Menu
▾
▴
obi-svn-commit — Mailing list to receive notices of commits to the OBI SVN.
You can subscribe to this list here.
| 2007 |
Jan
|
Feb
|
Mar
|
Apr
(3) |
May
(6) |
Jun
(29) |
Jul
(37) |
Aug
(20) |
Sep
(9) |
Oct
(24) |
Nov
(14) |
Dec
(39) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2008 |
Jan
(61) |
Feb
(64) |
Mar
(118) |
Apr
(92) |
May
(130) |
Jun
(106) |
Jul
(86) |
Aug
(32) |
Sep
(65) |
Oct
(126) |
Nov
(125) |
Dec
(82) |
| 2009 |
Jan
(118) |
Feb
(99) |
Mar
(140) |
Apr
(30) |
May
(25) |
Jun
(43) |
Jul
(152) |
Aug
(130) |
Sep
(43) |
Oct
(285) |
Nov
(214) |
Dec
(96) |
| 2010 |
Jan
(44) |
Feb
(26) |
Mar
(143) |
Apr
(24) |
May
(36) |
Jun
(42) |
Jul
(12) |
Aug
(29) |
Sep
(7) |
Oct
(24) |
Nov
(6) |
Dec
(27) |
| 2011 |
Jan
(4) |
Feb
(6) |
Mar
(28) |
Apr
(37) |
May
(27) |
Jun
(25) |
Jul
(68) |
Aug
(14) |
Sep
(8) |
Oct
(36) |
Nov
(10) |
Dec
(33) |
| 2012 |
Jan
(56) |
Feb
(14) |
Mar
(32) |
Apr
(22) |
May
(35) |
Jun
(41) |
Jul
(66) |
Aug
(1) |
Sep
(7) |
Oct
(6) |
Nov
(6) |
Dec
(4) |
| 2013 |
Jan
(9) |
Feb
(5) |
Mar
(21) |
Apr
(18) |
May
(24) |
Jun
(33) |
Jul
(4) |
Aug
(7) |
Sep
(17) |
Oct
(50) |
Nov
(18) |
Dec
(10) |
| 2014 |
Jan
(1) |
Feb
(3) |
Mar
(12) |
Apr
(2) |
May
(2) |
Jun
(2) |
Jul
|
Aug
(4) |
Sep
(2) |
Oct
(1) |
Nov
(3) |
Dec
(9) |
| 2015 |
Jan
(6) |
Feb
(2) |
Mar
(15) |
Apr
(2) |
May
(5) |
Jun
(4) |
Jul
(2) |
Aug
(5) |
Sep
(8) |
Oct
(3) |
Nov
(9) |
Dec
(18) |
| 2016 |
Jan
(3) |
Feb
(2) |
Mar
(15) |
Apr
(1) |
May
(4) |
Jun
(10) |
Jul
(2) |
Aug
(2) |
Sep
(5) |
Oct
(5) |
Nov
|
Dec
|
| 2017 |
Jan
(4) |
Feb
|
Mar
|
Apr
|
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: <jzh...@us...> - 2013-07-29 22:27:04
|
Revision: 3813
http://sourceforge.net/p/obi/code/3813
Author: jzheng24
Date: 2013-07-29 22:27:03 +0000 (Mon, 29 Jul 2013)
Log Message:
-----------
OBI ids assigned to newly added terms
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20130729.tab
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jzh...@us...> - 2013-07-29 22:26:24
|
Revision: 3812
http://sourceforge.net/p/obi/code/3812
Author: jzheng24
Date: 2013-07-29 22:26:21 +0000 (Mon, 29 Jul 2013)
Log Message:
-----------
Added 6 new assay terms requested by ENCODE.
Details of newly added terms, please see tracker:
https://sourceforge.net/p/obi/obi-terms/661/
Added obsolescence reason and set deprecated value data type as boolean of terms deprecated during CL/CLO/OBI alignment work (done by Matt)
Modified Paths:
--------------
trunk/src/ontology/branches/catalog-v001.xml
trunk/src/ontology/branches/obi.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jzh...@us...> - 2013-07-29 21:28:34
|
Revision: 3811
http://sourceforge.net/p/obi/code/3811
Author: jzheng24
Date: 2013-07-29 21:28:32 +0000 (Mon, 29 Jul 2013)
Log Message:
-----------
import miRNA from SO
Modified Paths:
--------------
trunk/src/ontology/branches/external-byhand.owl
trunk/src/ontology/branches/external.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jam...@us...> - 2013-07-29 15:01:54
|
Revision: 3810
http://sourceforge.net/p/obi/code/3810
Author: jamesaoverton
Date: 2013-07-29 15:01:53 +0000 (Mon, 29 Jul 2013)
Log Message:
-----------
Removed all references to 'information structural entity' from data prototype.
Modified Paths:
--------------
trunk/src/examples/development/data-prototype.owl
trunk/src/examples/development/data-prototype.pdf
trunk/src/examples/development/data-prototype.txt
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jam...@us...> - 2013-06-25 19:42:54
|
Revision: 3809
http://sourceforge.net/p/obi/code/3809
Author: jamesaoverton
Date: 2013-06-25 19:42:52 +0000 (Tue, 25 Jun 2013)
Log Message:
-----------
Jie asked for a couple of IRI changes to the data prototype.
Modified Paths:
--------------
trunk/src/examples/development/data-prototype.owl
trunk/src/examples/development/data-prototype.pdf
trunk/src/examples/development/data-prototype.txt
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jam...@us...> - 2013-06-25 14:16:48
|
Revision: 3808
http://sourceforge.net/p/obi/code/3808
Author: jamesaoverton
Date: 2013-06-25 14:16:43 +0000 (Tue, 25 Jun 2013)
Log Message:
-----------
Updated data prototype with categorical and textual examples, and from Jie's comments.
Modified Paths:
--------------
trunk/src/examples/development/data-prototype.owl
trunk/src/examples/development/data-prototype.pdf
trunk/src/examples/development/data-prototype.txt
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jam...@us...> - 2013-06-18 15:18:10
|
Revision: 3807
http://sourceforge.net/p/obi/code/3807
Author: jamesaoverton
Date: 2013-06-18 15:18:08 +0000 (Tue, 18 Jun 2013)
Log Message:
-----------
Added prediction and setting examples to data-prototype.
Modified Paths:
--------------
trunk/src/examples/development/data-prototype.owl
trunk/src/examples/development/data-prototype.pdf
trunk/src/examples/development/data-prototype.txt
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jam...@us...> - 2013-06-17 20:28:49
|
Revision: 3806
http://sourceforge.net/p/obi/code/3806
Author: jamesaoverton
Date: 2013-06-17 20:28:48 +0000 (Mon, 17 Jun 2013)
Log Message:
-----------
Removed determinate mass from data-prototype and added assay.
Modified Paths:
--------------
trunk/src/examples/development/data-prototype.owl
trunk/src/examples/development/data-prototype.pdf
trunk/src/examples/development/data-prototype.txt
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jam...@us...> - 2013-06-14 20:06:52
|
Revision: 3805
http://sourceforge.net/p/obi/code/3805
Author: jamesaoverton
Date: 2013-06-14 20:06:51 +0000 (Fri, 14 Jun 2013)
Log Message:
-----------
Fixed links in data-prototype, added PDF version.
Modified Paths:
--------------
trunk/src/examples/development/data-prototype.txt
Added Paths:
-----------
trunk/src/examples/development/data-prototype.pdf
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jam...@us...> - 2013-06-14 20:06:00
|
Revision: 3804
http://sourceforge.net/p/obi/code/3804
Author: jamesaoverton
Date: 2013-06-14 20:05:58 +0000 (Fri, 14 Jun 2013)
Log Message:
-----------
Updated SVN link.
Modified Paths:
--------------
trunk/src/tools/build/README.md
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jzh...@us...> - 2013-06-12 17:05:23
|
Revision: 3803
http://sourceforge.net/p/obi/code/3803
Author: jzheng24
Date: 2013-06-12 17:05:21 +0000 (Wed, 12 Jun 2013)
Log Message:
-----------
add axiom
'has part' some 'enzymatic ligation'
to class:'multiplex ligation-mediated amplification'
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jzh...@us...> - 2013-06-12 16:45:25
|
Revision: 3802
http://sourceforge.net/p/obi/code/3802
Author: jzheng24
Date: 2013-06-12 16:45:23 +0000 (Wed, 12 Jun 2013)
Log Message:
-----------
OBI ids were assigned to newly added terms
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20130612.tab
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jzh...@us...> - 2013-06-12 16:13:11
|
Revision: 3802
http://obi.svn.sourceforge.net/obi/?rev=3802&view=rev
Author: jzheng24
Date: 2013-06-12 16:13:04 +0000 (Wed, 12 Jun 2013)
Log Message:
-----------
make minor changes on axioms of 4 assays request by ENCODE project
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jzh...@us...> - 2013-06-12 05:31:19
|
Revision: 3801
http://obi.svn.sourceforge.net/obi/?rev=3801&view=rev
Author: jzheng24
Date: 2013-06-12 05:31:04 +0000 (Wed, 12 Jun 2013)
Log Message:
-----------
Add ENCODE project request terms.
Details see tracker:
https://sourceforge.net/tracker/?func=detail&aid=3611094&group_id=177891&atid=886178
Modified Paths:
--------------
trunk/src/ontology/branches/external-byhand.owl
trunk/src/ontology/branches/external.owl
trunk/src/ontology/branches/obi.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jzh...@us...> - 2013-06-11 18:25:52
|
Revision: 3800
http://obi.svn.sourceforge.net/obi/?rev=3800&view=rev
Author: jzheng24
Date: 2013-06-11 18:25:44 +0000 (Tue, 11 Jun 2013)
Log Message:
-----------
assign OBI ids to newly added terms for OBI/CLO alignment
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
Added Paths:
-----------
trunk/src/ontology/spreadsheets/new_ids/newIDs_20130611.tab
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mb...@us...> - 2013-06-11 16:47:44
|
Revision: 3799
http://obi.svn.sourceforge.net/obi/?rev=3799&view=rev
Author: mbrush
Date: 2013-06-11 16:47:35 +0000 (Tue, 11 Jun 2013)
Log Message:
-----------
minor edits to cultured cell classes, and made cultured cell population a child of processed material
Modified Paths:
--------------
trunk/src/ontology/branches/externalDerived.owl
trunk/src/ontology/branches/obi.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jzh...@us...> - 2013-06-10 23:42:56
|
Revision: 3798
http://obi.svn.sourceforge.net/obi/?rev=3798&view=rev
Author: jzheng24
Date: 2013-06-10 23:42:49 +0000 (Mon, 10 Jun 2013)
Log Message:
-----------
- protocol
1. change 'domain experts' to ?\226?\128?\152investigation agent?\226?\128?\153 in textual definition
2. remove duplicated logical axiom, has part some 'objective specification'
3. new example: PCR protocol, has objective specification, amplify DNA fragment of interest, has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR.
- participant under investigation
remove ?\226?\128?\152concretizes some ('intervention design' or 'observation design')?\226?\128?\153 axiom
changes were made according to 2013-6-10 dev call discussion.
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mb...@us...> - 2013-06-10 22:10:25
|
Revision: 3797
http://obi.svn.sourceforge.net/obi/?rev=3797&view=rev
Author: mbrush
Date: 2013-06-10 22:10:16 +0000 (Mon, 10 Jun 2013)
Log Message:
-----------
- remove "is_specified_output_of some 'material portioning'" from cell culture population
- removed specimen role from cultured cell population
- remove achieves_planned_objective some 'specimen collection objective' from establishing cell culture
- added 'cell freezing medium class, and added to specified input axiom on maintaining cell culture
- deleted three subclasses of maintaining cell culture (originally created for CLO but now not needed)
- added axiom to cultured cell population: 'participates in' some 'maintaining cell culture'
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jam...@us...> - 2013-06-10 20:02:15
|
Revision: 3796
http://obi.svn.sourceforge.net/obi/?rev=3796&view=rev
Author: jamesaoverton
Date: 2013-06-10 20:02:09 +0000 (Mon, 10 Jun 2013)
Log Message:
-----------
Added data prototype text and OWL file to 'examples/development'.
Added Paths:
-----------
trunk/src/examples/development/data-prototype.owl
trunk/src/examples/development/data-prototype.txt
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jam...@us...> - 2013-06-10 19:56:11
|
Revision: 3795
http://obi.svn.sourceforge.net/obi/?rev=3795&view=rev
Author: jamesaoverton
Date: 2013-06-10 19:56:04 +0000 (Mon, 10 Jun 2013)
Log Message:
-----------
Updated OBI core OWL file.
Modified Paths:
--------------
trunk/src/ontology/obi-view/obi-core/obi_core.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jam...@us...> - 2013-06-10 19:54:54
|
Revision: 3794
http://obi.svn.sourceforge.net/obi/?rev=3794&view=rev
Author: jamesaoverton
Date: 2013-06-10 19:54:48 +0000 (Mon, 10 Jun 2013)
Log Message:
-----------
Changing 'core.owl' to 'obi_core.owl'.
Modified Paths:
--------------
trunk/src/tools/build/README.md
trunk/src/tools/build/build.xml
trunk/src/tools/build/config.properties
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jam...@us...> - 2013-06-10 19:52:34
|
Revision: 3793
http://obi.svn.sourceforge.net/obi/?rev=3793&view=rev
Author: jamesaoverton
Date: 2013-06-10 19:52:28 +0000 (Mon, 10 Jun 2013)
Log Message:
-----------
Fixed a bug with named individuals for SPARQL tests.
Modified Paths:
--------------
trunk/src/tools/build/src/main/java/obi/SPARQLTest.java
trunk/src/tools/build/src/main/java/obi/Tester.java
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mb...@us...> - 2013-06-09 22:32:03
|
Revision: 3792
http://obi.svn.sourceforge.net/obi/?rev=3792&view=rev
Author: mbrush
Date: 2013-06-09 22:31:55 +0000 (Sun, 09 Jun 2013)
Log Message:
-----------
- minor edits, and added a cell population class (for CLO): a collection of cells of the same type that are co-located in the same location (adapted from PCO population: "A collection of organisms, all of the same species, that live in the same place.") . . . e.g. a collection of macrophages in a lymph nodes, a tube of white blood cell that were isolated from a mouse, a dish of cell line cells in culture
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mb...@us...> - 2013-06-06 17:27:00
|
Revision: 3791
http://obi.svn.sourceforge.net/obi/?rev=3791&view=rev
Author: mbrush
Date: 2013-06-06 17:26:53 +0000 (Thu, 06 Jun 2013)
Log Message:
-----------
- updated labels, definitions, and other metadata on cultured cell population classes in accordance with CLO-alignment outcomes
- updated establishing cell culture metadata (and that of children) to conform to CLO alignment outcomes
- created new classes - 'cell line culture' - for CLO to import, and 'primary cell culture
- made cell culture asserted child of processed material
- obsoleted all classes in old cell culture hierarchy (decided not needed in CLO alignment work)
- changed label and metadata on 'active cell culture' class to align with CLO alignment outcomes
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mb...@us...> - 2013-06-05 22:06:56
|
Revision: 3790
http://obi.svn.sourceforge.net/obi/?rev=3790&view=rev
Author: mbrush
Date: 2013-06-05 22:06:50 +0000 (Wed, 05 Jun 2013)
Log Message:
-----------
- added to editor note on device about distinction from reagents, reflecting outcomes of OBI core workshop. added similar editor note to reagent
- began updating cell line modeling to reflect outcomes of alignment work with CLO and CL
Modified Paths:
--------------
trunk/src/ontology/branches/obi.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
