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: <man...@us...> - 2008-05-08 14:17:06
|
Revision: 585
http://obi.svn.sourceforge.net/obi/?rev=585&view=rev
Author: manduchi
Date: 2008-05-08 07:16:32 -0700 (Thu, 08 May 2008)
Log Message:
-----------
Added 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: <jam...@us...> - 2008-05-08 14:00:29
|
Revision: 584
http://obi.svn.sourceforge.net/obi/?rev=584&view=rev
Author: jamesmalone
Date: 2008-05-08 07:00:16 -0700 (Thu, 08 May 2008)
Log Message:
-----------
Clean up of branch file. JM
Modified Paths:
--------------
trunk/src/ontology/branches/DataTransformation.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <al...@us...> - 2008-05-08 04:39:25
|
Revision: 583
http://obi.svn.sourceforge.net/obi/?rev=583&view=rev
Author: alanr
Date: 2008-05-07 21:39:31 -0700 (Wed, 07 May 2008)
Log Message:
-----------
obi.asd minor fix to path stuff
We had unsatisfiable classes which are resolved by edits to external.owl
These included: organism,viruses,bacteria,archaea,eukaryotes (plus some collateral damage)
Here's why:
Organism: equivalent viruses or bacteria or archaea or eukaryotes
siblings (because they were only subclass of material)
viruses
archaea
bacteria
eukaryotes
Disjoints then add (because that are the same level)
organism disjoint viruses
organism disjoint archaea
organism disjoint bacteria
organism disjoint eukaryotes
Organism is therefore the union of 4 things it is disjoint with. That leaves it empty.
Because it is *equivalent* to the union, each of them have to be empty too.
The repair was, in external.owl, to make viruses, bacteria, archaea,
eukaryotes subclass of organism, rather than material.
Modified Paths:
--------------
trunk/src/ontology/branches/disjoints.owl
trunk/src/ontology/branches/external.owl
trunk/src/tools/build/obi.asd
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <al...@us...> - 2008-05-08 04:17:14
|
Revision: 582
http://obi.svn.sourceforge.net/obi/?rev=582&view=rev
Author: alanr
Date: 2008-05-07 21:17:19 -0700 (Wed, 07 May 2008)
Log Message:
-----------
Paths in lisp code more rational.
obi: is trunk/ obi:build; is trunk/build obi:branches; is trunk/src/ontology/branches/
disjoints.owl gets put in branches directory
everything else generated goes in trunk/build
Modified Paths:
--------------
trunk/src/ontology/branches/AnnotationProperty.owl
trunk/src/ontology/branches/disjoints.owl
trunk/src/tools/build/add-disjoints.lisp
trunk/src/tools/build/modify-uris.pl
trunk/src/tools/build/obi.asd
trunk/src/tools/build/uri-report.lisp
trunk/src/tools/build/write-purls.lisp
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mco...@us...> - 2008-05-06 18:24:20
|
Revision: 581
http://obi.svn.sourceforge.net/obi/?rev=581&view=rev
Author: mcourtot
Date: 2008-05-06 11:24:23 -0700 (Tue, 06 May 2008)
Log Message:
-----------
removed extra ro import
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...> - 2008-05-06 15:46:11
|
Revision: 580
http://obi.svn.sourceforge.net/obi/?rev=580&view=rev
Author: daniel_schober
Date: 2008-05-06 08:46:18 -0700 (Tue, 06 May 2008)
Log Message:
-----------
added temperature bath def into correct annotation property
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: <p_r...@us...> - 2008-05-06 10:16:08
|
Revision: 579
http://obi.svn.sourceforge.net/obi/?rev=579&view=rev
Author: p_rocca_serra
Date: 2008-05-06 03:16:14 -0700 (Tue, 06 May 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/src/ontology/branches/AnnotationProperty.owl
trunk/src/ontology/branches/Biomaterial.owl
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...> - 2008-05-06 10:05:30
|
Revision: 578
http://obi.svn.sourceforge.net/obi/?rev=578&view=rev
Author: p_rocca_serra
Date: 2008-05-06 03:05:35 -0700 (Tue, 06 May 2008)
Log Message:
-----------
Modified Paths:
--------------
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...> - 2008-05-06 10:05:11
|
Revision: 577
http://obi.svn.sourceforge.net/obi/?rev=577&view=rev
Author: p_rocca_serra
Date: 2008-05-06 03:05:18 -0700 (Tue, 06 May 2008)
Log Message:
-----------
Modified Paths:
--------------
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: <p_r...@us...> - 2008-05-06 10:03:49
|
Revision: 576
http://obi.svn.sourceforge.net/obi/?rev=576&view=rev
Author: p_rocca_serra
Date: 2008-05-06 03:03:51 -0700 (Tue, 06 May 2008)
Log Message:
-----------
Modified Paths:
--------------
trunk/src/ontology/branches/AnnotationProperty.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <p_r...@us...> - 2008-05-06 10:01:07
|
Revision: 575
http://obi.svn.sourceforge.net/obi/?rev=575&view=rev
Author: p_rocca_serra
Date: 2008-05-06 03:01:10 -0700 (Tue, 06 May 2008)
Log Message:
-----------
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...> - 2008-05-06 09:38:25
|
Revision: 574
http://obi.svn.sourceforge.net/obi/?rev=574&view=rev
Author: p_rocca_serra
Date: 2008-05-06 02:38:14 -0700 (Tue, 06 May 2008)
Log Message:
-----------
changelog to biomaterial.owl
-metadata upgrade based on branch report
*Deprecated classes:
-obsoletion of virus (DNA virus, RNA virus,reverse transcribing virus), eukaryote (plant, animal, fungus, protist),viroid, cultivar,, procaryote(archaea, bacterium), _biomaterial(deprecated)
*Created Imports:
-viruses, Eukaryotes, Bacteria, Archaea, viroids
Known issue-> breaks naming convention
*Added Restrictions:
To class Organism where a necessary and sufficient condition has been added defining as the Union of (Eukaryotes or Bacteria or Archaea or Viruses)
*Added Classes for Evaluation purposes:
liver (OBI_302743) as child of multi-tissue structure
epithelium(OBI_302744) and adipose tissue (OBI_302745) as children of tissue
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: <al...@us...> - 2008-05-06 02:47:08
|
Revision: 573
http://obi.svn.sourceforge.net/obi/?rev=573&view=rev
Author: alanr
Date: 2008-05-05 19:47:10 -0700 (Mon, 05 May 2008)
Log Message:
-----------
fix debug print
Modified Paths:
--------------
trunk/src/tools/build/modify-uris.pl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mco...@us...> - 2008-05-05 18:43:26
|
Revision: 572
http://obi.svn.sourceforge.net/obi/?rev=572&view=rev
Author: mcourtot
Date: 2008-05-05 11:43:31 -0700 (Mon, 05 May 2008)
Log Message:
-----------
added definition sources for
ratio of collected to emitted light. Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
number of lost events computer: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
number of particles in subset: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
number of lost events electronic: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
parameter threshold: Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
electronic case report tabulation: CDISC glossary
electronic case report form: CDISC glossary
measured expression level: OBI Data transformation branch
Modified Paths:
--------------
trunk/src/ontology/branches/DigitalEntityPlus.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <p_r...@us...> - 2008-05-02 18:30:25
|
Revision: 571
http://obi.svn.sourceforge.net/obi/?rev=571&view=rev
Author: p_rocca_serra
Date: 2008-05-02 11:30:32 -0700 (Fri, 02 May 2008)
Log Message:
-----------
Added metadata corresponding to the 4 top classes from NCBI-tax
Modified Paths:
--------------
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...> - 2008-05-02 18:29:44
|
Revision: 570
http://obi.svn.sourceforge.net/obi/?rev=570&view=rev
Author: p_rocca_serra
Date: 2008-05-02 11:29:46 -0700 (Fri, 02 May 2008)
Log Message:
-----------
added Import from NCBI tax: Archaea,Bacteria,Eukaryotes,Viruses
Modified Paths:
--------------
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: <p_r...@us...> - 2008-05-02 18:28:00
|
Revision: 569
http://obi.svn.sourceforge.net/obi/?rev=569&view=rev
Author: p_rocca_serra
Date: 2008-05-02 11:28:04 -0700 (Fri, 02 May 2008)
Log Message:
-----------
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...> - 2008-05-02 16:42:29
|
Revision: 568
http://obi.svn.sourceforge.net/obi/?rev=568&view=rev
Author: p_rocca_serra
Date: 2008-05-02 09:42:36 -0700 (Fri, 02 May 2008)
Log Message:
-----------
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...> - 2008-05-02 11:03:49
|
Revision: 567
http://obi.svn.sourceforge.net/obi/?rev=567&view=rev
Author: p_rocca_serra
Date: 2008-05-02 04:03:52 -0700 (Fri, 02 May 2008)
Log Message:
-----------
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: <mco...@us...> - 2008-05-01 22:04:34
|
Revision: 566
http://obi.svn.sourceforge.net/obi/?rev=566&view=rev
Author: mcourtot
Date: 2008-05-01 15:04:38 -0700 (Thu, 01 May 2008)
Log Message:
-----------
removed extra preferred term for cell
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: <mco...@us...> - 2008-05-01 22:01:27
|
Revision: 565
http://obi.svn.sourceforge.net/obi/?rev=565&view=rev
Author: mcourtot
Date: 2008-05-01 15:01:15 -0700 (Thu, 01 May 2008)
Log Message:
-----------
removed extra definition of cell
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: <fgi...@us...> - 2008-05-01 09:36:04
|
Revision: 564
http://obi.svn.sourceforge.net/obi/?rev=564&view=rev
Author: fgibson_sf
Date: 2008-05-01 02:36:03 -0700 (Thu, 01 May 2008)
Log Message:
-----------
-Added relation has_part droplet_sorter to Flow-cytometry_sorter, according to
the definition of droplet_sorter
-Added definition source and editor to droplet_sorter
-Removed value of rdfs-comment to defintion source for laser
-Removed value of rdfs-comment to defintion source for helium_neon_ion_laser
-Removed value of rdfs-comment to editor note for flow_cytometer_analyzer
-Removed value of rdfs-comment to defintion source for gas laser
-Removed value of rdfs-comment to defintion source for argon_ion laser
-Added prefered term to liquid_chromatography_mass_spectrometry_platform
-Added relations to liquid_chromatography_mass_spectrometry_platform of has_part
liquid_chromatography_instrument and has_part mass_spectrometer
-Removed value of rdfs-comment to defintion source for obscuration_bar
-Added relation has_part obscuration_bar to flow_cytometer
-Added preferred term, definition editor and definition source to platform
-Added preferred term to DNA_microarray
-Added relation has_part micorarray to micorarray_platform
-Added preferred term, definition editor and definition source to micorarray_platform
-Removed the notion of sample from the defintion of temperature_control_bath
-Added definition source of temperature control bath
-Remved value of rdfs comment to definition source for ion_laser
Ontology is consistent
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...> - 2008-04-29 00:47:34
|
Revision: 563
http://obi.svn.sourceforge.net/obi/?rev=563&view=rev
Author: jgreenbaum
Date: 2008-04-28 17:47:39 -0700 (Mon, 28 Apr 2008)
Log Message:
-----------
Added Example.owl file as well
Added Paths:
-----------
trunk/src/tools/format-converters/xl2owl/Example.owl
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jgr...@us...> - 2008-04-29 00:46:13
|
Revision: 562
http://obi.svn.sourceforge.net/obi/?rev=562&view=rev
Author: jgreenbaum
Date: 2008-04-28 17:46:19 -0700 (Mon, 28 Apr 2008)
Log Message:
-----------
Updated the example files
Modified Paths:
--------------
trunk/src/tools/format-converters/xl2owl/Example.txt
Added Paths:
-----------
trunk/src/tools/format-converters/xl2owl/Example.txt.xtra
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <jgr...@us...> - 2008-04-29 00:38:17
|
Revision: 561
http://obi.svn.sourceforge.net/obi/?rev=561&view=rev
Author: jgreenbaum
Date: 2008-04-28 17:38:20 -0700 (Mon, 28 Apr 2008)
Log Message:
-----------
* Fixed bug regarding owl:disjointWith tags
* Fixed utf8 encoding issue
* Updated README
* Generated new binaries
* Changes reflected on webserver as well
Modified Paths:
--------------
trunk/bin/linux/xl2owl
trunk/bin/osx/xl2owl
trunk/bin/windows/xl2owl.exe
trunk/src/tools/format-converters/xl2owl/README
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.
|
