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: <dan...@us...> - 2008-05-20 13:55:12
|
Revision: 635
http://obi.svn.sourceforge.net/obi/?rev=635&view=rev
Author: daniel_schober
Date: 2008-05-20 06:55:19 -0700 (Tue, 20 May 2008)
Log Message:
-----------
In order to be able to create a few simple examples I have added the following device functions:
device function
instrument_function
microarray function
RNA microarray function
transcription analysis function
NMR spectroscopy function
metabolic profiling function
microscope function
polystyrene tube function
Modified Paths:
--------------
trunk/src/ontology/branches/OBI-Function.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <dan...@us...> - 2008-05-20 13:12:55
|
Revision: 634
http://obi.svn.sourceforge.net/obi/?rev=634&view=rev
Author: daniel_schober
Date: 2008-05-20 06:12:54 -0700 (Tue, 20 May 2008)
Log Message:
-----------
I renamed the utilises_instrument relation to utilises_device in order to reflect the broader scope of this relation. Its inverse 'is_instrument_for' was renamed accordingly to 'is_device_for'. For both the domain and range were also adjusted.
Modified Paths:
--------------
trunk/src/ontology/branches/Relations.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mco...@us...> - 2008-05-15 23:28:39
|
Revision: 633
http://obi.svn.sourceforge.net/obi/?rev=633&view=rev
Author: mcourtot
Date: 2008-05-15 16:27:25 -0700 (Thu, 15 May 2008)
Log Message:
-----------
modified format of definition field to be obo compliant
Modified Paths:
--------------
trunk/src/tools/build/generate-obo.lisp
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <man...@us...> - 2008-05-15 16:38:43
|
Revision: 632
http://obi.svn.sourceforge.net/obi/?rev=632&view=rev
Author: manduchi
Date: 2008-05-15 09:38:20 -0700 (Thu, 15 May 2008)
Log Message:
-----------
Reflects decisions from DT conference call on May 15
Modified Paths:
--------------
trunk/docs/developer/DT/GenePatternUseCases.xls
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <man...@us...> - 2008-05-15 16:24:19
|
Revision: 631
http://obi.svn.sourceforge.net/obi/?rev=631&view=rev
Author: manduchi
Date: 2008-05-15 09:24:14 -0700 (Thu, 15 May 2008)
Log Message:
-----------
Use Cases from Ricardo Pietrobon
Added Paths:
-----------
trunk/docs/developer/DT/PietrobonUseCases.pdf
trunk/docs/developer/DT/PietrobonUseCases.xmi
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <man...@us...> - 2008-05-15 15:13:47
|
Revision: 630
http://obi.svn.sourceforge.net/obi/?rev=630&view=rev
Author: manduchi
Date: 2008-05-15 07:28:15 -0700 (Thu, 15 May 2008)
Log Message:
-----------
EM finished review of files, need to discuss with branch terms from line 62 on
Modified Paths:
--------------
trunk/docs/developer/DT/GenePatternUseCases.xls
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <al...@us...> - 2008-05-15 14:17:31
|
Revision: 629
http://obi.svn.sourceforge.net/obi/?rev=629&view=rev
Author: alanr
Date: 2008-05-15 07:17:26 -0700 (Thu, 15 May 2008)
Log Message:
-----------
Should work after top level svn update
Modified Paths:
--------------
trunk/src/tools/build/generate-obo.lisp
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <al...@us...> - 2008-05-15 04:41:47
|
Revision: 628
http://obi.svn.sourceforge.net/obi/?rev=628&view=rev
Author: alanr
Date: 2008-05-14 21:41:53 -0700 (Wed, 14 May 2008)
Log Message:
-----------
tweak
Modified Paths:
--------------
trunk/src/tools/build/generate-obo.lisp
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <al...@us...> - 2008-05-15 04:38:47
|
Revision: 627
http://obi.svn.sourceforge.net/obi/?rev=627&view=rev
Author: alanr
Date: 2008-05-14 21:38:53 -0700 (Wed, 14 May 2008)
Log Message:
-----------
Partially done. (setq kb (load-kb-jena :obi)) (generate-obo)
Added Paths:
-----------
trunk/src/tools/build/generate-obo.lisp
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mco...@us...> - 2008-05-13 21:57:13
|
Revision: 626
http://obi.svn.sourceforge.net/obi/?rev=626&view=rev
Author: mcourtot
Date: 2008-05-13 14:55:54 -0700 (Tue, 13 May 2008)
Log Message:
-----------
added purl generation and lsw html report
Modified Paths:
--------------
trunk/src/tools/build/OBIrelease.sh
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <dan...@us...> - 2008-05-13 17:01:12
|
Revision: 625
http://obi.svn.sourceforge.net/obi/?rev=625&view=rev
Author: daniel_schober
Date: 2008-05-13 10:01:04 -0700 (Tue, 13 May 2008)
Log Message:
-----------
Implemented 5 new device and instrument terms as submitter by Phillippe:
TERM TO SUBMIT definition definition source definition editor example of usage
bead a bead is a device which is characterized by a round shape. depending on size,material and manufacturing process, beads may have a range of application OBI biomaterial branch prs PMID: 18446240.Single bead affinity detection (SINBAD) for the analysis of protein-protein interactions. PLoS ONE. 2008 Apr 30;3(4):e2061.
microtome A microtome is a mechanical instrument used to cut biological specimens into very thin segments for microscopic examination. Most microtomes use a steel blade and are used to prepare sections of animal or plant tissues for histology wikipedia:microtome prs PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
microscope a microscope is an instrument which magnifies objects too small to be viewed by the naked eye. microscope can be optical instrument but also electronic instruments. there are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope) adapted from wikipedia prs PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
microscope slide a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument OBI biomaterial branch prs PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay.
laboratory cage, rename 'animal cage' a laboratory cage is a device which defines an bounded habitat which is amenable to breeding and keeping laboratory animals during experimentation. cages may be made in various material and serve specific purpose (e.g metabolic cages). cages maybe equiped with additional devices such as water and food dispenser, weighing device OBI biomaterial branch prs PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice.
all metadata incomplete
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jgr...@us...> - 2008-05-13 16:40:17
|
Revision: 624
http://obi.svn.sourceforge.net/obi/?rev=624&view=rev
Author: jgreenbaum
Date: 2008-05-13 09:40:21 -0700 (Tue, 13 May 2008)
Log Message:
-----------
* Fixed handling of OBI_0000281 - curation_status instances
* Regenerated Linux & Windows binaries
* Replaced example files
* Updated web server
Modified Paths:
--------------
trunk/bin/linux/xl2owl
trunk/bin/windows/xl2owl.exe
trunk/src/tools/format-converters/xl2owl/Example.txt
trunk/src/tools/format-converters/xl2owl/xl2owl.pl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mco...@us...> - 2008-05-12 21:39:52
|
Revision: 623
http://obi.svn.sourceforge.net/obi/?rev=623&view=rev
Author: mcourtot
Date: 2008-05-12 14:39:56 -0700 (Mon, 12 May 2008)
Log Message:
-----------
added quality terms in the quality.owl file (moved from biomaterial.owl and therest.owl)
Modified Paths:
--------------
trunk/src/ontology/branches/Quality.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mco...@us...> - 2008-05-12 21:39:20
|
Revision: 622
http://obi.svn.sourceforge.net/obi/?rev=622&view=rev
Author: mcourtot
Date: 2008-05-12 14:39:11 -0700 (Mon, 12 May 2008)
Log Message:
-----------
removed quality terms, which have been moved to quality.owl file
Modified Paths:
--------------
trunk/src/ontology/branches/TheRest.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mco...@us...> - 2008-05-12 21:38:39
|
Revision: 621
http://obi.svn.sourceforge.net/obi/?rev=621&view=rev
Author: mcourtot
Date: 2008-05-12 14:38:34 -0700 (Mon, 12 May 2008)
Log Message:
-----------
moved radiocative to quality.owl file
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <dan...@us...> - 2008-05-12 15:01:06
|
Revision: 620
http://obi.svn.sourceforge.net/obi/?rev=620&view=rev
Author: daniel_schober
Date: 2008-05-12 08:01:08 -0700 (Mon, 12 May 2008)
Log Message:
-----------
...and made instrument function a subclass of device function.
Modified Paths:
--------------
trunk/src/ontology/branches/OBI-Function.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <dan...@us...> - 2008-05-12 14:59:26
|
Revision: 619
http://obi.svn.sourceforge.net/obi/?rev=619&view=rev
Author: daniel_schober
Date: 2008-05-12 07:58:51 -0700 (Mon, 12 May 2008)
Log Message:
-----------
Refined restriction on 'device' to 'has_function some device function'
Modified Paths:
--------------
trunk/src/ontology/branches/InstrumentAndPart.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <dan...@us...> - 2008-05-12 14:54:55
|
Revision: 618
http://obi.svn.sourceforge.net/obi/?rev=618&view=rev
Author: daniel_schober
Date: 2008-05-12 07:53:40 -0700 (Mon, 12 May 2008)
Log Message:
-----------
added 'device function'.
Modified Paths:
--------------
trunk/src/ontology/branches/OBI-Function.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <al...@us...> - 2008-05-11 23:58:30
|
Revision: 617
http://obi.svn.sourceforge.net/obi/?rev=617&view=rev
Author: alanr
Date: 2008-05-11 16:58:37 -0700 (Sun, 11 May 2008)
Log Message:
-----------
added create-superclasses.pl
Modified Paths:
--------------
trunk/src/tools/build/add-inferred-superclasses.lisp
Added Paths:
-----------
trunk/bin/create-superclasses.pl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <al...@us...> - 2008-05-11 23:11:25
|
Revision: 616
http://obi.svn.sourceforge.net/obi/?rev=616&view=rev
Author: alanr
Date: 2008-05-11 16:11:32 -0700 (Sun, 11 May 2008)
Log Message:
-----------
(write-inferred-superclasses kb path) - creates a new file at path with the inferred superclasses of all classes in ontology
Added Paths:
-----------
trunk/src/tools/build/add-inferred-superclasses.lisp
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <al...@us...> - 2008-05-11 22:26:22
|
Revision: 615
http://obi.svn.sourceforge.net/obi/?rev=615&view=rev
Author: alanr
Date: 2008-05-11 15:26:29 -0700 (Sun, 11 May 2008)
Log Message:
-----------
missed removing the separate condition utilizes_reagent some viruses when it was combined with PA
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <p_r...@us...> - 2008-05-11 22:19:24
|
Revision: 614
http://obi.svn.sourceforge.net/obi/?rev=614&view=rev
Author: p_rocca_serra
Date: 2008-05-11 15:19:25 -0700 (Sun, 11 May 2008)
Log Message:
-----------
PRS:11-05-2008: including a couple of imports from ENVO
Modified Paths:
--------------
trunk/src/ontology/branches/external.owl
trunk/src/ontology/branches/externalDerived.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <p_r...@us...> - 2008-05-11 22:18:36
|
Revision: 613
http://obi.svn.sourceforge.net/obi/?rev=613&view=rev
Author: p_rocca_serra
Date: 2008-05-11 15:18:41 -0700 (Sun, 11 May 2008)
Log Message:
-----------
Soil and Podzol imported from ENVO
Change to Biomaterial Definition
Following Alan 's feedback: The class "Epstein Barr virus transformed B cell" is unsatisfiable.
The error is that it currently says:
derives_from only CL_0000236
and is_output_of some 'establishing cell culture'
and utilizes_reagent some NCBITaxon_10239
Where it should say:
derives_from only CL_0000236
and is_output_of some
('establishing cell culture'
and utilizes_reagent some NCBITaxon_10239)
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <p_r...@us...> - 2008-05-11 17:39:29
|
Revision: 612
http://obi.svn.sourceforge.net/obi/?rev=612&view=rev
Author: p_rocca_serra
Date: 2008-05-11 10:39:33 -0700 (Sun, 11 May 2008)
Log Message:
-----------
removing <owl:imports rdf:resource="http://purl.obofoundry.org/obo"/> from BM.owl
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <p_r...@us...> - 2008-05-11 17:19:38
|
Revision: 611
http://obi.svn.sourceforge.net/obi/?rev=611&view=rev
Author: p_rocca_serra
Date: 2008-05-11 10:19:45 -0700 (Sun, 11 May 2008)
Log Message:
-----------
Philippe: 11-05-2008:
change log
Pellet Report: Inconsistencies found for Organism and Subclasses
Which include 2 classes under the branch which have become children of Organism or use one of Organism subclass to build restrictions (See EBV transformed B-Cell)
deleted
obsolete in-vivo,in-vitro
natural biomaterial
artificially engineered biomaterial
_defined class is needed
moved to instrument:
bead placed under device
hierarchical changes:
[person] is now a subclass of [organism]
[cell] (import) modified to be a subclass of [anatomical entity-cardinal part of organism]
cell component, blood plasma cell and
[multicellular entity of organism origin] should be deprecated (used to hold CARO:multitissue structure and portion of tissue as children
[multitissue structure] is a child of [anatomical entity-cardinal part of organism]
[liver],[adipose tissue] are children of [multissue structure]
[epithelium] is a child of [portion of tissue] (note: both are flagged as possible imports from CARO)
[environmental sample] is renamed to [environmental matter] and flagged to be a possible import from EnVO
entity of organismal origin have the following children: most which used to be children of "_defined class is needed"
Note1: Work is ongoing to set the restrictions.
Note2: The classifier could have done the job of placing the class in the hierarchy once the restrictions set.
Modified Paths:
--------------
trunk/src/ontology/branches/Biomaterial.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
