https://wiki.geneontology.org/api.php?action=feedcontributions&user=Nomi&feedformat=atomGO Wiki - User contributions [en]2024-03-29T13:53:47ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41161OEWG 201207032012-07-03T17:23:28Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Paola, Chris M., Ramona, Midori<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
** Nomi started working on this; Heiko will finish it.<br />
<br />
==Discussion==<br />
* Important announcement from Nomi: as of July 1, she has a new job (and thus will no longer be working on OBO-Edit). Nomi is now the program manager for KBase, a knowledgebase for predictive biology. (The project is based at LBNL, but in a different division.)<br />
** Heiko will take over as the OBO-Edit support person, but will only fix showstopper bugs--most of his time is spent working on next-generation ontology tools.<br />
** Heiko and Chris will continue to hold an OEWG meeting on the first Tuesday of each month, but it will become more of a general ontology support meeting (e.g., help with using OORT, TermGenie, phenotype ontologies, etc.)<br />
<br><br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
** Hard to attack this one when the people who report it won't give us any additional info, and no one in the OEWG has ever observed it themselves.<br />
* Ramona reviewed her bug reports and feature requests and updated priorities<br />
* Ramona said: "I haven't been doing much editing lately, but I have been using OE for making figures, and it has been behaving vary poorly. Crashing a lot. I will try to put together a more detailed report for you tomorrow, but I haven't had much time to investigate it systematically."<br />
** Removing oboedit_config/perspectives didn't help. Removing her whole oboedit_config directory helped only temporarily--then it started crashing again.<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=41160OBO-Edit Working Group Meeting Agenda and Minutes2012-07-03T17:22:49Z<p>Nomi: </p>
<hr />
<div>==Meeting Schedule for 2011-2==<br />
__NOTOC__<br />
<br />
The OBO-Edit Working Group currently meets the first Tuesday of the month (and sometimes the third Tuesday as well) at 8:30am California time (16:30 GMT), except as noted.<br />
<br />
==Future Meetings==<br />
August 7, 2012<br />
<br />
<br />
== Past Meetings in 2011-2==<br />
* [[OEWG_20120703 | July 3, 2012]]<br />
* [[OEWG_20120515 | June 5, 2012]]<br />
* [[OEWG_20120501 | May 1, 2012]]<br />
* [[OEWG_20120417 | April 17, 2012]] ('''NOTE: The US has switched to Daylight Savings Time''')<br />
* [[OEWG_20120306 | March 6, 2012]]<br />
* [[OEWG_20120221 | February 21, 2012]]<br />
* [[OEWG_20120207 | February 7, 2012]]<br />
* [[OEWG_20120117 | January 17, 2012]]<br />
* [[OEWG_20120103 | January 3, 2012]]<br />
* [[OEWG_20111207 | December 6, 2011]]<br />
* [[OEWG_20111101 | November 1, 2011]] ('''NOTE: If you are in the UK, the meeting will start at 15:30 rather than the usual 16:30, because the UK has gone off British Summer Time whereas the US still has another week on Daylight Savings Time.''')<br />
* [[OEWG_20111004 | October 4]]<br />
* [[OEWG_20110920 | September 20]] (no meeting September 6)<br />
* [[OEWG_20110830 | August 30]] (note FIFTH Tuesday)<br />
* [[OEWG_20110816 | August 16]]<br />
* [[OEWG_20110721 | Thursday, July 21, 8:30am PDT (usual time, different day)]]<br />
* [[OEWG_20110705| July 5]]<br />
* [[OEWG_20110621| June 21]]<br />
* [[OEWG_20110607| June 7]]<br />
* [[OEWG_20110517| May 17]]<br />
* [[OEWG_20110503| May 3]]<br />
<br />
* [[OEWG_20110419| April 19]]<br />
* [[OEWG_20110405| April 5]]<br />
<br />
* [[OEWG_20110315| March 15]]<br />
<br />
* [[OEWG_20110301| March 1]]<br />
<br />
*[[OEWG_20110208| February 8]]<br />
<br />
*[[OEWG_20110125| January 25]]<br />
<br />
*[[OEWG_20110111| January 11]]<br />
<br />
====Meetings in Past Years====<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 home page]]==<br />
<br />
[[Category:OBO-Edit_working_group]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41156OEWG 201207032012-07-03T15:56:14Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Paola, Chris M., Ramona, Midori<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
** Nomi started working on this; Heiko will finish it.<br />
<br />
==Discussion==<br />
* Important announcement from Nomi: as of July 1, she has a new job (and thus will no longer be working on OBO-Edit). Nomi is now the technical project manager for KBase, a knowledgebase for predictive biology. (The project is based at LBNL, but in a different division.)<br />
** Heiko will take over as the OBO-Edit support person, but will only fix showstopper bugs--most of his time is spent working on next-generation ontology tools.<br />
** Heiko and Chris will continue to hold an OEWG meeting on the first Tuesday of each month, but it will become more of a general ontology support meeting (e.g., help with using OORT, TermGenie, phenotype ontologies, etc.)<br />
<br><br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
** Hard to attack this one when the people who report it won't give us any additional info, and no one in the OEWG has ever observed it themselves.<br />
* Ramona reviewed her bug reports and feature requests and updated priorities<br />
* Ramona said: "I haven't been doing much editing lately, but I have been using OE for making figures, and it has been behaving vary poorly. Crashing a lot. I will try to put together a more detailed report for you tomorrow, but I haven't had much time to investigate it systematically."<br />
** Removing oboedit_config/perspectives didn't help. Removing her whole oboedit_config directory helped only temporarily--then it started crashing again.<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41155OEWG 201207032012-07-03T15:55:11Z<p>Nomi: </p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Paola, Chris M., Ramona, Midori<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
** Nomi started working on this; Heiko will finish it.<br />
<br />
==Discussion==<br />
* Important announcement from Nomi: as of July 1, she has a new job (and thus will no longer be working on OBO-Edit). Nomi is now the technical project manager for KBase, a knowledgebase for predictive biology. (The project is based at LBNL, but in a different division.)<br />
** Heiko will take over as the OBO-Edit support person, but will only fix showstopper bugs--most of his time is spent working on next-generation ontology tools.<br />
** Heiko and Chris will continue to hold an OEWG meeting on the first Tuesday of each month, but it will become more of a general ontology support meeting (e.g., help with using OORT, TermGenie, phenotype ontologies, etc.)<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
* Ramona reviewed her bug reports and feature requests and updated priorities<br />
* Ramona said: "I haven't been doing much editing lately, but I have been using OE for making figures, and it has been behaving vary poorly. Crashing a lot. I will try to put together a more detailed report for you tomorrow, but I haven't had much time to investigate it systematically."<br />
** Removing oboedit_config/perspectives didn't help. Removing her whole oboedit_config directory helped only temporarily--then it started crashing again.<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41154OEWG 201207032012-07-03T15:48:30Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Paola, Chris M., Ramona, Midori<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
<br />
==Future work==<br />
<br />
==Discussion==<br />
* Important announcement from Nomi<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
* Ramona reviewed her bug reports and feature requests and updated priorities<br />
* Ramona said: "I haven't been doing much editing lately, but I have been using OE for making figures, and it has been behaving vary poorly. Crashing a lot. I will try to put together a more detailed report for you tomorrow, but I haven't had much time to investigate it systematically."<br />
** Removing oboedit_config/perspectives didn't help. Removing her whole oboedit_config directory helped only temporarily--then it started crashing again.<br />
<br />
* OEWG meeting will continue once a month but will become more of a general ontology support meeting (e.g., help with using OORT, TermGenie, phenotype ontologies, etc.)<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41153OEWG 201207032012-07-03T15:47:15Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Paola, Chris M., Ramona, Midori<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
<br />
==Future work==<br />
<br />
==Discussion==<br />
* Important announcement from Nomi<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
* Ramona reviewed her bug reports and feature requests and updated priorities<br />
* Ramona said: "I haven't been doing much editing lately, but I have been using OE for making figures, and it has been behaving vary poorly. Crashing a lot. I will try to put together a more detailed report for you tomorrow, but I haven't had much time to investigate it systematically."<br />
** Removing oboedit_config/perspectives didn't help. Removing her whole oboedit_config directory helped only temporarily--then it started crashing again.<br />
<br />
* OEWG meeting will continue once a month but will become more of a general ontology support meeting (e.g., help with using OORT, phenotype ontologies, etc.)<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41152OEWG 201207032012-07-03T15:43:40Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Paola, Chris M., Ramona, Midori<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
<br />
==Future work==<br />
<br />
==Discussion==<br />
* Important announcement from Nomi<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
* Ramona reviewed her bug reports and feature requests and updated priorities<br />
* Ramona said: "I haven't been doing much editing lately, but I have been using OE for making figures, and it has been behaving vary poorly. Crashing a lot. I will try to put together a more detailed report for you tomorrow, but I haven't had much time to investigate it systematically."<br />
** Removing oboedit_config/perspectives didn't help. Removing her whole oboedit_config directory helped only temporarily--then it started crashing again.<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41151OEWG 201207032012-07-03T15:33:00Z<p>Nomi: /* OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Paola, Chris M., Ramona, Midori<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
<br />
==Future work==<br />
<br />
==Discussion==<br />
* Important announcement from Nomi<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
* Ramona reviewed her bug reports and feature requests and updated priorities<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41150OEWG 201207032012-07-03T15:32:47Z<p>Nomi: /* OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Chris M., Ramona, Midori<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
<br />
==Future work==<br />
<br />
==Discussion==<br />
* Important announcement from Nomi<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
* Ramona reviewed her bug reports and feature requests and updated priorities<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41149OEWG 201207032012-07-03T15:31:10Z<p>Nomi: /* Future work */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
<br />
==Future work==<br />
<br />
==Discussion==<br />
* Important announcement from Nomi<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
* Ramona reviewed her bug reports and feature requests and updated priorities<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41148OEWG 201207032012-07-03T15:30:53Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
<br />
==Future work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3487566&group_id=36855&atid=418257 is_Obsolete not recognized in verification check]<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3411578&group_id=36855&atid=418257 Different warnings from Verification Manager and Text Editor]<br />
<br />
==Discussion==<br />
* Important announcement from Nomi<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
* Ramona reviewed her bug reports and feature requests and updated priorities<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=41126OBO-Edit Working Group Meeting Agenda and Minutes2012-06-27T18:19:14Z<p>Nomi: </p>
<hr />
<div>==Meeting Schedule for 2011-2==<br />
__NOTOC__<br />
<br />
The OBO-Edit Working Group currently meets the first Tuesday of the month (and sometimes the third Tuesday as well) at 8:30am California time (16:30 GMT), except as noted.<br />
<br />
==Future Meetings==<br />
<br />
[[OEWG_20120703 | July 3, 2012]]<br />
<br />
== Past Meetings in 2011-2==<br />
* [[OEWG_20120515 | June 5, 2012]]<br />
* [[OEWG_20120501 | May 1, 2012]]<br />
* [[OEWG_20120417 | April 17, 2012]] ('''NOTE: The US has switched to Daylight Savings Time''')<br />
* [[OEWG_20120306 | March 6, 2012]]<br />
* [[OEWG_20120221 | February 21, 2012]]<br />
* [[OEWG_20120207 | February 7, 2012]]<br />
* [[OEWG_20120117 | January 17, 2012]]<br />
* [[OEWG_20120103 | January 3, 2012]]<br />
* [[OEWG_20111207 | December 6, 2011]]<br />
* [[OEWG_20111101 | November 1, 2011]] ('''NOTE: If you are in the UK, the meeting will start at 15:30 rather than the usual 16:30, because the UK has gone off British Summer Time whereas the US still has another week on Daylight Savings Time.''')<br />
* [[OEWG_20111004 | October 4]]<br />
* [[OEWG_20110920 | September 20]] (no meeting September 6)<br />
* [[OEWG_20110830 | August 30]] (note FIFTH Tuesday)<br />
* [[OEWG_20110816 | August 16]]<br />
* [[OEWG_20110721 | Thursday, July 21, 8:30am PDT (usual time, different day)]]<br />
* [[OEWG_20110705| July 5]]<br />
* [[OEWG_20110621| June 21]]<br />
* [[OEWG_20110607| June 7]]<br />
* [[OEWG_20110517| May 17]]<br />
* [[OEWG_20110503| May 3]]<br />
<br />
* [[OEWG_20110419| April 19]]<br />
* [[OEWG_20110405| April 5]]<br />
<br />
* [[OEWG_20110315| March 15]]<br />
<br />
* [[OEWG_20110301| March 1]]<br />
<br />
*[[OEWG_20110208| February 8]]<br />
<br />
*[[OEWG_20110125| January 25]]<br />
<br />
*[[OEWG_20110111| January 11]]<br />
<br />
====Meetings in Past Years====<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 home page]]==<br />
<br />
[[Category:OBO-Edit_working_group]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41125OEWG 201207032012-06-27T17:44:47Z<p>Nomi: /* Current work */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary files that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
<br />
==Future work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3487566&group_id=36855&atid=418257 is_Obsolete not recognized in verification check]<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3411578&group_id=36855&atid=418257 Different warnings from Verification Manager and Text Editor]<br />
<br />
==Discussion==<br />
* Important announcement from Nomi<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120703&diff=41108OEWG 201207032012-06-26T18:12:45Z<p>Nomi: Created page with "== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT == __NOTOC__ Conference call numbers:<br /> US: 1 866 953 9688<br /> UK: 0808 238 6001<br /> PIN: 801561<br /..."</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, July 3, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Current work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3537901&group_id=36855&atid=418260 Custom dictionaries]<br />
** OBO-Edit has two dictionaries that it uses to check for misspelled words in term names, definitions, etc. One is the "standard" dictionary distributed with OBO-Edit; the other is the "user" dictionary that each user can add words to (it starts out empty), which is stored in ~/oboedit_config/dict.<br />
** Some ontologies have a lot of specialized terms that users would like OBO-Edit to recognize so that it didn't flag them as misspelled. This request is to allow users to specify (via the Configuration Manager) additional custom dictionary/ies that OBO-Edit will read. (Any words that the user adds to the dictionary from inside OBO-Edit will still be stored in user.dict.)<br />
<br />
==Future work==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3487566&group_id=36855&atid=418257 is_Obsolete not recognized in verification check]<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3411578&group_id=36855&atid=418257 Different warnings from Verification Manager and Text Editor]<br />
<br />
==Discussion==<br />
* Important announcement from Nomi<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Most important unfixed bug: problem on some Windows 7 computers<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=41023OBO-Edit Working Group Meeting Agenda and Minutes2012-06-11T17:12:23Z<p>Nomi: /* Future Meetings */</p>
<hr />
<div>==Meeting Schedule for 2011-2==<br />
__NOTOC__<br />
<br />
The OBO-Edit Working Group currently meets the first Tuesday of the month (and sometimes the third Tuesday as well) at 8:30am California time (16:30 GMT), except as noted.<br />
<br />
==Future Meetings==<br />
<br />
July 3, 2012<br />
<br />
== Past Meetings in 2011-2==<br />
* [[OEWG_20120515 | June 5, 2012]]<br />
* [[OEWG_20120501 | May 1, 2012]]<br />
* [[OEWG_20120417 | April 17, 2012]] ('''NOTE: The US has switched to Daylight Savings Time''')<br />
* [[OEWG_20120306 | March 6, 2012]]<br />
* [[OEWG_20120221 | February 21, 2012]]<br />
* [[OEWG_20120207 | February 7, 2012]]<br />
* [[OEWG_20120117 | January 17, 2012]]<br />
* [[OEWG_20120103 | January 3, 2012]]<br />
* [[OEWG_20111207 | December 6, 2011]]<br />
* [[OEWG_20111101 | November 1, 2011]] ('''NOTE: If you are in the UK, the meeting will start at 15:30 rather than the usual 16:30, because the UK has gone off British Summer Time whereas the US still has another week on Daylight Savings Time.''')<br />
* [[OEWG_20111004 | October 4]]<br />
* [[OEWG_20110920 | September 20]] (no meeting September 6)<br />
* [[OEWG_20110830 | August 30]] (note FIFTH Tuesday)<br />
* [[OEWG_20110816 | August 16]]<br />
* [[OEWG_20110721 | Thursday, July 21, 8:30am PDT (usual time, different day)]]<br />
* [[OEWG_20110705| July 5]]<br />
* [[OEWG_20110621| June 21]]<br />
* [[OEWG_20110607| June 7]]<br />
* [[OEWG_20110517| May 17]]<br />
* [[OEWG_20110503| May 3]]<br />
<br />
* [[OEWG_20110419| April 19]]<br />
* [[OEWG_20110405| April 5]]<br />
<br />
* [[OEWG_20110315| March 15]]<br />
<br />
* [[OEWG_20110301| March 1]]<br />
<br />
*[[OEWG_20110208| February 8]]<br />
<br />
*[[OEWG_20110125| January 25]]<br />
<br />
*[[OEWG_20110111| January 11]]<br />
<br />
====Meetings in Past Years====<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 home page]]==<br />
<br />
[[Category:OBO-Edit_working_group]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=41001OBO-Edit Working Group Meeting Agenda and Minutes2012-06-05T15:41:59Z<p>Nomi: </p>
<hr />
<div>==Meeting Schedule for 2011-2==<br />
__NOTOC__<br />
<br />
The OBO-Edit Working Group currently meets the first Tuesday of the month (and sometimes the third Tuesday as well) at 8:30am California time (16:30 GMT), except as noted.<br />
<br />
==Future Meetings==<br />
<br />
== Past Meetings in 2011-2==<br />
* [[OEWG_20120515 | June 5, 2012]]<br />
* [[OEWG_20120501 | May 1, 2012]]<br />
* [[OEWG_20120417 | April 17, 2012]] ('''NOTE: The US has switched to Daylight Savings Time''')<br />
* [[OEWG_20120306 | March 6, 2012]]<br />
* [[OEWG_20120221 | February 21, 2012]]<br />
* [[OEWG_20120207 | February 7, 2012]]<br />
* [[OEWG_20120117 | January 17, 2012]]<br />
* [[OEWG_20120103 | January 3, 2012]]<br />
* [[OEWG_20111207 | December 6, 2011]]<br />
* [[OEWG_20111101 | November 1, 2011]] ('''NOTE: If you are in the UK, the meeting will start at 15:30 rather than the usual 16:30, because the UK has gone off British Summer Time whereas the US still has another week on Daylight Savings Time.''')<br />
* [[OEWG_20111004 | October 4]]<br />
* [[OEWG_20110920 | September 20]] (no meeting September 6)<br />
* [[OEWG_20110830 | August 30]] (note FIFTH Tuesday)<br />
* [[OEWG_20110816 | August 16]]<br />
* [[OEWG_20110721 | Thursday, July 21, 8:30am PDT (usual time, different day)]]<br />
* [[OEWG_20110705| July 5]]<br />
* [[OEWG_20110621| June 21]]<br />
* [[OEWG_20110607| June 7]]<br />
* [[OEWG_20110517| May 17]]<br />
* [[OEWG_20110503| May 3]]<br />
<br />
* [[OEWG_20110419| April 19]]<br />
* [[OEWG_20110405| April 5]]<br />
<br />
* [[OEWG_20110315| March 15]]<br />
<br />
* [[OEWG_20110301| March 1]]<br />
<br />
*[[OEWG_20110208| February 8]]<br />
<br />
*[[OEWG_20110125| January 25]]<br />
<br />
*[[OEWG_20110111| January 11]]<br />
<br />
====Meetings in Past Years====<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 home page]]==<br />
<br />
[[Category:OBO-Edit_working_group]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=41000OEWG 201205152012-06-05T15:38:57Z<p>Nomi: /* OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Ramona [the UK had a bank holiday]<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3487566&group_id=36855&atid=418257 is_Obsolete not recognized in verification check]<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3411578&group_id=36855&atid=418257 Different warnings from Verification Manager and Text Editor]<br />
<br />
==Discussion==<br />
<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Next bugs/features to focus on?<br />
** [http://sourceforge.net/tracker/?words=tracker_browse&sort=priority&sortdir=desc&offset=0&group_id=36855&atid=418257&assignee=&status=1&category=&artgroup=&keyword=&submitter=&artifact_id=0 Bugs sorted in descending order by priority]<br />
** [http://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=418260&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=1&category=&artgroup=&submitter=&keyword=&artifact_id=&submit=Filter Feature requests sorted in descending order by priority]<br />
** Could use re-prioritization<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40999OEWG 201205152012-06-05T15:36:46Z<p>Nomi: /* OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Ramona<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3487566&group_id=36855&atid=418257 is_Obsolete not recognized in verification check]<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3411578&group_id=36855&atid=418257 Different warnings from Verification Manager and Text Editor]<br />
<br />
==Discussion==<br />
<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Next bugs/features to focus on?<br />
** [http://sourceforge.net/tracker/?words=tracker_browse&sort=priority&sortdir=desc&offset=0&group_id=36855&atid=418257&assignee=&status=1&category=&artgroup=&keyword=&submitter=&artifact_id=0 Bugs sorted in descending order by priority]<br />
** [http://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=418260&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=1&category=&artgroup=&submitter=&keyword=&artifact_id=&submit=Filter Feature requests sorted in descending order by priority]<br />
** Could use re-prioritization<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40990OEWG 201205152012-06-04T17:52:22Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3487566&group_id=36855&atid=418257 is_Obsolete not recognized in verification check]<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3411578&group_id=36855&atid=418257 Different warnings from Verification Manager and Text Editor]<br />
<br />
==Discussion==<br />
<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Next bugs/features to focus on?<br />
** [http://sourceforge.net/tracker/?words=tracker_browse&sort=priority&sortdir=desc&offset=0&group_id=36855&atid=418257&assignee=&status=1&category=&artgroup=&keyword=&submitter=&artifact_id=0 Bugs sorted in descending order by priority]<br />
** [http://sourceforge.net/tracker/?limit=25&func=&group_id=36855&atid=418260&assignee=&status=&category=&artgroup=&keyword=&submitter=&artifact_id=&assignee=&status=1&category=&artgroup=&submitter=&keyword=&artifact_id=&submit=Filter Feature requests sorted in descending order by priority]<br />
** Could use re-prioritization<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40989OEWG 201205152012-06-04T17:50:37Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3487566&group_id=36855&atid=418257 is_Obsolete not recognized in verification check]<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3411578&group_id=36855&atid=418257 Different warnings from Verification Manager and Text Editor]<br />
<br />
==Discussion==<br />
<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
* Next bugs to focus on? [http://sourceforge.net/tracker/?words=tracker_browse&sort=priority&sortdir=desc&offset=0&group_id=36855&atid=418257&assignee=&status=1&category=&artgroup=&keyword=&submitter=&artifact_id=0 Bugs sorted in descending order by priority]<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40988OEWG 201205152012-06-04T17:50:09Z<p>Nomi: /* Currently working on */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3487566&group_id=36855&atid=418257 is_Obsolete not recognized in verification check]<br />
* [http://sourceforge.net/tracker/?func=detail&aid=3411578&group_id=36855&atid=418257 Different warnings from Verification Manager and Text Editor]<br />
<br />
==Discussion==<br />
<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40987OEWG 201205152012-06-04T17:11:39Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
<br />
==Discussion==<br />
<br />
* Released [http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%202.2/ OBO-Edit 2.2] on May 24 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
** Several OEWG members said that it works for them<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40934OEWG 201205152012-05-28T21:19:42Z<p>Nomi: /* Currently working on */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
<br />
==Discussion==<br />
<br />
* Latest official release: 2.2 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40933OEWG 201205152012-05-28T21:19:22Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* Ramona reported that the reasoner seems much slower than it used to (took over a minute to reason over plant_ontology.obo).<br />
** Nomi tried it and it ran as fast as ever (about 5 seconds for plant_ontology.obo). Not sure why it's going so slowly for Ramona.<br />
<br />
==Discussion==<br />
<br />
* Latest official release: 2.2 (I was going to call it 2.1.1 but decided that was too confusing)<br />
** Passes the usual unit tests<br />
** Mike Cherry tested it in the pipeline and said it seemed fine<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40770OEWG 201205152012-05-15T05:43:04Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* Ramona reported that the reasoner seems much slower than it used to (took over a minute to reason over plant_ontology.obo).<br />
** Nomi tried it and it ran as fast as ever (about 5 seconds for plant_ontology.obo). Not sure why it's going so slowly for Ramona.<br />
<br />
==Discussion==<br />
<br />
* I would like to do another OBO-Edit official release soon (which I'll call 2.2 because 2.1.1 is too confusing)<br />
** Please try out release 2.2-rc1 and report any problems: http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/2.2-rc1/<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=40769OBO-Edit Working Group Meeting Agenda and Minutes2012-05-15T05:42:22Z<p>Nomi: </p>
<hr />
<div>==Meeting Schedule for 2011-2==<br />
__NOTOC__<br />
<br />
The OBO-Edit Working Group currently meets the first Tuesday of the month (and sometimes the third Tuesday as well) at 8:30am California time (16:30 GMT), except as noted.<br />
<br />
==Future Meetings==<br />
* [[OEWG_20120515 | June 5, 2012]]<br />
<br />
<br />
== Past Meetings in 2011-2==<br />
* [[OEWG_20120501 | May 1, 2012]]<br />
* [[OEWG_20120417 | April 17, 2012]] ('''NOTE: The US has switched to Daylight Savings Time''')<br />
* [[OEWG_20120306 | March 6, 2012]]<br />
* [[OEWG_20120221 | February 21, 2012]]<br />
* [[OEWG_20120207 | February 7, 2012]]<br />
* [[OEWG_20120117 | January 17, 2012]]<br />
* [[OEWG_20120103 | January 3, 2012]]<br />
* [[OEWG_20111207 | December 6, 2011]]<br />
* [[OEWG_20111101 | November 1, 2011]] ('''NOTE: If you are in the UK, the meeting will start at 15:30 rather than the usual 16:30, because the UK has gone off British Summer Time whereas the US still has another week on Daylight Savings Time.''')<br />
* [[OEWG_20111004 | October 4]]<br />
* [[OEWG_20110920 | September 20]] (no meeting September 6)<br />
* [[OEWG_20110830 | August 30]] (note FIFTH Tuesday)<br />
* [[OEWG_20110816 | August 16]]<br />
* [[OEWG_20110721 | Thursday, July 21, 8:30am PDT (usual time, different day)]]<br />
* [[OEWG_20110705| July 5]]<br />
* [[OEWG_20110621| June 21]]<br />
* [[OEWG_20110607| June 7]]<br />
* [[OEWG_20110517| May 17]]<br />
* [[OEWG_20110503| May 3]]<br />
<br />
* [[OEWG_20110419| April 19]]<br />
* [[OEWG_20110405| April 5]]<br />
<br />
* [[OEWG_20110315| March 15]]<br />
<br />
* [[OEWG_20110301| March 1]]<br />
<br />
*[[OEWG_20110208| February 8]]<br />
<br />
*[[OEWG_20110125| January 25]]<br />
<br />
*[[OEWG_20110111| January 11]]<br />
<br />
====Meetings in Past Years====<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 home page]]==<br />
<br />
[[Category:OBO-Edit_working_group]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40768OEWG 201205152012-05-14T22:50:08Z<p>Nomi: </p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, June 5, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* Ramona reported that the reasoner seems much slower than it used to (took over a minute to reason over plant_ontology.obo).<br />
** Nomi tried it and it ran as fast as ever (about 5 seconds for plant_ontology.obo). Not sure why it's going so slowly for Ramona.<br />
<br />
==Discussion==<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Please try out the latest beta and report any problems: http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/2.1.1-b10/<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40767OEWG 201205152012-05-14T22:49:32Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 15, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* Ramona reported that the reasoner seems much slower than it used to (took over a minute to reason over plant_ontology.obo).<br />
** Nomi tried it and it ran as fast as ever (about 5 seconds for plant_ontology.obo). Not sure why it's going so slowly for Ramona.<br />
<br />
==Discussion==<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Please try out the latest beta and report any problems: http://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/2.1.1-b10/<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40766OEWG 201205152012-05-14T21:28:57Z<p>Nomi: /* Fixed or newly added since last meeting */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 15, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it [http://sourceforge.net/tracker/?func=detail&aid=3526720&group_id=36855&atid=418260 doesn't find cycles that involve implied links found by the reasoner].<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* Ramona reported that the reasoner seems much slower than it used to (took over a minute to reason over plant_ontology.obo).<br />
** Nomi tried it and it ran as fast as ever (about 5 seconds for plant_ontology.obo). Not sure why it's going so slowly for Ramona.<br />
<br />
==Discussion==<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40765OEWG 201205152012-05-14T21:24:01Z<p>Nomi: /* Currently working on */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 15, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it doesn't find cycles that involve implied links found by the reasoner.<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* Ramona reported that the reasoner seems much slower than it used to (took over a minute to reason over plant_ontology.obo).<br />
** Nomi tried it and it ran as fast as ever (about 5 seconds for plant_ontology.obo). Not sure why it's going so slowly for Ramona.<br />
<br />
==Discussion==<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40764OEWG 201205152012-05-14T21:23:05Z<p>Nomi: /* Fixed or newly added since last meeting */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 15, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it doesn't find cycles that involve implied links found by the reasoner.<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3384594&aid=3517323&group_id=36855 Name redundancy check not working in Text Editor]<br />
** It was checking for name redundancy when called with no arg (i.e., invoked from Verification Manager; check all terms) but not when called on a specific term (i.e., from Text Editor).<br />
<br />
==Currently working on==<br />
* Ramona reported that the reasoner seems much slower than it used to. Nomi is investigating.<br />
<br />
==Discussion==<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40758OEWG 201205152012-05-14T16:59:07Z<p>Nomi: /* Currently working on */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 15, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it doesn't find cycles that involve implied links found by the reasoner.<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
<br />
==Currently working on==<br />
* Ramona reported that the reasoner seems much slower than it used to. Nomi is investigating.<br />
<br />
==Discussion==<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40757OEWG 201205012012-05-14T05:16:46Z<p>Nomi: </p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 1, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Ramona, Paola<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** "Regardless of what I select in the first drop-down menu (self, type, parent, child), my only options are Namespace, Is intersection, Is necessary, Is implied, and Is redundant."<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** I fixed this, but have one question: I know parent and child should show all the options (Name, Synonym, etc.), but what about Type?<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** The Cycle Check verification check doesn't find cycles (tight or loose)<br />
** Tests on OBO-Edit versions as far back as 2.0 have not turned up any version in which this worked. Perhaps it worked at some point before release 2.0.<br />
** If this has been broken for that long, is it important to fix?<br />
*** Ramona said that they have been having problems where there were cycles in their ontology that OE didn't catch and then when they loaded the ontology into Amigo, it complained. She thinks this is an important thing to fix.<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly, as his description was brief.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I downloaded the latest gaz.obo and it roundtripped fine, with all 88 remarks.<br />
** I then tried adding more remarks to gaz.obo, and again all 176 remarks roundtripped fine.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that Michael added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on--for example, something else overwrote the saved file.<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
* Ramona mentioned that she sometimes pastes the wrong text into the text editor and tries Undo but instead of undoing her text edit, it undoes the last change she made to the ontology. She wishes she could just undo the last text change.<br />
** Nomi encouraged Ramona to submit a Feature Request for this, but said that the way the edit history is tracked, it would not be easy to add this kind of small-grained edits to the Undo history list. She suggested that Ramona try editing in Manual Commit mode instead of Autocommit mode if she wants to be able to discard unwanted text edits.<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40756OEWG 201205152012-05-14T05:16:30Z<p>Nomi: </p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 15, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it doesn't find cycles that involve implied links found by the reasoner.<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
<br />
==Currently working on==<br />
<br />
<br />
==Discussion==<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40755OEWG 201205152012-05-14T05:14:23Z<p>Nomi: /* OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it doesn't find cycles that involve implied links found by the reasoner.<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
<br />
==Currently working on==<br />
<br />
<br />
==Discussion==<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120515&diff=40754OEWG 201205152012-05-14T02:56:42Z<p>Nomi: Created page with "== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT == __NOTOC__ Conference call numbers:<br /> US: 1 866 953 9688<br /> UK: 0808 238 6001<br /> PIN: 801561<br />..."</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Ramona, Paola<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** New cycle check method finds (possibly mixed-relationship) cycles by checking for objects that are descendants of one of their own children.<br />
** The check works whether or not you have the reasoner on, but it doesn't find cycles that involve implied links found by the reasoner.<br />
** The new cycle check is set by default to run on save and on manual verification; other times (e.g., on reasoner change) can be added by the user via the Verification Manager configuration panel.<br />
<br />
==Currently working on==<br />
<br />
<br />
==Discussion==<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes&diff=40753OBO-Edit Working Group Meeting Agenda and Minutes2012-05-14T02:51:30Z<p>Nomi: </p>
<hr />
<div>==Meeting Schedule for 2011-2==<br />
__NOTOC__<br />
<br />
The OBO-Edit Working Group currently meets the first Tuesday of the month (and sometimes the third Tuesday as well) at 8:30am California time (16:30 GMT), except as noted.<br />
<br />
==Future Meetings==<br />
* [[OEWG_20120515 | May 15, 2012?]]<br />
<br />
<br />
== Past Meetings in 2011-2==<br />
* [[OEWG_20120501 | May 1, 2012]]<br />
* [[OEWG_20120417 | April 17, 2012]] ('''NOTE: The US has switched to Daylight Savings Time''')<br />
* [[OEWG_20120306 | March 6, 2012]]<br />
* [[OEWG_20120221 | February 21, 2012]]<br />
* [[OEWG_20120207 | February 7, 2012]]<br />
* [[OEWG_20120117 | January 17, 2012]]<br />
* [[OEWG_20120103 | January 3, 2012]]<br />
* [[OEWG_20111207 | December 6, 2011]]<br />
* [[OEWG_20111101 | November 1, 2011]] ('''NOTE: If you are in the UK, the meeting will start at 15:30 rather than the usual 16:30, because the UK has gone off British Summer Time whereas the US still has another week on Daylight Savings Time.''')<br />
* [[OEWG_20111004 | October 4]]<br />
* [[OEWG_20110920 | September 20]] (no meeting September 6)<br />
* [[OEWG_20110830 | August 30]] (note FIFTH Tuesday)<br />
* [[OEWG_20110816 | August 16]]<br />
* [[OEWG_20110721 | Thursday, July 21, 8:30am PDT (usual time, different day)]]<br />
* [[OEWG_20110705| July 5]]<br />
* [[OEWG_20110621| June 21]]<br />
* [[OEWG_20110607| June 7]]<br />
* [[OEWG_20110517| May 17]]<br />
* [[OEWG_20110503| May 3]]<br />
<br />
* [[OEWG_20110419| April 19]]<br />
* [[OEWG_20110405| April 5]]<br />
<br />
* [[OEWG_20110315| March 15]]<br />
<br />
* [[OEWG_20110301| March 1]]<br />
<br />
*[[OEWG_20110208| February 8]]<br />
<br />
*[[OEWG_20110125| January 25]]<br />
<br />
*[[OEWG_20110111| January 11]]<br />
<br />
====Meetings in Past Years====<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 home page]]==<br />
<br />
[[Category:OBO-Edit_working_group]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40738OEWG 201205012012-05-09T18:28:03Z<p>Nomi: /* Fixed or newly added since last meeting */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Ramona, Paola<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** "Regardless of what I select in the first drop-down menu (self, type, parent, child), my only options are Namespace, Is intersection, Is necessary, Is implied, and Is redundant."<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** I fixed this, but have one question: I know parent and child should show all the options (Name, Synonym, etc.), but what about Type?<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** The Cycle Check verification check doesn't find cycles (tight or loose)<br />
** Tests on OBO-Edit versions as far back as 2.0 have not turned up any version in which this worked. Perhaps it worked at some point before release 2.0.<br />
** If this has been broken for that long, is it important to fix?<br />
*** Ramona said that they have been having problems where there were cycles in their ontology that OE didn't catch and then when they loaded the ontology into Amigo, it complained. She thinks this is an important thing to fix.<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly, as his description was brief.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I downloaded the latest gaz.obo and it roundtripped fine, with all 88 remarks.<br />
** I then tried adding more remarks to gaz.obo, and again all 176 remarks roundtripped fine.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that Michael added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on--for example, something else overwrote the saved file.<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
* Ramona mentioned that she sometimes pastes the wrong text into the text editor and tries Undo but instead of undoing her text edit, it undoes the last change she made to the ontology. She wishes she could just undo the last text change.<br />
** Nomi encouraged Ramona to submit a Feature Request for this, but said that the way the edit history is tracked, it would not be easy to add this kind of small-grained edits to the Undo history list. She suggested that Ramona try editing in Manual Commit mode instead of Autocommit mode if she wants to be able to discard unwanted text edits.<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40474OEWG 201205012012-05-01T15:59:59Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Ramona, Paola<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** "Regardless of what I select in the first drop-down menu (self, type, parent, child), my only options are Namespace, Is intersection, Is necessary, Is implied, and Is redundant."<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** I fixed this, but have one question: I know parent and child should show all the options (Name, Synonym, etc.), but what about Type?<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** The Cycle Check verification check doesn't find cycles (tight or loose)<br />
** Tests on OBO-Edit versions as far back as 2.0 have not turned up any version in which this worked. Perhaps it worked at some point before release 2.0.<br />
** If this has been broken for that long, is it important to fix?<br />
*** Ramona said that they have been having problems where there were cycles in their ontology that OE didn't catch and then when they loaded the ontology into Amigo, it complained. She thinks this is an important thing to fix.<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly, as his description was brief.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I downloaded the latest gaz.obo and it roundtripped fine, with all 88 remarks.<br />
** I then tried adding more remarks to gaz.obo, and again all 176 remarks roundtripped fine.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that Michael added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on--for example, something else overwrote the saved file.<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
* Ramona mentioned that she sometimes pastes the wrong text into the text editor and tries Undo but instead of undoing her text edit, it undoes the last change she made to the ontology. She wishes she could just undo the last text change.<br />
** Nomi encouraged Ramona to submit a Feature Request for this, but said that the way the edit history is tracked, it would not be easy to add this kind of small-grained edits to the Undo history list. She suggested that Ramona try editing in Manual Commit mode instead of Autocommit mode if she wants to be able to discard unwanted text edits.<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40473OEWG 201205012012-05-01T15:57:50Z<p>Nomi: /* Currently working on */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Ramona, Paola<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** "Regardless of what I select in the first drop-down menu (self, type, parent, child), my only options are Namespace, Is intersection, Is necessary, Is implied, and Is redundant."<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** I fixed this, but have one question: I know parent and child should show all the options (Name, Synonym, etc.), but what about Type?<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** The Cycle Check verification check doesn't find cycles (tight or loose)<br />
** Tests on OBO-Edit versions as far back as 2.0 have not turned up any version in which this worked. Perhaps it worked at some point before release 2.0.<br />
** If this has been broken for that long, is it important to fix?<br />
*** Ramona said that they have been having problems where there were cycles in their ontology that OE didn't catch and then when they loaded the ontology into Amigo, it complained. She thinks this is an important thing to fix.<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly, as his description was brief.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I downloaded the latest gaz.obo and it roundtripped fine, with all 88 remarks.<br />
** I then tried adding more remarks to gaz.obo, and again all 176 remarks roundtripped fine.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that Michael added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on--for example, something else overwrote the saved file.<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40472OEWG 201205012012-05-01T15:57:08Z<p>Nomi: /* OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: Nomi, Heiko, Ramona, Paola<br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** "Regardless of what I select in the first drop-down menu (self, type, parent, child), my only options are Namespace, Is intersection, Is necessary, Is implied, and Is redundant."<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** I fixed this, but have one question: I know parent and child should show all the options (Name, Synonym, etc.), but what about Type?<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** The Cycle Check verification check doesn't find cycles (tight or loose)<br />
** Tests on OBO-Edit versions as far back as 2.0 have not turned up any version in which this worked. Perhaps it worked at some point before release 2.0.<br />
** If this has been broken for that long, is it important to fix?<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly, as his description was brief.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I downloaded the latest gaz.obo and it roundtripped fine, with all 88 remarks.<br />
** I then tried adding more remarks to gaz.obo, and again all 176 remarks roundtripped fine.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that Michael added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on--for example, something else overwrote the saved file.<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40437OEWG 201205012012-05-01T05:06:34Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** "Regardless of what I select in the first drop-down menu (self, type, parent, child), my only options are Namespace, Is intersection, Is necessary, Is implied, and Is redundant."<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** I fixed this, but have one question: I know parent and child should show all the options (Name, Synonym, etc.), but what about Type?<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** The Cycle Check verification check doesn't find cycles (tight or loose)<br />
** Tests on OBO-Edit versions as far back as 2.0 have not turned up any version in which this worked. Perhaps it worked at some point before release 2.0.<br />
** If this has been broken for that long, is it important to fix?<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly, as his description was brief.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I downloaded the latest gaz.obo and it roundtripped fine, with all 88 remarks.<br />
** I then tried adding more remarks to gaz.obo, and again all 176 remarks roundtripped fine.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that Michael added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on--for example, something else overwrote the saved file.<br />
<br />
* I would like to do another OBO-Edit official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40428OEWG 201205012012-04-30T17:29:08Z<p>Nomi: </p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** "Regardless of what I select in the first drop-down menu (self, type, parent, child), my only options are Namespace, Is intersection, Is necessary, Is implied, and Is redundant."<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** I fixed this, but have one question: I know parent and child should show all the options (Name, Synonym, etc.), but what about Type?<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521113&aid=3517323&group_id=36855 Cycle Check doesn't work]<br />
** The Cycle Check verification check doesn't find cycles (tight or loose)<br />
** Tests on OBO-Edit versions as far back as 2.0 have not turned up any version in which this worked. Perhaps it worked at some point before release 2.0.<br />
** If this has been broken for that long, is it important to fix?<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly, as his description was brief.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I downloaded the latest gaz.obo and it roundtripped fine, with all 88 remarks.<br />
** I then tried adding more remarks to gaz.obo, and again all 176 remarks roundtripped fine.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that Michael added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on--for example, something else overwrote the saved file.<br />
<br />
* I would like to do another official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
** Any other pressing bug fixes to get into this release?<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40427OEWG 201205012012-04-30T17:24:11Z<p>Nomi: </p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** "Regardless of what I select in the first drop-down menu (self, type, parent, child), my only options are Namespace, Is intersection, Is necessary, Is implied, and Is redundant."<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** I fixed this, but have one question: I know parent and child should show all the options (Name, Synonym, etc.), but what about Type?<br />
<br />
==Currently working on==<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly, as his description was brief.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I was unable to download gaz.obo from the URL Michael gave me: http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/environmental/ (and Michael said the latest commit of it failed--maybe a SourceForge problem?)<br />
** I tried adding the remark lines that Michael sent me to gene_ontology_write.obo (which, like gaz.obo, is big) and roundtripping, and that worked fine.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that were added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on.<br />
<br />
* I would like to do another official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40367OEWG 201205012012-04-29T05:25:07Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** "Regardless of what I select in the first drop-down menu (self, type, parent, child), my only options are Namespace, Is intersection, Is necessary, Is implied, and Is redundant."<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** I fixed this, but have one question: I know parent and child should show all the options (Name, Synonym, etc.), but what about Type?<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly, as his description was brief.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I was unable to download gaz.obo from the URL Michael gave me: http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/environmental/ (and Michael said the latest commit of it failed--maybe a SourceForge problem?)<br />
** I tried adding the remark lines that Michael sent me to gene_ontology_write.obo (which, like gaz.obo, is big) and roundtripping, and that worked fine.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that were added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on.<br />
<br />
* I would like to do another official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40366OEWG 201205012012-04-29T05:22:31Z<p>Nomi: </p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** "Regardless of what I select in the first drop-down menu (self, type, parent, child), my only options are Namespace, Is intersection, Is necessary, Is implied, and Is redundant."<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** I fixed this, but have one question: I know parent and child should show all the options (Name, Synonym, etc.), but what about Type?<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that were added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I was unable to download gaz.obo from the URL Michael gave me: http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/environmental/ (and Michael said the latest commit of it failed--maybe a SourceForge problem?)<br />
<br />
* I would like to do another official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40365OEWG 201205012012-04-29T04:54:10Z<p>Nomi: </p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, May 2, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** Almost fixed<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that were added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I was unable to download gaz.obo from the URL Michael gave me: http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/environmental/ (and Michael said the latest commit of it failed--maybe a SourceForge problem?)<br />
<br />
* I would like to do another official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40364OEWG 201205012012-04-29T04:53:45Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, April 17, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** Almost fixed<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that were added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I was unable to download gaz.obo from the URL Michael gave me: http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/environmental/ (and Michael said the latest commit of it failed--maybe a SourceForge problem?)<br />
<br />
* I would like to do another official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40363OEWG 201205012012-04-29T04:49:44Z<p>Nomi: /* Discussion */</p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, April 17, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** Almost fixed<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that were added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I was unable to download gaz.obo from http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/environmental/ (and Michael said the latest commit of it failed--maybe a SourceForge problem?)<br />
<br />
* I would like to do another official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomihttps://wiki.geneontology.org/index.php?title=OEWG_20120501&diff=40362OEWG 201205012012-04-29T04:49:29Z<p>Nomi: </p>
<hr />
<div>== OBO-Edit Working Group Meeting: Tuesday, April 17, 2012, 8:30am PDT ==<br />
__NOTOC__<br />
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: Nomi Harris<br /><br />
Minutes: Nomi<br /><br />
Attendees: <br /><br />
<br />
== Bug and Feature Trackers ==<br />
<br />
* [http://sourceforge.net/tracker/?atid=418257&group_id=36855&func=browse OE Bug tracker]<br />
* [http://sourceforge.net/tracker/?func=browse&group_id=36855&atid=418260 OE Feature tracker]<br />
<br />
==Fixed or newly added since last meeting==<br />
* Remove Redundant Links panel<br />
** [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517323&group_id=36855 Remove Redundant Links Panel doesn't refresh when it should]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3147642&group_id=36855&atid=418257 'Select all' not working in Remove Redundant Links panel]<br />
** [http://sourceforge.net/tracker/index.php?func=detail&aid=3520750&group_id=36855&atid=418257 Remove Redundant Link doesn't always remove the right link]<br />
*** Was this even tested??<br />
** Undo wouldn't undo even one deletion done in Remove Redundant Links<br />
*** The way links were being removed (by creating multiple(!) TermMacroHistoryItems), the removal couldn't be undone. If you deleted even a single link, Undo wouldn't restore it.<br />
*** I have improved this behavior--you can now undo single deletions. However, if you delete multiple links at a time, Undo only successfully undoes the last one. I'm not sure why.<br />
**** Tracker item for remaining issue: [http://sourceforge.net/tracker/?func=detail&atid=418257&aid=3517324&group_id=36855 Undo only restores last link removed in Remove Redundant Links]<br />
*** As a beneficial side effect of improving the Undoableness, I expect link deletion to be faster than it was.<br />
<br />
* Fixed data format to use 24 hours for writing ISO 8601 dates (e.g., creation_date). (Heiko)<br />
<br />
==Currently working on==<br />
* [http://sourceforge.net/tracker/?func=detail&atid=3521387&aid=3517323&group_id=36855 link filter not working properly]<br />
** I broke this in 2.1.1-b7 as a side effect of fixing another bug: [http://sourceforge.net/tracker/?func=detail&atid=3487892&aid=3517323&group_id=36855 In compound ancestor/descendant queries, relation list bad]<br />
** Almost fixed<br />
<br />
==Discussion==<br />
* Michael Ashburner reported that when he added two more remark: lines to gaz.obo (in a text editor) and then roundtripped it through OBO-Edit, it lost the last two remark: lines he put in.<br />
** I am not completely sure I interpreted the scenario correctly.<br />
** There is nothing in OE that limits how many remark lines you can have, and at any rate it seems odd that it would forget the last two remarks that were added (they are not the last two in the list, they are both somewhere in the middle of the list), so I suspect that there's a non-OE problem going on.<br />
** He was using an extremely old version of OE but said that he also tried the latest version and had the same problem.<br />
** I was unable to download gaz.obo from http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/environmental/ (and Michael said the latest commit of it failed--maybe a SourceForge problem?)<br />
* I would like to do another official release soon (which I think I'll call 2.2 because 2.1.1 is too confusing)<br />
<br />
==Links==<br />
[[OBO-Edit_Working_Group_Meeting_Agenda_and_Minutes|Back to OEWG meeting agenda and minutes list]]</div>Nomi