------
updated EuPath application
Modified Paths:
--------------
trunk/docs/papers/release/Manuscript 2014.doc
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From: <bjo...@us...> - 2015-08-02 21:25:07
|
Revision: 3993
http://sourceforge.net/p/obi/code/3993
Author: bjoernpeters
Date: 2015-08-02 21:25:05 +0000 (Sun, 02 Aug 2015)
Log Message:
-----------
final read through; moved sections around for plos one; removed the evidence ontology part which should be its own paper; adressed remaining comments where possible.
Modified Paths:
--------------
trunk/docs/papers/release/Manuscript 2014.doc
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/csort.MYI
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/misc.MYD
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/misc.MYI
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/refs.MYI
trunk/docs/papers/release/release.Data/Trash/Trash.Data/rdb/refs_ext.MYI
trunk/docs/papers/release/release.Data/rdb/csort.MYD
trunk/docs/papers/release/release.Data/rdb/csort.MYI
trunk/docs/papers/release/release.Data/rdb/jterms.MYI
trunk/docs/papers/release/release.Data/rdb/misc.MYD
trunk/docs/papers/release/release.Data/rdb/misc.MYI
trunk/docs/papers/release/release.Data/rdb/refs.MYD
trunk/docs/papers/release/release.Data/rdb/refs.MYI
trunk/docs/papers/release/release.Data/rdb/refs_ext.MYD
trunk/docs/papers/release/release.Data/rdb/refs_ext.MYI
trunk/docs/papers/release/release.Data/rdb/terms.MYD
trunk/docs/papers/release/release.Data/rdb/terms.MYI
trunk/docs/papers/release/release.enl
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From: <jzh...@us...> - 2015-07-28 14:37:32
|
Revision: 3992
http://sourceforge.net/p/obi/code/3992
Author: jzheng24
Date: 2015-07-28 14:37:30 +0000 (Tue, 28 Jul 2015)
Log Message:
-----------
changes made based on the trackers:
https://sourceforge.net/p/obi/obi-terms/767/
https://sourceforge.net/p/obi/obi-terms/757/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2015-07-15 18:10:30
|
Revision: 3992
http://sourceforge.net/p/obi/code/3992
Author: jzheng24
Date: 2015-07-15 18:10:28 +0000 (Wed, 15 Jul 2015)
Log Message:
-----------
changes made based on the trackers:
https://sourceforge.net/p/obi/obi-terms/767/
https://sourceforge.net/p/obi/obi-terms/757/
https://sourceforge.net/p/obi/obi-terms/102/
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
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From: <jzh...@us...> - 2015-06-08 15:14:27
|
Revision: 3991
http://sourceforge.net/p/obi/code/3991
Author: jzheng24
Date: 2015-06-08 15:14:26 +0000 (Mon, 08 Jun 2015)
Log Message:
-----------
update term labels based on OBI 2015-04-13 release
Modified Paths:
--------------
trunk/docs/papers/release/OBI-core.cmap
trunk/docs/papers/release/OBI-core.jpg
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From: <jam...@us...> - 2015-06-08 14:09:36
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Revision: 3990
http://sourceforge.net/p/obi/code/3990
Author: jamesaoverton
Date: 2015-06-08 14:09:35 +0000 (Mon, 08 Jun 2015)
Log Message:
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Add GO:0001047 'core promoter binding' to imports
Modified Paths:
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trunk/src/ontology/branches/OntoFox_inputs/GO_input.txt
trunk/src/ontology/branches/OntoFox_outputs/GO_imports.owl
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