https://wiki.geneontology.org/api.php?action=feedcontributions&user=Amina&feedformat=atomGO Wiki - User contributions [en]2024-03-29T04:58:50ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=OEWG_20110125&diff=32747OEWG 201101252010-12-22T03:27:50Z<p>Amina: Created page with 'OBO-Edit Working Group, Tuesday January 25th, 2011 8.30 a.m. PDT Conference call details: New GOC conference call numbers US: 1 866 953 9688 UK: 0808 238 6001 pin: 801561 Agend…'</p>
<hr />
<div>OBO-Edit Working Group, Tuesday January 25th, 2011 8.30 a.m. PDT<br />
<br />
Conference call details: New GOC conference call numbers<br />
US: 1 866 953 9688<br />
UK: 0808 238 6001<br />
pin: 801561<br />
<br />
Agenda/Chair:<br />
Minutes:<br />
Attendees:<br />
<br />
==Action items carried over==<br />
<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [https://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
<br />
==Discussion items==<br />
<br />
<br />
<br />
<br />
== Demo ==<br />
<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20110111&diff=32746OEWG 201101112010-12-22T03:26:47Z<p>Amina: Created page with 'OBO-Edit Working Group, Tuesday January 11th, 2011 8.30 a.m. PDT Conference call details: New GOC conference call numbers US: 1 866 953 9688 UK: 0808 238 6001 pin: 801561 Agend…'</p>
<hr />
<div>OBO-Edit Working Group, Tuesday January 11th, 2011 8.30 a.m. PDT<br />
<br />
Conference call details: New GOC conference call numbers<br />
US: 1 866 953 9688<br />
UK: 0808 238 6001<br />
pin: 801561<br />
<br />
Agenda/Chair:<br />
Minutes:<br />
Attendees:<br />
<br />
==Action items carried over==<br />
<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [https://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
<br />
==Discussion items==<br />
<br />
<br />
<br />
<br />
== Demo ==<br />
<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=32745OBO-Edit Working Group Meeting Agenda and Minutes2010-12-22T03:24:54Z<p>Amina: </p>
<hr />
<div>====[[OBO-Edit_Working_Group_weekly_meeting_minutes/agenda_rota|Meeting minutes/agenda rota]]====<br />
<br />
==Meeting Schedule for 2011==<br />
<br />
==Future Meetings Schedule==<br />
<br />
*[[OEWG_20110111| January 11]]<br />
<br />
*[[OEWG_20110125| January 25]]<br />
<br />
<br />
== Past Meetings ==<br />
<br />
<br />
<br />
<br />
<br />
<br />
====Previous Year Meetings====<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2010 | Meeting Minutes from 2010]]<br><br />
<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2009 | Meeting Minutes from 2009]]<br><br />
<br />
[[Web_chat_transcripts | Web Chat Transcripts]]<br />
<br />
==[[OBO-Edit|Back to OBO-Edit wiki mainpage]]==</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=32744OBO-Edit Working Group Meeting Agenda and Minutes2010-12-22T03:20:33Z<p>Amina: </p>
<hr />
<div>====[[OBO-Edit_Working_Group_weekly_meeting_minutes/agenda_rota|Meeting minutes/agenda rota]]====<br />
<br />
==Meeting Schedule for 2011==<br />
<br />
<br />
===Future Meetings Schedule===<br />
<br />
*[[OEWG_20110111| January 11]]<br />
<br />
*[[OEWG_20110125| January 25]]<br />
<br />
<br />
==== Past Meetings ====<br />
<br />
<br />
<br />
<br />
<br />
<br />
====Previous Year Meetings====<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2010 | Meeting Minutes from 2010]]<br><br />
<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2009 | Meeting Minutes from 2009]]<br><br />
<br />
[[Web_chat_transcripts | Web Chat Transcripts]]<br />
<br />
==[[OBO-Edit|Back to OBO-Edit wiki mainpage]]==</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2010&diff=32743OBO-Edit Working Group Meeting Agenda and Minutes 20102010-12-22T03:16:34Z<p>Amina: Created page with '== OBO-Edit Working Group 2010 Meetings == * January 12 * January 19 * January 26 * February 02 *[[OE…'</p>
<hr />
<div>== OBO-Edit Working Group 2010 Meetings ==<br />
<br />
*[[OEWG_20100112| January 12]]<br />
<br />
*[[OEWG_20100119| January 19]]<br />
<br />
*[[OEWG_20100126| January 26]]<br />
<br />
*[[OEWG_20100202| February 02]]<br />
<br />
*[[OEWG_20100216| February 16]]<br />
<br />
*[[OEWG_20100302| March 02]]<br />
<br />
*[[OEWG_20100309| March 09]]<br />
<br />
*[[OEWG_20100316| March 16]]<br />
<br />
*[[OEWG_20100330| March 30]]<br />
<br />
*[[OEWG_20100413| April 13]]<br />
<br />
*[[OEWG_20100504| May 04]]<br />
<br />
*[[OEWG_20100511| May 11]]<br />
<br />
*[[OEWG_20100525| May 25]]<br />
<br />
*[[OEWG_20100608| June 08]]<br />
<br />
*[[OEWG_20100720| July 20]]<br />
<br />
*[[OEWG_20100803| August 03]]<br />
<br />
*[[OEWG_20100817| August 17]]<br />
<br />
*[[OEWG_20100908| September 8-9th GOC Meeting]]<br />
<br />
*[[OEWG_20100928| September 28]]<br />
<br />
*[[OEWG_20101207| December 07]]<br />
<br />
*[[OEWG_20101213| December 14]]<br />
<br />
*[[OEWG_20101221| December 21]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=32742OBO-Edit Working Group Meeting Agenda and Minutes2010-12-22T03:03:43Z<p>Amina: </p>
<hr />
<div>====[[OBO-Edit_Working_Group_weekly_meeting_minutes/agenda_rota|Meeting minutes/agenda rota]]====<br />
<br />
==Meeting Schedule for 2010==<br />
<br />
<br />
===Future Meetings Schedule===<br />
<br />
*[[OEWG_20110111| January 11]]<br />
<br />
*[[OEWG_20110125| January 25]]<br />
<br />
<br />
<br />
==== Past Meetings ====<br />
<br />
*[[OEWG_20100112| January 12]]<br />
<br />
*[[OEWG_20100119| January 19]]<br />
<br />
*[[OEWG_20100126| January 26]]<br />
<br />
*[[OEWG_20100202| February 02]]<br />
<br />
*[[OEWG_20100216| February 16]]<br />
<br />
*[[OEWG_20100302| March 02]]<br />
<br />
*[[OEWG_20100309| March 09]]<br />
<br />
*[[OEWG_20100316| March 16]]<br />
<br />
*[[OEWG_20100330| March 30]]<br />
<br />
*[[OEWG_20100413| April 13]]<br />
<br />
*[[OEWG_20100504| May 04]]<br />
<br />
*[[OEWG_20100511| May 11]]<br />
<br />
*[[OEWG_20100525| May 25]]<br />
<br />
*[[OEWG_20100608| June 08]]<br />
<br />
*[[OEWG_20100720| July 20]]<br />
<br />
*[[OEWG_20100803| August 03]]<br />
<br />
*[[OEWG_20100817| August 17]]<br />
<br />
*[[OEWG_20100908| September 8-9th GOC Meeting]]<br />
<br />
*[[OEWG_20100928| September 28]]<br />
<br />
*[[OEWG_20101207| December 07]]<br />
<br />
*[[OEWG_20101213| December 14]]<br />
<br />
*[[OEWG_20101221| December 21]]<br />
<br />
====Previous Year Meetings====<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2010 | Meeting Minutes from 2010]]<br><br />
<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2009 | Meeting Minutes from 2009]]<br><br />
<br />
[[Web_chat_transcripts | Web Chat Transcripts]]<br />
<br />
==[[OBO-Edit|Back to OBO-Edit wiki mainpage]]==</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101221&diff=32741OEWG 201012212010-12-21T20:56:21Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 21st, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: <br><br />
Attendees: Midori, Nomi, Chris, Laurel, Harold, Alex<br />
<br />
==Action items carried over==<br />
<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [https://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
<br />
==Discussion items==<br />
* Development Updates <br />
** auto complete selection flaky - Fixed<br />
** xps editing bugs - Fixed<br />
<br />
* Terry<br />
** Graph Editor causes OBO-Edit to freeze<br />
** is_a closure link filers <br />
<br />
*Harold<br />
** RBR freezes on GO - Amina tested this and RBR does not cause a freeze.<br />
<br />
* Graph Editor bugs<br />
** Alex, Harold, Midori have problems with GO loaded<br />
** if all you use the reasoner is to show redundant links it does not need the full functionality of the reasoner.<br />
** RBR good for xps reasoner<br />
<br />
* Terry asks about is_a cycles that are logically wrong not picked up by RBR bu picked up by LPR - is_a and develops relation - RBR does not pick it up.<br />
** Chris: this should be a verification check<br />
<br />
* Chris: common reasoner tasks by users<br />
<br />
* Uncommited text edits bug back<br />
** the working group was able to replicate this only with the camphor catabolism ontology. <br />
** click on a xps term - load another ontology to replicate bug.<br />
<br />
<br />
<br />
<br />
== Demo ==<br />
<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101221&diff=32739OEWG 201012212010-12-21T16:46:43Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 21st, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: <br><br />
Attendees: Midori, Nomi, Chris, Laurel, Harold, Alex<br />
<br />
==Action items carried over==<br />
<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [https://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
<br />
==Discussion items==<br />
* Development Updates <br />
** auto complete selection flaky - Fixed<br />
** xps editing bugs - Fixed<br />
<br />
* Terry<br />
** Graph Editor causes OBO-Edit to freeze<br />
** is_a closure link filers <br />
<br />
*Harold<br />
** RBR freezes on GO - Amina tested this and RBR does not cause a freeze.<br />
<br />
* Graph Editor bugs<br />
<br />
== Demo ==<br />
<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101221&diff=32734OEWG 201012212010-12-20T19:20:35Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 21st, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [https://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
<br />
==Discussion items==<br />
* Development Updates <br />
** auto complete selection flaky - Fixed<br />
** xps editing bugs - Fixed<br />
<br />
<br />
== Demo ==<br />
<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101221&diff=32733OEWG 201012212010-12-20T19:19:50Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 21st, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
* Development Updates <br />
** auto complete selection flaky - Fixed<br />
** xps editing bugs - Fixed<br />
<br />
<br />
== Demo ==<br />
<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=32732OBO-Edit Working Group Meeting Agenda and Minutes2010-12-20T19:19:00Z<p>Amina: </p>
<hr />
<div>====[[OBO-Edit_Working_Group_weekly_meeting_minutes/agenda_rota|Meeting minutes/agenda rota]]====<br />
<br />
==Meeting Schedule for 2010==<br />
<br />
<br />
===Future Meetings Schedule===<br />
<br />
*[[OEWG_20101221| December 21]]<br />
<br />
<br />
==== Past Meetings ====<br />
<br />
*[[OEWG_20100112| January 12]]<br />
<br />
*[[OEWG_20100119| January 19]]<br />
<br />
*[[OEWG_20100126| January 26]]<br />
<br />
*[[OEWG_20100202| February 02]]<br />
<br />
*[[OEWG_20100216| February 16]]<br />
<br />
*[[OEWG_20100302| March 02]]<br />
<br />
*[[OEWG_20100309| March 09]]<br />
<br />
*[[OEWG_20100316| March 16]]<br />
<br />
*[[OEWG_20100330| March 30]]<br />
<br />
*[[OEWG_20100413| April 13]]<br />
<br />
*[[OEWG_20100504| May 04]]<br />
<br />
*[[OEWG_20100511| May 11]]<br />
<br />
*[[OEWG_20100525| May 25]]<br />
<br />
*[[OEWG_20100608| June 08]]<br />
<br />
*[[OEWG_20100720| July 20]]<br />
<br />
*[[OEWG_20100803| August 03]]<br />
<br />
*[[OEWG_20100817| August 17]]<br />
<br />
*[[OEWG_20100908| September 8-9th GOC Meeting]]<br />
<br />
*[[OEWG_20100928| September 28]]<br />
<br />
*[[OEWG_20101207| December 07]]<br />
<br />
*[[OEWG_20101213| December 14]]<br />
<br />
<br />
<br />
====Previous Year Meetings====<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2009 | Meeting Minutes from 2009]]<br><br />
[[Web_chat_transcripts | Web Chat Transcripts]]<br />
<br />
==[[OBO-Edit|Back to OBO-Edit wiki mainpage]]==</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Editv2.1beta7&diff=32702OBO-Editv2.1beta72010-12-17T00:22:48Z<p>Amina: </p>
<hr />
<div>= Status =<br />
This page tracks items I'm currently working on. It is a moving target for beta 7 development dictated by the bug and feature tracker on sourceforge. <br />
<br />
= TO Dos =<br />
* transfer OEWG meeting calendar to GO Calendar<br />
<br />
<br />
= Current work =<br />
* [https://sourceforge.net/tracker/?func=detail&aid=3029689&group_id=36855&atid=418257 Subset manager - subset name change not saved] <font color = blue> Done </font><br />
* [https://sourceforge.net/tracker/index.php?func=detail&aid=3049416&group_id=36855&atid=418257 Selection from auto-complete search menu flaky] <font color = blue> Done </font><br />
* [https://sourceforge.net/tracker/?func=detail&aid=2823197&group_id=36855&atid=418257 Some disjoint_from relationships impossible to delete]<br />
<br />
<br />
== Bugs ==<br />
* High Priority:<br />
**[http://sourceforge.net/tracker/?func=detail&aid=3076730&group_id=36855&atid=418257 Filter on save problems OE b4 - ID: 3076730]<font color = blue> Done </font><br />
**[https://sourceforge.net/tracker/?func=detail&aid=2971364&group_id=36855&atid=418257 b4 - still having problems committing text edits]<font color = blue> Done </font><br />
**[https://sourceforge.net/tracker/?func=detail&aid=2948445&group_id=36855&atid=418257 Loss of intersection status on merge]<font color = blue> Done </font><br />
**[https://sourceforge.net/tracker/?func=detail&aid=2745699&group_id=36855&atid=418257 2.0 graph viewer now shows only one parent]<font color = blue> Done </font><br />
<br />
* Necessary Fixes<br />
** [https://sourceforge.net/tracker/?func=detail&aid=3038713&group_id=36855&atid=418257 Cross product editor broken in beta 5]<font color = blue> Done </font><br />
** [https://sourceforge.net/tracker/?func=detail&aid=3049402&group_id=36855&atid=418257 Delete option gone from parent plugin]<font color = blue> Done </font><br />
*[]<br />
<br />
== Features ==<br />
<br />
<br />
<br />
== Plans and TBD ==<br />
<br />
[[OBO-Edit_Release_Timeline]]<br />
<br />
[http://wiki.geneontology.org/index.php/OBO-Edit OBO-Edit Wiki Mainpage]<br />
[[Category:OBO-Edit]]<br />
[[Category:Software]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Editv2.1beta7&diff=32701OBO-Editv2.1beta72010-12-17T00:00:06Z<p>Amina: </p>
<hr />
<div>= Status =<br />
This page tracks items I'm currently working on. It is a moving target for beta 7 development dictated by the bug and feature tracker on sourceforge. <br />
<br />
= TO Dos =<br />
* transfer OEWG meeting calendar to GO Calendar<br />
<br />
<br />
= Current work =<br />
* [https://sourceforge.net/tracker/?func=detail&aid=3029689&group_id=36855&atid=418257 Subset manager - subset name change not saved] <font color = blue> Done </font><br />
* [https://sourceforge.net/tracker/index.php?func=detail&aid=3049416&group_id=36855&atid=418257 Selection from auto-complete search menu flaky] <font color = blue> Done </font><br />
* [https://sourceforge.net/tracker/?func=detail&aid=2823197&group_id=36855&atid=418257 Some disjoint_from relationships impossible to delete]<br />
<br />
<br />
== Bugs ==<br />
* High Priority:<br />
**[http://sourceforge.net/tracker/?func=detail&aid=3076730&group_id=36855&atid=418257 Filter on save problems OE b4 - ID: 3076730]<font color = blue> In progress </font><br />
**[https://sourceforge.net/tracker/?func=detail&aid=2971364&group_id=36855&atid=418257 b4 - still having problems committing text edits]<font color = blue> Done </font><br />
**[https://sourceforge.net/tracker/?func=detail&aid=2948445&group_id=36855&atid=418257 Loss of intersection status on merge]<font color = blue> Done </font><br />
**[https://sourceforge.net/tracker/?func=detail&aid=2745699&group_id=36855&atid=418257 2.0 graph viewer now shows only one parent]<font color = blue> Done </font><br />
<br />
* Necessary Fixes<br />
** [https://sourceforge.net/tracker/?func=detail&aid=3038713&group_id=36855&atid=418257 Cross product editor broken in beta 5]<font color = blue> Done </font><br />
** [https://sourceforge.net/tracker/?func=detail&aid=3049402&group_id=36855&atid=418257 Delete option gone from parent plugin]<font color = blue> Done </font><br />
*[]<br />
<br />
== Features ==<br />
<br />
<br />
<br />
== Plans and TBD ==<br />
<br />
[[OBO-Edit_Release_Timeline]]<br />
<br />
[http://wiki.geneontology.org/index.php/OBO-Edit OBO-Edit Wiki Mainpage]<br />
[[Category:OBO-Edit]]<br />
[[Category:Software]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101213&diff=32623OEWG 201012132010-12-14T16:58:57Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 14th, 2010 8.30 a.m. PDT <br><br />
<br />
== Teleconference details only for Tuesday Dec 14th ==<br />
BBOP ReadyTalk<br><br />
US Toll-Free Number: 8667401260 (U.S. & Canada)<br><br />
US Toll Number: 3032480285<br><br><br />
UK Toll-Free Number: 08004960576<br><br />
UK Toll Number: 02070844345<br><br><br />
<br />
Your Access Code: 1867508<br><br />
Your Passcode: 8653<br><br />
<br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
* Updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
* Unable to get OBOEdit to read dictionaries (might be machine specific for Becky)<br />
** Becky reset system dictionaries through the Configuration Editor - Error with having a high memory allocation - setting memory to 1600M and then Saving Configuration fixed the error.<br />
<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
== OEWG regular call numbers not applicable tomorrow ==<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=32621OBO-Edit Working Group Meeting Agenda and Minutes2010-12-14T16:36:36Z<p>Amina: </p>
<hr />
<div>====[[OBO-Edit_Working_Group_weekly_meeting_minutes/agenda_rota|Meeting minutes/agenda rota]]====<br />
<br />
==Meeting Schedule for 2010==<br />
<br />
<br />
===Future Meetings Schedule===<br />
<br />
<br />
*[[OEWG_20101213| December 14]]<br />
<br />
*[[OEWG_20101221| December 21]]<br />
<br />
<br />
==== Past Meetings ====<br />
<br />
*[[OEWG_20100112| January 12]]<br />
<br />
*[[OEWG_20100119| January 19]]<br />
<br />
*[[OEWG_20100126| January 26]]<br />
<br />
*[[OEWG_20100202| February 02]]<br />
<br />
*[[OEWG_20100216| February 16]]<br />
<br />
*[[OEWG_20100302| March 02]]<br />
<br />
*[[OEWG_20100309| March 09]]<br />
<br />
*[[OEWG_20100316| March 16]]<br />
<br />
*[[OEWG_20100330| March 30]]<br />
<br />
*[[OEWG_20100413| April 13]]<br />
<br />
*[[OEWG_20100504| May 04]]<br />
<br />
*[[OEWG_20100511| May 11]]<br />
<br />
*[[OEWG_20100525| May 25]]<br />
<br />
*[[OEWG_20100608| June 08]]<br />
<br />
*[[OEWG_20100720| July 20]]<br />
<br />
*[[OEWG_20100803| August 03]]<br />
<br />
*[[OEWG_20100817| August 17]]<br />
<br />
*[[OEWG_20100908| September 8-9th GOC Meeting]]<br />
<br />
*[[OEWG_20100928| September 28]]<br />
<br />
*[[OEWG_20101207| December 07]]<br />
<br />
<br />
<br />
====Previous Year Meetings====<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2009 | Meeting Minutes from 2009]]<br><br />
[[Web_chat_transcripts | Web Chat Transcripts]]<br />
<br />
==[[OBO-Edit|Back to OBO-Edit wiki mainpage]]==</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=32620OBO-Edit Working Group Meeting Agenda and Minutes2010-12-14T16:36:14Z<p>Amina: </p>
<hr />
<div>====[[OBO-Edit_Working_Group_weekly_meeting_minutes/agenda_rota|Meeting minutes/agenda rota]]====<br />
<br />
==Meeting Schedule for 2010==<br />
<br />
<br />
===Future Meetings Schedule===<br />
<br />
<br />
*[[OEWG_20101214| December 14]]<br />
<br />
*[[OEWG_20101221| December 21]]<br />
<br />
<br />
==== Past Meetings ====<br />
<br />
*[[OEWG_20100112| January 12]]<br />
<br />
*[[OEWG_20100119| January 19]]<br />
<br />
*[[OEWG_20100126| January 26]]<br />
<br />
*[[OEWG_20100202| February 02]]<br />
<br />
*[[OEWG_20100216| February 16]]<br />
<br />
*[[OEWG_20100302| March 02]]<br />
<br />
*[[OEWG_20100309| March 09]]<br />
<br />
*[[OEWG_20100316| March 16]]<br />
<br />
*[[OEWG_20100330| March 30]]<br />
<br />
*[[OEWG_20100413| April 13]]<br />
<br />
*[[OEWG_20100504| May 04]]<br />
<br />
*[[OEWG_20100511| May 11]]<br />
<br />
*[[OEWG_20100525| May 25]]<br />
<br />
*[[OEWG_20100608| June 08]]<br />
<br />
*[[OEWG_20100720| July 20]]<br />
<br />
*[[OEWG_20100803| August 03]]<br />
<br />
*[[OEWG_20100817| August 17]]<br />
<br />
*[[OEWG_20100908| September 8-9th GOC Meeting]]<br />
<br />
*[[OEWG_20100928| September 28]]<br />
<br />
*[[OEWG_20101207| December 07]]<br />
<br />
<br />
<br />
====Previous Year Meetings====<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2009 | Meeting Minutes from 2009]]<br><br />
[[Web_chat_transcripts | Web Chat Transcripts]]<br />
<br />
==[[OBO-Edit|Back to OBO-Edit wiki mainpage]]==</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101213&diff=32618OEWG 201012132010-12-14T16:31:43Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 14th, 2010 8.30 a.m. PDT <br><br />
<br />
== Teleconference details only for Tuesday Dec 14th ==<br />
BBOP ReadyTalk<br><br />
US Toll-Free Number: 8667401260 (U.S. & Canada)<br><br />
US Toll Number: 3032480285<br><br><br />
UK Toll-Free Number: 08004960576<br><br />
UK Toll Number: 02070844345<br><br><br />
<br />
Your Access Code: 1867508<br><br />
Your Passcode: 8653<br><br />
<br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
* Updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
<br />
<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
== OEWG regular call numbers not applicable tomorrow ==<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101213&diff=32590OEWG 201012132010-12-13T23:31:15Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 13th, 2010 8.30 a.m. PDT <br><br />
<br />
== Teleconference details only for Tuesday Dec 13th ==<br />
BBOP ReadyTalk<br><br />
US Toll-Free Number: 8667401260 (U.S. & Canada)<br><br />
US Toll Number: 3032480285<br><br><br />
UK Toll-Free Number: 08004960576<br><br />
UK Toll Number: 02070844345<br><br><br />
<br />
Your Access Code: 1867508<br><br />
Your Passcode: 8653<br><br />
<br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
* Updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
<br />
<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
== OEWG regular call numbers not applicable tomorrow ==<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101213&diff=32580OEWG 201012132010-12-13T21:59:14Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 13th, 2010 8.30 a.m. PDT <br><br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
* Updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
<br />
<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101213&diff=32577OEWG 201012132010-12-13T21:37:10Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 13th, 2010 8.30 a.m. PDT <br><br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
Midori using 2.1beta1 and Ramona is using beta6<br />
<br />
* Updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
<br />
<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101213&diff=32576OEWG 201012132010-12-13T21:36:15Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 13th, 2010 8.30 a.m. PDT <br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
Midori using 2.1beta1 and Ramona is using beta6<br />
<br />
* Updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
<br />
<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101213&diff=32575OEWG 201012132010-12-13T21:35:56Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 13th, 2010 8.30 a.m. PDT <br><br />
<br />
<br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
Midori using 2.1beta1 and Ramona is using beta6<br />
<br />
* Updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
<br />
<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101213&diff=32573OEWG 201012132010-12-13T21:35:35Z<p>Amina: Created page with 'OBO-Edit Working Group, Tuesday December 7th, 2010 8.30 a.m. PDT <br> Agenda/Chair: Amina<br> Minutes: Amina <br> Attendees: Midori, Ramona, Chris, Amina, Marcus, Laurel ==Ac…'</p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 7th, 2010 8.30 a.m. PDT <br><br />
<br />
<br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: Midori, Ramona, Chris, Amina, Marcus, Laurel<br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
Midori using 2.1beta1 and Ramona is using beta6<br />
<br />
* Updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
<br />
<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=32571OBO-Edit Working Group Meeting Agenda and Minutes2010-12-13T21:31:32Z<p>Amina: </p>
<hr />
<div>====[[OBO-Edit_Working_Group_weekly_meeting_minutes/agenda_rota|Meeting minutes/agenda rota]]====<br />
<br />
==Meeting Schedule for 2010==<br />
<br />
<br />
===Future Meetings Schedule===<br />
<br />
*[[OEWG_20101207| December 07]]<br />
<br />
*[[OEWG_20101213| December 13]]<br />
<br />
*[[OEWG_20101221| December 21]]<br />
<br />
<br />
==== Past Meetings ====<br />
<br />
*[[OEWG_20100112| January 12]]<br />
<br />
*[[OEWG_20100119| January 19]]<br />
<br />
*[[OEWG_20100126| January 26]]<br />
<br />
*[[OEWG_20100202| February 02]]<br />
<br />
*[[OEWG_20100216| February 16]]<br />
<br />
*[[OEWG_20100302| March 02]]<br />
<br />
*[[OEWG_20100309| March 09]]<br />
<br />
*[[OEWG_20100316| March 16]]<br />
<br />
*[[OEWG_20100330| March 30]]<br />
<br />
*[[OEWG_20100413| April 13]]<br />
<br />
*[[OEWG_20100504| May 04]]<br />
<br />
*[[OEWG_20100511| May 11]]<br />
<br />
*[[OEWG_20100525| May 25]]<br />
<br />
*[[OEWG_20100608| June 08]]<br />
<br />
*[[OEWG_20100720| July 20]]<br />
<br />
*[[OEWG_20100803| August 03]]<br />
<br />
*[[OEWG_20100817| August 17]]<br />
<br />
*[[OEWG_20100908| September 8-9th GOC Meeting]]<br />
<br />
*[[OEWG_20100928| September 28]]<br />
<br />
<br />
<br />
====Previous Year Meetings====<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2009 | Meeting Minutes from 2009]]<br><br />
[[Web_chat_transcripts | Web Chat Transcripts]]<br />
<br />
==[[OBO-Edit|Back to OBO-Edit wiki mainpage]]==</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101207&diff=32447OEWG 201012072010-12-07T21:56:14Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 7th, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: Midori, Ramona, Chris, Amina, Marcus, Laurel<br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
Midori using 2.1beta1 and Ramona is using beta6<br />
<br />
* General updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
<br />
* disjoint relation deletion - feature request<br />
<br />
* Ramona: deletion of parent links in Parent Editor.<br />
* Laurel: OBO Format questions for Chris.<br />
* Jane: graph viewer, cross product editor and user dictionary fixes.<br />
* Harold: highlight reasoner that should be used.<br />
<br />
<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101207&diff=32440OEWG 201012072010-12-07T17:09:38Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 7th, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: Midori, Ramona, Chris, Amina, Marcus, Laurel<br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
Midori using 2.1beta1 and Ramona is using beta6<br />
<br />
* General updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
<br />
* disjoint relation deletion - feature request<br />
<br />
* Ramona: deletion of parent links in Parent Editor.<br />
* Laurel: OBO Format questions for Chris.<br />
* Jane: graph viewer, cross product editor and user dictionary fixes.<br />
<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101207&diff=32434OEWG 201012072010-12-07T16:34:36Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 7th, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: Midori, Ramona, Chris, Amina<br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
Midori using 2.1beta1 and Ramona is using beta6<br />
<br />
* General updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101207&diff=32433OEWG 201012072010-12-07T16:32:10Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 7th, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
* General updates from development and working group members.<br />
* http://wiki.geneontology.org/index.php/OBO-Editv2.1beta7<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101207&diff=32432OEWG 201012072010-12-07T15:57:39Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday December 7th, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: Amina <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
* v2.1beta7 release<br />
<br />
== Bug and Feature Tracker Updates ==<br />
<br />
<br />
<br />
==Discussion items==<br />
* General updates from development and working group members.<br />
<br />
== Demo ==<br />
No demo scheduled.<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=32431OBO-Edit Working Group Meeting Agenda and Minutes2010-12-07T15:56:27Z<p>Amina: </p>
<hr />
<div>====[[OBO-Edit_Working_Group_weekly_meeting_minutes/agenda_rota|Meeting minutes/agenda rota]]====<br />
<br />
==Meeting Schedule for 2010==<br />
<br />
<br />
===Future Meetings Schedule===<br />
<br />
*[[OEWG_20101207| December 07]]<br />
<br />
*[[OEWG_20101221| December 21]]<br />
<br />
<br />
==== Past Meetings ====<br />
<br />
*[[OEWG_20100112| January 12]]<br />
<br />
*[[OEWG_20100119| January 19]]<br />
<br />
*[[OEWG_20100126| January 26]]<br />
<br />
*[[OEWG_20100202| February 02]]<br />
<br />
*[[OEWG_20100216| February 16]]<br />
<br />
*[[OEWG_20100302| March 02]]<br />
<br />
*[[OEWG_20100309| March 09]]<br />
<br />
*[[OEWG_20100316| March 16]]<br />
<br />
*[[OEWG_20100330| March 30]]<br />
<br />
*[[OEWG_20100413| April 13]]<br />
<br />
*[[OEWG_20100504| May 04]]<br />
<br />
*[[OEWG_20100511| May 11]]<br />
<br />
*[[OEWG_20100525| May 25]]<br />
<br />
*[[OEWG_20100608| June 08]]<br />
<br />
*[[OEWG_20100720| July 20]]<br />
<br />
*[[OEWG_20100803| August 03]]<br />
<br />
*[[OEWG_20100817| August 17]]<br />
<br />
*[[OEWG_20100908| September 8-9th GOC Meeting]]<br />
<br />
*[[OEWG_20100928| September 28]]<br />
<br />
<br />
<br />
====Previous Year Meetings====<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2009 | Meeting Minutes from 2009]]<br><br />
[[Web_chat_transcripts | Web Chat Transcripts]]<br />
<br />
==[[OBO-Edit|Back to OBO-Edit wiki mainpage]]==</div>Aminahttps://wiki.geneontology.org/index.php?title=V2.1_fixes_and_updates&diff=32353V2.1 fixes and updates2010-12-01T20:19:22Z<p>Amina: </p>
<hr />
<div>=== OBO-Edit v2.1 RELEASE NOTES === <br />
<br />
<br />
== What's New in OBO-Edit v2.1-beta7 ==<br />
<br />
Bug Fixes: <br />
[ geneontology-Bugs-3076730 ] Filter on save problems OE b4 <br><br />
<br />
[ geneontology-Bugs-2948445 ] Loss of intersection status on merge<br><br />
<br />
[ geneontology-Bugs-3029689 ] Subset manager - subset name change not saved<br><br />
<br />
[ geneontology-Bugs-2745699 ] 2.0 graph viewer now shows only one parent<br><br />
<br />
[ geneontology-Bugs-3049416 ] Selection from auto-complete search menu flaky<br><br />
<br />
[ geneontology-Bugs-2815514 ] overzealous autosave<br><br />
<br />
[ geneontology-Bugs-2722517 ] autocomplete term selection in search panel<br><br />
<br />
[ geneontology-Bugs-2685810 ] Graph Editor - Move option not working for multiple terms<br><br />
<br />
[ geneontology-Bugs-2840516 ] no way to get to genus term while defining xps<br><br />
fuzzy purple ball == cotton ball icon == Go To term button. Correct tooltip message added for both genus and differentia terms.<br />
Spanning to the term in OTE works well now, provided the OTE is in global mode.<br><br />
<br />
Fixes in progress:<br><br />
[ geneontology-Bugs-2971364 ] b4 - still having problems committing text edits<br><br />
<br />
<br />
== What's New in OBO-Edit v2.1-beta6 ==<br />
<br />
Bug Fixes: Fixed comments being eliminated from load cycle.<br><br />
<br />
<br />
== What's New in OBO-Edit v2.1-beta5 ==<br />
<br />
Bug Fixes: <br><br />
[ geneontology-Bugs-3011139 ] delete term not deleting<br><br />
[ geneontology-Bugs-3017846 ] Ubuntu 10.04 crashes<br><br />
[ geneontology-Bugs-3007375 ] spontaneous cross products<br><br />
[ geneontology-Bugs-2996789 ] Search Panel look-ahead keyboard selection problem<br><br />
[ geneontology-Bugs-2997272 ] not all typedefs are shown in relationship branch<br><br />
[ geneontology-Bugs-3000534 ] Search function (arrow key select)<br><br />
[ geneontology-Bugs-3000571 ] problem with config manager display- 2.1 b4<br><br />
[ geneontology-Bugs-2996688 ] Comments section being duplicated with is_a closure p<br><br />
[ geneontology-Bugs-2996593 ] Weird search results OE beta 4<br><br />
[ geneontology-Bugs-2990477 ] spontaneous replication of upper level terms<br><br />
[ geneontology-Bugs-3035323 ] OE 2.1 beta 2 - clone problems<br><br />
[ geneontology-Bugs-3035322 ] 2.1 betas - GraphViz problem<br><br />
<br />
obo2obo: allowdangling true by default for input and output files.<br><br />
v2.1b5 onwards the comments are overwritten. The order in which the files are loaded dictates precedence. In the OBOEdit Advanced file load menu, if file1 and file2 both have different comments for a particular term - and file2 is below file1 in the load list - the definition from file2 will hold.<br><br />
<br />
<br />
*IMPORTANT* ANNOUNCEMENT FOR v2.1x on Importing Settings From Previous Versions<br><br />
<br />
Config directory located in the users home directory and called "oboedit_config".<br />
Settings from the previous releases (OBO-Edit 1. 2.0 or 2.0 beta versions) are located in the <br />
configuration folder found at the default application installation location of your operating system. <br />
You can import the perspective and layout settings from previous versions to the folder called "oboedit_config".<br />
* Please note the config folder naming convention is not consistent with previous version.* <br />
Config files can also be reset when required through the Configuration Manager.<br />
<br />
<br />
<br />
== 2.1 beta1 through beta4 Bug Fixes ==<br />
<br />
[geneontology-Bugs-2899760] Too easy to make link to self in graph editor<br><br />
[geneontology-Bugs-2971221] eliminate possibility to create is_a relationships to self<br><br />
Text Editor and Parent Editor are now in sync<br><br />
[ geneontology-Bugs-2971364 ] b3 - problems committing text edits<br><br />
[ geneontology-Bugs-2987680 ] spontaneous intersection_of terms when cloning<br><br />
[ geneontology-Bugs-2922369 ] Is_a closure not working as expected<br><br />
[ geneontology-Bugs-2908106 ] OBO-merge fail<br><br />
[ geneontology-Bugs-2915594] Not saving<br><br />
[ geneontology-Bugs-2968827 ] saving implied links<br><br />
[ geneontology-Bugs-2952892 ] Reasoning with union_of terms<br><br />
[ geneontology-Bugs-2949754 ] Verification plugin dictionary - problem with quickfixes<br><br />
[ geneontology-Bugs-2922331 ] No log file for OE2.1beta2<br><br />
[ geneontology-Bugs-2874878 ] Missing log files in Mac<br><br />
[ geneontology-Bugs-2610787] disjointness violations not detected<br><br />
[ geneontology-Bugs-2821857] disjoint violations not being checked by RBR<br><br />
[ geneontology-Bugs-2941032] Functionality - application does not run on windows 7<br><br />
[ geneontology-Bugs-2915594 ] Not saving<br><br />
[ geneontology-Bugs-2914257 ] When a term is cloned, intersections become relationships<br><br />
[ geneontology-Bugs-2828905 ] verification config in 2.1 test release<br><br />
[ geneontology-Bugs-2869195 ] text editor is not working<br><br />
[ geneontology-Bugs-2864861 ] replaced_by statement causing problems in SO<br><br />
[ geneontology-Bugs-2840516 ] no way to get to genus term while defing xps<br><br />
[ geneontology-Bugs-2840500 ] relation name vanishes<br><br />
[ geneontology-Bugs-2908106 ] OBO-merge fail<br><br />
[ geneontology-Bugs-2610787] disjointness violations not detected<br><br />
[ geneontology-Bugs-2821857] disjoint violations not being checked by RBR<br><br />
[ geneontology-Bugs-2749049] disjoinedness check working?<br><br />
[ geneontology-Bugs-2750699 ] config manager memory settings option out of sync<br><br />
[ geneontology-Bugs-2785074 ] OBO-Edit2-rc still present<br><br />
[ geneontology-Bugs-2787869 ] very minor bug with saving filters<br><br />
[ geneontology-Bugs-2812189 ] GAZ.obo not displayed correctly in OBOEdit2.0<br><br />
[ geneontology-Bugs-2824732 ] obodiff is broken!<br><br />
[ geneontology-Bugs-2818616] stop panel changes if click on top<br><br />
[ geneontology-Bugs-2814791] OBO merge doesn't work!<br><br />
[ geneontology-Bugs-2805373] Assert implied links - color table rows<br><br />
[ geneontology-Bugs-2818549] parent search ignores relationship type<br><br />
[ geneontology-Bugs-2815689] change tracker save <br><br />
[ geneontology-Bugs-2805371] Assert implied links - resize<br><br />
[ geneontology-Bugs-2801684] OBO-Merge generates null-pointer exception<br><br />
[ geneontology-Bugs-2790372] Mac version 2 does not generate log files<br><br />
[ geneontology-Bugs-2749070] reasoner active even in OFF mode<br><br />
[ geneontology-Bugs-2722323] assert implied links pop-up hogs focus and halts editing<br><br />
[ geneontology-Bugs-2787869] very minor bug with saving filters<br><br />
[ geneontology-Bugs-2815829] Simplify 'save implied links'<br><br />
[ geneontology-Bugs-2722318] OTE local mode indication not intuitive<br><br />
- Fixed bug that stopped the box at the bottom of the history browser from appearing unless another component was clicked on. <br><br />
- flaky xp commit<br><br />
- graph viewer issue<br><br />
- filtering union_of cycles in OTE<br><br />
- lock view selection behavior<br><br />
- fixed root detection algorithm to detect inverse relations and display root<br><br />
(Part of OE2.0 - history browser minor bugs - ID: 2507044)<br><br />
- Fixed the history browser html message so it shows 'name (id)' rather then 'id (id)'.<br />
(Part of OE2.0 - history browser minor bugs - ID: 2507044)<br />
- Graphviz uses a lot of memory when you assign dbxrefs: ID: 2057452<br />
The Graphviz interface redraws have been removed for the bulk addition of dbxrefs. <br><br />
Now there is only one redraw at the end of the bulk process.<br><br />
- Added new feature to OBOMerge so that it reports if any term has been edited in both the live and branch files. <br><br />
- Added new feature to TermMergeHistoryItem, so it can update substitution tags that mention any term that<br><br />
is in the process of being subsumed in a merge. Fixes bug: ID: 2790775<br><br />
<br />
<br />
== Features ==<br />
<br />
<br />
- Parent Editor and Cross Product Text Editor component are now in synch and warn regarding changes made in either component <br><br />
<br />
- Graph Viewer Improvements<br />
-- Renamed "Succinct" configuration option to "Trim reasoner-generated (implied) links from display".<br><br />
--> Removed reasoner dependency from displaying all-types panels and showing ancestors upto root<br><br />
<br />
- New Default Global Term Renderer for highlighting terms with cross product definitions<br><br />
<br />
- Cross Product Editor -> Go to Genus term button<br><br />
<br />
- J. Deegan committed new Tag Filter code. This feature enables <br><br />
users to choose which tags are saved out into OBO files. The GUI is in the <br />
'save as' dialog. There is still some work to do to make the GUI look less intimidating. Also, though the feature has been<br />
carefully tested, further testing will be required in case an obscure bug is causing parts of<br />
the data not to be saved out at all. I have not yet run the JUnit tests. When this code is released we should warn in-house users to<br />
watch diffs carefully for lost tags. <br><br />
<br />
- Assert Implied Links Component<br><br />
-- Displays impled links table and asserts selected links.<br><br />
-- Row sorting enabled (ascending and descending) for Child and Parent name columns<br><br />
-- Clicking the more info icon brings up the explanation for the reasoner made link in the Explanation Component and highlights the link in the Graph Editor<br><br />
<br />
- New Reasoner Modes (IN PROGRESS - WILL BE AVAILABLE in the next release)<br><br />
-- Two new options that represent step-wise and continuous incremental reasoning<br><br />
-- Activate incremental reasoning by selecting the "Avtivate Incremental Reasoning" checkbox through the Reasoner Manager<br><br />
-- Users have a choice between activating continuous incremental reasoning or partial/step reasoning modes. If neither of these options are selected incremental reasoning is off by default.<br><br />
<br />
- New option in Advanced Save - Perform is_a closure (behaviour under testing for various use cases)<br><br />
-- Performs is_a closure for all cross-referenced terms while saving<br><br />
<br />
- Changed naming coventions for Advanced Save - Save implied links:<br><br />
-- "Realize links" changed to "Assert Implied Links"<br><br />
-- "Save for presentation" changed to "Save trimmed links"<br><br />
<br />
- Lock/Unlock Layout option<br><br />
-- Locking the layout freezes current application layout and prevents addition/removal of components.<br><br />
<br />
- Scroll Lock for the Ontology Tree Editor<br><br />
-- Select any term in the OTE; right-click for Lock View option which enforces a scroll lock on the path currently displayed.<br><br />
<br />
- NEW Configuration directory location: users home directory/oboedit_config<br><br />
- Cloning behavior corrected - clones now persist on the same branch as the original term. <br></div>Aminahttps://wiki.geneontology.org/index.php?title=V2.1_fixes_and_updates&diff=32352V2.1 fixes and updates2010-12-01T20:13:21Z<p>Amina: Created page with '=== OBO-Edit v2.1 RELEASE NOTES === ================================ What's New in OBO-Edit v2.1-beta7 ================================ Bug Fixes: [ geneontology-Bugs-307673…'</p>
<hr />
<div>=== OBO-Edit v2.1 RELEASE NOTES === <br />
<br />
================================<br />
What's New in OBO-Edit v2.1-beta7<br />
================================<br />
Bug Fixes: <br />
[ geneontology-Bugs-3076730 ] Filter on save problems OE b4<br />
<br />
[ geneontology-Bugs-2948445 ] Loss of intersection status on merge<br />
<br />
[ geneontology-Bugs-3029689 ] Subset manager - subset name change not saved<br />
<br />
[ geneontology-Bugs-2745699 ] 2.0 graph viewer now shows only one parent<br />
<br />
[ geneontology-Bugs-3049416 ] Selection from auto-complete search menu flaky<br />
<br />
[ geneontology-Bugs-2815514 ] overzealous autosave<br />
<br />
[ geneontology-Bugs-2722517 ] autocomplete term selection in search panel<br />
<br />
[ geneontology-Bugs-2685810 ] Graph Editor - Move option not working for multiple terms<br />
<br />
[ geneontology-Bugs-2840516 ] no way to get to genus term while defining xps<br />
fuzzy purple ball == cotton ball icon == Go To term button. Correct tooltip message added for both genus and differentia terms.<br />
Spanning to the term in OTE works well now, provided the OTE is in global mode.<br />
<br />
[ geneontology-Bugs- ]<br />
[ geneontology-Bugs- ]<br />
[ geneontology-Bugs- ]<br />
[ geneontology-Bugs- ]<br />
<br />
[ geneontology-Bugs- ]<br />
Fixes in progress:<br />
HIGH PRIORITY<br />
[ geneontology-Bugs-2971364 ] b4 - still having problems committing text edits<br />
[ geneontology-Bugs- ]<br />
<br />
<br />
[ geneontology-Bugs- ]<br />
<br />
<br />
<br />
================================<br />
What's New in OBO-Edit v2.1-beta6<br />
================================<br />
Bug Fixes: Fixed comments being eliminated from load cycle.<br />
<br />
================================<br />
What's New in OBO-Edit v2.1-beta5<br />
================================<br />
Bug Fixes: <br />
[ geneontology-Bugs-3011139 ] delete term not deleting<br />
[ geneontology-Bugs-3017846 ] Ubuntu 10.04 crashes<br />
[ geneontology-Bugs-3007375 ] spontaneous cross products<br />
[ geneontology-Bugs-2996789 ] Search Panel look-ahead keyboard selection problem<br />
[ geneontology-Bugs-2997272 ] not all typedefs are shown in relationship branch<br />
[ geneontology-Bugs-3000534 ] Search function (arrow key select)<br />
[ geneontology-Bugs-3000571 ] problem with config manager display- 2.1 b4<br />
[ geneontology-Bugs-2996688 ] Comments section being duplicated with is_a closure p<br />
[ geneontology-Bugs-2996593 ] Weird search results OE beta 4<br />
[ geneontology-Bugs-2990477 ] spontaneous replication of upper level terms<br />
[ geneontology-Bugs-3035323 ] OE 2.1 beta 2 - clone problems<br />
[ geneontology-Bugs-3035322 ] 2.1 betas - GraphViz problem<br />
<br />
obo2obo: allowdangling true by default for input and output files.<br />
v2.1b5 onwards the comments are overwritten. The order in which the files are loaded dictates precedence. In the OBOEdit Advanced file load menu, if file1 and file2 both have different comments for a particular term - and file2 is below file1 in the load list - the definition from file2 will hold.<br />
<br />
===================================================================================<br />
*IMPORTANT* ANNOUNCEMENT FOR v2.1x on Importing Settings From Previous Versions<br />
===================================================================================<br />
Config directory located in the users home directory and called "oboedit_config".<br />
Settings from the previous releases (OBO-Edit 1. 2.0 or 2.0 beta versions) are located in the <br />
configuration folder found at the default application installation location of your operating system. <br />
You can import the perspective and layout settings from previous versions to the folder called "oboedit_config".<br />
* Please note the config folder naming convention is not consistent with previous version.* <br />
Config files can also be reset when required through the Configuration Manager.<br />
<br />
<br />
============<br />
2.1 beta1 through beta4 Bug Fixes<br />
============<br />
[geneontology-Bugs-2899760] Too easy to make link to self in graph editor<br />
[geneontology-Bugs-2971221] eliminate possibility to create is_a relationships to self<br />
Text Editor and Parent Editor are now in sync<br />
[ geneontology-Bugs-2971364 ] b3 - problems committing text edits<br />
[ geneontology-Bugs-2987680 ] spontaneous intersection_of terms when cloning<br />
[ geneontology-Bugs-2922369 ] Is_a closure not working as expected<br />
[ geneontology-Bugs-2908106 ] OBO-merge fail<br />
[ geneontology-Bugs-2915594] Not saving<br />
[ geneontology-Bugs-2968827 ] saving implied links<br />
[ geneontology-Bugs-2952892 ] Reasoning with union_of terms<br />
[ geneontology-Bugs-2949754 ] Verification plugin dictionary - problem with quickfixes<br />
[ geneontology-Bugs-2922331 ] No log file for OE2.1beta2<br />
[ geneontology-Bugs-2874878 ] Missing log files in Mac<br />
[ geneontology-Bugs-2610787] disjointness violations not detected<br />
[ geneontology-Bugs-2821857] disjoint violations not being checked by RBR<br />
[ geneontology-Bugs-2941032] Functionality - application does not run on windows 7<br />
[ geneontology-Bugs-2915594 ] Not saving<br />
[ geneontology-Bugs-2914257 ] When a term is cloned, intersections become relationships<br />
[ geneontology-Bugs-2828905 ] verification config in 2.1 test release<br />
[ geneontology-Bugs-2869195 ] text editor is not working<br />
[ geneontology-Bugs-2864861 ] replaced_by statement causing problems in SO<br />
[ geneontology-Bugs-2840516 ] no way to get to genus term while defing xps<br />
[ geneontology-Bugs-2840500 ] relation name vanishes<br />
[ geneontology-Bugs-2908106 ] OBO-merge fail<br />
[ geneontology-Bugs-2610787] disjointness violations not detected<br />
[ geneontology-Bugs-2821857] disjoint violations not being checked by RBR<br />
[ geneontology-Bugs-2749049] disjoinedness check working?<br />
[ geneontology-Bugs-2750699 ] config manager memory settings option out of sync<br />
[ geneontology-Bugs-2785074 ] OBO-Edit2-rc still present<br />
[ geneontology-Bugs-2787869 ] very minor bug with saving filters<br />
[ geneontology-Bugs-2812189 ] GAZ.obo not displayed correctly in OBOEdit2.0<br />
[ geneontology-Bugs-2824732 ] obodiff is broken!<br />
[ geneontology-Bugs-2818616] stop panel changes if click on top<br />
[ geneontology-Bugs-2814791] OBO merge doesn't work!<br />
[ geneontology-Bugs-2805373] Assert implied links - color table rows<br />
[ geneontology-Bugs-2818549] parent search ignores relationship type<br />
[ geneontology-Bugs-2815689] change tracker save <br />
[ geneontology-Bugs-2805371] Assert implied links - resize<br />
[ geneontology-Bugs-2801684] OBO-Merge generates null-pointer exception<br />
[ geneontology-Bugs-2790372] Mac version 2 does not generate log files<br />
[ geneontology-Bugs-2749070] reasoner active even in OFF mode<br />
[ geneontology-Bugs-2722323] assert implied links pop-up hogs focus and halts editing<br />
[ geneontology-Bugs-2787869] very minor bug with saving filters<br />
[ geneontology-Bugs-2815829] Simplify 'save implied links'<br />
[ geneontology-Bugs-2722318] OTE local mode indication not intuitive<br />
- Fixed bug that stopped the box at the bottom of the history browser from appearing unless another component was clicked on. <br />
- flaky xp commit<br />
- graph viewer issue<br />
- filtering union_of cycles in OTE<br />
- lock view selection behavior<br />
- fixed root detection algorithm to detect inverse relations and display root<br />
(Part of OE2.0 - history browser minor bugs - ID: 2507044)<br />
- Fixed the history browser html message so it shows 'name (id)' rather then 'id (id)'.<br />
(Part of OE2.0 - history browser minor bugs - ID: 2507044)<br />
- Graphviz uses a lot of memory when you assign dbxrefs: ID: 2057452<br />
The Graphviz interface redraws have been removed for the bulk addition of dbxrefs. <br />
Now there is only one redraw at the end of the bulk process.<br />
- Added new feature to OBOMerge so that it reports if any term has been edited in both the live and branch files. <br />
- Added new feature to TermMergeHistoryItem, so it can update substitution tags that mention any term that<br />
is in the process of being subsumed in a merge. Fixes bug: ID: 2790775<br />
<br />
<br />
============<br />
Features<br />
============<br />
<br />
- Parent Editor and Cross Product Text Editor component are now in synch and warn regarding changes made in either component<br />
<br />
- Graph Viewer Improvements<br />
-- Renamed "Succinct" configuration option to "Trim reasoner-generated (implied) links from display".<br />
--> Removed reasoner dependency from displaying all-types panels and showing ancestors upto root<br />
<br />
- New Default Global Term Renderer for highlighting terms with cross product definitions<br />
<br />
- Cross Product Editor -> Go to Genus term button<br />
<br />
- J. Deegan committed new Tag Filter code. This feature enables <br />
users to choose which tags are saved out into OBO files. The GUI is in the <br />
'save as' dialog. There is still some work to do to make the GUI look less intimidating. Also, though the feature has been<br />
carefully tested, further testing will be required in case an obscure bug is causing parts of<br />
the data not to be saved out at all. I have not yet run the JUnit tests. When this code is released we should warn in-house users to<br />
watch diffs carefully for lost tags. <br />
<br />
- Assert Implied Links Component<br />
-- Displays impled links table and asserts selected links.<br />
-- Row sorting enabled (ascending and descending) for Child and Parent name columns<br />
-- Clicking the more info icon brings up the explanation for the reasoner made link in the Explanation Component and highlights the link in the Graph Editor<br />
<br />
- New Reasoner Modes (IN PROGRESS - WILL BE AVAILABLE in the next release)<br />
-- Two new options that represent step-wise and continuous incremental reasoning<br />
-- Activate incremental reasoning by selecting the "Avtivate Incremental Reasoning" checkbox through the Reasoner Manager<br />
-- Users have a choice between activating continuous incremental reasoning or partial/step reasoning modes. If neither of these options are selected incremental reasoning is off by default.<br />
<br />
- New option in Advanced Save - Perform is_a closure (behaviour under testing for various use cases)<br />
-- Performs is_a closure for all cross-referenced terms while saving<br />
<br />
- Changed naming coventions for Advanced Save - Save implied links:<br />
-- "Realize links" changed to "Assert Implied Links"<br />
-- "Save for presentation" changed to "Save trimmed links"<br />
<br />
- Lock/Unlock Layout option<br />
-- Locking the layout freezes current application layout and prevents addition/removal of components.<br />
<br />
- Scroll Lock for the Ontology Tree Editor<br />
-- Select any term in the OTE; right-click for Lock View option which enforces a scroll lock on the path currently displayed.<br />
<br />
- NEW Configuration directory location: users home directory/oboedit_config<br />
<br />
- Cloning behavior corrected - clones now persist on the same branch as the original term. <br />
<br />
<br />
============<br />
To Do<br />
============<br />
Documentation:<br />
- user.dict usage and backup info<br />
- Assert Implied Links Component<br />
- Update Advanced Save interface options<br />
<br />
Troubleshooting- add note about:<br />
https://sourceforge.net/tracker2/index.php?func=detail&aid=2683791&group_id=36855&atid=418257<br />
<br />
Known Issues - Upcoming fixes<br />
Parent Editor and Text Editor not in sync.<br />
Ontology Tree Editor - Name unnamed terms<br />
Renaming terms problematic in Text Editor</div>Aminahttps://wiki.geneontology.org/index.php?title=Software_Group_progress_report_for_2010&diff=32351Software Group progress report for 20102010-12-01T20:12:54Z<p>Amina: /* OBO-Edit */</p>
<hr />
<div>== Management ==<br />
<br />
* Created a timeline [[SWUG_Timeline_2010-2011]]<br />
<br />
== Annotation Support ==<br />
<br />
=== Database ===<br />
<br />
=== Production (Stuart, Gail, Ben, Mike C) ===<br />
<br />
#Rebuilt goweb-dev (not replaced)<br />
#*Upgraded OS from RH 32-bit -> RH 64bit<br />
#*Upgraded mysql from 5.0 -> 5.1<br />
#Replaced GO loading machine<br />
#* (old) goad = PowerEdge 1850, 2x2.8GHz Dual Core Intel Xeon, 12GB RAM, 2x300GB disks<br />
#* (new) claret = PowerEdge R610, 2x2.53GHz Quad Core Intel E5540 Xeon, 24GB RAM, 4x500GB disks (64bit OS)<br />
#** sucessfully tested loading on claret<br />
#** have also done initial testing on load-qfo replacement for loading sequences into godb<br />
#Ordered 2 machines to replace GO frontends, goweb1/goweb2<br />
#*Anticipated that these machines will be into production by the end of 2010.<br />
#During process of moving to new machines, the OS, Mysql, and other software were upgraded to the lastest versions.<br />
#Worked on testing and installing of Amigo 1.8 (required 64bit OS for clucene-based searching)<br />
#Made several upgrades to GAF filtering script<br />
#* update from GAF 1.0 -> 2.0<br />
#* added the following feature_types<br />
#** gene_product<br />
#** polypeptide<br />
#* added the following evidence codes: IMR, IRD<br />
#* added qualifier 'rapid_divergence'<br />
# Put in place filter-paint-associations.pl script<br />
<br />
=== Schema Overhaul ===<br />
<br />
[[Schema Overhaul]]<br />
<br />
#SQL schema creation into postgres through a java program<br />
#generation of TSV files through [[Schema_Overhaul#OBO_Access_Layer]] except the following tables (in progress)<br />
#*ontology_imports, ontology_subset, all_only_relationship, never_some_relationship , relation_chain<br />
#[[Schema_Overhaul#OBO_Access_Layer]] is in progress<br />
#loading of TSV files into postgres<br />
#incremental update of the GOLD database (in progress)<br />
#Command Line Interface is built<br />
#Basic Admin servlet interface is built to run the db operations through a web interface (in progress)<br />
<br />
(this may belong in a separate report - add here for now anyway)<br />
<br />
=== Annotation QC ===<br />
<br />
* v1 of [[Taxon_Constraint_Check_Engine] in production. v2 (java rewrite) in progress<br />
* [[Function_to_Process_Inference_Engine]] in production<br />
* [[Annotation_Rule_Engine]]<br />
** current and proposed checks now captured in the annotation xml file<br />
<br />
=== AmiGO ===<br />
<br />
* See [[AmiGO_1_9]]<br />
* See [[Full_Text_Indexing_Progress]]<br />
<br />
=== Website ===<br />
<br />
*Overhaul with different layout, some organisational changes, more easily accessed menu navigation, vertical rhythm<br />
*New documentation for ontology relations, structure<br />
*Updating of tools list (hampered by lack of new tool submissions)<br />
<br />
=== Workflow Support ===<br />
<br />
* Created a basic [[GO_Galaxy_Environment]]<br />
** integrated map2slim<br />
** integrated slim-creator<br />
** integrated enrichment tools<br />
*** GO TermFinder<br />
*** Ontologizer<br />
<br />
=== MOOSE libraries ===<br />
<br />
* Ontology slimmer<br />
* Ontology and annotation slimmer (map2slim)<br />
* Added algorithms of transitive closure and transitive reduction for use by slimming scripts<br />
* Started some preliminary support for basic boolean logic (for creating bucket terms)<br />
<br />
== Reference Genome Support ==<br />
<br />
=== RefG in AmiGO ===<br />
<br />
<br />
* Loading Trees (SVEN)<br />
** Matching IDs<br />
*** Currently ~64% of of the ids are being matched after the new QFO load.<br />
*** Noticed that 1970 proteins are in more then one group (ie YEAST|SGD:S000006392|UniProtKB:Q06580). Informed Paul Thomas.<br />
** Report Pages<br />
*** 2. Concurrent annotation: Code written, not part of load yet.<br />
**** Some group name in file provided by Pascale Gaudet are not in group list. Informed Paul Thomas.<br />
*** 8. 'Date comprehensively annotated' for groups that can provide this information: Have no idea where this data is<br />
<br />
<br />
* js phylo views: work in progress on dev machine (nothing public yet, rapidly changing alpha versions). See: [[AmiGO_Phylotrees]].<br />
* existing refg pages: to be dropped--no further work<br />
* [[AmiGO_and_QuickGO_Integration]] SETH/TONY<br />
<br />
MARY TO FILL IN<br />
<br />
=== Paint ===<br />
<br />
SUZI TO FILL IN<br />
<br />
== Ontology Support ==<br />
<br />
=== TermGenie ===<br />
<br />
See [[Compositional_Term_Submission_Tool]]<br />
<br />
* Created initial prototype, in use by ontology group and annotators<br />
* Integrated autocomplete<br />
* Added involved_in template<br />
<br />
=== OBO-Edit ===<br />
<br />
*[http://wiki.geneontology.org/index.php/OBO-Edit_Release_Timeline Release Tracker]<br />
*[http://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=418257&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=1&category=&artgroup=&submitter=&keyword=&artifact_id=&submit=Filter Bug tracker highlighting upcoming fixes based on priority]<br />
*2010 fixes, features and updates: [[v2.1 fixes and updates]]<br />
<br />
=== Transition to OWL ===<br />
<br />
See [[Transition_to_OWL]]<br />
* Initiated plan for ontology support in next cycle [[Software_Group_2010_Future_Plans#Plan]]<br />
* first draft of obof1.4 guide http://www.geneontology.org/GO.format.obo-1_4.shtml<br />
* formal spec of obo syntax and owl mapping: http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html<br />
* rewritten parser and obo2owl converter, 100% java http://code.google.com/p/oboformat/<br />
<br />
<br />
<br />
[[Category:Reports]]</div>Aminahttps://wiki.geneontology.org/index.php?title=Software_Group_progress_report_for_2010&diff=32350Software Group progress report for 20102010-12-01T20:12:38Z<p>Amina: /* OBO-Edit */</p>
<hr />
<div>== Management ==<br />
<br />
* Created a timeline [[SWUG_Timeline_2010-2011]]<br />
<br />
== Annotation Support ==<br />
<br />
=== Database ===<br />
<br />
=== Production (Stuart, Gail, Ben, Mike C) ===<br />
<br />
#Rebuilt goweb-dev (not replaced)<br />
#*Upgraded OS from RH 32-bit -> RH 64bit<br />
#*Upgraded mysql from 5.0 -> 5.1<br />
#Replaced GO loading machine<br />
#* (old) goad = PowerEdge 1850, 2x2.8GHz Dual Core Intel Xeon, 12GB RAM, 2x300GB disks<br />
#* (new) claret = PowerEdge R610, 2x2.53GHz Quad Core Intel E5540 Xeon, 24GB RAM, 4x500GB disks (64bit OS)<br />
#** sucessfully tested loading on claret<br />
#** have also done initial testing on load-qfo replacement for loading sequences into godb<br />
#Ordered 2 machines to replace GO frontends, goweb1/goweb2<br />
#*Anticipated that these machines will be into production by the end of 2010.<br />
#During process of moving to new machines, the OS, Mysql, and other software were upgraded to the lastest versions.<br />
#Worked on testing and installing of Amigo 1.8 (required 64bit OS for clucene-based searching)<br />
#Made several upgrades to GAF filtering script<br />
#* update from GAF 1.0 -> 2.0<br />
#* added the following feature_types<br />
#** gene_product<br />
#** polypeptide<br />
#* added the following evidence codes: IMR, IRD<br />
#* added qualifier 'rapid_divergence'<br />
# Put in place filter-paint-associations.pl script<br />
<br />
=== Schema Overhaul ===<br />
<br />
[[Schema Overhaul]]<br />
<br />
#SQL schema creation into postgres through a java program<br />
#generation of TSV files through [[Schema_Overhaul#OBO_Access_Layer]] except the following tables (in progress)<br />
#*ontology_imports, ontology_subset, all_only_relationship, never_some_relationship , relation_chain<br />
#[[Schema_Overhaul#OBO_Access_Layer]] is in progress<br />
#loading of TSV files into postgres<br />
#incremental update of the GOLD database (in progress)<br />
#Command Line Interface is built<br />
#Basic Admin servlet interface is built to run the db operations through a web interface (in progress)<br />
<br />
(this may belong in a separate report - add here for now anyway)<br />
<br />
=== Annotation QC ===<br />
<br />
* v1 of [[Taxon_Constraint_Check_Engine] in production. v2 (java rewrite) in progress<br />
* [[Function_to_Process_Inference_Engine]] in production<br />
* [[Annotation_Rule_Engine]]<br />
** current and proposed checks now captured in the annotation xml file<br />
<br />
=== AmiGO ===<br />
<br />
* See [[AmiGO_1_9]]<br />
* See [[Full_Text_Indexing_Progress]]<br />
<br />
=== Website ===<br />
<br />
*Overhaul with different layout, some organisational changes, more easily accessed menu navigation, vertical rhythm<br />
*New documentation for ontology relations, structure<br />
*Updating of tools list (hampered by lack of new tool submissions)<br />
<br />
=== Workflow Support ===<br />
<br />
* Created a basic [[GO_Galaxy_Environment]]<br />
** integrated map2slim<br />
** integrated slim-creator<br />
** integrated enrichment tools<br />
*** GO TermFinder<br />
*** Ontologizer<br />
<br />
=== MOOSE libraries ===<br />
<br />
* Ontology slimmer<br />
* Ontology and annotation slimmer (map2slim)<br />
* Added algorithms of transitive closure and transitive reduction for use by slimming scripts<br />
* Started some preliminary support for basic boolean logic (for creating bucket terms)<br />
<br />
== Reference Genome Support ==<br />
<br />
=== RefG in AmiGO ===<br />
<br />
<br />
* Loading Trees (SVEN)<br />
** Matching IDs<br />
*** Currently ~64% of of the ids are being matched after the new QFO load.<br />
*** Noticed that 1970 proteins are in more then one group (ie YEAST|SGD:S000006392|UniProtKB:Q06580). Informed Paul Thomas.<br />
** Report Pages<br />
*** 2. Concurrent annotation: Code written, not part of load yet.<br />
**** Some group name in file provided by Pascale Gaudet are not in group list. Informed Paul Thomas.<br />
*** 8. 'Date comprehensively annotated' for groups that can provide this information: Have no idea where this data is<br />
<br />
<br />
* js phylo views: work in progress on dev machine (nothing public yet, rapidly changing alpha versions). See: [[AmiGO_Phylotrees]].<br />
* existing refg pages: to be dropped--no further work<br />
* [[AmiGO_and_QuickGO_Integration]] SETH/TONY<br />
<br />
MARY TO FILL IN<br />
<br />
=== Paint ===<br />
<br />
SUZI TO FILL IN<br />
<br />
== Ontology Support ==<br />
<br />
=== TermGenie ===<br />
<br />
See [[Compositional_Term_Submission_Tool]]<br />
<br />
* Created initial prototype, in use by ontology group and annotators<br />
* Integrated autocomplete<br />
* Added involved_in template<br />
<br />
=== OBO-Edit ===<br />
<br />
*[http://wiki.geneontology.org/index.php/OBO-Edit_Release_Timeline Release Tracker]<br />
*[http://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=418257&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=1&category=&artgroup=&submitter=&keyword=&artifact_id=&submit=Filter Bug tracker highlighting upcoming fixes based on priority]<br />
*2010 fixes, features and updates [[2.1 fixes and updates]]<br />
<br />
=== Transition to OWL ===<br />
<br />
See [[Transition_to_OWL]]<br />
* Initiated plan for ontology support in next cycle [[Software_Group_2010_Future_Plans#Plan]]<br />
* first draft of obof1.4 guide http://www.geneontology.org/GO.format.obo-1_4.shtml<br />
* formal spec of obo syntax and owl mapping: http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html<br />
* rewritten parser and obo2owl converter, 100% java http://code.google.com/p/oboformat/<br />
<br />
<br />
<br />
[[Category:Reports]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_2.1_fixes_and_updates&diff=32349OBO-Edit 2.1 fixes and updates2010-12-01T20:12:28Z<p>Amina: Created page with '=== OBO-Edit v2.1 RELEASE NOTES === ================================ What's New in OBO-Edit v2.1-beta7 ================================ Bug Fixes: [ geneontology-Bugs-307673…'</p>
<hr />
<div>=== OBO-Edit v2.1 RELEASE NOTES === <br />
<br />
================================<br />
What's New in OBO-Edit v2.1-beta7<br />
================================<br />
Bug Fixes: <br />
[ geneontology-Bugs-3076730 ] Filter on save problems OE b4<br />
<br />
[ geneontology-Bugs-2948445 ] Loss of intersection status on merge<br />
<br />
[ geneontology-Bugs-3029689 ] Subset manager - subset name change not saved<br />
<br />
[ geneontology-Bugs-2745699 ] 2.0 graph viewer now shows only one parent<br />
<br />
[ geneontology-Bugs-3049416 ] Selection from auto-complete search menu flaky<br />
<br />
[ geneontology-Bugs-2815514 ] overzealous autosave<br />
<br />
[ geneontology-Bugs-2722517 ] autocomplete term selection in search panel<br />
<br />
[ geneontology-Bugs-2685810 ] Graph Editor - Move option not working for multiple terms<br />
<br />
[ geneontology-Bugs-2840516 ] no way to get to genus term while defining xps<br />
fuzzy purple ball == cotton ball icon == Go To term button. Correct tooltip message added for both genus and differentia terms.<br />
Spanning to the term in OTE works well now, provided the OTE is in global mode.<br />
<br />
[ geneontology-Bugs- ]<br />
[ geneontology-Bugs- ]<br />
[ geneontology-Bugs- ]<br />
[ geneontology-Bugs- ]<br />
<br />
[ geneontology-Bugs- ]<br />
Fixes in progress:<br />
HIGH PRIORITY<br />
[ geneontology-Bugs-2971364 ] b4 - still having problems committing text edits<br />
[ geneontology-Bugs- ]<br />
<br />
<br />
[ geneontology-Bugs- ]<br />
<br />
<br />
<br />
================================<br />
What's New in OBO-Edit v2.1-beta6<br />
================================<br />
Bug Fixes: Fixed comments being eliminated from load cycle.<br />
<br />
================================<br />
What's New in OBO-Edit v2.1-beta5<br />
================================<br />
Bug Fixes: <br />
[ geneontology-Bugs-3011139 ] delete term not deleting<br />
[ geneontology-Bugs-3017846 ] Ubuntu 10.04 crashes<br />
[ geneontology-Bugs-3007375 ] spontaneous cross products<br />
[ geneontology-Bugs-2996789 ] Search Panel look-ahead keyboard selection problem<br />
[ geneontology-Bugs-2997272 ] not all typedefs are shown in relationship branch<br />
[ geneontology-Bugs-3000534 ] Search function (arrow key select)<br />
[ geneontology-Bugs-3000571 ] problem with config manager display- 2.1 b4<br />
[ geneontology-Bugs-2996688 ] Comments section being duplicated with is_a closure p<br />
[ geneontology-Bugs-2996593 ] Weird search results OE beta 4<br />
[ geneontology-Bugs-2990477 ] spontaneous replication of upper level terms<br />
[ geneontology-Bugs-3035323 ] OE 2.1 beta 2 - clone problems<br />
[ geneontology-Bugs-3035322 ] 2.1 betas - GraphViz problem<br />
<br />
obo2obo: allowdangling true by default for input and output files.<br />
v2.1b5 onwards the comments are overwritten. The order in which the files are loaded dictates precedence. In the OBOEdit Advanced file load menu, if file1 and file2 both have different comments for a particular term - and file2 is below file1 in the load list - the definition from file2 will hold.<br />
<br />
===================================================================================<br />
*IMPORTANT* ANNOUNCEMENT FOR v2.1x on Importing Settings From Previous Versions<br />
===================================================================================<br />
Config directory located in the users home directory and called "oboedit_config".<br />
Settings from the previous releases (OBO-Edit 1. 2.0 or 2.0 beta versions) are located in the <br />
configuration folder found at the default application installation location of your operating system. <br />
You can import the perspective and layout settings from previous versions to the folder called "oboedit_config".<br />
* Please note the config folder naming convention is not consistent with previous version.* <br />
Config files can also be reset when required through the Configuration Manager.<br />
<br />
<br />
============<br />
2.1 beta1 through beta4 Bug Fixes<br />
============<br />
[geneontology-Bugs-2899760] Too easy to make link to self in graph editor<br />
[geneontology-Bugs-2971221] eliminate possibility to create is_a relationships to self<br />
Text Editor and Parent Editor are now in sync<br />
[ geneontology-Bugs-2971364 ] b3 - problems committing text edits<br />
[ geneontology-Bugs-2987680 ] spontaneous intersection_of terms when cloning<br />
[ geneontology-Bugs-2922369 ] Is_a closure not working as expected<br />
[ geneontology-Bugs-2908106 ] OBO-merge fail<br />
[ geneontology-Bugs-2915594] Not saving<br />
[ geneontology-Bugs-2968827 ] saving implied links<br />
[ geneontology-Bugs-2952892 ] Reasoning with union_of terms<br />
[ geneontology-Bugs-2949754 ] Verification plugin dictionary - problem with quickfixes<br />
[ geneontology-Bugs-2922331 ] No log file for OE2.1beta2<br />
[ geneontology-Bugs-2874878 ] Missing log files in Mac<br />
[ geneontology-Bugs-2610787] disjointness violations not detected<br />
[ geneontology-Bugs-2821857] disjoint violations not being checked by RBR<br />
[ geneontology-Bugs-2941032] Functionality - application does not run on windows 7<br />
[ geneontology-Bugs-2915594 ] Not saving<br />
[ geneontology-Bugs-2914257 ] When a term is cloned, intersections become relationships<br />
[ geneontology-Bugs-2828905 ] verification config in 2.1 test release<br />
[ geneontology-Bugs-2869195 ] text editor is not working<br />
[ geneontology-Bugs-2864861 ] replaced_by statement causing problems in SO<br />
[ geneontology-Bugs-2840516 ] no way to get to genus term while defing xps<br />
[ geneontology-Bugs-2840500 ] relation name vanishes<br />
[ geneontology-Bugs-2908106 ] OBO-merge fail<br />
[ geneontology-Bugs-2610787] disjointness violations not detected<br />
[ geneontology-Bugs-2821857] disjoint violations not being checked by RBR<br />
[ geneontology-Bugs-2749049] disjoinedness check working?<br />
[ geneontology-Bugs-2750699 ] config manager memory settings option out of sync<br />
[ geneontology-Bugs-2785074 ] OBO-Edit2-rc still present<br />
[ geneontology-Bugs-2787869 ] very minor bug with saving filters<br />
[ geneontology-Bugs-2812189 ] GAZ.obo not displayed correctly in OBOEdit2.0<br />
[ geneontology-Bugs-2824732 ] obodiff is broken!<br />
[ geneontology-Bugs-2818616] stop panel changes if click on top<br />
[ geneontology-Bugs-2814791] OBO merge doesn't work!<br />
[ geneontology-Bugs-2805373] Assert implied links - color table rows<br />
[ geneontology-Bugs-2818549] parent search ignores relationship type<br />
[ geneontology-Bugs-2815689] change tracker save <br />
[ geneontology-Bugs-2805371] Assert implied links - resize<br />
[ geneontology-Bugs-2801684] OBO-Merge generates null-pointer exception<br />
[ geneontology-Bugs-2790372] Mac version 2 does not generate log files<br />
[ geneontology-Bugs-2749070] reasoner active even in OFF mode<br />
[ geneontology-Bugs-2722323] assert implied links pop-up hogs focus and halts editing<br />
[ geneontology-Bugs-2787869] very minor bug with saving filters<br />
[ geneontology-Bugs-2815829] Simplify 'save implied links'<br />
[ geneontology-Bugs-2722318] OTE local mode indication not intuitive<br />
- Fixed bug that stopped the box at the bottom of the history browser from appearing unless another component was clicked on. <br />
- flaky xp commit<br />
- graph viewer issue<br />
- filtering union_of cycles in OTE<br />
- lock view selection behavior<br />
- fixed root detection algorithm to detect inverse relations and display root<br />
(Part of OE2.0 - history browser minor bugs - ID: 2507044)<br />
- Fixed the history browser html message so it shows 'name (id)' rather then 'id (id)'.<br />
(Part of OE2.0 - history browser minor bugs - ID: 2507044)<br />
- Graphviz uses a lot of memory when you assign dbxrefs: ID: 2057452<br />
The Graphviz interface redraws have been removed for the bulk addition of dbxrefs. <br />
Now there is only one redraw at the end of the bulk process.<br />
- Added new feature to OBOMerge so that it reports if any term has been edited in both the live and branch files. <br />
- Added new feature to TermMergeHistoryItem, so it can update substitution tags that mention any term that<br />
is in the process of being subsumed in a merge. Fixes bug: ID: 2790775<br />
<br />
<br />
============<br />
Features<br />
============<br />
<br />
- Parent Editor and Cross Product Text Editor component are now in synch and warn regarding changes made in either component<br />
<br />
- Graph Viewer Improvements<br />
-- Renamed "Succinct" configuration option to "Trim reasoner-generated (implied) links from display".<br />
--> Removed reasoner dependency from displaying all-types panels and showing ancestors upto root<br />
<br />
- New Default Global Term Renderer for highlighting terms with cross product definitions<br />
<br />
- Cross Product Editor -> Go to Genus term button<br />
<br />
- J. Deegan committed new Tag Filter code. This feature enables <br />
users to choose which tags are saved out into OBO files. The GUI is in the <br />
'save as' dialog. There is still some work to do to make the GUI look less intimidating. Also, though the feature has been<br />
carefully tested, further testing will be required in case an obscure bug is causing parts of<br />
the data not to be saved out at all. I have not yet run the JUnit tests. When this code is released we should warn in-house users to<br />
watch diffs carefully for lost tags. <br />
<br />
- Assert Implied Links Component<br />
-- Displays impled links table and asserts selected links.<br />
-- Row sorting enabled (ascending and descending) for Child and Parent name columns<br />
-- Clicking the more info icon brings up the explanation for the reasoner made link in the Explanation Component and highlights the link in the Graph Editor<br />
<br />
- New Reasoner Modes (IN PROGRESS - WILL BE AVAILABLE in the next release)<br />
-- Two new options that represent step-wise and continuous incremental reasoning<br />
-- Activate incremental reasoning by selecting the "Avtivate Incremental Reasoning" checkbox through the Reasoner Manager<br />
-- Users have a choice between activating continuous incremental reasoning or partial/step reasoning modes. If neither of these options are selected incremental reasoning is off by default.<br />
<br />
- New option in Advanced Save - Perform is_a closure (behaviour under testing for various use cases)<br />
-- Performs is_a closure for all cross-referenced terms while saving<br />
<br />
- Changed naming coventions for Advanced Save - Save implied links:<br />
-- "Realize links" changed to "Assert Implied Links"<br />
-- "Save for presentation" changed to "Save trimmed links"<br />
<br />
- Lock/Unlock Layout option<br />
-- Locking the layout freezes current application layout and prevents addition/removal of components.<br />
<br />
- Scroll Lock for the Ontology Tree Editor<br />
-- Select any term in the OTE; right-click for Lock View option which enforces a scroll lock on the path currently displayed.<br />
<br />
- NEW Configuration directory location: users home directory/oboedit_config<br />
<br />
- Cloning behavior corrected - clones now persist on the same branch as the original term. <br />
<br />
<br />
============<br />
To Do<br />
============<br />
Documentation:<br />
- user.dict usage and backup info<br />
- Assert Implied Links Component<br />
- Update Advanced Save interface options<br />
<br />
Troubleshooting- add note about:<br />
https://sourceforge.net/tracker2/index.php?func=detail&aid=2683791&group_id=36855&atid=418257<br />
<br />
Known Issues - Upcoming fixes<br />
Parent Editor and Text Editor not in sync.<br />
Ontology Tree Editor - Name unnamed terms<br />
Renaming terms problematic in Text Editor</div>Aminahttps://wiki.geneontology.org/index.php?title=Software_Group_progress_report_for_2010&diff=32348Software Group progress report for 20102010-12-01T20:06:19Z<p>Amina: /* OBO-Edit */</p>
<hr />
<div>== Management ==<br />
<br />
* Created a timeline [[SWUG_Timeline_2010-2011]]<br />
<br />
== Annotation Support ==<br />
<br />
=== Database ===<br />
<br />
=== Production (Stuart, Gail, Ben, Mike C) ===<br />
<br />
#Rebuilt goweb-dev (not replaced)<br />
#*Upgraded OS from RH 32-bit -> RH 64bit<br />
#*Upgraded mysql from 5.0 -> 5.1<br />
#Replaced GO loading machine<br />
#* (old) goad = PowerEdge 1850, 2x2.8GHz Dual Core Intel Xeon, 12GB RAM, 2x300GB disks<br />
#* (new) claret = PowerEdge R610, 2x2.53GHz Quad Core Intel E5540 Xeon, 24GB RAM, 4x500GB disks (64bit OS)<br />
#** sucessfully tested loading on claret<br />
#** have also done initial testing on load-qfo replacement for loading sequences into godb<br />
#Ordered 2 machines to replace GO frontends, goweb1/goweb2<br />
#*Anticipated that these machines will be into production by the end of 2010.<br />
#During process of moving to new machines, the OS, Mysql, and other software were upgraded to the lastest versions.<br />
#Worked on testing and installing of Amigo 1.8 (required 64bit OS for clucene-based searching)<br />
#Made several upgrades to GAF filtering script<br />
#* update from GAF 1.0 -> 2.0<br />
#* added the following feature_types<br />
#** gene_product<br />
#** polypeptide<br />
#* added the following evidence codes: IMR, IRD<br />
#* added qualifier 'rapid_divergence'<br />
# Put in place filter-paint-associations.pl script<br />
<br />
=== Schema Overhaul ===<br />
<br />
[[Schema Overhaul]]<br />
<br />
#SQL schema creation into postgres through a java program<br />
#generation of TSV files through [[Schema_Overhaul#OBO_Access_Layer]] except the following tables (in progress)<br />
#*ontology_imports, ontology_subset, all_only_relationship, never_some_relationship , relation_chain<br />
#[[Schema_Overhaul#OBO_Access_Layer]] is in progress<br />
#loading of TSV files into postgres<br />
#incremental update of the GOLD database (in progress)<br />
#Command Line Interface is built<br />
#Basic Admin servlet interface is built to run the db operations through a web interface (in progress)<br />
<br />
(this may belong in a separate report - add here for now anyway)<br />
<br />
=== Annotation QC ===<br />
<br />
* v1 of [[Taxon_Constraint_Check_Engine] in production. v2 (java rewrite) in progress<br />
* [[Function_to_Process_Inference_Engine]] in production<br />
* [[Annotation_Rule_Engine]]<br />
** current and proposed checks now captured in the annotation xml file<br />
<br />
=== AmiGO ===<br />
<br />
* See [[AmiGO_1_9]]<br />
* See [[Full_Text_Indexing_Progress]]<br />
<br />
=== Website ===<br />
<br />
*Overhaul with different layout, some organisational changes, more easily accessed menu navigation, vertical rhythm<br />
*New documentation for ontology relations, structure<br />
*Updating of tools list (hampered by lack of new tool submissions)<br />
<br />
=== Workflow Support ===<br />
<br />
* Created a basic [[GO_Galaxy_Environment]]<br />
** integrated map2slim<br />
** integrated slim-creator<br />
** integrated enrichment tools<br />
*** GO TermFinder<br />
*** Ontologizer<br />
<br />
=== MOOSE libraries ===<br />
<br />
* Ontology slimmer<br />
* Ontology and annotation slimmer (map2slim)<br />
* Added algorithms of transitive closure and transitive reduction for use by slimming scripts<br />
* Started some preliminary support for basic boolean logic (for creating bucket terms)<br />
<br />
== Reference Genome Support ==<br />
<br />
=== RefG in AmiGO ===<br />
<br />
<br />
* Loading Trees (SVEN)<br />
** Matching IDs<br />
*** Currently ~64% of of the ids are being matched after the new QFO load.<br />
*** Noticed that 1970 proteins are in more then one group (ie YEAST|SGD:S000006392|UniProtKB:Q06580). Informed Paul Thomas.<br />
** Report Pages<br />
*** 2. Concurrent annotation: Code written, not part of load yet.<br />
**** Some group name in file provided by Pascale Gaudet are not in group list. Informed Paul Thomas.<br />
*** 8. 'Date comprehensively annotated' for groups that can provide this information: Have no idea where this data is<br />
<br />
<br />
* js phylo views: work in progress on dev machine (nothing public yet, rapidly changing alpha versions). See: [[AmiGO_Phylotrees]].<br />
* existing refg pages: to be dropped--no further work<br />
* [[AmiGO_and_QuickGO_Integration]] SETH/TONY<br />
<br />
MARY TO FILL IN<br />
<br />
=== Paint ===<br />
<br />
SUZI TO FILL IN<br />
<br />
== Ontology Support ==<br />
<br />
=== TermGenie ===<br />
<br />
See [[Compositional_Term_Submission_Tool]]<br />
<br />
* Created initial prototype, in use by ontology group and annotators<br />
* Integrated autocomplete<br />
* Added involved_in template<br />
<br />
=== OBO-Edit ===<br />
<br />
*[http://wiki.geneontology.org/index.php/OBO-Edit_Release_Timeline Release Tracker]<br />
*[http://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=418257&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=1&category=&artgroup=&submitter=&keyword=&artifact_id=&submit=Filter Bug tracker]<br />
<br />
=== Transition to OWL ===<br />
<br />
See [[Transition_to_OWL]]<br />
* Initiated plan for ontology support in next cycle [[Software_Group_2010_Future_Plans#Plan]]<br />
* first draft of obof1.4 guide http://www.geneontology.org/GO.format.obo-1_4.shtml<br />
* formal spec of obo syntax and owl mapping: http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html<br />
* rewritten parser and obo2owl converter, 100% java http://code.google.com/p/oboformat/<br />
<br />
<br />
<br />
[[Category:Reports]]</div>Aminahttps://wiki.geneontology.org/index.php?title=Software_Group_progress_report_for_2010&diff=32335Software Group progress report for 20102010-12-01T18:08:56Z<p>Amina: /* OBO-Edit */</p>
<hr />
<div>== Management ==<br />
<br />
* Created a timeline [[SWUG_Timeline_2010-2011]]<br />
<br />
== Annotation Support ==<br />
<br />
=== Database ===<br />
<br />
=== Production (Stuart, Gail, Ben, Mike C) ===<br />
<br />
#Rebuilt goweb-dev (not replaced)<br />
#*Upgraded OS from RH 32-bit -> RH 64bit<br />
#*Upgraded mysql from 5.0 -> 5.1<br />
#Replaced GO loading machine<br />
#* (old) goad = PowerEdge 1850, 2x2.8GHz Dual Core Intel Xeon, 12GB RAM, 2x300GB disks<br />
#* (new) claret = PowerEdge R610, 2x2.53GHz Quad Core Intel E5540 Xeon, 24GB RAM, 4x500GB disks (64bit OS)<br />
#** sucessfully tested loading on claret<br />
#** have also done initial testing on load-qfo replacement for loading sequences into godb<br />
#Ordered 2 machines to replace GO frontends, goweb1/goweb2<br />
#*Anticipated that these machines will be into production by the end of 2010.<br />
#During process of moving to new machines, the OS, Mysql, and other software were upgraded to the lastest versions.<br />
#Worked on testing and installing of Amigo 1.8 (required 64bit OS for clucene-based searching)<br />
#Made several upgrades to GAF filtering script<br />
#* update from GAF 1.0 -> 2.0<br />
#* added the following feature_types<br />
#** gene_product<br />
#** polypeptide<br />
#* added the following evidence codes: IMR, IRD<br />
#* added qualifier 'rapid_divergence'<br />
# Put in place filter-paint-associations.pl script<br />
<br />
=== Schema Overhaul ===<br />
<br />
[[Schema Overhaul]]<br />
<br />
#SQL schema creation into postgres through a java program<br />
#generation of TSV files through [[Schema_Overhaul#OBO_Access_Layer]] except the following tables (in progress)<br />
#*ontology_imports, ontology_subset, all_only_relationship, never_some_relationship , relation_chain<br />
#[[Schema_Overhaul#OBO_Access_Layer]] is in progress<br />
#loading of TSV files into postgres<br />
#incremental update of the GOLD database (in progress)<br />
#Command Line Interface is built<br />
#Basic Admin servlet interface is built to run the db operations through a web interface (in progress)<br />
<br />
(this may belong in a separate report - add here for now anyway)<br />
<br />
=== Annotation QC ===<br />
<br />
* v1 of [[Taxon_Constraint_Check_Engine] in production. v2 (java rewrite) in progress<br />
* [[Function_to_Process_Inference_Engine]] in production<br />
* [[Annotation_Rule_Engine]]<br />
** current and proposed checks now captured in the annotation xml file<br />
<br />
=== AmiGO ===<br />
<br />
* See [[AmiGO_1_9]]<br />
* See [[Full_Text_Indexing_Progress]]<br />
<br />
=== Website ===<br />
<br />
*Overhaul with different layout, some organisational changes, more easily accessed menu navigation, vertical rhythm<br />
*New documentation for ontology relations, structure<br />
*Updating of tools list (hampered by lack of new tool submissions)<br />
<br />
=== Workflow Support ===<br />
<br />
* Created a basic [[GO_Galaxy_Environment]]<br />
** integrated map2slim<br />
** integrated slim-creator<br />
** integrated enrichment tools<br />
*** GO TermFinder<br />
*** Ontologizer<br />
<br />
=== MOOSE libraries ===<br />
<br />
* Ontology slimmer<br />
* Ontology and annotation slimmer (map2slim)<br />
* Added algorithms of transitive closure and transitive reduction for use by slimming scripts<br />
* Started some preliminary support for basic boolean logic (for creating bucket terms)<br />
<br />
== Reference Genome Support ==<br />
<br />
=== RefG in AmiGO ===<br />
<br />
<br />
* Loading Trees (SVEN)<br />
** Matching IDs<br />
*** Currently ~64% of of the ids are being matched after the new QFO load.<br />
*** Noticed that 1970 proteins are in more then one group (ie YEAST|SGD:S000006392|UniProtKB:Q06580). Informed Paul Thomas.<br />
** Report Pages<br />
*** 2. Concurrent annotation: Code written, not part of load yet.<br />
**** Some group name in file provided by Pascale Gaudet are not in group list. Informed Paul Thomas.<br />
*** 8. 'Date comprehensively annotated' for groups that can provide this information: Have no idea where this data is<br />
<br />
<br />
* js phylo views: work in progress on dev machine (nothing public yet, rapidly changing alpha versions). See: [[AmiGO_Phylotrees]].<br />
* existing refg pages: to be dropped--no further work<br />
* [[AmiGO_and_QuickGO_Integration]] SETH/TONY<br />
<br />
MARY TO FILL IN<br />
<br />
=== Paint ===<br />
<br />
SUZI TO FILL IN<br />
<br />
== Ontology Support ==<br />
<br />
=== TermGenie ===<br />
<br />
See [[Compositional_Term_Submission_Tool]]<br />
<br />
* Created initial prototype, in use by ontology group and annotators<br />
* Integrated autocomplete<br />
* Added involved_in template<br />
<br />
=== OBO-Edit ===<br />
<br />
*[http://wiki.geneontology.org/index.php/OBO-Edit_Release_Timeline Release Tracker]<br />
*[ Bugs recently fixed]<br />
*[ ]<br />
<br />
=== Transition to OWL ===<br />
<br />
See [[Transition_to_OWL]]<br />
* Initiated plan for ontology support in next cycle [[Software_Group_2010_Future_Plans#Plan]]<br />
* first draft of obof1.4 guide http://www.geneontology.org/GO.format.obo-1_4.shtml<br />
* formal spec of obo syntax and owl mapping: http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html<br />
* rewritten parser and obo2owl converter, 100% java http://code.google.com/p/oboformat/<br />
<br />
<br />
<br />
[[Category:Reports]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Editv2.1beta7&diff=32072OBO-Editv2.1beta72010-11-24T01:40:49Z<p>Amina: </p>
<hr />
<div>= Status =<br />
This page tracks items I'm currently working on. It is a moving target for beta 7 development dictated by the bug and feature tracker on sourceforge. <br />
<br />
* Oct 1st Friday Update: All the bugs listed below are fixed - I'm running some tests and will make a release when I'm sure everything is running ok.<br />
<br />
= Current work =<br />
* [https://sourceforge.net/tracker/?func=detail&aid=3029689&group_id=36855&atid=418257 Subset manager - subset name change not saved] <font color = blue> Done </font><br />
* [https://sourceforge.net/tracker/index.php?func=detail&aid=3049416&group_id=36855&atid=418257 Selection from auto-complete search menu flaky] <font color = blue> Done </font><br />
* [https://sourceforge.net/tracker/?func=detail&aid=2823197&group_id=36855&atid=418257 Some disjoint_from relationships impossible to delete]<br />
<br />
<br />
== Bugs ==<br />
* High Priority:<br />
**[http://sourceforge.net/tracker/?func=detail&aid=3076730&group_id=36855&atid=418257 Filter on save problems OE b4 - ID: 3076730]<font color = blue> In progress </font><br />
**[https://sourceforge.net/tracker/?func=detail&aid=2971364&group_id=36855&atid=418257 b4 - still having problems committing text edits]<font color = blue> Done </font><br />
**[https://sourceforge.net/tracker/?func=detail&aid=2948445&group_id=36855&atid=418257 Loss of intersection status on merge]<font color = blue> Done </font><br />
**[https://sourceforge.net/tracker/?func=detail&aid=2745699&group_id=36855&atid=418257 2.0 graph viewer now shows only one parent]<font color = blue> Done </font><br />
<br />
* Necessary Fixes<br />
** [https://sourceforge.net/tracker/?func=detail&aid=3038713&group_id=36855&atid=418257 Cross product editor broken in beta 5]<font color = blue> Done </font><br />
** [https://sourceforge.net/tracker/?func=detail&aid=3049402&group_id=36855&atid=418257 Delete option gone from parent plugin]<font color = blue> Done </font><br />
*[]<br />
<br />
== Features ==<br />
<br />
<br />
<br />
== Plans and TBD ==<br />
<br />
[[OBO-Edit_Release_Timeline]]<br />
<br />
[http://wiki.geneontology.org/index.php/OBO-Edit OBO-Edit Wiki Mainpage]<br />
[[Category:OBO-Edit]]<br />
[[Category:Software]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Editv2.1_Official_Release&diff=32071OBO-Editv2.1 Official Release2010-11-24T01:38:46Z<p>Amina: Created page with '= Status = This page tracks items I'm currently working on. = Current work = == Bugs == * High Priority: == Features == == Plans and TBD == [http://wiki.geneontology.org/i…'</p>
<hr />
<div>= Status =<br />
This page tracks items I'm currently working on.<br />
<br />
<br />
= Current work =<br />
<br />
== Bugs ==<br />
* High Priority:<br />
<br />
== Features ==<br />
<br />
<br />
<br />
== Plans and TBD ==<br />
[http://wiki.geneontology.org/index.php?title=OBO-Editv2.1beta7&action=submit Release Timeline]<br />
<br />
<br />
[http://wiki.geneontology.org/index.php/OBO-Edit OBO-Edit Wiki Mainpage]<br />
[[Category:OBO-Edit]]<br />
[[Category:Software]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Editv2.2_Official_Release&diff=32070OBO-Editv2.2 Official Release2010-11-24T01:38:39Z<p>Amina: Created page with '= Status = This page tracks items I'm currently working on. = Current work = == Bugs == * High Priority: == Features == == Plans and TBD == [http://wiki.geneontology.org/i…'</p>
<hr />
<div>= Status =<br />
This page tracks items I'm currently working on.<br />
<br />
<br />
= Current work =<br />
<br />
== Bugs ==<br />
* High Priority:<br />
<br />
== Features ==<br />
<br />
<br />
<br />
== Plans and TBD ==<br />
[http://wiki.geneontology.org/index.php?title=OBO-Editv2.1beta7&action=submit Release Timeline]<br />
<br />
<br />
[http://wiki.geneontology.org/index.php/OBO-Edit OBO-Edit Wiki Mainpage]<br />
[[Category:OBO-Edit]]<br />
[[Category:Software]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Release_Tracker&diff=32069OBO-Edit Release Tracker2010-11-24T01:37:53Z<p>Amina: </p>
<hr />
<div>*[[OBO-Edit Release Timeline]]<br />
*[[OBO-Editv2.1beta7]]<br />
*[[OBO-Editv2.1rc1]]<br />
*[[OBO-Editv2.1 Official Release]]<br />
*[[OBO-Editv2.2 Official Release]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101129&diff=32068OEWG 201011292010-11-24T01:37:02Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday November 29th, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
<br />
<br />
== Bug and Feature Tracker Updates ==<br />
* High priority editing, merge, xps bugs fixed in 2.1beta7<br />
<br />
<br />
==Discussion items==<br />
<br />
* [https://sourceforge.net/tracker/?func=detail&aid=1944186&group_id=36855&atid=418257 OTE oversensitive to unintended "dragging" between terms]<br />
* [https://sourceforge.net/tracker/?func=detail&aid=2823197&group_id=36855&atid=418257 Some disjoint_from relationships impossible to delete]<br />
<br />
<br />
== Demo ==<br />
<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101129&diff=32067OEWG 201011292010-11-24T01:28:26Z<p>Amina: </p>
<hr />
<div>OBO-Edit Working Group, Tuesday November 29th, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
<br />
<br />
== Bug and Feature Tracker Updates ==<br />
* High priority editing, merge, xps bugs fixed in 2.1beta7<br />
<br />
<br />
==Discussion items==<br />
<br />
* [https://sourceforge.net/tracker/?func=detail&aid=1944186&group_id=36855&atid=418257 OTE oversensitive to unintended "dragging" between terms]<br />
*<br />
<br />
<br />
== Demo ==<br />
<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OEWG_20101129&diff=32063OEWG 201011292010-11-24T01:09:41Z<p>Amina: Created page with 'OBO-Edit Working Group, Tuesday November 29th, 2010 8.30 a.m. PDT <br> Conference call details: New GOC conference call numbers<br> US: 1 866 953 9688 <br> UK: 0808 238 6001<br>…'</p>
<hr />
<div>OBO-Edit Working Group, Tuesday November 29th, 2010 8.30 a.m. PDT <br><br />
<br />
Conference call details: New GOC conference call numbers<br><br />
US: 1 866 953 9688 <br><br />
UK: 0808 238 6001<br><br />
pin: 801561<br><br />
<br />
Agenda/Chair: Amina<br><br />
Minutes: <br><br />
Attendees: <br />
<br />
==Action items carried over==<br />
<br />
<br />
== Bug and Feature Tracker Updates ==<br />
* High priority editing, merge, xps bugs fixed in 2.1beta7<br />
<br />
<br />
==Discussion items==<br />
<br />
<br />
== Demo ==<br />
<br />
<br />
<br />
<br />
==Action Items==<br />
<br />
<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG Meeting agenda and minutes List]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=32062OBO-Edit Working Group Meeting Agenda and Minutes2010-11-24T01:09:30Z<p>Amina: </p>
<hr />
<div>====[[OBO-Edit_Working_Group_weekly_meeting_minutes/agenda_rota|Meeting minutes/agenda rota]]====<br />
<br />
==Meeting Schedule for 2010==<br />
<br />
<br />
===Future Meetings Schedule===<br />
<br />
<br />
*[[OEWG_20101129| November 29]]<br />
<br />
*[[OEWG_20101207| December 07]]<br />
<br />
*[[OEWG_20101221| December 21]]<br />
<br />
<br />
==== Past Meetings ====<br />
<br />
*[[OEWG_20100112| January 12]]<br />
<br />
*[[OEWG_20100119| January 19]]<br />
<br />
*[[OEWG_20100126| January 26]]<br />
<br />
*[[OEWG_20100202| February 02]]<br />
<br />
*[[OEWG_20100216| February 16]]<br />
<br />
*[[OEWG_20100302| March 02]]<br />
<br />
*[[OEWG_20100309| March 09]]<br />
<br />
*[[OEWG_20100316| March 16]]<br />
<br />
*[[OEWG_20100330| March 30]]<br />
<br />
*[[OEWG_20100413| April 13]]<br />
<br />
*[[OEWG_20100504| May 04]]<br />
<br />
*[[OEWG_20100511| May 11]]<br />
<br />
*[[OEWG_20100525| May 25]]<br />
<br />
*[[OEWG_20100608| June 08]]<br />
<br />
*[[OEWG_20100720| July 20]]<br />
<br />
*[[OEWG_20100803| August 03]]<br />
<br />
*[[OEWG_20100817| August 17]]<br />
<br />
*[[OEWG_20100908| September 8-9th GOC Meeting]]<br />
<br />
*[[OEWG_20100928| September 28]]<br />
<br />
<br />
<br />
====Previous Year Meetings====<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2009 | Meeting Minutes from 2009]]<br><br />
[[Web_chat_transcripts | Web Chat Transcripts]]<br />
<br />
==[[OBO-Edit|Back to OBO-Edit wiki mainpage]]==</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=32025OBO-Edit Working Group Meeting Agenda and Minutes2010-11-23T16:44:39Z<p>Amina: </p>
<hr />
<div>====[[OBO-Edit_Working_Group_weekly_meeting_minutes/agenda_rota|Meeting minutes/agenda rota]]====<br />
<br />
==Meeting Schedule for 2010==<br />
<br />
<br />
===Future Meetings Schedule===<br />
<br />
<br />
*[[OEWG_20101123| November 29]]<br />
<br />
*[[OEWG_20101207| December 07]]<br />
<br />
*[[OEWG_20101221| December 21]]<br />
<br />
<br />
==== Past Meetings ====<br />
<br />
*[[OEWG_20100112| January 12]]<br />
<br />
*[[OEWG_20100119| January 19]]<br />
<br />
*[[OEWG_20100126| January 26]]<br />
<br />
*[[OEWG_20100202| February 02]]<br />
<br />
*[[OEWG_20100216| February 16]]<br />
<br />
*[[OEWG_20100302| March 02]]<br />
<br />
*[[OEWG_20100309| March 09]]<br />
<br />
*[[OEWG_20100316| March 16]]<br />
<br />
*[[OEWG_20100330| March 30]]<br />
<br />
*[[OEWG_20100413| April 13]]<br />
<br />
*[[OEWG_20100504| May 04]]<br />
<br />
*[[OEWG_20100511| May 11]]<br />
<br />
*[[OEWG_20100525| May 25]]<br />
<br />
*[[OEWG_20100608| June 08]]<br />
<br />
*[[OEWG_20100720| July 20]]<br />
<br />
*[[OEWG_20100803| August 03]]<br />
<br />
*[[OEWG_20100817| August 17]]<br />
<br />
*[[OEWG_20100908| September 8-9th GOC Meeting]]<br />
<br />
*[[OEWG_20100928| September 28]]<br />
<br />
<br />
<br />
====Previous Year Meetings====<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2009 | Meeting Minutes from 2009]]<br><br />
[[Web_chat_transcripts | Web Chat Transcripts]]<br />
<br />
==[[OBO-Edit|Back to OBO-Edit wiki mainpage]]==</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=32003OBO-Edit Working Group Meeting Agenda and Minutes2010-11-20T00:02:11Z<p>Amina: </p>
<hr />
<div>====[[OBO-Edit_Working_Group_weekly_meeting_minutes/agenda_rota|Meeting minutes/agenda rota]]====<br />
<br />
==Meeting Schedule for 2010==<br />
<br />
<br />
===Future Meetings Schedule===<br />
<br />
<br />
*[[OEWG_20101123| November 23]]<br />
<br />
*[[OEWG_20101207| December 07]]<br />
<br />
*[[OEWG_20101221| December 21]]<br />
<br />
<br />
==== Past Meetings ====<br />
<br />
*[[OEWG_20100112| January 12]]<br />
<br />
*[[OEWG_20100119| January 19]]<br />
<br />
*[[OEWG_20100126| January 26]]<br />
<br />
*[[OEWG_20100202| February 02]]<br />
<br />
*[[OEWG_20100216| February 16]]<br />
<br />
*[[OEWG_20100302| March 02]]<br />
<br />
*[[OEWG_20100309| March 09]]<br />
<br />
*[[OEWG_20100316| March 16]]<br />
<br />
*[[OEWG_20100330| March 30]]<br />
<br />
*[[OEWG_20100413| April 13]]<br />
<br />
*[[OEWG_20100504| May 04]]<br />
<br />
*[[OEWG_20100511| May 11]]<br />
<br />
*[[OEWG_20100525| May 25]]<br />
<br />
*[[OEWG_20100608| June 08]]<br />
<br />
*[[OEWG_20100720| July 20]]<br />
<br />
*[[OEWG_20100803| August 03]]<br />
<br />
*[[OEWG_20100817| August 17]]<br />
<br />
*[[OEWG_20100908| September 8-9th GOC Meeting]]<br />
<br />
*[[OEWG_20100928| September 28]]<br />
<br />
<br />
<br />
====Previous Year Meetings====<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes_2009 | Meeting Minutes from 2009]]<br><br />
[[Web_chat_transcripts | Web Chat Transcripts]]<br />
<br />
==[[OBO-Edit|Back to OBO-Edit wiki mainpage]]==</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Summary&diff=31891OBO-Edit Working Group Summary2010-11-16T19:12:19Z<p>Amina: </p>
<hr />
<div>3 July 2006<br />
==Purpose==<br />
;What is the group’s purpose?<br />
:This group guides the development of OBO-Edit to ensure usability and accessibility for a dynamic user group.<br />
;What makes this group necessary and unique?<br />
:OBO-Edit has become sufficiently complex, and sufficiently widely used, that we needed to move beyond the ad hoc development/testing approach that worked previously. This group ensures that OBO-Edit develops in directions that address the needs of its diverse and growing user community.<br />
;What is the lifespan?<br />
:This group will exist as long as OBO-Edit is undergoing active development. At present we assume that's equivalent to the lifespan of the GO project.<br />
==Group Leader==<br />
Midori Harris<br><br />
Decisions are made by consensus among group members.<br />
<br />
==Subscribe==<br />
;Subscribe to the working group mailing list on Sourceforge:<br />
https://sourceforge.net/mailarchive/forum.php?forum_name=geneontology-oboedit-working-group<br />
<br />
;OBO-Edit Working Group Meeting Calendar:<br />
[http://www.google.com/calendar/embed?src=cDN1bXNkOG45bDMyYW5kbGR1M2xqcjNuazhAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ View the OBO-Edit calendar]<br />
<br />
<br />
==Activities==<br />
<br />
;What are the key deliverables of this group?<br />
*Testing: We beta-test each version of OBO-Edit, and determine whether/when a version is ready for official release.<br />
*Assigning priorities for future OBO-Edit development tasks, such as new features. OBO-Edit is being used by many groups (e.g. GO, PO, PATO, NCBO) whose priorities must be taken into consideration.<br />
*User training: we are writing documentation, and plan to produce online tutorials and organize 'webinars' and live training workshops.<br />
;What criteria are used to set priorities?<br />
New feature requests are tracked at [https://sourceforge.net/tracker/?group_id=36855&atid=418260 SourceForge]. Criteria include how many people would use a feature, how much it would improve the speed or accuracy of their work, and how much it would help future development. Bug fixes always have high priority. Additional criteria may emerge. <br />
==Members==<br />
*Amina Abdulla (BBOP)<br />
*Chris Mungall (BBOP)<br />
*Midori Harris (GO Ed., EBI)<br />
*Jennifer Deegan (GO Ed., EBI)<br />
*Nomi Harris (BBOP)<br />
*Shuly Avraham (Gramene)<br />
*Rama Balakrishnan (SGD)<br />
*Carol Bastiani (WB)<br />
*Tanya Berardini (TAIR)<br />
*Karen Christie (SGD)<br />
*Alex Diehl (MGI)<br />
*Harold Drabkin (MGI)<br />
*Karen Eilbeck (SO)<br />
*Petra Fey (DDB)<br />
*Melissa Haendel (ZFIN)<br />
*Amelia Ireland (GO Ed., EBI)<br />
*Pankaj Jaiswal (Gramene)<br />
*Ranjana Kishore (WB)<br />
*Jane Lomax (GO Ed., EBI)<br />
*John Osborne<br />
*David Osumi-Sutherland (FlyBase)<br />
*Victoria Petri (RGD)<br />
*Erika Feltrin (TRAIT)<br />
<br />
Aim is at least one representative from each MOD. One becomes a member by volunteering; we don't want the group to get too much bigger, but so far no one's been denied entry (and we'd hate to do that).<br />
<br />
==Meeting calendar==<br />
<br />
*WebEx chat/screen sharing interface for demos in conjunction with conference call every Tuesday at 9:30am PST/PDT<br />
*Email in between meetings<br />
<br />
==Metrics of success==<br />
*Most important metric: Stable releases of OBO-Edit<br />
*Other metrics: bugs fixed; features implemented; documentation produced<br />
==Linkages==<br />
*GO Editors - main users of OBO-Edit within GOC<br />
*Annotators - some do content development; others use OBO-Edit for searching GO<br />
*OBO ontology developers - i.e. OBO-Edit users, both within and outside GOC (some overlap with GO annotators)<br />
*Software development group (Berkeley)<br />
*Production database/software group (Stanford)<br />
==Process==<br />
Decision-making is by consensus following discussion via email and conference calls. All email is on the [https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group mailing list]<br />
<br />
Tools: Using WebEx. Conference calls & email; professional webinar hosting will help a lot with sharing experience among ourselves and training others.<br />
<br />
OBO-Edit testing follows steps:<br />
<br />
1. automated testing<br />
2. manual testing<br />
a. 'pre-testing' (one curator)<br />
b. test commonly used editing tasks (several curators)<br />
c. test all items in test suite (several curators)<br />
d. test new features (several curators)<br />
<br />
If a version fails automated tests, or if bugs turn up in manual<br />
testing, Amina does bug fixes and the procedures starts again with the<br />
next version.<br />
<br />
Note: automated and manual testing suites are being developed by the<br />
working group. We will soon make more specifics available, probably on<br />
a wiki page.<br />
<br />
[[Category:OBO-Edit working group|OBO-Edit Working Group main page]]<br />
[[Category:Working Groups]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Summary&diff=31890OBO-Edit Working Group Summary2010-11-16T19:11:59Z<p>Amina: </p>
<hr />
<div>3 July 2006<br />
==Purpose==<br />
;What is the group’s purpose?<br />
:This group guides the development of OBO-Edit to ensure usability and accessibility for a dynamic user group.<br />
;What makes this group necessary and unique?<br />
:OBO-Edit has become sufficiently complex, and sufficiently widely used, that we needed to move beyond the ad hoc development/testing approach that worked previously. This group ensures that OBO-Edit develops in directions that address the needs of its diverse and growing user community.<br />
;What is the lifespan?<br />
:This group will exist as long as OBO-Edit is undergoing active development. At present we assume that's equivalent to the lifespan of the GO project.<br />
==Group Leader==<br />
Midori Harris<br><br />
Decisions are made by consensus among group members.<br />
<br />
==Subscribe==<br />
;Subscribe to the working group mailing list on Sourceforge: <br><br />
https://sourceforge.net/mailarchive/forum.php?forum_name=geneontology-oboedit-working-group<br />
<br />
;OBO-Edit Working Group Meeting Calendar:<br><br />
[http://www.google.com/calendar/embed?src=cDN1bXNkOG45bDMyYW5kbGR1M2xqcjNuazhAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ View the OBO-Edit calendar]<br />
<br />
<br />
==Activities==<br />
<br />
;What are the key deliverables of this group?<br />
*Testing: We beta-test each version of OBO-Edit, and determine whether/when a version is ready for official release.<br />
*Assigning priorities for future OBO-Edit development tasks, such as new features. OBO-Edit is being used by many groups (e.g. GO, PO, PATO, NCBO) whose priorities must be taken into consideration.<br />
*User training: we are writing documentation, and plan to produce online tutorials and organize 'webinars' and live training workshops.<br />
;What criteria are used to set priorities?<br />
New feature requests are tracked at [https://sourceforge.net/tracker/?group_id=36855&atid=418260 SourceForge]. Criteria include how many people would use a feature, how much it would improve the speed or accuracy of their work, and how much it would help future development. Bug fixes always have high priority. Additional criteria may emerge. <br />
==Members==<br />
*Amina Abdulla (BBOP)<br />
*Chris Mungall (BBOP)<br />
*Midori Harris (GO Ed., EBI)<br />
*Jennifer Deegan (GO Ed., EBI)<br />
*Nomi Harris (BBOP)<br />
*Shuly Avraham (Gramene)<br />
*Rama Balakrishnan (SGD)<br />
*Carol Bastiani (WB)<br />
*Tanya Berardini (TAIR)<br />
*Karen Christie (SGD)<br />
*Alex Diehl (MGI)<br />
*Harold Drabkin (MGI)<br />
*Karen Eilbeck (SO)<br />
*Petra Fey (DDB)<br />
*Melissa Haendel (ZFIN)<br />
*Amelia Ireland (GO Ed., EBI)<br />
*Pankaj Jaiswal (Gramene)<br />
*Ranjana Kishore (WB)<br />
*Jane Lomax (GO Ed., EBI)<br />
*John Osborne<br />
*David Osumi-Sutherland (FlyBase)<br />
*Victoria Petri (RGD)<br />
*Erika Feltrin (TRAIT)<br />
<br />
Aim is at least one representative from each MOD. One becomes a member by volunteering; we don't want the group to get too much bigger, but so far no one's been denied entry (and we'd hate to do that).<br />
<br />
==Meeting calendar==<br />
<br />
*WebEx chat/screen sharing interface for demos in conjunction with conference call every Tuesday at 9:30am PST/PDT<br />
*Email in between meetings<br />
<br />
==Metrics of success==<br />
*Most important metric: Stable releases of OBO-Edit<br />
*Other metrics: bugs fixed; features implemented; documentation produced<br />
==Linkages==<br />
*GO Editors - main users of OBO-Edit within GOC<br />
*Annotators - some do content development; others use OBO-Edit for searching GO<br />
*OBO ontology developers - i.e. OBO-Edit users, both within and outside GOC (some overlap with GO annotators)<br />
*Software development group (Berkeley)<br />
*Production database/software group (Stanford)<br />
==Process==<br />
Decision-making is by consensus following discussion via email and conference calls. All email is on the [https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group mailing list]<br />
<br />
Tools: Using WebEx. Conference calls & email; professional webinar hosting will help a lot with sharing experience among ourselves and training others.<br />
<br />
OBO-Edit testing follows steps:<br />
<br />
1. automated testing<br />
2. manual testing<br />
a. 'pre-testing' (one curator)<br />
b. test commonly used editing tasks (several curators)<br />
c. test all items in test suite (several curators)<br />
d. test new features (several curators)<br />
<br />
If a version fails automated tests, or if bugs turn up in manual<br />
testing, Amina does bug fixes and the procedures starts again with the<br />
next version.<br />
<br />
Note: automated and manual testing suites are being developed by the<br />
working group. We will soon make more specifics available, probably on<br />
a wiki page.<br />
<br />
[[Category:OBO-Edit working group|OBO-Edit Working Group main page]]<br />
[[Category:Working Groups]]</div>Aminahttps://wiki.geneontology.org/index.php?title=OBO-Edit&diff=31889OBO-Edit2010-11-16T19:04:39Z<p>Amina: /* Working group */</p>
<hr />
<div><big>'''OBO-Edit Wiki'''</big><br />
<br />
A central repository for OBO-Edit developer info, announcements, and technical information.<br />
<br />
== Releases ==<br />
*[[Release Tracker]]<br />
*[https://sourceforge.net/projects/geneontology/files/ Download the latest version from Sourceforge]<br />
<br />
<br />
== Announcements ==<br />
*[[OBO-Edit: v2.1 Release Notes]]<br />
* [http://www.bioontology.org/wiki/index.php/A_practical_introduction_to_OBO-Edit2 A_practical_introduction_to_OBO-Edit2]<br />
* [[OBO-Edit 2.0 Official Release Available for download]]<br />
* [[OBO-Edit: Help document OBO-Edit 2]]<br />
* [[OBO-Edit: Versioning Proposal]]--versioning for OBO ontology files (not for OBO-Edit)<br />
* [[OBO-Edit: Long Term Goals]]<br />
* [[OBO-Edit: Potential Refactoring]]<br />
* [[OBO-Edit 2.0 Development Roadmap]]<br />
* [[OBO-Edit: Code Overhaul]]<br />
* [[Regulates icons in OBO-Edit]]<br />
* [[Ideas page]]<br />
<br />
<br />
== Code and Trackers ==<br />
* [[OBO-Edit: Getting the Source Code]]<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse Bug tracker]<br />
* [https://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 Feature tracker]<br />
* [http://geneontology.svn.sourceforge.net/viewvc/geneontology/java/oboedit/trunk/ Browse OBO-Edit code in SourceForge svn repository]<br />
* [http://www.oboedit.org/api/ API docs for OBO, BBOP, and OBO-Edit]<br />
* [[OBO-Edit_Developer_Area]]<br />
<br />
<br />
== Working group ==<br />
* [[OBO-Edit Working Group Summary]]<br />
* [[OBO-Edit Working Group Meeting Agenda and Minutes]]<br />
<br />
== User articles ==<br />
* [[OBO-Edit: FAQ]]<br />
* [[OBO-Edit: Tips]]<br />
<br />
<br />
== Teaching Resources ==<br />
* [[OBO-Edit: References/Teaching Resources]]<br />
<br />
<br />
== Technical articles and documentation ==<br />
* [[OBO-Edit: Arcana for User's Guide]]<br />
* [[OBO-Edit: Making OBO-Edit Installers]]<br />
* [[OBO-Edit: Adding to the OBO-Edit help guide]]<br />
* [[OBO-Edit: Getting Old Source Code from CVS]]<br />
<br />
* [[OBO-Edit: Writing Plugins for OBO-Edit 2.0]]<br />
* [[OBO-Edit: Installing the Term Image Plugin]]<br />
<br />
* [[OBO-Edit: Reusable Components in BBOP]]<br />
* [[OBO-Edit: The Filtering System]]<br />
* [[OBO-Edit: Reasoner Overview]]<br />
* [[OBO-Edit: OBO Parser - Getting Started]]<br />
<br />
* [[OBO-Edit: UML Diagrams]]<br />
* [[OBO-Edit Datamodel Interfaces Diagram]]<br />
* [[OBO-Edit: Intersections in the OBO-Edit datamodel]]<br />
<br />
* [[OBO: 1.3 Whiteboard for OBO 1.3 features and proposals]]<br />
<br />
<br />
== Mailing lists ==<br />
* [http://groups.google.com/group/obo-edit-dev obo-edit-dev] Google group for OBO-Edit developers<br />
* [https://lists.sourceforge.net/lists/listinfo/geneontology-oboedit-working-group OBO-Edit Working Group mailing list (SourceForge)]<br />
<br />
<br />
== Old pages ==<br />
* [[OBO-Edit Working Group Meeting Agenda and Minutes 2009]]<br />
* OBO-Edit Working Group [[Web chat transcripts]]<br />
* [[OBO-Edit 2.0 Testing Tasks]]<br />
* [[OBO-Edit: 2.0 TODO]]<br />
* [[OBO-Edit: OBO-Edit 2.0 Feature Request Prioritization]]<br />
* [[OBO-Edit 1.1 Testing Tasks]]<br />
* [[OBO-Edit: Proposals for Designing a New Filtering Interface]] DONE - NO LONGER RELEVANT<br />
<br />
[[Category:Software]]<br />
[[Category:SWUG Product]]</div>Amina