https://wiki.geneontology.org/api.php?action=feedcontributions&user=MC&feedformat=atomGO Wiki - User contributions [en]2024-03-28T20:04:26ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Ontology_meeting_2017-02-16&diff=63176Ontology meeting 2017-02-162017-02-14T16:13:00Z<p>MC: Created page with "Attendees: Regrets: Bluejeans: https://bluejeans.com/164681006 ==Tickets for discussion at this meeting:== See https://github.com/geneontology/go-ontology/projects/1, co..."</p>
<hr />
<div>Attendees:<br />
<br />
Regrets: <br />
<br />
<br />
Bluejeans: https://bluejeans.com/164681006<br />
<br />
==Tickets for discussion at this meeting:==<br />
<br />
See https://github.com/geneontology/go-ontology/projects/1, column labeled "Ontology Call February 16th, 2017" on the right<br />
#[https://github.com/geneontology/go-ontology/issues/12948 EC:1.14.12 is being used as an xref in multiple enzyme activities]<br />
#[https://github.com/geneontology/molecular_function_refactoring Update on MF refactoring]<br />
#[https://github.com/geneontology/go-ontology/issues/12976 regulation by pattern]<br />
#[https://github.com/geneontology/go-ontology/issues/12995 semantic difference between catalytic activity MF and BP]<br />
#[https://github.com/geneontology/go-ontology/issues/12975 response to other organism]<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2017-01-19&diff=62958Ontology meeting 2017-01-192017-01-17T15:51:46Z<p>MC: Created page with "Attendees: Regrets: Bluejeans: https://bluejeans.com/164681006 ==Tickets for discussion at this meeting:== See https://github.com/geneontology/go-ontology/projects/1, col..."</p>
<hr />
<div>Attendees:<br />
<br />
Regrets:<br />
<br />
<br />
Bluejeans: https://bluejeans.com/164681006<br />
<br />
==Tickets for discussion at this meeting:==<br />
<br />
See https://github.com/geneontology/go-ontology/projects/1, column labeled "Ontology Call January 19, 2017" on the right<br />
<br />
#[https://github.com/geneontology/go-ontology/issues/12788 Contact for UniProt annotations]<br />
#[https://github.com/geneontology/go-ontology/issues/12341 Bridging ChEBI to Pro]<br />
#[https://github.com/geneontology/go-ontology/issues/12922 Phosphate versus phophate ion]<br />
#[https://github.com/geneontology/go-ontology/issues/12890 relationship between adenylate cyclase and cAMP biosynthetic process]<br />
#[https://github.com/geneontology/go-ontology/issues/12859 Remove all single-step BP classes]<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_editor%27s_conference_call_minutes_2017&diff=62957Ontology editor's conference call minutes 20172017-01-17T15:47:28Z<p>MC: Created page with "*Jan 12 *Jan 19 Category:Meetings Category:Ontology"</p>
<hr />
<div>*[[Ontology meeting 2017-01-12|Jan 12]]<br />
*[[Ontology meeting 2017-01-19|Jan 19]]<br />
<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_Development&diff=62956Ontology Development2017-01-17T15:46:48Z<p>MC: /* Editor's Conference calls-weekly NOW ON THURSDAYS, 8:30-9:15 AM PST */</p>
<hr />
<div>This group's purpose is to ensure that the Gene Ontology represents biology in a way that is useful for gene product annotation of reference genomes and other MODs using the GO for annotation. The group serves as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO. Members of the group are responsible for reporting areas of the GO that need development and for suggesting changes and additions to the GO as needs arise. Members of the group serve as biological experts in domains that are covered by their organism. They are responsible for reviewing changes to be sure that they accurately reflect our current understanding of biology.<br />
<br />
==Content Development ==<br />
===Projects===<br />
====High Priority/Ongoing====<br />
*[[Cell Cycle]] (Val, Pombe experts, GOEds)<br />
*[[Enzymes and EC mappings]]<br />
*[https://github.com/geneontology/synapse Synapse project] (Synapse experts, DavidOS, Becky Foulger)<br />
*Extracellular RNA-containing vesicles (Paola, Aleks and community experts)<br />
*Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts)<br />
*Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts)<br />
<br />
====Medium Priority====<br />
*[[Non-symbiotic multi-organism processes]] (Jane, David OS)<br />
<br />
====Low priority====<br />
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)<br />
*[[microbial ontology development and annotation]]<br />
<br />
====Recently completed projects====<br />
*[[Uberon alignment]] (DavidH)<br />
*Addition of cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]<br />
**[[Cell cross-products]], [[Cell-type specific GO terms]] (Jane, Paola, Alex, Chris, DavidOS)<br />
**[[Adding missing CHEBI xps]]<br />
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)<br />
*[[Virus terms|Virus-related term overhaul]], [[Virus_ontology_devt_July_2012|Phage Terms]] (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others)<br />
*[[Neurobiology Project]] (David, Tanya, Jane, Paola, DavidOS)<br />
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013<br />
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012<br />
*[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group) <br />
*[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan)<br />
*Rework disjoint terms as [http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded in discussion on GO list] (Jane).<br />
*[[:Category:Content MENGO|MENGO collaboration]] (Jane)<br />
<br />
====Proposed content work====<br />
A list of topics that we propose to address, but for which a timeline has not been set<br />
<br />
*Peripheral nervous system development<br />
*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology. <br />
*Overhaul [[translation]], similar to what's being done for transcription. [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1891512&group_id=36855| SF 1891512] is closed, but notes some issues for consideration. (midori 2010-10-04)<br />
* [[Recombination and DNA repair]]<br />
* [[RNA processes]]<br />
* [[Bile formation and secretion processes]]<br />
* [[protein and peptidyl amino acid modification / protein processing]]<br />
* [[Response to drug]]<br />
* [[Polyketide synthases]]<br />
* [[cell growth/proliferation/division]]<br />
* [[oxidoreductases]]<br />
<br />
==Guides, Training and Documentation==<br />
<br />
*[[:Category:Curator Guides|Curator guides]]<br />
*[[Editor_Guide]]<br />
*[[Editor_file_guide]]<br />
*[[Protege_setup_for_GO_Eds|Protege setup for GO Eds]]<br />
*[[Ontology Documentation Drafts]] - for working on documentation of ontology content that will become part of the web-based documentation<br />
*[[New Ontology Editor Training]]<br />
*[[Ontology Editing Examples|Ontology Editing Examples: Regulation of a pathway by regulation of enzyme activity]]<br />
*[[Guidelines on 'protein complex' terms]]<br />
*[[Content Meeting Documentation|Guidance for organizing content meetings]] (old doc, but basic principles still apply)<br />
<br />
==Other Ontology Development Group Activities==<br />
===QC===<br />
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)<br />
*[[Jenkins]]<br />
<br />
===TermGenie===<br />
*[[Template-able Requests Prior To TG]]<br />
<br />
===Website===<br />
*[[Editorial-type sections copied over from the GO website ontology documentation: MF]]<br />
<br />
===Protege===<br />
*[[Protege workshop]] Jan. 2012<br />
*[[Ontology_workshop_Jan_2013]]<br />
*[[Protege Feature Requirements]]<br />
<br />
[[Category:Ontology]]<br />
<br />
===LEGO===<br />
*[[Regulation]]<br />
<br />
*[[Noctua_meeting_140929|Modelling complex annotations in LEGO/noctua - meeting 140929]]<br />
<br />
===Annotation extensions===<br />
*[[Terms that could be obsoleted if information was collected as annotation extension]]<br />
<br />
==Meetings==<br />
===Cambridge Editors' meetings - weekly Tuesday 10-11 AM===<br />
<br />
*[[CamEds Ontology meeting 2012-06-19|June 19]]<br />
*[[CamEds Ontology meeting 2012-06-26|June 26]]<br />
*[[CamEds Ontology meeting 2012-07-3|July 3]]<br />
*[[CamEds Ontology meeting 2012-07-17|July 17]]<br />
*[[CamEds Ontology meeting 2012-07-31|July 31]]<br />
*[[CamEds Ontology meeting 2012-08-31|August 7]]<br />
*[[CamEds Ontology meeting 2012-10-24|October 24]]<br />
<br />
<br />
===SourceForge Meetings: Fortnightly, Wednesdays, 4:30-5:15pm BST - now fortnightly, Mondays, 4-5pm BST===<br />
<br />
*[[SourceForge meeting 2013-07-24|July 24]]<br />
*[[SourceForge meeting 2013-09-04|Sept 4]]<br />
*[[SourceForge meeting 2013-09-11|Sept 11]]<br />
*[[SourceForge meeting 2013-09-25|Sept 25]]<br />
*[[SourceForge meeting 2013-10-09|Oct 9]]<br />
*[[SourceForge meeting 2013-10-30|Oct 30]]<br />
*[[SourceForge meeting 2013-12-11|Dec 11th]]<br />
*[[SourceForge meeting 2014-01-29|Jan 29th]]<br />
*[[SourceForge meeting 2014-02-12|Feb 12th]]<br />
*[[SourceForge meeting 2014-02-26|Feb 26th]]<br />
*[[SourceForge meeting 2014-04-23|Apr 23rd]]<br />
*[[SourceForge meeting 2014-05-14|May 14th]]<br />
*[[SourceForge meeting 2014-06-25|June 25th]]<br />
*[[SourceForge meeting 2014-09-10|Sept 10th]]<br />
*[[SourceForge meeting 2014-09-24|Sept 24th]]<br />
*[[SourceForge meeting 2014-10-22|Oct 22nd]]<br />
*[[SourceForge meeting 2015-02-11|Feb 11th]]<br />
*[[SourceForge meeting 2015-02-25|Feb 25th]]<br />
*[[SourceForge meeting 2015-03-11|Mar 11th]]<br />
*[[SourceForge meeting 2015-03-25|Mar 25th]]<br />
*[[SourceForge meeting 2015-04-22|Apr 22nd]]<br />
*[[SourceForge meeting 2015-04-29|Apr 29th]]<br />
*[[SourceForge meeting 2015-06-22|Jun 22nd]]<br />
*[[SourceForge meeting 2015-12-14|Dec 14th]]<br />
<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]<br />
<br />
===Editor's Conference calls-weekly NOW ON THURSDAYS, 8:30-9:15 AM PST===<br />
<br />
*[[Ontology editor's conference call minutes 2011|2011 minutes]]<br />
*[[Ontology editor's conference call minutes Jan-June 2012|Jan-June 2012 minutes]]<br />
*[[Ontology editor's conference call minutes July-Dec 2012|July-Dec 2012 minutes]]<br />
*[[Ontology editor's conference call minutes Jan-June 2013|Jan-June 2013 minutes]]<br />
*[[Ontology editor's conference call minutes July-Dec 2013|July-Dec 2013 minutes]]<br />
*[[Ontology editor's conference call minutes Jan-June 2014|Jan-June 2014 minutes]]<br />
*[[Ontology editor's conference call minutes July-Dec 2014|July-Dec 2014 minutes]]<br />
*[[Ontology editor's conference call minutes Jan-June 2015|Jan-June 2015 minutes]]<br />
*[[Ontology editor's conference call minutes July-Dec 2015|July-Dec 2015 minutes]]<br />
*[[Ontology editor's conference call minutes Jan-June 2016|Jan-June 2016 minutes]]<br />
*[[Ontology editor's conference call minutes July-Dec 2016|July-Dec 2016 minutes]]<br />
*[[Ontology editor's conference call minutes Jan-June 2017|Jan-June 2017 minutes]]<br />
<br />
==Useful Links==<br />
*[[Completed ontology content work]]<br />
*[[SF + TG Rota for Gene Ontology requests]]<br />
*[[Ontology_Development_Reports|Ontology Development Reports]] (discontinued Nov 2010)<br />
<br />
[[Category:Ontology]]<br />
<br />
==Administrative==<br />
*[[Ontology Development group summary]]<br />
*[[Meeting_minutes:_general_topics|Miscellaneous meeting minutes]]<br />
<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2017-01-12&diff=62947Ontology meeting 2017-01-122017-01-12T16:39:44Z<p>MC: /* Update from Melanie on EBI editors status */</p>
<hr />
<div>Attendees:<br />
<br />
Regrets:<br />
<br />
<br />
Bluejeans: https://bluejeans.com/164681006<br />
<br />
==Update from Melanie on EBI editors status==<br />
<br />
The following labels were created/used on the ontology tracker at https://github.com/geneontology/go-ontology/issues: <br />
* curator-request (Paul indicated those should be highest priority) <br />
* MF refactoring <br />
* wrapping-up (non trivial work has already been done on ticket by PR, DOS or MC it'd be more efficient for one of them to close it instead of passing it on) <br />
* low priority <br />
<br />
and labels indicating estimated time: <br />
* time low (<2h) <br />
* time medium (requires discussion with submitter but feasible in a day if communication fast enough) <br />
* time high (>1 day) <br />
* time unknown (external dependencies) <br />
<br />
Based on this, we anticipate that Paola and Melanie should be able to wrap their tickets up, though some are dependent on external efforts and therefore remain uncertain. <br />
David has 106 tickets open, including 41 curator requests which we agreed should take priority. Based on his current workload, he is aiming at coordinating an MF refactoring work week early February, possibly coordinating with Phil Lord and Robert Stevens who he mentioned are working on a refactoring proposal as well.<br />
<br />
==Tickets for discussion at this meeting:==<br />
<br />
See https://github.com/geneontology/go-ontology/projects/1, column labeled "Ontology Call January 12, 2017" on the right<br />
<br />
#[https://github.com/geneontology/go-ontology/issues/12211 Move editors file to this repo on GitHub]<br />
#[https://github.com/geneontology/go-ontology/issues/12788 Contact for UniProt annotations]<br />
#[https://github.com/geneontology/go-ontology/issues/12880 Protege documentation needs updating and ID issue]<br />
#[https://github.com/geneontology/go-ontology/issues/12808 Ghost relations in the OBO file]<br />
#[https://github.com/geneontology/go-ontology/issues/12341 Bridging ChEBI to Pro]<br />
#[https://github.com/geneontology/go-ontology/issues/12811 Merge directly_activates/inhibits relations into directly_positively/negatively_regulates]<br />
<br />
Is anyone else having trouble using the OBO annotation plug-in in Protege 5.0.0? <br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2017-01-12&diff=62946Ontology meeting 2017-01-122017-01-12T16:39:07Z<p>MC: /* Update from Melanie on EBI editors status */</p>
<hr />
<div>Attendees:<br />
<br />
Regrets:<br />
<br />
<br />
Bluejeans: https://bluejeans.com/164681006<br />
<br />
==Update from Melanie on EBI editors status==<br />
<br />
The following labels were created/used on the ontology tracker at https://github.com/geneontology/go-ontology/issues: <br />
- curator-request (Paul indicated those should be highest priority) <br />
- MF refactoring <br />
- wrapping-up (non trivial work has already been done on ticket by PR, DOS or MC it'd be more efficient for one of them to close it instead of passing it on) <br />
- low priority <br />
<br />
and labels indicating estimated time: <br />
- time low (<2h) <br />
- time medium (requires discussion with submitter but feasible in a day if communication fast enough) <br />
- time high (>1 day) <br />
- time unknown (external dependencies) <br />
<br />
Based on this, we anticipate that Paola and Melanie should be able to wrap their tickets up, though some are dependent on external efforts and therefore remain uncertain. <br />
David has 106 tickets open, including 41 curator requests which we agreed should take priority. Based on his current workload, he is aiming at coordinating an MF refactoring work week early February, possibly coordinating with Phil Lord and Robert Stevens who he mentioned are working on a refactoring proposal as well.<br />
<br />
==Tickets for discussion at this meeting:==<br />
<br />
See https://github.com/geneontology/go-ontology/projects/1, column labeled "Ontology Call January 12, 2017" on the right<br />
<br />
#[https://github.com/geneontology/go-ontology/issues/12211 Move editors file to this repo on GitHub]<br />
#[https://github.com/geneontology/go-ontology/issues/12788 Contact for UniProt annotations]<br />
#[https://github.com/geneontology/go-ontology/issues/12880 Protege documentation needs updating and ID issue]<br />
#[https://github.com/geneontology/go-ontology/issues/12808 Ghost relations in the OBO file]<br />
#[https://github.com/geneontology/go-ontology/issues/12341 Bridging ChEBI to Pro]<br />
#[https://github.com/geneontology/go-ontology/issues/12811 Merge directly_activates/inhibits relations into directly_positively/negatively_regulates]<br />
<br />
Is anyone else having trouble using the OBO annotation plug-in in Protege 5.0.0? <br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-12-01&diff=62558Ontology meeting 2016-12-012016-11-29T16:11:27Z<p>MC: </p>
<hr />
<div>Attendees: <br />
<br />
Regrets: <br />
<br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
==End of EBI subcontract - plans to wrap up==<br />
<br />
End of subcontract end of February 2017. EBI GO editors (DOS, Paola, Melanie) will step off the GO rotas (GH, TG, Helpdesk) starting December 12th to allow wrap-up of existing tickets concomittently with other tasks.<br />
<br />
==Tickets for discussion at this meeting:==<br />
<br />
#[https://github.com/geneontology/go-ontology/issues/12815 Add check for identical definitions in ontology file?]<br />
#[https://github.com/geneontology/go-ontology/issues/12766 Review MF term GO:0050827 'toxin receptor binding']<br />
#[https://github.com/geneontology/go-ontology/issues/12808 Ghost relations in the obo-file]<br />
#[https://github.com/geneontology/go-ontology/issues/12786 Discussion of 'positive regulation' and 'maintenance']<br />
#[https://github.com/geneontology/go-ontology/issues/12721 MP: (recently removed ) parentage in amino acid metabolism]<br />
#[https://github.com/geneontology/go-ontology/issues/12811 Merge directly_activates/inhibits relations into directly_positively/negatively_regulates.]<br />
<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-12-01&diff=62557Ontology meeting 2016-12-012016-11-29T15:47:39Z<p>MC: Created page with "Attendees: Regrets: GoToMeeting invite: https://global.gotomeeting.com/join/859015101 End of EBI subcontract -plans to wrap up Tickets for discussion at this meeting:..."</p>
<hr />
<div>Attendees: <br />
<br />
Regrets: <br />
<br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
End of EBI subcontract -plans to wrap up<br />
<br />
Tickets for discussion at this meeting:<br />
<br />
#[https://github.com/geneontology/go-ontology/issues/12786 Discussion of 'positive regulation' and 'maintenance']<br />
<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_Development&diff=62556Ontology Development2016-11-29T15:46:30Z<p>MC: </p>
<hr />
<div>This group's purpose is to ensure that the Gene Ontology represents biology in a way that is useful for gene product annotation of reference genomes and other MODs using the GO for annotation. The group serves as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO. Members of the group are responsible for reporting areas of the GO that need development and for suggesting changes and additions to the GO as needs arise. Members of the group serve as biological experts in domains that are covered by their organism. They are responsible for reviewing changes to be sure that they accurately reflect our current understanding of biology.<br />
<br />
==Content Development ==<br />
===Projects===<br />
====High Priority/Ongoing====<br />
*[[Cell Cycle]] (Val, Pombe experts, GOEds)<br />
*[[Enzymes and EC mappings]]<br />
*[https://github.com/geneontology/synapse Synapse project] (Synapse experts, DavidOS, Becky Foulger)<br />
*Extracellular RNA-containing vesicles (Paola, Aleks and community experts)<br />
*Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts)<br />
*Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts)<br />
<br />
====Medium Priority====<br />
*[[Non-symbiotic multi-organism processes]] (Jane, David OS)<br />
<br />
====Low priority====<br />
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)<br />
*[[microbial ontology development and annotation]]<br />
<br />
====Recently completed projects====<br />
*[[Uberon alignment]] (DavidH)<br />
*Addition of cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]<br />
**[[Cell cross-products]], [[Cell-type specific GO terms]] (Jane, Paola, Alex, Chris, DavidOS)<br />
**[[Adding missing CHEBI xps]]<br />
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)<br />
*[[Virus terms|Virus-related term overhaul]], [[Virus_ontology_devt_July_2012|Phage Terms]] (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others)<br />
*[[Neurobiology Project]] (David, Tanya, Jane, Paola, DavidOS)<br />
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013<br />
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012<br />
*[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group) <br />
*[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan)<br />
*Rework disjoint terms as [http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded in discussion on GO list] (Jane).<br />
*[[:Category:Content MENGO|MENGO collaboration]] (Jane)<br />
<br />
====Proposed content work====<br />
A list of topics that we propose to address, but for which a timeline has not been set<br />
<br />
*Peripheral nervous system development<br />
*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology. <br />
*Overhaul [[translation]], similar to what's being done for transcription. [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1891512&group_id=36855| SF 1891512] is closed, but notes some issues for consideration. (midori 2010-10-04)<br />
* [[Recombination and DNA repair]]<br />
* [[RNA processes]]<br />
* [[Bile formation and secretion processes]]<br />
* [[protein and peptidyl amino acid modification / protein processing]]<br />
* [[Response to drug]]<br />
* [[Polyketide synthases]]<br />
* [[cell growth/proliferation/division]]<br />
* [[oxidoreductases]]<br />
<br />
==Guides, Training and Documentation==<br />
<br />
*[[:Category:Curator Guides|Curator guides]]<br />
*[[Editor_Guide]]<br />
*[[Editor_file_guide]]<br />
*[[Protege_setup_for_GO_Eds|Protege setup for GO Eds]]<br />
*[[Ontology Documentation Drafts]] - for working on documentation of ontology content that will become part of the web-based documentation<br />
*[[New Ontology Editor Training]]<br />
*[[Ontology Editing Examples|Ontology Editing Examples: Regulation of a pathway by regulation of enzyme activity]]<br />
*[[Guidelines on 'protein complex' terms]]<br />
*[[Content Meeting Documentation|Guidance for organizing content meetings]] (old doc, but basic principles still apply)<br />
<br />
==Other Ontology Development Group Activities==<br />
===QC===<br />
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)<br />
*[[Jenkins]]<br />
<br />
===TermGenie===<br />
*[[Template-able Requests Prior To TG]]<br />
<br />
===Website===<br />
*[[Editorial-type sections copied over from the GO website ontology documentation: MF]]<br />
<br />
===Protege===<br />
*[[Protege workshop]] Jan. 2012<br />
*[[Ontology_workshop_Jan_2013]]<br />
*[[Protege Feature Requirements]]<br />
<br />
[[Category:Ontology]]<br />
<br />
===LEGO===<br />
*[[Regulation]]<br />
<br />
*[[Noctua_meeting_140929|Modelling complex annotations in LEGO/noctua - meeting 140929]]<br />
<br />
===Annotation extensions===<br />
*[[Terms that could be obsoleted if information was collected as annotation extension]]<br />
<br />
==Meetings==<br />
===Cambridge Editors' meetings - weekly Tuesday 10-11 AM===<br />
<br />
*[[CamEds Ontology meeting 2012-06-19|June 19]]<br />
*[[CamEds Ontology meeting 2012-06-26|June 26]]<br />
*[[CamEds Ontology meeting 2012-07-3|July 3]]<br />
*[[CamEds Ontology meeting 2012-07-17|July 17]]<br />
*[[CamEds Ontology meeting 2012-07-31|July 31]]<br />
*[[CamEds Ontology meeting 2012-08-31|August 7]]<br />
*[[CamEds Ontology meeting 2012-10-24|October 24]]<br />
<br />
<br />
===SourceForge Meetings: Fortnightly, Wednesdays, 4:30-5:15pm BST - now fortnightly, Mondays, 4-5pm BST===<br />
<br />
*[[SourceForge meeting 2013-07-24|July 24]]<br />
*[[SourceForge meeting 2013-09-04|Sept 4]]<br />
*[[SourceForge meeting 2013-09-11|Sept 11]]<br />
*[[SourceForge meeting 2013-09-25|Sept 25]]<br />
*[[SourceForge meeting 2013-10-09|Oct 9]]<br />
*[[SourceForge meeting 2013-10-30|Oct 30]]<br />
*[[SourceForge meeting 2013-12-11|Dec 11th]]<br />
*[[SourceForge meeting 2014-01-29|Jan 29th]]<br />
*[[SourceForge meeting 2014-02-12|Feb 12th]]<br />
*[[SourceForge meeting 2014-02-26|Feb 26th]]<br />
*[[SourceForge meeting 2014-04-23|Apr 23rd]]<br />
*[[SourceForge meeting 2014-05-14|May 14th]]<br />
*[[SourceForge meeting 2014-06-25|June 25th]]<br />
*[[SourceForge meeting 2014-09-10|Sept 10th]]<br />
*[[SourceForge meeting 2014-09-24|Sept 24th]]<br />
*[[SourceForge meeting 2014-10-22|Oct 22nd]]<br />
*[[SourceForge meeting 2015-02-11|Feb 11th]]<br />
*[[SourceForge meeting 2015-02-25|Feb 25th]]<br />
*[[SourceForge meeting 2015-03-11|Mar 11th]]<br />
*[[SourceForge meeting 2015-03-25|Mar 25th]]<br />
*[[SourceForge meeting 2015-04-22|Apr 22nd]]<br />
*[[SourceForge meeting 2015-04-29|Apr 29th]]<br />
*[[SourceForge meeting 2015-06-22|Jun 22nd]]<br />
*[[SourceForge meeting 2015-12-14|Dec 14th]]<br />
<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]<br />
<br />
===Editor's Conference calls-weekly NOW ON THURSDAYS, 8:30-9:15 AM PST===<br />
<br />
*[[Ontology editor's conference call minutes 2011|2011 minutes]]<br />
*[[Ontology editor's conference call minutes Jan-June 2012|Jan-June 2012 minutes]]<br />
*[[Ontology editor's conference call minutes July-Dec 2012|July-Dec 2012 minutes]]<br />
*[[Ontology editor's conference call minutes Jan-June 2013|Jan-June 2013 minutes]]<br />
*[[Ontology editor's conference call minutes July-Dec 2013|July-Dec 2013 minutes]]<br />
*[[Ontology editor's conference call minutes Jan-June 2014|Jan-June 2014 minutes]]<br />
*[[Ontology editor's conference call minutes July-Dec 2014|July-Dec 2014 minutes]]<br />
*[[Ontology editor's conference call minutes Jan-June 2015|Jan-June 2015 minutes]]<br />
*[[Ontology editor's conference call minutes July-Dec 2015|July-Dec 2015 minutes]]<br />
*[[Ontology editor's conference call minutes Jan-June 2016|Jan-June 2016 minutes]]<br />
*[[Ontology meeting 2016-07-07|Jul 07]] Cancelled<br />
*[[Ontology meeting 2016-07-14|Jul 14]] Cancelled<br />
*[[Ontology meeting 2016-07-21|Jul 21]]<br />
*[[Ontology meeting 2016-07-28|Jul 28]]<br />
*[[Ontology meeting 2016-08-04|Aug 4]] Cancelled<br />
*[[Ontology meeting 2016-08-11|Aug 11]] Cancelled<br />
*[[Ontology meeting 2016-08-18|Aug 18]]<br />
*[[Ontology meeting 2016-08-25|Aug 25]] <br />
*[[Ontology meeting 2016-09-01|Sep 1]] Cancelled due to Hinxton LEGO/Noctua workshop<br />
*[[Ontology meeting 2016-09-08|Sep 8]]<br />
*[[Ontology meeting 2016-09-15|Sep 15]]<br />
*[[Ontology meeting 2016-09-22|Sep 22]]<br />
*[[Ontology meeting 2016-09-29|Sep 29]]<br />
*[[Ontology meeting 2016-10-06|Oct 6]]<br />
*[[Ontology meeting 2016-10-13|Oct 13]]<br />
*[[Ontology meeting 2016-10-20|Oct 20]]<br />
*[[Ontology meeting 2016-10-27|Oct 27]]<br />
*[[Ontology meeting 2016-11-03|Nov 3]] Cancelled due to traveling to GOC meeting<br />
*[[Ontology meeting 2016-11-10|Nov 10]]<br />
*[[Ontology meeting 2016-11-17|Nov 17]]<br />
*[[Ontology meeting 2016-11-24|Nov 24]] Thanksgiving<br />
*[[Ontology meeting 2016-12-01|Dec 01]]<br />
<br />
==Useful Links==<br />
*[[Completed ontology content work]]<br />
*[[SF + TG Rota for Gene Ontology requests]]<br />
*[[Ontology_Development_Reports|Ontology Development Reports]] (discontinued Nov 2010)<br />
<br />
[[Category:Ontology]]<br />
<br />
==Administrative==<br />
*[[Ontology Development group summary]]<br />
*[[Meeting_minutes:_general_topics|Miscellaneous meeting minutes]]<br />
<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-11-16&diff=62519Manager Call 2016-11-162016-11-17T09:57:13Z<p>MC: /* Bluejeans URL */</p>
<hr />
<div>=Bluejeans URL=<br />
*https://bluejeans.com/588333403<br />
<br />
'''Agenda:''' Kimberly Van Auken<br />
<br />
'''Minutes:''' Moni Munoz-Torres<br />
<br />
'''Present:''' Paul, Kimberly, Suzi, Huaiyu, David H, Chris, Melanie, Moni, Paola.<br />
<br />
=Agenda=<br />
==Annotation Tools==<br />
*This issue is wrt a response to a request from Peter Karp to list his group's annotation tool on the GO website.<br />
*What should be listed on the website? See http://geneontology.org/faq/where-can-i-find-software-allow-me-make-or-edit-go-annotations<br />
**The current FAQ on this only specifically mentions CANTO: http://geneontology.org/faq/where-can-i-find-software-allow-me-make-or-edit-go-annotations<br />
<br />
<pre><br />
- For the GO-help issue, see http://jira.geneontology.org/browse/GO-1379<br />
- For historical context, this FAQ was ported over from the old website and last updated on October 14 of 2014.<br />
- The answer we should add to this FAQ is that curators can use Noctua. Given that there is not yet a system / plan in place to open Noctua for the public to contribute annotations, in the mean time we can list Canto, Cacao, Protein2GO, and Pathway Tools (http://pathwaytools.com/)<br />
- Paul: Add comments informing curators that if you have a small number of annotations, you can send them to us, see "here". If you want to start a new effort, let us know “here”.<br />
- Moni: Let’s send them through the decision tree we created and added to the 'Contributing to GO' page! This will allow them to contribute their annotations in the most efficient way. <br />
<br />
ToDo: Send Paul contact info for Pathway Tools to be added to registry at Elixir (Melanie did this? MC: yes, done :)).<br />
</pre><br />
<br />
*Note that we also do mention other tools on our FAQ page for performing enrichment analyses for species not included in the drop-down list on the website<br />
**http://geneontology.org/faq/how-can-i-do-term-enrichment-analysis-species-not-present-list-amigo<br />
<br />
<pre><br />
- Proposal (Paola): general recommendation for endorsing software for use of GOC resources should be that at least one of the members of GOC has used it.<br />
- ToDo: Make the FAQ (http://geneontology.org/faq/how-can-i-do-term-enrichment-analysis-species-not-present-list-amigo) match what’s on the Enrichment Analysis Help Page at http://geneontology.org/page/go-enrichment-analysis<br />
</pre><br />
<br />
<br />
*From Minutes of last call?<br />
**Genomespace looks a bit too much like an environment in which tools can be linked rather than a registry per se.<br />
**We propose to use the Elixir registry assuming we can punctually request to add content. (Melanie sent email to Jon) If it's only a handful of request we can add on a case by case, if it's more than that we can revisit this issue.<br />
<br />
==2016 Year-End Progress Reports==<br />
*Formats? <br />
**Google docs<br />
**Wiki pages<br />
<br />
<pre><br />
- ToDo: create Google Doc per institution, and also a separate document where all efforts will be combined and summarized.<br />
- As we ask institutions to prepare their individual documents, ask them to follow a template. Suzi will prepare the templates and add them to this directory: <br />
https://drive.google.com/drive/u/1/folders/0B8kRPmmvPJU3SzNuZ0YzVVJEOWc<br />
</pre><br />
<br />
==Food for thought==<br />
*What is the biggest challenge for ontology development?<br />
*What is the biggest challenge for annotation?<br />
*What tool is most urgently needed?<br />
*How can we be consumers and users of GO ourselves? (eat our own dog food?)<br />
<br />
<pre><br />
- Suzi: suggestion to set up main and large-scope goals for the year. Addressing the questions in the agenda. Suzi requests that everyone thinks of these questions. <br />
- Paul suggests that these goals should be organized on the GOC Projects page at https://github.com/orgs/geneontology/projects<br />
</pre><br />
<br />
[[Category: GO Managers Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-11-16&diff=62518Manager Call 2016-11-162016-11-17T09:21:54Z<p>MC: </p>
<hr />
<div>=Bluejeans URL=<br />
*https://bluejeans.com/588333403<br />
<br />
'''Agenda:''' Kimberly Van Auken<br />
<br />
'''Minutes:''' Moni Munoz-Torres<br />
<br />
'''Present:''' Paul, Kimberly, Suzi, Huaiyu, David H, Chris, Melanie, Moni. <br />
<br />
=Agenda=<br />
==Annotation Tools==<br />
*This issue is wrt a response to a request from Peter Karp to list his group's annotation tool on the GO website.<br />
*What should be listed on the website? See http://geneontology.org/faq/where-can-i-find-software-allow-me-make-or-edit-go-annotations<br />
**The current FAQ on this only specifically mentions CANTO: http://geneontology.org/faq/where-can-i-find-software-allow-me-make-or-edit-go-annotations<br />
<br />
<pre><br />
- For the GO-help issue, see http://jira.geneontology.org/browse/GO-1379<br />
- For historical context, this FAQ was ported over from the old website and last updated on October 14 of 2014.<br />
- The answer we should add to this FAQ is that curators can use Noctua. Given that there is not yet a system / plan in place to open Noctua for the public to contribute annotations, in the mean time we can list Canto, Cacao, Protein2GO, and Pathway Tools (http://pathwaytools.com/)<br />
- Paul: Add comments informing curators that if you have a small number of annotations, you can send them to us, see "here". If you want to start a new effort, let us know “here”.<br />
- Moni: Let’s send them through the decision tree we created and added to the 'Contributing to GO' page! This will allow them to contribute their annotations in the most efficient way. <br />
<br />
ToDo: Send Paul contact info for Pathway Tools to be added to registry at Elixir (Melanie did this? MC: yes, done :)).<br />
</pre><br />
<br />
*Note that we also do mention other tools on our FAQ page for performing enrichment analyses for species not included in the drop-down list on the website<br />
**http://geneontology.org/faq/how-can-i-do-term-enrichment-analysis-species-not-present-list-amigo<br />
<br />
<pre><br />
- Proposal (Paola): general recommendation for endorsing software for use of GOC resources should be that at least one of the members of GOC has used it.<br />
- ToDo: Make the FAQ (http://geneontology.org/faq/how-can-i-do-term-enrichment-analysis-species-not-present-list-amigo) match what’s on the Enrichment Analysis Help Page at http://geneontology.org/page/go-enrichment-analysis<br />
</pre><br />
<br />
<br />
*From Minutes of last call?<br />
**Genomespace looks a bit too much like an environment in which tools can be linked rather than a registry per se.<br />
**We propose to use the Elixir registry assuming we can punctually request to add content. (Melanie sent email to Jon) If it's only a handful of request we can add on a case by case, if it's more than that we can revisit this issue.<br />
<br />
==2016 Year-End Progress Reports==<br />
*Formats? <br />
**Google docs<br />
**Wiki pages<br />
<br />
<pre><br />
- ToDo: create Google Doc per institution, and also a separate document where all efforts will be combined and summarized.<br />
- As we ask institutions to prepare their individual documents, ask them to follow a template. Suzi will prepare the templates and add them to this directory: <br />
https://drive.google.com/drive/u/1/folders/0B8kRPmmvPJU3SzNuZ0YzVVJEOWc<br />
</pre><br />
<br />
==Food for thought==<br />
*What is the biggest challenge for ontology development?<br />
*What is the biggest challenge for annotation?<br />
*What tool is most urgently needed?<br />
*How can we be consumers and users of GO ourselves? (eat our own dog food?)<br />
<br />
<pre><br />
- Suzi: suggestion to set up main and large-scope goals for the year. Addressing the questions in the agenda. Suzi requests that everyone thinks of these questions. <br />
- Paul suggests that these goals should be organized on the GOC Projects page at https://github.com/orgs/geneontology/projects<br />
</pre><br />
<br />
[[Category: GO Managers Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-11-10&diff=62496Ontology meeting 2016-11-102016-11-09T10:00:09Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes: <br />
<br />
Regrets: <br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
===GitHub projects page (we'll try to follow this, as a test): https://github.com/geneontology/go-ontology/projects/1===<br />
Agenda below is there as backup.<br />
<br />
===Debrief from GOC meeting: ontology group update and breakout session on ontology priorities===<br />
<br />
For reference, minutes are here: https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#<br />
<br />
===Discussion of 'positive regulation' and 'maintenance' from last annotation call===<br />
<br />
See http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2016-10-25#Discussion_of_Outstanding_github_Tickets_2<br />
<br />
===Modified Proteins Proposal===<br />
The proposal was not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives. <br />
<br />
<br />
# Continue to add these terms by hand. Unsustainable?<br />
# Figure out a way to add these terms automatically. Use PRO?, Chebi?, PsiMod?, will this lead to annotation inconsistency. Probably.<br />
# Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.<br />
# Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.<br />
<br />
We discussed three possible semantic interpretations of modified protein binding terms:<br />
<br />
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#heading=h.vzsyf1ss0k8h<br />
<br />
Number 2 in this list - binds to the modified part of a protein - had the most support. Example: SH2 domain confers binding to phospho-tryosine in the context of a specific peptide motif: https://en.wikipedia.org/wiki/SH2_domain<br />
<br />
For terms like this, we could add a comment that it should only be used where there is high confidence that binding is to the modification + protein (simple dependency on phosphorylation of target is not sufficient but one that localizes the domain by deletion/mutagenesis analysis of the protein is). This still leaves the question of how detailed we should get in specifying the target (see histone binding).<br />
<br />
===Follow-up: contacts for UniProt annotations===<br />
Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#Update:_contacts_for_UniProt_annotations<br />
<br />
AI from last call was "Sylvain will discuss with Chris and David H at the GOC meeting". Any news on this please?<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-11-02&diff=62389Manager Call 2016-11-022016-11-02T15:44:28Z<p>MC: </p>
<hr />
<div>=Bluejeans URL=<br />
*https://bluejeans.com/588333403<br />
<br />
=Agenda=<br />
==USC Meeting==<br />
*Current agenda page: http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda<br />
*Remote participants? Use Bluejeans?<br />
<br />
==Annotation Tools==<br />
*What should be listed on the website? See http://geneontology.org/faq/where-can-i-find-software-allow-me-make-or-edit-go-annotations<br />
**The current FAQ on this only specifically mentions CANTO: http://geneontology.org/faq/where-can-i-find-software-allow-me-make-or-edit-go-annotations<br />
<br />
==Minutes==<br />
<br />
Genomespace looks a bit too much like an environment in which tools can be linked rather than a registry per se.<br />
<br />
We propose to use the Elixir registry assuming we can punctually request to add content. (Melanie sent email to Jon) If it's only a handful of request we can add on a case by case, if it's more than that we can revisit this issue.<br />
<br />
[[Category:GO Managers Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-11-02&diff=62388Manager Call 2016-11-022016-11-02T15:21:39Z<p>MC: </p>
<hr />
<div>=Bluejeans URL=<br />
*https://bluejeans.com/588333403<br />
<br />
=Agenda=<br />
==USC Meeting==<br />
*Current agenda page: http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda<br />
*Remote participants? Use Bluejeans?<br />
<br />
==Annotation Tools==<br />
*What should be listed on the website? See http://geneontology.org/faq/where-can-i-find-software-allow-me-make-or-edit-go-annotations<br />
**The current FAQ on this only specifically mentions CANTO: http://geneontology.org/faq/where-can-i-find-software-allow-me-make-or-edit-go-annotations<br />
<br />
==Minutes==<br />
<br />
Genomespace looks a bit too much like an environment in which tools can be linked rather than a registry per se.<br />
<br />
We propose to use the Elixir registry assuming we can have a login to add content. If it's only a handful of request we can add on a case by case, if it's more than that we can revisit this issue.<br />
<br />
[[Category:GO Managers Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-10-13&diff=62085Ontology meeting 2016-10-132016-10-12T12:55:16Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes:<br />
<br />
Regrets:<br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
<br />
===Update: contacts for UniProt annotations===<br />
<br />
As already mentioned, we should email the GOA helpdesk at goa@ebi.ac.uk for annotations assigned specifically by EBI UniProt (GOA) curators.<br />
Where annotations by SIB UniProt curators are or may be involved, please email help@uniprot.org. They distribute updates to all UniProt curators (GOA + SIB). I added this info to the Google spreadsheet (https://docs.google.com/spreadsheets/d/1nAquF0oXHU6d638Q97ZeQ7K7DOhuru84-rOMEL4A114/edit#gid=0), but we opted not to include email contacts on the corresponding GitHub page (https://github.com/geneontology/go-ontology/blob/master/curator_group_contacts.tsv).<br />
<br />
===Update: membership go-ontology mailing-list===<br />
<br />
Do we want to restrict membership of the list or should it be a public one? (The current list of subscribers can be accessed upon logging in https://mailman.stanford.edu/mailman/listinfo/go-ontology)<br />
<br />
===Pending TG requests===<br />
<br />
Just a note so we don't forget to deal with these:<br />
<br />
regulation of memory terms (requested by Helen Attrill, FlyBase)<br />
<br />
heteroreceptor complex assembly/disassembly (requested by Paul Denny, UCL)<br />
<br />
===Follow-up: GitHub projects===<br />
<br />
See background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-06#GitHub_Projects<br />
<br />
Paola added one card each to the 3 columns in https://github.com/geneontology/go-ontology/projects/1. Feel free to add as an experiment, and/or we could go over those. Then we can see how this works for us.<br />
<br />
Melanie: https://github.com/geneontology/go-ontology/issues/12723 "hypusine pathway", discussed with David Hill and thought worthwhile to bring to editors call.<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-10-13&diff=62084Ontology meeting 2016-10-132016-10-12T12:42:20Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes:<br />
<br />
Regrets:<br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
<br />
===Build problems===<br />
<br />
If not fixed yet<br />
<br />
===Update: contacts for UniProt annotations===<br />
<br />
As already mentioned, we should email the GOA helpdesk at goa@ebi.ac.uk for annotations assigned specifically by EBI UniProt (GOA) curators.<br />
Where annotations by SIB UniProt curators are or may be involved, please email help@uniprot.org. They distribute updates to all UniProt curators (GOA + SIB). I added this info to the Google spreadsheet (https://docs.google.com/spreadsheets/d/1nAquF0oXHU6d638Q97ZeQ7K7DOhuru84-rOMEL4A114/edit#gid=0), but we opted not to include email contacts on the corresponding GitHub page (https://github.com/geneontology/go-ontology/blob/master/curator_group_contacts.tsv).<br />
<br />
===Update: membership go-ontology mailing-list===<br />
<br />
Do we want to restrict membership of the list or should it be a public one? (The current list of subscribers can be accessed upon logging in https://mailman.stanford.edu/mailman/listinfo/go-ontology)<br />
<br />
===Pending TG requests===<br />
<br />
Just a note so we don't forget to deal with these:<br />
<br />
regulation of memory terms (requested by Helen Attrill, FlyBase)<br />
<br />
heteroreceptor complex assembly/disassembly (requested by Paul Denny, UCL)<br />
<br />
===Follow-up: GitHub projects===<br />
<br />
See background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-06#GitHub_Projects<br />
<br />
Paola added one card each to the 3 columns in https://github.com/geneontology/go-ontology/projects/1. Feel free to add as an experiment, and/or we could go over those. Then we can see how this works for us.<br />
<br />
Melanie: https://github.com/geneontology/go-ontology/issues/12723 "hypusine pathway", discussed with David Hill and thought worthwhile to bring to editors call.<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-10-13&diff=62076Ontology meeting 2016-10-132016-10-12T08:00:43Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes:<br />
<br />
Regrets:<br />
<br />
<br />
===Update: contacts for UniProt annotations===<br />
<br />
As already mentioned, we should email the GOA helpdesk at goa@ebi.ac.uk for annotations assigned specifically by EBI UniProt (GOA) curators.<br />
Where annotations by SIB UniProt curators are or may be involved, please email help@uniprot.org. They distribute updates to all UniProt curators (GOA + SIB). I added this info to the Google spreadsheet (https://docs.google.com/spreadsheets/d/1nAquF0oXHU6d638Q97ZeQ7K7DOhuru84-rOMEL4A114/edit#gid=0), but we opted not to include email contacts on the corresponding GitHub page (https://github.com/geneontology/go-ontology/blob/master/curator_group_contacts.tsv).<br />
<br />
===Update: membership go-ontology mailing-list===<br />
<br />
Do we want to restrict membership of the list or should it be a public one?<br />
<br />
===Pending TG requests===<br />
<br />
Just a note so we don't forget to deal with these:<br />
<br />
regulation of memory terms (requested by Helen Attrill, FlyBase)<br />
<br />
heteroreceptor complex assembly/disassembly (requested by Paul Denny, UCL)<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-10-13&diff=62075Ontology meeting 2016-10-132016-10-12T08:00:30Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes:<br />
<br />
Regrets:<br />
<br />
<br />
===Update: contacts for UniProt annotations===<br />
<br />
As already mentioned, we should email the GOA helpdesk at goa@ebi.ac.uk for annotations assigned specifically by EBI UniProt (GOA) curators.<br />
Where annotations by SIB UniProt curators are or may be involved, please email help@uniprot.org. They distribute updates to all UniProt curators (GOA + SIB). I added this info to the Google spreadsheet (https://docs.google.com/spreadsheets/d/1nAquF0oXHU6d638Q97ZeQ7K7DOhuru84-rOMEL4A114/edit#gid=0), but we opted not to include email contacts on the corresponding GitHub page (https://github.com/geneontology/go-ontology/blob/master/curator_group_contacts.tsv).<br />
<br />
===Update: membership go-ontology mailing-list===<br />
<br />
Who is narjiszehra at gmail.com? Do we want to restrict membership of the list or should it be a public one?<br />
<br />
===Pending TG requests===<br />
<br />
Just a note so we don't forget to deal with these:<br />
<br />
regulation of memory terms (requested by Helen Attrill, FlyBase)<br />
<br />
heteroreceptor complex assembly/disassembly (requested by Paul Denny, UCL)<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-10-05&diff=62001Manager Call 2016-10-052016-10-05T15:45:48Z<p>MC: </p>
<hr />
<div>=Bluejeans URL - NEW!!=<br />
*https://bluejeans.com/588333403<br />
<br />
=Agenda=<br />
==USC Meeting==<br />
*Attendees: all checked? <br />
*Current agenda page: http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda<br />
<br />
==NAR paper==<br />
* Link to Google doc: https://docs.google.com/document/d/1K0oG6rDWS_OxNnecdcXRh-ChECAwco48RPXtlJfNwQo<br />
<br />
==Review Trello board==<br />
<br />
* Discuss possible replacements: Waffle, GitHub-projects<br />
* Report from task team: ChrisM, Kimberly, Moni<br />
<br />
==Noctua annotations are live==<br />
*As of this morning the production Noctua annotations for mouse have gone live in MGI.<br />
*Please let David H know if you spot any issues.<br />
<br />
=Minutes=<br />
<br />
==USC meeting==<br />
* 1 800 number for hotel doesn’t work from abroad, Paul will put new number on wiki<br />
<br />
* Seth/Chris will be there immediately before the meeting for a ‘hackathon’. Could do some sort of the LEGO software if Jim can make it on that day. To add to day 1 agenda.<br />
* Paul: will add grant overview/funding to day 1 (big picture)<br />
* Judy: Darren from PRO is coming<br />
* Marcus (ECO) can only attend first day<br />
<br />
<br />
Chris sent email to GO directors mentioning only David Hill left as editor on March 1st. Plan to train new editors? Maybe AGR editors could be trained more formally. For example Sue Bello and Stan (RGD) have worked on fork from DO to include OMIM terms. Central DO editor looks at it and merges it in or not. Editor keeps gatekeeping while allowing edits by others.<br />
Proposal from Chris: have training session before March for AGR editors, or wider training session. Maybe one person from each MOD could be a designated editor and come to this session.<br />
<br />
Would be useful to present some sort of plan at November meeting. Kimberly: should also include discussion of annotations (calls, resources…)<br />
-> Paul will include this in the big picture presentation on first day<br />
<br />
==NAR paper==<br />
* DL October 24<br />
* Missing: “promotion” to users. Practical bit: what should they care about reference proteome, what does the website allows them to do… Highlight “service to users”. Contributions for this section welcome. Paul to assign people to specific parts to get more response. All to contribute.<br />
<br />
==Waffle/Github project==<br />
Report pushed to next call.<br />
<br />
==Production annotation from Noctua now loaded in MGI==<br />
* Some small issues (e.g. using causally upstream doesn’t generate annotation, attribution) but everything that comes out seems correct and curators are happy about that.<br />
* Judy: many Noctua tickets open, Suzi: we are looking to hire, Seth is overloaded atm.<br />
* Chris: also big changes coming in march: retire mysql, move ontology to github… big switches in production pipeline.<br />
<br />
[[Category: GO Managers Meetings]]<br />
<br />
'''Present''': Melanie, Chris, David Hill, Huaiyu, Judy, Kimberly, Moni, Paola, Pascale, Paul, Suzi, Pascale<br />
<br />
Minutes by Melanie</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-10-05&diff=62000Manager Call 2016-10-052016-10-05T15:45:01Z<p>MC: </p>
<hr />
<div>=Bluejeans URL - NEW!!=<br />
*https://bluejeans.com/588333403<br />
<br />
=Agenda=<br />
==USC Meeting==<br />
*Attendees: all checked? <br />
*Current agenda page: http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda<br />
<br />
==NAR paper==<br />
* Link to Google doc: https://docs.google.com/document/d/1K0oG6rDWS_OxNnecdcXRh-ChECAwco48RPXtlJfNwQo<br />
<br />
==Review Trello board==<br />
<br />
* Discuss possible replacements: Waffle, GitHub-projects<br />
* Report from task team: ChrisM, Kimberly, Moni<br />
<br />
==Noctua annotations are live==<br />
*As of this morning the production Noctua annotations for mouse have gone live in MGI.<br />
*Please let David H know if you spot any issues.<br />
<br />
=Minutes=<br />
<br />
==USC meeting==<br />
* 1 800 number for hotel doesn’t work from abroad, Paul will put new number on wiki<br />
<br />
* Seth/Chris will be there immediately before the meeting for a ‘hackathon’. Could do some sort of the LEGO software if Jim can make it on that day. To add to day 1 agenda.<br />
* Paul: will add grant overview/funding to day 1 (big picture)<br />
* Judy: Darren from PRO is coming<br />
* Marcus (ECO) can only attend first day<br />
<br />
<br />
Chris sent email to GO directors mentioning only David Hill left as editor on March 1st. Plan to train new editors? Maybe AGR editors could be trained more formally. For example Sue Bello and Stan (RGD) have worked on from from DO to include OMIM terms. Central DO editor looks at it and merges it in or not. Editor keeps gatekeeping while allowing edits by others.<br />
Proposal from Chris: have training session before March for AGR editors, or wider training session. Maybe one person from each MOD could be a designated editor and come to this session.<br />
<br />
Would be useful to present some sort of plan at November meeting. Kimberly: should also include discussion of annotations (calls, resources…)<br />
-> Paul will include this in the big picture presentation on first day<br />
<br />
==NAR paper==<br />
* DL October 24<br />
* Missing: “promotion” to users. Practical bit: what should they care about reference proteome, what does the website allows them to do… Highlight “service to users”. Contributions for this section welcome. Paul to assign people to specific parts to get more response. All to contribute.<br />
<br />
==Waffle/Github project==<br />
Report pushed to next call.<br />
<br />
==Production annotation from Noctua now loaded in MGI==<br />
* Some small issues (e.g. using causally upstream doesn’t generate annotation, attribution) but everything that comes out seems correct and curators are happy about that.<br />
* Judy: many Noctua tickets open, Suzi: we are looking to hire, Seth is overloaded atm.<br />
* Chris: also big changes coming in march: retire mysql, move ontology to github… big switches in production pipeline.<br />
<br />
[[Category: GO Managers Meetings]]<br />
<br />
'''Present''': Melanie, Chris, David Hill, Huaiyu, Judy, Kimberly, Moni, Paola, Pascale, Paul, Suzi, Pascale<br />
<br />
Minutes by Melanie</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-10-05&diff=61955Manager Call 2016-10-052016-10-04T10:24:32Z<p>MC: </p>
<hr />
<div>=Agenda=<br />
==USC Meeting==<br />
*Attendees: all checked? <br />
*Current agenda page: http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda<br />
<br />
==NAR paper==<br />
* Link to Google doc: https://docs.google.com/document/d/1K0oG6rDWS_OxNnecdcXRh-ChECAwco48RPXtlJfNwQo<br />
<br />
==Review Trello board==<br />
<br />
* Discuss possible replacements: Waffle, GitHub-projects<br />
* Report from task team: ChrisM, Kimberly, Moni<br />
<br />
=Minutes=<br />
<br />
[[Category: GO Managers Meetings]]<br />
<br />
'''Present''': <br />
<br />
Minutes by</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-10-05&diff=61954Manager Call 2016-10-052016-10-04T10:24:02Z<p>MC: Created page with "=Agenda= ==USC Meeting== *Attendees: all checked? *Current agenda page: http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda ==NAR paper== * Link to Go..."</p>
<hr />
<div>=Agenda=<br />
==USC Meeting==<br />
*Attendees: all checked? <br />
*Current agenda page: http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda<br />
<br />
==NAR paper==<br />
* Link to Google doc: https://docs.google.com/document/d/1K0oG6rDWS_OxNnecdcXRh-ChECAwco48RPXtlJfNwQo<br />
<br />
==Review Trello board==<br />
<br />
* Discuss possible replacements: Waffle, GitHub-projects<br />
* Report from task team: ChrisM, Kimberly, Moni<br />
<br />
=Minutes=<br />
<br />
[[Category: GO Managers Meetings]]<br />
<br />
'''Present''': <br />
<br />
Minutes by <br />
<br />
==</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-09-29&diff=61926Ontology meeting 2016-09-292016-09-30T11:08:49Z<p>MC: added concerns about ontology call merge</p>
<hr />
<div>Attendees: Paola, Tanya, Harold, Melanie, DavidOS, DavidH, PaulT, Chris<br />
<br />
Regrets: Moni, Jim<br />
<br />
Minutes: Tanya<br />
<br />
===Follow-up: Reinstate daily report of terms and stats===<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
The ticket says that this is fixed, but no one has seen the report. Chris, any news on this one please?<br />
<br />
Some progress. See ticket for details.<br />
<br />
===Follow-up: Modified proteins===<br />
<br />
See background discussion here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-09-15#Modified_proteins<br />
<br />
At the time of writing, comments are still missing from some ontology group members. Please review the document here and comment, even if it's just to say that you agree with everything.<br />
<br />
https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit<br />
<br />
Then Paola will wrap up (or we could do it as a group) and we’ll present, whether it’s at an annotation call, by email to the wider group, in person at the GOC meeting, or all of the above.<br />
<br />
Chris needs to comment and then Paola can wrap up.<br />
<br />
===EC2GO annotation problems===<br />
<br />
Current EC2GO annotations are done using the xrefs from the GO ontology file. Main problem occurs if EC number contains one or more dashes, if a gene product is associated with an EC number (from UniProt files, Trembl record for instance), then it becomes associated<br />
to ALL of the GO terms that have that match the non-dash numbers.<br />
<br />
http://geneontology.org/external2go/ec2go<br />
<br />
What generates these annotations? Need to track down the script. Possibly one written by Chris, Heiko, someone else? This problem should be corrected at the source.<br />
<br />
Archeology: Found email thread titled '[go-ontology] Ec2GO mappings' March 9, 2015 - Harold raised issue, Chris <br />
generated some reports. <br />
go-ec-dash-no-generic-ec-parent.txt -- cases such as the one above where we have a dash xref but no corresponding <br />
generic xref<br />
go-ec-dash-inconsistent-with-generic.txt -- cases where the dash xref and generic xref exist but the GO term for the <br />
dash does not sit under the GO term for the generic<br />
<br />
Also, http://wiki.geneontology.org/index.php/Ontology_meeting_2016-02-25#ec2GO_Clean_up<br />
<br />
Action items from there:<br />
<br />
AI #1: Chris will remove ALL EC xrefs in the GO file that have a dash in the number, look like this<br />
xref: EC:2.-.-.-<br />
xref: EC:2.1.-.-<br />
xref: EC:2.2.3.-<br />
<br />
AI #2: Review 250 cases where there are GO terms with more than one FULL EC number (eyeball they are in different<br />
categories). Harold will look at these, Chris will send. (HJD and DPH have 1100 enzymes to add for Peifen.)<br />
<br />
AI #3: Do NOT add EC terms without dashes to new terms.<br />
<br />
===RHEA update request===<br />
<br />
Where are we?<br />
<br />
Chris went back over his plan presented at the Bar Harbour meeting in 2013. This attempted to hack representation of stochiometry <br />
and bidirectional relations into full logical definitions staying within OWL-EL. On reviewing these seem overly complex and may be <br />
unsafe (they may cause incorrect inference when the inputs/output of one reaction are all present in another).<br />
<br />
We decided to simply add subclassing axioms rather than equivalent class expressions. There are two ways to do this: <br />
1. Keep bidirectionality: using a pattern that translates the rxn X + Y -> A + B into <br />
SubClassOf has_participant_collection some ((has_component some X) and (has_component some Y))<br />
SubClassOf has_participant_collection some ((has_component some A) and (has_component some B))<br />
2. Encode directionality reflecting how these reactions are conventionally drawn and their predominant direcion under physiological conditions.<br />
i.g. Translate the rxn X + Y -> A + B into <br />
SubClassOf has_input some X<br />
SubClassOf has_input some Y<br />
SubClassOf has_output some A<br />
SubClassOf has_output some B<br />
<br />
After discussion, we decided to go with the latter, although review later if we run into inference problems (e.g. from use in LEGO to mean opposite direction). <br />
This approach maintains OBO compatibility and as easy to work with. We should probably add a standard comment to all terms explaining the design decision.<br />
Note: the first approach may also have its problems: reciprocal reactions would have the same axiomatisation.<br />
<br />
Neither approach => us autoclassification, but we may be able to find cases (e.g. transporters) where we could come up with full logical definitions that work.<br />
Where does classification come from?<br />
We agreed that we should extract classification from EC wherever possible. We can do this for Rhea reactions wherever they have a mapping to an EC <br />
- or an EC used as a classification.<br />
<br />
Open question: should we also create an experimental translation using cardinality constraints<br />
e.g. X + Y -> A + B becomes:<br />
<br />
EquivalentTo: (has_participant_collection some ((has_component exactly 1 X) and (has_component exactly 1 Y)) <br />
and has_participant_collection some ((has_component exactly 1 A) and (has_component exactly 1 B))<br />
<br />
One for the reasoner competition? Scaling might be OK if we treat MF axiomatisation as a separate module.<br />
<br />
===Consolidation of group calls into one (on USC agenda)===<br />
<br />
Intent to merge all the calls into one? LEGO, Annotation, PAINT, and Ontology Development calls into one GO call.<br />
<br />
Yes, that was the intent. Concerns that merging the ontology call with the rest is too much (different audiences, different topics from annotations related calls) - to be discussed at the USC meeting.<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-08-25&diff=61599Ontology meeting 2016-08-252016-08-25T16:15:28Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Regrets:<br />
<br />
Minutes: Paola<br />
<br />
<br />
===xref error===<br />
<br />
These keep coming in at commit:<br />
<br />
:: ERROR: valid-id-space: bad xref: :develops_from Line: xref: :develops_from<br />
<br />
:: ERROR: valid-id-space: bad xref: :part_of Line: xref: :part_of<br />
<br />
===TG freeform===<br />
<br />
Following up on last week's discussion (see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#TG_freeform), these were the action items:<br />
<br />
"FreeForm is currently broken so needs to be closed down. But could still be useful if fixed, e.g. for protein complexes (better for Birgit to add). AI: Chris to post ticket detailing problems and to look into whether there is some easy way to fix."<br />
<br />
Chris - could you update us please? In the meantime, shall I (Paola) send another reminder to go-consortium NOT to use the tool?<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
Val says "many people use the "protein complex" term, and would expect that to retrieve complexes like the ribosome and the spliceosome and telomerase (I suspect)<br />
<br />
Is it possible to define a protein complex as a complex which has only proteins, or protein and RNA components?<br />
<br />
so <br />
protein complex<br />
--ribonucleoprotein complex<br />
<br />
Would that be crazy? then everything can go under protein complex, unless we know that it has an RNA component, then it moves down...<br />
<br />
This way people will retrieve all protein complexes with the protein complex term.<br />
<br />
Similarly <br />
protein-DNA complex (telosome), which is currently not retrieved by a "protein complex" search. I doubt there are any biologists who would not describe the telosome as a 'protein complex'<br />
https://en.wikipedia.org/wiki/Shelterin<br />
<br />
but you would not currently retrieve it with a protein complex search.."<br />
<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
* See Inferences Changes Report for: 2016-08-24 - e.g.<br />
<br />
<pre><br />
[Term]<br />
+id: GO:0075251 ! uredospore formation<br />
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process<br />
</pre><br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
Please read ahead of meeting, I needed a little time to wrap my head around this. (Tanya)<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
<br />
==Minutes==<br />
<br />
===Protein complexes===<br />
Proposal:<br />
<br />
macromolecular complex: update definition to say it contains at least one protein<br />
<br />
protein complex: add user friendly comment “those are complexes containing *only* proteins,if you are looking for a more general term please consider parent ‘macromolecular complex’<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-08-25&diff=61594Ontology meeting 2016-08-252016-08-25T15:20:40Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Regrets:<br />
<br />
Minutes: Paola<br />
<br />
<br />
===xref error===<br />
<br />
These keep coming in at commit:<br />
<br />
:: ERROR: valid-id-space: bad xref: :develops_from Line: xref: :develops_from<br />
<br />
:: ERROR: valid-id-space: bad xref: :part_of Line: xref: :part_of<br />
<br />
===TG freeform===<br />
<br />
Following up on last week's discussion (see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#TG_freeform), these were the action items:<br />
<br />
"FreeForm is currently broken so needs to be closed down. But could still be useful if fixed, e.g. for protein complexes (better for Birgit to add). AI: Chris to post ticket detailing problems and to look into whether there is some easy way to fix."<br />
<br />
Chris - could you update us please? In the meantime, shall I (Paola) send another reminder to go-consortium NOT to use the tool?<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
Val says "many people use the "protein complex" term, and would expect that to retrieve complexes like the ribosome and the spliceosome and telomerase (I suspect)<br />
<br />
Is it possible to define a protein complex as a complex which has only proteins, or protein and RNA components?<br />
<br />
so <br />
protein complex<br />
--ribonucleoprotein complex<br />
<br />
Would that be crazy? then everything can go under protein complex, unless we know that it has an RNA component, then it moves down...<br />
<br />
This way people will retrieve all protein complexes with the protein complex term.<br />
<br />
Similarly <br />
protein-DNA complex (telosome), which is currently not retrieved by a "protein complex" search. I doubt there are any biologists who would not describe the telosome as a 'protein complex'<br />
https://en.wikipedia.org/wiki/Shelterin<br />
<br />
but you would not currently retrieve it with a protein complex search.."<br />
<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
Please read ahead of meeting, I needed a little time to wrap my head around this. (Tanya)<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
<br />
<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-08-25&diff=61591Ontology meeting 2016-08-252016-08-25T14:50:13Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Regrets:<br />
<br />
Minutes: Paola<br />
<br />
<br />
===xref error===<br />
<br />
These keep coming in at commit:<br />
<br />
:: ERROR: valid-id-space: bad xref: :develops_from Line: xref: :develops_from<br />
<br />
:: ERROR: valid-id-space: bad xref: :part_of Line: xref: :part_of<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
Val says "many people use the "protein complex" term, and would expect that to retrieve complexes like the ribosome and the spliceosome and telomerase (I suspect)<br />
<br />
Is it possible to define a protein complex as a complex which has only proteins, or protein and RNA components?<br />
<br />
so <br />
protein complex<br />
--ribonucleoprotein complex<br />
<br />
Would that be crazy? then everything can go under protein complex, unless we know that it has an RNA component, then it moves down...<br />
<br />
This way people will retrieve all protein complexes with the protein complex term.<br />
<br />
Similarly <br />
protein-DNA complex (telosome), which is currently not retrieved by a "protein complex" search. I doubt there are any biologists who would not describe the telosome as a 'protein complex'<br />
https://en.wikipedia.org/wiki/Shelterin<br />
<br />
but you would not currently retrieve it with a protein complex search.."<br />
<br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
Please read ahead of meeting, I needed a little time to wrap my head around this. (Tanya)<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
===TG freeform===<br />
<br />
Following up on last week's discussion (see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#TG_freeform), these were the action items:<br />
<br />
"FreeForm is currently broken so needs to be closed down. But could still be useful if fixed, e.g. for protein complexes (better for Birgit to add). AI: Chris to post ticket detailing problems and to look into whether there is some easy way to fix."<br />
<br />
Chris - could you update us please? In the meantime, shall I (Paola) send another reminder to go-consortium NOT to use the tool?<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=2016_Hinxton_LEGO/Noctua_Training_Logistics&diff=615442016 Hinxton LEGO/Noctua Training Logistics2016-08-24T07:47:37Z<p>MC: /* Attendees */</p>
<hr />
<div>This training will take place at the EBI Campus in Hinxton, Cambridgeshire, UK from August 31st through September 2nd. <br />
Please contact Claire O'Donovan with details of your accommodation requirements. <br />
<br />
The Agenda for this Training Workshop can be found here: http://wiki.geneontology.org/index.php/2016_Hinxton_LEGO/Noctua_Training_Agenda<br />
<br />
= Transportation =<br />
<br />
==Airports==<br />
<br />
[http://www.heathrowairport.com Heathrow Airport]<br />
<br />
[http://www.stanstedairport.com Stansted]<br />
<br />
[http://www.londoncityairport.com London City]<br />
<br />
==Ground transportation== <br />
<br />
[http://www.nationalexpress.com National Express coaches]<br />
<br />
[http://www.nationalrail.co.uk Train Information]<br />
<br />
[http://www.theaa.com/route-planner/index.jsp AA Route planner]<br />
<br />
==Taxi Companies==<br />
<br />
Panther Taxis <br />
Website: www.panthertaxis.co.uk <br />
Tel: +44 (0)1223 715715<br />
<br />
Sawston Cab Co Ltd (Airport Specialist) <br />
Email: info@sawstoncabcoltd.co.uk <br />
Tel: +44 (0)1223 517008<br />
<br />
==Attendees==<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Dates<br />
|!Arrival at Heathrow<br />
|-<br />
|David Hill<br />
|MGI<br />
| all<br />
|10:00 am Tues<br />
|<br />
|-<br />
|Judith Blake<br />
|MGI<br />
| all<br />
| 9:00 am Tues<br />
|-<br />
|Kimberly Van Auken<br />
|Wormbase<br />
| all<br />
|<br />
|-<br />
|Seth Carbon<br />
|LBNL<br />
| all<br />
| <br />
|-<br />
|Chris Mungall<br />
|LBNL<br />
| all<br />
| 2:10 pm Tues<br />
|-<br />
|Moni Munoz-Torres<br />
|LBNL<br />
| 08/31 - 09/01<br />
|<br />
|-<br />
|Midori Harris<br />
|PomBase<br />
| all<br />
| <br />
|-<br />
|Ruth Lovering<br />
|UCL<br />
| all<br />
| <br />
|-<br />
|Rachael Huntley <br />
|UCL<br />
| 08/31 - 09/01<br />
| <br />
|-<br />
|Barbara Czub<br />
|UCL<br />
| all<br />
| <br />
|-<br />
|Helen Attrill<br />
|FlyBase<br />
| all<br />
| <br />
|-<br />
|Giulia Antonazzo<br />
|FlyBase<br />
| all<br />
| <br />
|-<br />
|Paul Thomas<br />
|USC<br />
| all<br />
| <br />
|-<br />
|Val Wood<br />
|PomBase<br />
| all<br />
| <br />
|-<br />
|Jacky Hayles<br />
|Crick Inst.<br />
|all<br />
| <br />
|-<br />
|Antonia Lock<br />
|PomBase<br />
|all<br />
| <br />
|-<br />
|Melanie Courtot<br />
|EMBL-EBI<br />
|day 1<br />
|<br />
|}<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Logistics&diff=613912016 Los Angeles GOC Meeting Logistics2016-08-10T10:53:01Z<p>MC: </p>
<hr />
<div>=GOC Meeting, Los Angeles, November 4-6, 2016=<br />
<br />
* Location: <br />
** University of Southern California<br />
<br />
==Registration==<br />
Registration site not available yet.<br />
<br />
==Consortium dinner Friday November 4==<br />
<br />
<br />
==Planned Schedule== <br />
<br />
* '''Friday November 4''': <br />
:* Meeting will run from 9am to 5pm.<br />
:* Consortium Dinner will follow.<br />
<br />
*'''Saturday November 5''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Sunday November 6''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
==Meeting Venue and Directions==<br />
* University of Southern California, Ray I. Irani Hall, room 101.<br />
<br />
===Arriving===<br />
<br />
<br />
===Meeting Dinner===<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Would you be able to attend an adjoining Noctua/LEGO workshop the day before the meeting?<br />
! The day after?<br />
|-<br />
| Shur-Jen Wang<br />
| Rat Genome Database<br />
| Yes<br />
|<br />
<br />
|-<br />
| Paul Thomas<br />
| USC<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| LBNL<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| Jackson Laboratory<br />
|No<br />
|Yes<br />
|-<br />
| Mike Cherry<br />
| Stanford<br />
|<br />
|<br />
|-<br />
| Paul Sternberg<br />
| Caltech<br />
|<br />
|<br />
|-<br />
| Chris Mungall<br />
| LBNL<br />
|<br />
| Yes<br />
|-<br />
| Seth Carbon<br />
| LBNL<br />
|<br />
|<br />
|-<br />
| Stacia Engel<br />
| Stanford, SGD<br />
|<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WB, Caltech<br />
| Yes<br />
| Yes<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
|<br />
|<br />
|-<br />
| Leonore Reiser<br />
| TAIR<br />
|<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| The Jackson Laboratory<br />
| No<br />
| Yes<br />
|<br />
|-<br />
| Fiona McCarthy<br />
| AgBase<br />
| No<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| No<br />
| Yes<br />
|<br />
|-<br />
|}<br />
<br />
NOT attending:<br />
<br />
Moni Munoz-Torres - Previous commitment to attend http://www.icg-11.org/<br />
<br />
Melanie Courtot<br />
<br />
==Accommodations==<br />
* We will arrange for a group rate at the Radisson Hotel across the street from the campus. Stay tuned for details.<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Logistics&diff=613902016 Los Angeles GOC Meeting Logistics2016-08-10T10:52:35Z<p>MC: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Los Angeles, November 4-6, 2016=<br />
<br />
* Location: <br />
** University of Southern California<br />
<br />
==Registration==<br />
Registration site not available yet.<br />
<br />
==Consortium dinner Friday November 4==<br />
<br />
<br />
==Planned Schedule== <br />
<br />
* '''Friday November 4''': <br />
:* Meeting will run from 9am to 5pm.<br />
:* Consortium Dinner will follow.<br />
<br />
*'''Saturday November 5''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Sunday November 6''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<br />
<br />
==Meeting Venue and Directions==<br />
* University of Southern California, Ray I. Irani Hall, room 101.<br />
<br />
===Arriving===<br />
<br />
<br />
===Meeting Dinner===<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Would you be able to attend an adjoining Noctua/LEGO workshop the day before the meeting?<br />
! The day after?<br />
|-<br />
| Shur-Jen Wang<br />
| Rat Genome Database<br />
| Yes<br />
|<br />
<br />
|-<br />
| Paul Thomas<br />
| USC<br />
|<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| LBNL<br />
|<br />
|<br />
|-<br />
| Judy Blake<br />
| Jackson Laboratory<br />
|No<br />
|Yes<br />
|-<br />
| Mike Cherry<br />
| Stanford<br />
|<br />
|<br />
|-<br />
| Paul Sternberg<br />
| Caltech<br />
|<br />
|<br />
|-<br />
| Chris Mungall<br />
| LBNL<br />
|<br />
| Yes<br />
|-<br />
| Seth Carbon<br />
| LBNL<br />
|<br />
|<br />
|-<br />
| Stacia Engel<br />
| Stanford, SGD<br />
|<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WB, Caltech<br />
| Yes<br />
| Yes<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
|<br />
|<br />
|-<br />
| Leonore Reiser<br />
| TAIR<br />
|<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
|<br />
|<br />
|-<br />
| David Hill<br />
| The Jackson Laboratory<br />
| No<br />
| Yes<br />
|<br />
|-<br />
| Fiona McCarthy<br />
| AgBase<br />
| No<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| No<br />
| Yes<br />
|<br />
|-<br />
|}<br />
<br />
NOT attending:<br />
<br />
Moni Munoz-Torres - Previous commitment to attend http://www.icg-11.org/<br />
Melanie Courtot<br />
<br />
==Accommodations==<br />
* We will arrange for a group rate at the Radisson Hotel across the street from the campus. Stay tuned for details.<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-08-17&diff=61347Manager Call 2016-08-172016-08-08T09:12:05Z<p>MC: Created page with "=Agenda= ==GOA isoforms files== See https://github.com/geneontology/go-site/issues/190#issuecomment-235598926 The goa_{species} and goa_{species}_isoform GAFs have been merge..."</p>
<hr />
<div>=Agenda=<br />
<br />
==GOA isoforms files==<br />
See https://github.com/geneontology/go-site/issues/190#issuecomment-235598926<br />
The goa_{species} and goa_{species}_isoform GAFs have been merged into a single file. This means that the files available from the GOA and GOC sites would be different, which will inevitably lead to confusion among users. File name should be changed.<br />
<br />
==Proposal for GO REFs==<br />
(Brought up by Moni on last mangers call)<br />
* Maintaining the current GO_REF file in SVN relies completely on input from a GOC member. <br />
* Need to move GO_REF to a more stable place. <br />
* Numerous URL redirects continue to prove a less than efficient system. <br />
* Proposal to move from current GO_REF to DOI record to ensure permanency.<br />
All, please consider Moni's proposal above, add comments or alternative suggestions here, and we can discuss again in 2 weeks.<br />
<br />
==NAR paper==<br />
* Link to Google doc: https://docs.google.com/document/d/1K0oG6rDWS_OxNnecdcXRh-ChECAwco48RPXtlJfNwQo<br />
All, please add subjects to cover, paragraphs if you have at hand. Aim at having a full list of what we want to cover by August 15.<br />
<br />
=Minutes=<br />
<br />
Attendees: <br />
<br />
Minutes: <br />
<br />
<br />
<br />
<br />
[[Category:GO Managers Meetings ]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-07-21&diff=61204Ontology meeting 2016-07-212016-07-21T10:56:36Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes: <br />
<br />
Regrets: Paola<br />
<br />
===Slim versioning===<br />
<br />
interPro wants to release new version of slim, but would like to maintain access to old one. Should version IRI PURLs resolve?<br />
Which relations should be kept?<br />
E.g. http://www.geneontology.org/ontology/subsets/goslim_metagenomics.obo<br />
<br />
[Term]<br />
<br />
id: GO:0001071<br />
<br />
is_a: GO:0003674 ! molecular_function<br />
<br />
relationship: has_part GO:0003676 ! nucleic acid binding<br />
<br />
relationship: part_of GO:0008150 ! biological_process<br />
<br />
===Assertion or inference?===<br />
<br />
Should we assert the is_a or let the reasoner do the job? Also confirm Jenkins check is disabled.<br />
<br />
[Term]<br />
<br />
id: GO:0090685<br />
<br />
name: RNA localization to nucleus<br />
<br />
namespace: biological_process<br />
<br />
def: "A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus." [GOD:mah, PMID:26305931]<br />
<br />
synonym: "RNA localisation to nucleus" EXACT [GOC:mah]<br />
<br />
is_a: GO:0006403 ! RNA localization<br />
<br />
intersection_of: GO:0006403 ! RNA localization<br />
<br />
intersection_of: has_target_end_location GO:0005634 ! nucleus<br />
<br />
===Request for obsoletion ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/1059<br />
<br />
https://github.com/geneontology/go-ontology/issues/12533<br />
<br />
Val said "I often wonder with terms like this, if there is no difference between the process<br />
DNA replication initiation<br />
and<br />
DNA replication initiation from late origin<br />
except via regulation<br />
<br />
should the term <br />
DNA replication initiation from late origin<br />
exist, or should we only have the regulation terms in GO?"<br />
<br />
Midori said "The mechanism and involved gene products are the same at early origins and at late origins, so there is no differentium to distinguish "initiation at late origin" from "initiation"."<br />
<br />
<br />
===Xrefs to Reactome===<br />
<br />
Looks like this wasn't fully addressed yet. See email thread here:<br />
While Peter is on site at Jax, we should devise and action plan for this.<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007619.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007620.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007621.html<br />
<br />
And this GH issue:<br />
<br />
https://github.com/geneontology/go-ontology/issues/12518<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]<br />
<br />
===Review capitalisation of terms ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/12541<br />
<br />
https://github.com/geneontology/go-ontology/issues/12540<br />
<br />
<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-07-21&diff=61203Ontology meeting 2016-07-212016-07-21T10:47:02Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes: <br />
<br />
Regrets: Paola<br />
<br />
===Slim versioning===<br />
<br />
interPro wants to release new version of slim, but would like to maintain access to old one. Should version IRI PURLs resolve?<br />
<br />
===Assertion or inference?===<br />
<br />
Should we assert the is_a or let the reasoner do the job? Also confirm Jenkins check is disabled.<br />
<br />
[Term]<br />
<br />
id: GO:0090685<br />
<br />
name: RNA localization to nucleus<br />
<br />
namespace: biological_process<br />
<br />
def: "A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus." [GOD:mah, PMID:26305931]<br />
<br />
synonym: "RNA localisation to nucleus" EXACT [GOC:mah]<br />
<br />
is_a: GO:0006403 ! RNA localization<br />
<br />
intersection_of: GO:0006403 ! RNA localization<br />
<br />
intersection_of: has_target_end_location GO:0005634 ! nucleus<br />
<br />
===Request for obsoletion ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/1059<br />
<br />
https://github.com/geneontology/go-ontology/issues/12533<br />
<br />
Val said "I often wonder with terms like this, if there is no difference between the process<br />
DNA replication initiation<br />
and<br />
DNA replication initiation from late origin<br />
except via regulation<br />
<br />
should the term <br />
DNA replication initiation from late origin<br />
exist, or should we only have the regulation terms in GO?"<br />
<br />
Midori said "The mechanism and involved gene products are the same at early origins and at late origins, so there is no differentium to distinguish "initiation at late origin" from "initiation"."<br />
<br />
<br />
===Xrefs to Reactome===<br />
<br />
Looks like this wasn't fully addressed yet. See email thread here:<br />
While Peter is on site at Jax, we should devise and action plan for this.<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007619.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007620.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007621.html<br />
<br />
And this GH issue:<br />
<br />
https://github.com/geneontology/go-ontology/issues/12518<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]<br />
<br />
===Review capitalisation of terms ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/12541<br />
<br />
https://github.com/geneontology/go-ontology/issues/12540<br />
<br />
<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-07-21&diff=61202Ontology meeting 2016-07-212016-07-21T10:31:06Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes: <br />
<br />
Regrets: Paola<br />
<br />
===Assertion or inference?===<br />
<br />
Should we assert the is_a or let the reasoner do the job? Also confirm Jenkins check is disabled.<br />
<br />
[Term]<br />
<br />
id: GO:0090685<br />
<br />
name: RNA localization to nucleus<br />
<br />
namespace: biological_process<br />
<br />
def: "A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus." [GOD:mah, PMID:26305931]<br />
<br />
synonym: "RNA localisation to nucleus" EXACT [GOC:mah]<br />
<br />
is_a: GO:0006403 ! RNA localization<br />
<br />
intersection_of: GO:0006403 ! RNA localization<br />
<br />
intersection_of: has_target_end_location GO:0005634 ! nucleus<br />
<br />
===Request for obsoletion ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/1059<br />
<br />
https://github.com/geneontology/go-ontology/issues/12533<br />
<br />
Val said "I often wonder with terms like this, if there is no difference between the process<br />
DNA replication initiation<br />
and<br />
DNA replication initiation from late origin<br />
except via regulation<br />
<br />
should the term <br />
DNA replication initiation from late origin<br />
exist, or should we only have the regulation terms in GO?"<br />
<br />
Midori said "The mechanism and involved gene products are the same at early origins and at late origins, so there is no differentium to distinguish "initiation at late origin" from "initiation"."<br />
<br />
<br />
===Xrefs to Reactome===<br />
<br />
Looks like this wasn't fully addressed yet. See email thread here:<br />
While Peter is on site at Jax, we should devise and action plan for this.<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007619.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007620.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007621.html<br />
<br />
And this GH issue:<br />
<br />
https://github.com/geneontology/go-ontology/issues/12518<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]<br />
<br />
===Review capitalisation of terms ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/12541<br />
<br />
https://github.com/geneontology/go-ontology/issues/12540<br />
<br />
<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-07-21&diff=61201Ontology meeting 2016-07-212016-07-21T10:28:57Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes: <br />
<br />
Regrets: Paola<br />
<br />
===Assertion or inference?===<br />
<br />
Should we assert the is_a or let the reasoner do the job? Also confirm Jenkins check is disabled.<br />
<br />
[Term]<br />
<br />
id: GO:0090685<br />
<br />
name: RNA localization to nucleus<br />
<br />
namespace: biological_process<br />
<br />
def: "A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus." [GOD:mah, PMID:26305931]<br />
<br />
synonym: "RNA localisation to nucleus" EXACT [GOC:mah]<br />
<br />
is_a: GO:0006403 ! RNA localization<br />
<br />
intersection_of: GO:0006403 ! RNA localization<br />
<br />
intersection_of: has_target_end_location GO:0005634 ! nucleus<br />
<br />
<br />
<br />
===Xrefs to Reactome===<br />
<br />
Looks like this wasn't fully addressed yet. See email thread here:<br />
While Peter is on site at Jax, we should devise and action plan for this.<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007619.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007620.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007621.html<br />
<br />
And this GH issue:<br />
<br />
https://github.com/geneontology/go-ontology/issues/12518<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]<br />
<br />
===Review capitalisation of terms ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/12541<br />
<br />
https://github.com/geneontology/go-ontology/issues/12540<br />
<br />
===Request for obsoletion ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/1059<br />
<br />
https://github.com/geneontology/go-ontology/issues/12533<br />
<br />
Val said "I often wonder with terms like this, if there is no difference between the process<br />
DNA replication initiation<br />
and<br />
DNA replication initiation from late origin<br />
except via regulation<br />
<br />
should the term <br />
DNA replication initiation from late origin<br />
exist, or should we only have the regulation terms in GO?"<br />
<br />
Midori said "The mechanism and involved gene products are the same at early origins and at late origins, so there is no differentium to distinguish "initiation at late origin" from "initiation"."<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-07-21&diff=61200Ontology meeting 2016-07-212016-07-21T10:28:32Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes: <br />
<br />
Regrets: Paola<br />
<br />
===Assertion or inference?===<br />
<br />
Should we assert the is_a or let the reasoner do the job? Also confirm Jenkins check is disabled.<br />
<br />
[Term]<br />
+id: GO:0090685<br />
<br />
+name: RNA localization to nucleus<br />
<br />
+namespace: biological_process<br />
<br />
+def: "A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus." [GOD:mah, PMID:26305931]<br />
<br />
+synonym: "RNA localisation to nucleus" EXACT [GOC:mah]<br />
<br />
+is_a: GO:0006403 ! RNA localization<br />
<br />
+intersection_of: GO:0006403 ! RNA localization<br />
<br />
+intersection_of: has_target_end_location GO:0005634 ! nucleus<br />
<br />
<br />
<br />
===Xrefs to Reactome===<br />
<br />
Looks like this wasn't fully addressed yet. See email thread here:<br />
While Peter is on site at Jax, we should devise and action plan for this.<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007619.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007620.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007621.html<br />
<br />
And this GH issue:<br />
<br />
https://github.com/geneontology/go-ontology/issues/12518<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]<br />
<br />
===Review capitalisation of terms ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/12541<br />
<br />
https://github.com/geneontology/go-ontology/issues/12540<br />
<br />
===Request for obsoletion ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/1059<br />
<br />
https://github.com/geneontology/go-ontology/issues/12533<br />
<br />
Val said "I often wonder with terms like this, if there is no difference between the process<br />
DNA replication initiation<br />
and<br />
DNA replication initiation from late origin<br />
except via regulation<br />
<br />
should the term <br />
DNA replication initiation from late origin<br />
exist, or should we only have the regulation terms in GO?"<br />
<br />
Midori said "The mechanism and involved gene products are the same at early origins and at late origins, so there is no differentium to distinguish "initiation at late origin" from "initiation"."<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-07-21&diff=61199Ontology meeting 2016-07-212016-07-21T10:27:51Z<p>MC: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes: <br />
<br />
Regrets: Paola<br />
<br />
===Assertion or inference?===<br />
<br />
Should we assert the is_a or let the reasoner do the job? Also confirm Jenkins check is disabled.<br />
<br />
[Term]<br />
+id: GO:0090685<br />
+name: RNA localization to nucleus<br />
+namespace: biological_process<br />
+def: "A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus." [GOD:mah, PMID:26305931]<br />
+synonym: "RNA localisation to nucleus" EXACT [GOC:mah]<br />
+is_a: GO:0006403 ! RNA localization<br />
+intersection_of: GO:0006403 ! RNA localization<br />
+intersection_of: has_target_end_location GO:0005634 ! nucleus<br />
+created_by: tanyaberardini<br />
+creation_date: 2016-07-19T17:00:49Z<br />
<br />
===Xrefs to Reactome===<br />
<br />
Looks like this wasn't fully addressed yet. See email thread here:<br />
While Peter is on site at Jax, we should devise and action plan for this.<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007619.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007620.html<br />
<br />
https://mailman.stanford.edu/pipermail/go-ontology/2016-June/007621.html<br />
<br />
And this GH issue:<br />
<br />
https://github.com/geneontology/go-ontology/issues/12518<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]<br />
<br />
===Review capitalisation of terms ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/12541<br />
<br />
https://github.com/geneontology/go-ontology/issues/12540<br />
<br />
===Request for obsoletion ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/1059<br />
<br />
https://github.com/geneontology/go-ontology/issues/12533<br />
<br />
Val said "I often wonder with terms like this, if there is no difference between the process<br />
DNA replication initiation<br />
and<br />
DNA replication initiation from late origin<br />
except via regulation<br />
<br />
should the term <br />
DNA replication initiation from late origin<br />
exist, or should we only have the regulation terms in GO?"<br />
<br />
Midori said "The mechanism and involved gene products are the same at early origins and at late origins, so there is no differentium to distinguish "initiation at late origin" from "initiation"."<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-07-20&diff=61197Manager Call 2016-07-202016-07-20T15:57:54Z<p>MC: </p>
<hr />
<div>=Agenda=<br />
==Last meeting==<br />
http://wiki.geneontology.org/index.php/Manager_Call_2016-07-06<br />
Were the two agenda items resolved ? <br />
* Identifier space in GO annotations (GAF, GPAD)<br />
* Protein Complexes<br />
<br />
==Protein Complex annotation guidelines (proposed)==<br />
*[[Macromolecular_complex_annotation_July_2016]]<br />
<br />
==Noctua Workshops==<br />
*Add extra days at USC meeting for a Noctua workshop?<br />
*Have two workshops in the UK? It seems like the number of people wanting to attend is going to be large.<br />
<br />
==NAR paper: GO update==<br />
* put ideas here: https://docs.google.com/document/d/1K0oG6rDWS_OxNnecdcXRh-ChECAwco48RPXtlJfNwQo/edit?usp=sharing<br />
<br />
<br />
=Minutes=<br />
== ID space in GO annotations ==<br />
in progress, to be kept open and reconvene at next call.<br />
David H: each coding MGI has a UniProt ID in the dbxref column. Would be easy to mine this field. Was to do with PAINT and loading GPI file (follow-up on LEGO call discussion from Suzi)<br />
'''AI: David H to add this in the documentation for the GPI''': Any gene coding should have a dbxref to UniProt<br />
== Protein complexes ==<br />
Pascale: when she PAINTs she doesn’t use a lot of contributes_to. However when you don’t know much about complex you would annotate all subunits, but if you know you would annotate only the right one, which seems uneven -> sometimes more information if we know less.<br />
Paul: said he would write something up. Need something to formalise the propagation rule, difference if multiple subunits are responsible for function but not all of them in the complex, vs we don’t know which ones are involved and we propagate to all. If complex has function that is not found in specific subunit, then we want to use contributes_to as some gene products do contributes to the complex activity. Then other case where you just don’t know, and annotation was made to complex as we don’t know which subunits are involved: in this case we also used contributes_to but maybe we should have a weaker qualifier, e.g., may_contribute_to?<br />
<br />
In the case where we don’t know, how do we derive gene level annotation from complex level annotation?<br />
<br />
=> we need some way to distinguish between cases: compound activity from complex, specific activity from specific subunits, or we don’t know.<br />
=> '''AI: Paul will add text to [[Macromolecular_complex_annotation_July_2016]]'''<br />
<br />
== Noctua workshops ==<br />
- doodle poll for UK workshop, only handful of dates seem to work.<br />
- should we add a day to USC workshop? David H: we need to reach curators who may not attend GOC meeting<br />
- get people to register for USC meeting to gauge target audience. Kimberly to add to logistics of meeting “would you attend a Noctua workshop before or after?” - Done<br />
<br />
== invitation for NAR update==<br />
Paul started google doc. Deadline September 15th but we probably have a few weeks after that, so October 1st.<br />
AI for all to go through what we said last time and what we want to emphasise as being done since then. '''DL: August 15th for adding ideas/create outline.'''<br />
<br />
[[Category:GO Managers Meetings ]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-07-21&diff=61149Ontology meeting 2016-07-212016-07-15T10:47:13Z<p>MC: </p>
<hr />
<div>Attendees:<br />
Minutes: <br />
Regrets: Paola<br />
<br />
<br />
===Review capitalisation of terms ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/12541<br />
<br />
https://github.com/geneontology/go-ontology/issues/12540<br />
<br />
===Request for obsoletion ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/1059<br />
<br />
https://github.com/geneontology/go-ontology/issues/12533<br />
<br />
Val said "I often wonder with terms like this, if there is no difference between the process<br />
DNA replication initiation<br />
and<br />
DNA replication initiation from late origin<br />
except via regulation<br />
<br />
should the term <br />
DNA replication initiation from late origin<br />
exist, or should we only have the regulation terms in GO?"<br />
<br />
Midori said "The mechanism and involved gene products are the same at early origins and at late origins, so there is no differentium to distinguish "initiation at late origin" from "initiation"."<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-07-21&diff=61148Ontology meeting 2016-07-212016-07-15T10:46:59Z<p>MC: </p>
<hr />
<div>Attendees:<br />
Minutes: <br />
Regrets: Paola<br />
<br />
<br />
===Review capitalisation of terms ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/12541<br />
<br />
https://github.com/geneontology/go-ontology/issues/12540<br />
<br />
===Request for obsoletion ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/1059<br />
<br />
https://github.com/geneontology/go-ontology/issues/12533<br />
<br />
Val said "I often wonder with terms like this, if there is no difference between the process<br />
DNA replication initiation<br />
and<br />
DNA replication initiation from late origin<br />
except via regulation<br />
<br />
should the term <br />
DNA replication initiation from late origin<br />
exist, or should we only have the regulation terms in GO?"<br />
<br />
Midi said "The mechanism and involved gene products are the same at early origins and at late origins, so there is no differentium to distinguish "initiation at late origin" from "initiation"."<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-07-21&diff=61147Ontology meeting 2016-07-212016-07-15T08:10:35Z<p>MC: </p>
<hr />
<div>Attendees:<br />
Minutes: <br />
Regrets: Paola<br />
<br />
<br />
===Review capitalisation of terms ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/12541<br />
<br />
https://github.com/geneontology/go-ontology/issues/12540<br />
<br />
<br />
<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-07-21&diff=61146Ontology meeting 2016-07-212016-07-15T08:10:27Z<p>MC: Created page with "Attendees: Minutes: Regrets: Paola ===Review capitalisation of terms === https://github.com/geneontology/go-ontology/issues/12541 https://github.com/geneontology/go-ontol..."</p>
<hr />
<div>Attendees:<br />
Minutes: <br />
Regrets: Paola<br />
<br />
<br />
===Review capitalisation of terms ===<br />
<br />
<br />
https://github.com/geneontology/go-ontology/issues/12541<br />
https://github.com/geneontology/go-ontology/issues/12540<br />
<br />
<br />
<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>MChttps://wiki.geneontology.org/index.php?title=Data_Capture_Working_Group&diff=61140Data Capture Working Group2016-07-13T14:02:04Z<p>MC: /* Data Capture Working Group */</p>
<hr />
<div>[[Category:Advocacy and Outreach]] [[Category:Working Groups]]<br />
<br />
= Data Capture Working Group=<br />
<br />
This working group has been formed to ensure an effective way to welcome contributions from GOC and non-GOC researchers alike, beyond the initial contact via GitHub tracker / GO Contact form. We aim to help users to better understand the resources of the GOC and facilitate a path to formatting and depositing contributions.<br />
<br />
The members of this group are: <br />
* Monica Munoz-Torres (Coordinator)<br />
* Kimberly Van Auken<br />
* Judith Blake<br />
* Seth Carbon<br />
* Ruth Lovering<br />
* Chris Mungall<br />
* Valerie Wood<br />
* Claire O'Donovan<br />
* Pankaj Jaiswal<br />
* Melanie Courtot<br />
<br />
<br />
==Conference Calls Notes==<br />
* [[Non-GOC Contributions Call 2016-04-27 | Conference Call 2016-04-27]]<br />
* [[Data Capture Call 2016-05-10| Conference Call 2016-05-10]]<br />
* [[Data Capture Call 2016-05-25| Conference Call 2016-05-25]]<br />
* [[Data Capture Call 2016-06-22| Conference Call 2016-06-22]]</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-07-06&diff=61109Manager Call 2016-07-062016-07-06T14:20:13Z<p>MC: </p>
<hr />
<div>[[Manager_Call_2016-06-15|Previous call minutes]]<br />
<br />
[[Category:GO Managers Meetings ]]<br />
[http://wiki.geneontology.org/index.php/Manager_Call_2016-06-1 Minutes from the previous GO Managers Meeting can be found here].<br />
GO Managers meet using the GO Phone Conference Line from Jackson Laboratory.<br />
<br />
= Agenda =<br />
==Identifier space in GO annotations (GAF, GPAD)==<br />
<br />
We discussed to allow all IDs to be used in AE, provided we can get GPIs from everyone, ticket filed: https://github.com/geneontology/go-site/issues/194<br />
<br />
I (Melanie) talked with Tony S., and as discussed during the data capture call our GPI files don't include cross-references (too many of them to do so). We could envision a solution if it were possible to get a list of those cross-references that are needed specifically, and create a GPI with only those.<br />
<br />
== Protein Complexes ==<br />
<br />
We discussed propagating functions, BP and CC annotations on a complex to the individual gene products, using the contibutes_to qualifier.<br />
<br />
I (Melanie) discussed this with Claire, Sandra and Birgit and there are concerns that while ok for CC, the process/functions (using the contributes_to qualifier) could be confusing for users as a lot of people don't see these qualifiers - they'll only get as far a Protein X has a catalytic function associated with it and stop there. <br />
<br />
= Minutes =<br />
<br />
'''Attendees''':<br />
<br />
'''Regrets''': <br />
<br />
'''Agenda''': | '''Minutes''':</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-07-06&diff=61108Manager Call 2016-07-062016-07-06T14:19:14Z<p>MC: </p>
<hr />
<div>[[Manager_Call_2016-06-15|Previous call minutes]]<br />
<br />
[[Category:GO Managers Meetings ]]<br />
[http://wiki.geneontology.org/index.php/Manager_Call_2016-06-1 Minutes from the previous GO Managers Meeting can be found here].<br />
GO Managers meet using the GO Phone Conference Line from Jackson Laboratory.<br />
<br />
= Agenda =<br />
==Identifier space in GO annotations (GAF, GPAD)==<br />
<br />
We discussed to allow all IDs to be used in AE, provided we can get GPIs from everyone, ticket filed: https://github.com/geneontology/go-site/issues/194<br />
<br />
I (Melanie) talked with Tony S., and as discussed during the data capture call our GPI files don't include cross-references (too many of them to do so). We could envision a solution if it were possible to get a list of those cross-references that are needed specifically, and create a GPI with only those.<br />
<br />
== Protein Complexes ==<br />
<br />
We discussed propagating functions, BP and CC annotations on a complex to the individual gene products, using the contibutes_to qualifier.<br />
<br />
I (Melanie) discussed this with Claire, Sandra and Birgit and there are concerns that while ok for CC, the process/functions (using the contributes_to qualifier) could be confusing for users as a lot of people don't see these qualifiers - they'll only get as far a Protein X has a catalytic function associated with it and stop there. <br />
<br />
= Minutes =<br />
<br />
'''Attendees''':<br />
<br />
'''Regrets''': <br />
<br />
'''Agenda''': Moni | '''Minutes''':</div>MChttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-06-28&diff=61100Annotation Conf. Call 2016-06-282016-06-30T14:31:19Z<p>MC: </p>
<hr />
<div>=Bluejeans URL=<br />
https://bluejeans.com/993661940<br />
<br />
=Agenda=<br />
==Annotation Consistency Exercise==<br />
*[http://www.ncbi.nlm.nih.gov/pubmed/27146270 Drosophila SLC22A Transporter Is a Memory Suppressor Gene that Influences Cholinergic Neurotransmission to the Mushroom Bodies.]<br />
'''Abstract''' The mechanisms that constrain memory formation are of special interest because they provide insights into the brain's memory management systems and potential avenues for correcting cognitive disorders. RNAi knockdown in the Drosophila mushroom body neurons (MBn) of a newly discovered memory suppressor gene, Solute Carrier DmSLC22A, a member of the organic cation transporter family, enhances olfactory memory expression, while overexpression inhibits it. The protein localizes to the dendrites of the MBn, surrounding the presynaptic terminals of cholinergic afferent fibers from projection neurons (Pn). Cell-based expression assays show that this plasma membrane protein transports cholinergic compounds with the highest affinity among several in vitro substrates. Feeding flies choline or inhibiting acetylcholinesterase in Pn enhances memory, an effect blocked by overexpression of the transporter in the MBn. The data argue that DmSLC22A is a memory suppressor protein that limits memory formation by helping to terminate cholinergic neurotransmission at the Pn:MBn synapse.<br />
*'''How to capture biological process aspects of memory?'''<br />
**The paper identifies a ‘memory suppressor gene’ (Solute Carrier 22A of Drosophila (DmSLC22A) (FlyBase:CG7442; FBgn0037140). How to capture the biology described - memory, learning, conditioning? What new terms are needed to capture the process? Alternatively, is it better to capture these experiments only as phenotypes?<br />
** Leave the expression/mechanistic sections and have a look at these four sections of this paper:<br />
***Drosophila CG7442 Is a Memory Suppressor Gene Functioning in MBn and DAn<br />
***Drosophila CG7442 Overexpression Impairs Memory<br />
***DmSLC22A Regulates Both Memory Acquisition and Retention<br />
***DmSLC22A Modulates Memory Strength by Regulating Cholinergic Neurotransmission in the MB Calyx<br />
<br />
'''Annotations'''<br />
{| border=1 cell-padding=5 cell-spacing=10<br />
|-<br />
! Gene/Marker Name<br />
! GO term<br />
! Evidence Code<br />
! With/From<br />
! Annotation Extension <br />
! Comment<br />
|-<br />
|Biological Process<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of olfactory memory retention<br />
| <br />
| <br />
|<br />
|(not forgetting)?<br />
|-<br />
| SLC22A<br />
| NT:positive regulation of memory acquisition<br />
| <br />
| <br />
|<br />
|(learning?)<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory retention<br />
| <br />
| <br />
|<br />
|(memory)<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:regulation of memory acquisition<br />
| IMP <br />
| <br />
| <br />
|<br />
|-<br />
| SLC22A<br />
| NT:regulation of memory retention<br />
| IMP<br />
| <br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of anesthesia-resistant memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| regulation of olfactory learning (GO:0090328)<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:positive regulation of rate of learning<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| AChE<br />
| NT:negative regulation of memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IGI<br />
| AChE<br />
|<br />
|<br />
|-<br />
| AChE<br />
| NT:negative regulation of memory<br />
| IGI<br />
| SLC22A<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| negative regulation of synaptic transmission, cholinergic (GO:0032223)<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:neurotransmitter transport involved in regulation of memory<br />
| IC<br />
| GO:0005277|GO:0015220|GO:NT: negative regulation of memory<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:cholinergic synaptic transmission involved in regulation of memory<br />
| <br />
| <br />
|<br />
| This one's a "maybe"<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IMP/IDA<br />
| <br />
| part_of (olfactory learning)<br />
|<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of olfactory learning<br />
| IMP/IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| memory (GO:0007613)<br />
| IMP<br />
| <br />
| occurs_in(a/b MBn), occurs_in(a'/b' MBn), happens_during(adult life stage)|occurs_in(DAn),happens_during(adult life stage)<br />
|<br />
|- <br />
| SLC22A<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine uptake involved in memory acquisition rate enhancement?<br />
| <br />
| <br />
| occurs_in(a/b MBn), occurs_in(a'/b' MBn), happens_during(adult life stage)|occurs_in(DAn),happens_during(adult life stage)<br />
| <br />
|- <br />
| SLC22A<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine uptake involved in memory retention suppression?<br />
| <br />
| occurs_in(a/b MBn), occurs_in(a'/b' MBn), happens_during(adult life stage)|occurs_in(DAn),happens_during(adult life stage)<br />
|<br />
|<br />
|- <br />
| AChE<br />
| memory (GO:0007613)<br />
| IMP<br />
|<br />
|<br />
| How to express an extracellular synaptic region between two different neurons via annotation extensions?<br />
|- <br />
| AChE<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine catabolism involved in memory acquisition rate enhancement?<br />
| <br />
|<br />
|<br />
|<br />
|- <br />
| AChE<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine catabolism involved in memory retention suppression?<br />
| <br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of olfactory memory <br />
| IMP<br />
| <br />
| acts_on_population_of mushroom body neuron; dopamine neuron<br />
| olfactory memory,pos. reg., children of olfactory learning (GO:0008355). From Fig1,2 (MbN and DpN need to be component terms).<br />
|- <br />
| SLC22A<br />
| NT:positive regulation of olfactory learning<br />
| IMP<br />
| <br />
|<br />
| child of olfactory learning (GO:0008355). From fig 5c. Rate of learning is impaired in knockdown.<br />
|- <br />
| SLC22A<br />
| regulation of synaptic transmission, cholinergic (GO:0032222)<br />
| IMP<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| NT: choline uptake?<br />
| IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| dopamine uptake (GO:0015872)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| histamine uptake (GO:0051615)<br />
| IDA<br />
| <br />
| <br />
|<br />
|- <br />
| SLC22A<br />
| NT: amino-acid betaine uptake?<br />
| IDA<br />
| <br />
|<br />
|<br />
|-<br />
| Molecular Function<br />
|-<br />
| SLC22A<br />
| amino-acid betaine transmembrane transporter activity (GO:0015199)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity (GO:0005277)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| choline transmembrane transporter activity (GO:0015220)<br />
| IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| dopamine transmembrane transporter activity (GO:0005329)<br />
| IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| NT: histamine transmembrane transporter activity<br />
| IDA<br />
| <br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity (GO:0005277)<br />
| IDA/IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| choline transmembrane transporter activity<br />
| IDA <br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity<br />
| IDA<br />
|<br />
| <br />
|<br />
|- <br />
| SLC22A<br />
| choline transmembrane transporter activity (GO:0015220)<br />
| IDA<br />
| <br />
| <br />
| <br />
|- <br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity (GO:0005277)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| Cellular Component<br />
|-<br />
| SLC22A<br />
| dendrite (GO:0030425)<br />
| IDA<br />
| <br />
| part_of (calyx of adult mushroom body)<br />
|<br />
|- <br />
| SLC22A<br />
| plasma membrane (GO:0005886)<br />
| IDA<br />
|<br />
|<br />
| <br />
|-<br />
| SLC22A<br />
| dendrite (GO:0030425)<br />
| IDA<br />
|<br />
| part_of(cholinergic neuron), part_of (calyx of adult mushroom body)<br />
|<br />
|- <br />
| SLC22A<br />
| dendrite (GO:0030425)<br />
| IDA<br />
| <br />
| part_of(a/b MBn),part_of(a'/b' MBn)<br />
|<br />
|- <br />
| SLC22A<br />
| NT:dendrite plasma membrane<br />
| IC<br />
| GO:0030425,GO:0005277,GO:0051630<br />
| part_of(a/b MBn),part_of(a'/b' MBn)<br />
| Would need to use GO_REF:0000036<br />
|- <br />
|}<br />
<br />
*Other comments: "Not clear what the differences between memory retention and learning."<br />
I really don't understand the stuff about interference and forgetting.<br />
Overall I'm not fully convinced the set of memory BP annotations is self-consistent and sensible.<br />
Annotations like increased/decreased olfactory memory for RNAi and overexpressors should be phenotype annotation<br />
<br />
==Protein Binding Annotations==<br />
*Review [http://geneontology.org/page/go-annotation-conventions#binding Protein Binding Annotation Guidelines]<br />
*The following statement in our protein binding annotation guidelines does not hold for some annotation groups:<br />
The 'with' column (8) and the annotation extension column (16) should be used only for direct interactions and only when the binding <br />
relationship is not already included in the GO term and/or definition. See "column 16 documentation for relationship types to use when <br />
adding IDs in the annotation extension column (16). <br />
*Some groups do annotate protein binding from experiments that do not assess direct physical interactions, such as co-IP.<br />
*Proposal has been made to update documentation to be clearer about how the GOC members annotate protein binding.<br />
*Any objections to updating the documentation? Suggestions for clearer wording?<br />
<br />
=Minutes=<br />
*On call: Alice, Bob, David OS, Edith, Elena, Giulia, Helen, Kimberly, Li, Melanie, Midori, Paola, Petra, Rebecca, Sabrina, Shur-Jen, Stacia, Stan, Tanya<br />
<br />
==Annotation Consistency Exercise==<br />
*Molecular Function and Cellular Component annotations were all generally the same; no problems there<br />
*Biological Process annotations generated more discussion<br />
**Consensus seemed to be that this is an area of the ontology that would benefit from further development, with input from experts in the learning and memory field <br />
***There is a NeuroBehavior Ontology - who uses that ontology and would it be helpful for GO to work with that? <br />
**Paper raises the issue of what specific aspects of memory we want to capture in GO<br />
***Memory acquisition?<br />
***Memory retention?<br />
***Memory interference?<br />
**We also want to make sure we understand how the results of assays used to assess different aspects of learning and memory inform BP term choice<br />
**Tentative plan: compare learning and memory papers across organisms to find commonalities that could be used to develop GO BP<br />
<br />
==Protein Binding Documentation==<br />
*Review of different group's practices for capturing protein binding annotations indicates that there are still some differences with respect to what interactions groups capture<br />
*Some groups are more inclusive than others based largely on methodology and interpretation of author intent<br />
*Another contributing factor is whether or not groups have another mechanism in place, e.g. BioGrid or IntAct, to capture these physical interactions. Would be good to follow-up with IntAct to confirm what interactions they export to GOC and why.<br />
<br />
===== I asked Sandra for more details and she said:<br />
<br />
From http://www.ebi.ac.uk/intact/about/faq?conversationContext=5#8<br />
<br />
'''How are binary interactions selected for export to UniProtKB/GOA records?'''<br />
All binary interactions evidences in the IntAct database, including those generated by Spoke expansion of co-complex data, are clustered to produce a non- redundant set of protein pairs. Each binary pair is then scored, using a simple addition of the cumulated value of a weighted score for the interaction detection method and the interaction type for each interaction evidence associated with that binary pair. Only experimental data is scored, inferred interactions, for example, would not be scored, and any low confidence data, or data manually tagged by a curator for exclusion from the process, are also not scored. Isoforms and post-processed protein chains are regarded as individual proteins for scoring purposes. <br />
Score weightings were determined using the PSI-MI CV<br />
<br />
Once the interactions have been scored, a cut-off filter of 9 has been established, below which the interaction is not exported to UniProtKB and to the Gene Ontology annotation files. Additional rules ensure that any protein pair scoring above 9 must also include at least one evidence of a binary pair, excluding spoke expanded data, before export to UniProtKB/GOA.<br />
<br />
These criteria ensure that<br />
* Only experimental data is used for making the decision to export the protein pair to UniProtKB/GOA as a true binary interacting pair<br />
* The export decision is always based on at least two pieces of experimental data. A single evidence cannot score highly enough to trigger an export<br />
* An export cannot be triggered if the protein pair only ever co-occurs in larger complexes, there must be at least one evidence that the proteins are probably in physical contact.<br />
<br />
IMEx will only call an interaction 'direct' when performed with 2 purified molecules in vitro so any method using whole cells or cell lysates would not be regarded as direct. The described methodology will give you binary i.e. either direct or involved in the same small complex. =====<br />
<br />
*Consensus was, though, that this is an area of annotation where it is okay to have some differences but the documentation should reflect this<br />
*ACTION ITEM: Draft new statement explaining diverse GOC approach to protein binding annotations. Review at a future call to make sure everyone is okay with it.<br />
<br />
[[Category: Annotation Working Group]]</div>MChttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-06-28&diff=61099Annotation Conf. Call 2016-06-282016-06-30T14:29:49Z<p>MC: </p>
<hr />
<div>=Bluejeans URL=<br />
https://bluejeans.com/993661940<br />
<br />
=Agenda=<br />
==Annotation Consistency Exercise==<br />
*[http://www.ncbi.nlm.nih.gov/pubmed/27146270 Drosophila SLC22A Transporter Is a Memory Suppressor Gene that Influences Cholinergic Neurotransmission to the Mushroom Bodies.]<br />
'''Abstract''' The mechanisms that constrain memory formation are of special interest because they provide insights into the brain's memory management systems and potential avenues for correcting cognitive disorders. RNAi knockdown in the Drosophila mushroom body neurons (MBn) of a newly discovered memory suppressor gene, Solute Carrier DmSLC22A, a member of the organic cation transporter family, enhances olfactory memory expression, while overexpression inhibits it. The protein localizes to the dendrites of the MBn, surrounding the presynaptic terminals of cholinergic afferent fibers from projection neurons (Pn). Cell-based expression assays show that this plasma membrane protein transports cholinergic compounds with the highest affinity among several in vitro substrates. Feeding flies choline or inhibiting acetylcholinesterase in Pn enhances memory, an effect blocked by overexpression of the transporter in the MBn. The data argue that DmSLC22A is a memory suppressor protein that limits memory formation by helping to terminate cholinergic neurotransmission at the Pn:MBn synapse.<br />
*'''How to capture biological process aspects of memory?'''<br />
**The paper identifies a ‘memory suppressor gene’ (Solute Carrier 22A of Drosophila (DmSLC22A) (FlyBase:CG7442; FBgn0037140). How to capture the biology described - memory, learning, conditioning? What new terms are needed to capture the process? Alternatively, is it better to capture these experiments only as phenotypes?<br />
** Leave the expression/mechanistic sections and have a look at these four sections of this paper:<br />
***Drosophila CG7442 Is a Memory Suppressor Gene Functioning in MBn and DAn<br />
***Drosophila CG7442 Overexpression Impairs Memory<br />
***DmSLC22A Regulates Both Memory Acquisition and Retention<br />
***DmSLC22A Modulates Memory Strength by Regulating Cholinergic Neurotransmission in the MB Calyx<br />
<br />
'''Annotations'''<br />
{| border=1 cell-padding=5 cell-spacing=10<br />
|-<br />
! Gene/Marker Name<br />
! GO term<br />
! Evidence Code<br />
! With/From<br />
! Annotation Extension <br />
! Comment<br />
|-<br />
|Biological Process<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of olfactory memory retention<br />
| <br />
| <br />
|<br />
|(not forgetting)?<br />
|-<br />
| SLC22A<br />
| NT:positive regulation of memory acquisition<br />
| <br />
| <br />
|<br />
|(learning?)<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory retention<br />
| <br />
| <br />
|<br />
|(memory)<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:regulation of memory acquisition<br />
| IMP <br />
| <br />
| <br />
|<br />
|-<br />
| SLC22A<br />
| NT:regulation of memory retention<br />
| IMP<br />
| <br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of anesthesia-resistant memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| regulation of olfactory learning (GO:0090328)<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:positive regulation of rate of learning<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| AChE<br />
| NT:negative regulation of memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IGI<br />
| AChE<br />
|<br />
|<br />
|-<br />
| AChE<br />
| NT:negative regulation of memory<br />
| IGI<br />
| SLC22A<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| negative regulation of synaptic transmission, cholinergic (GO:0032223)<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:neurotransmitter transport involved in regulation of memory<br />
| IC<br />
| GO:0005277|GO:0015220|GO:NT: negative regulation of memory<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:cholinergic synaptic transmission involved in regulation of memory<br />
| <br />
| <br />
|<br />
| This one's a "maybe"<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IMP/IDA<br />
| <br />
| part_of (olfactory learning)<br />
|<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of olfactory learning<br />
| IMP/IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| memory (GO:0007613)<br />
| IMP<br />
| <br />
| occurs_in(a/b MBn), occurs_in(a'/b' MBn), happens_during(adult life stage)|occurs_in(DAn),happens_during(adult life stage)<br />
|<br />
|- <br />
| SLC22A<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine uptake involved in memory acquisition rate enhancement?<br />
| <br />
| <br />
| occurs_in(a/b MBn), occurs_in(a'/b' MBn), happens_during(adult life stage)|occurs_in(DAn),happens_during(adult life stage)<br />
| <br />
|- <br />
| SLC22A<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine uptake involved in memory retention suppression?<br />
| <br />
| occurs_in(a/b MBn), occurs_in(a'/b' MBn), happens_during(adult life stage)|occurs_in(DAn),happens_during(adult life stage)<br />
|<br />
|<br />
|- <br />
| AChE<br />
| memory (GO:0007613)<br />
| IMP<br />
|<br />
|<br />
| How to express an extracellular synaptic region between two different neurons via annotation extensions?<br />
|- <br />
| AChE<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine catabolism involved in memory acquisition rate enhancement?<br />
| <br />
|<br />
|<br />
|<br />
|- <br />
| AChE<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine catabolism involved in memory retention suppression?<br />
| <br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of olfactory memory <br />
| IMP<br />
| <br />
| acts_on_population_of mushroom body neuron; dopamine neuron<br />
| olfactory memory,pos. reg., children of olfactory learning (GO:0008355). From Fig1,2 (MbN and DpN need to be component terms).<br />
|- <br />
| SLC22A<br />
| NT:positive regulation of olfactory learning<br />
| IMP<br />
| <br />
|<br />
| child of olfactory learning (GO:0008355). From fig 5c. Rate of learning is impaired in knockdown.<br />
|- <br />
| SLC22A<br />
| regulation of synaptic transmission, cholinergic (GO:0032222)<br />
| IMP<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| NT: choline uptake?<br />
| IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| dopamine uptake (GO:0015872)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| histamine uptake (GO:0051615)<br />
| IDA<br />
| <br />
| <br />
|<br />
|- <br />
| SLC22A<br />
| NT: amino-acid betaine uptake?<br />
| IDA<br />
| <br />
|<br />
|<br />
|-<br />
| Molecular Function<br />
|-<br />
| SLC22A<br />
| amino-acid betaine transmembrane transporter activity (GO:0015199)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity (GO:0005277)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| choline transmembrane transporter activity (GO:0015220)<br />
| IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| dopamine transmembrane transporter activity (GO:0005329)<br />
| IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| NT: histamine transmembrane transporter activity<br />
| IDA<br />
| <br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity (GO:0005277)<br />
| IDA/IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| choline transmembrane transporter activity<br />
| IDA <br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity<br />
| IDA<br />
|<br />
| <br />
|<br />
|- <br />
| SLC22A<br />
| choline transmembrane transporter activity (GO:0015220)<br />
| IDA<br />
| <br />
| <br />
| <br />
|- <br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity (GO:0005277)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| Cellular Component<br />
|-<br />
| SLC22A<br />
| dendrite (GO:0030425)<br />
| IDA<br />
| <br />
| part_of (calyx of adult mushroom body)<br />
|<br />
|- <br />
| SLC22A<br />
| plasma membrane (GO:0005886)<br />
| IDA<br />
|<br />
|<br />
| <br />
|-<br />
| SLC22A<br />
| dendrite (GO:0030425)<br />
| IDA<br />
|<br />
| part_of(cholinergic neuron), part_of (calyx of adult mushroom body)<br />
|<br />
|- <br />
| SLC22A<br />
| dendrite (GO:0030425)<br />
| IDA<br />
| <br />
| part_of(a/b MBn),part_of(a'/b' MBn)<br />
|<br />
|- <br />
| SLC22A<br />
| NT:dendrite plasma membrane<br />
| IC<br />
| GO:0030425,GO:0005277,GO:0051630<br />
| part_of(a/b MBn),part_of(a'/b' MBn)<br />
| Would need to use GO_REF:0000036<br />
|- <br />
|}<br />
<br />
*Other comments: "Not clear what the differences between memory retention and learning."<br />
I really don't understand the stuff about interference and forgetting.<br />
Overall I'm not fully convinced the set of memory BP annotations is self-consistent and sensible.<br />
Annotations like increased/decreased olfactory memory for RNAi and overexpressors should be phenotype annotation<br />
<br />
==Protein Binding Annotations==<br />
*Review [http://geneontology.org/page/go-annotation-conventions#binding Protein Binding Annotation Guidelines]<br />
*The following statement in our protein binding annotation guidelines does not hold for some annotation groups:<br />
The 'with' column (8) and the annotation extension column (16) should be used only for direct interactions and only when the binding <br />
relationship is not already included in the GO term and/or definition. See "column 16 documentation for relationship types to use when <br />
adding IDs in the annotation extension column (16). <br />
*Some groups do annotate protein binding from experiments that do not assess direct physical interactions, such as co-IP.<br />
*Proposal has been made to update documentation to be clearer about how the GOC members annotate protein binding.<br />
*Any objections to updating the documentation? Suggestions for clearer wording?<br />
<br />
=Minutes=<br />
*On call: Alice, Bob, David OS, Edith, Elena, Giulia, Helen, Kimberly, Li, Melanie, Midori, Paola, Petra, Rebecca, Sabrina, Shur-Jen, Stacia, Stan, Tanya<br />
<br />
==Annotation Consistency Exercise==<br />
*Molecular Function and Cellular Component annotations were all generally the same; no problems there<br />
*Biological Process annotations generated more discussion<br />
**Consensus seemed to be that this is an area of the ontology that would benefit from further development, with input from experts in the learning and memory field <br />
***There is a NeuroBehavior Ontology - who uses that ontology and would it be helpful for GO to work with that? <br />
**Paper raises the issue of what specific aspects of memory we want to capture in GO<br />
***Memory acquisition?<br />
***Memory retention?<br />
***Memory interference?<br />
**We also want to make sure we understand how the results of assays used to assess different aspects of learning and memory inform BP term choice<br />
**Tentative plan: compare learning and memory papers across organisms to find commonalities that could be used to develop GO BP<br />
<br />
==Protein Binding Documentation==<br />
*Review of different group's practices for capturing protein binding annotations indicates that there are still some differences with respect to what interactions groups capture<br />
*Some groups are more inclusive than others based largely on methodology and interpretation of author intent<br />
*Another contributing factor is whether or not groups have another mechanism in place, e.g. BioGrid or IntAct, to capture these physical interactions. Would be good to follow-up with IntAct to confirm what interactions they export to GOC and why.<br />
<br />
===== I asked Sandra for more details and she said:<br />
<br />
From http://www.ebi.ac.uk/intact/about/faq?conversationContext=5#8<br />
> How are binary interactions selected for export to UniProtKB/GOA records?<br />
><br />
> All binary interactions evidences in the IntAct database, including those generated by Spoke expansion of co-complex data, are clustered to produce a non- redundant set of protein pairs. Each binary pair is then scored, using a simple addition of the cumulated value of a weighted score for the interaction detection method and the interaction type for each interaction evidence associated with that binary pair. Only experimental data is scored, inferred interactions, for example, would not be scored, and any low confidence data, or data manually tagged by a curator for exclusion from the process, are also not scored. Isoforms and post-processed protein chains are regarded as individual proteins for scoring purposes. <br />
Score weightings were determined using the PSI-MI CV<br />
<br />
Once the interactions have been scored, a cut-off filter of 9 has been established, below which the interaction is not exported to UniProtKB and to the Gene Ontology annotation files. Additional rules ensure that any protein pair scoring above 9 must also include at least one evidence of a binary pair, excluding spoke expanded data, before export to UniProtKB/GOA.<br />
<br />
These criteria ensure that<br />
* Only experimental data is used for making the decision to export the protein pair to UniProtKB/GOA as a true binary interacting pair<br />
* The export decision is always based on at least two pieces of experimental data. A single evidence cannot score highly enough to trigger an export<br />
* An export cannot be triggered if the protein pair only ever co-occurs in larger complexes, there must be at least one evidence that the proteins are probably in physical contact.<br />
<br />
IMEx will only call an interaction 'direct' when performed with 2 purified molecules in vitro so any method using whole cells or cell lysates would not be regarded as direct. The described methodology will give you binary i.e. either direct or involved in the same small complex. =====<br />
<br />
*Consensus was, though, that this is an area of annotation where it is okay to have some differences but the documentation should reflect this<br />
*ACTION ITEM: Draft new statement explaining diverse GOC approach to protein binding annotations. Review at a future call to make sure everyone is okay with it.<br />
<br />
[[Category: Annotation Working Group]]</div>MChttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-06-28&diff=61098Annotation Conf. Call 2016-06-282016-06-30T14:29:07Z<p>MC: </p>
<hr />
<div>=Bluejeans URL=<br />
https://bluejeans.com/993661940<br />
<br />
=Agenda=<br />
==Annotation Consistency Exercise==<br />
*[http://www.ncbi.nlm.nih.gov/pubmed/27146270 Drosophila SLC22A Transporter Is a Memory Suppressor Gene that Influences Cholinergic Neurotransmission to the Mushroom Bodies.]<br />
'''Abstract''' The mechanisms that constrain memory formation are of special interest because they provide insights into the brain's memory management systems and potential avenues for correcting cognitive disorders. RNAi knockdown in the Drosophila mushroom body neurons (MBn) of a newly discovered memory suppressor gene, Solute Carrier DmSLC22A, a member of the organic cation transporter family, enhances olfactory memory expression, while overexpression inhibits it. The protein localizes to the dendrites of the MBn, surrounding the presynaptic terminals of cholinergic afferent fibers from projection neurons (Pn). Cell-based expression assays show that this plasma membrane protein transports cholinergic compounds with the highest affinity among several in vitro substrates. Feeding flies choline or inhibiting acetylcholinesterase in Pn enhances memory, an effect blocked by overexpression of the transporter in the MBn. The data argue that DmSLC22A is a memory suppressor protein that limits memory formation by helping to terminate cholinergic neurotransmission at the Pn:MBn synapse.<br />
*'''How to capture biological process aspects of memory?'''<br />
**The paper identifies a ‘memory suppressor gene’ (Solute Carrier 22A of Drosophila (DmSLC22A) (FlyBase:CG7442; FBgn0037140). How to capture the biology described - memory, learning, conditioning? What new terms are needed to capture the process? Alternatively, is it better to capture these experiments only as phenotypes?<br />
** Leave the expression/mechanistic sections and have a look at these four sections of this paper:<br />
***Drosophila CG7442 Is a Memory Suppressor Gene Functioning in MBn and DAn<br />
***Drosophila CG7442 Overexpression Impairs Memory<br />
***DmSLC22A Regulates Both Memory Acquisition and Retention<br />
***DmSLC22A Modulates Memory Strength by Regulating Cholinergic Neurotransmission in the MB Calyx<br />
<br />
'''Annotations'''<br />
{| border=1 cell-padding=5 cell-spacing=10<br />
|-<br />
! Gene/Marker Name<br />
! GO term<br />
! Evidence Code<br />
! With/From<br />
! Annotation Extension <br />
! Comment<br />
|-<br />
|Biological Process<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of olfactory memory retention<br />
| <br />
| <br />
|<br />
|(not forgetting)?<br />
|-<br />
| SLC22A<br />
| NT:positive regulation of memory acquisition<br />
| <br />
| <br />
|<br />
|(learning?)<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory retention<br />
| <br />
| <br />
|<br />
|(memory)<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:regulation of memory acquisition<br />
| IMP <br />
| <br />
| <br />
|<br />
|-<br />
| SLC22A<br />
| NT:regulation of memory retention<br />
| IMP<br />
| <br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of anesthesia-resistant memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| regulation of olfactory learning (GO:0090328)<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:positive regulation of rate of learning<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| AChE<br />
| NT:negative regulation of memory<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IGI<br />
| AChE<br />
|<br />
|<br />
|-<br />
| AChE<br />
| NT:negative regulation of memory<br />
| IGI<br />
| SLC22A<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| negative regulation of synaptic transmission, cholinergic (GO:0032223)<br />
| IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:neurotransmitter transport involved in regulation of memory<br />
| IC<br />
| GO:0005277|GO:0015220|GO:NT: negative regulation of memory<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| NT:cholinergic synaptic transmission involved in regulation of memory<br />
| <br />
| <br />
|<br />
| This one's a "maybe"<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of memory<br />
| IMP/IDA<br />
| <br />
| part_of (olfactory learning)<br />
|<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of olfactory learning<br />
| IMP/IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| memory (GO:0007613)<br />
| IMP<br />
| <br />
| occurs_in(a/b MBn), occurs_in(a'/b' MBn), happens_during(adult life stage)|occurs_in(DAn),happens_during(adult life stage)<br />
|<br />
|- <br />
| SLC22A<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine uptake involved in memory acquisition rate enhancement?<br />
| <br />
| <br />
| occurs_in(a/b MBn), occurs_in(a'/b' MBn), happens_during(adult life stage)|occurs_in(DAn),happens_during(adult life stage)<br />
| <br />
|- <br />
| SLC22A<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine uptake involved in memory retention suppression?<br />
| <br />
| occurs_in(a/b MBn), occurs_in(a'/b' MBn), happens_during(adult life stage)|occurs_in(DAn),happens_during(adult life stage)<br />
|<br />
|<br />
|- <br />
| AChE<br />
| memory (GO:0007613)<br />
| IMP<br />
|<br />
|<br />
| How to express an extracellular synaptic region between two different neurons via annotation extensions?<br />
|- <br />
| AChE<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine catabolism involved in memory acquisition rate enhancement?<br />
| <br />
|<br />
|<br />
|<br />
|- <br />
| AChE<br />
| NT: negative regulation of acetylcholine receptor signaling pathway via acetylcholine catabolism involved in memory retention suppression?<br />
| <br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| NT:negative regulation of olfactory memory <br />
| IMP<br />
| <br />
| acts_on_population_of mushroom body neuron; dopamine neuron<br />
| olfactory memory,pos. reg., children of olfactory learning (GO:0008355). From Fig1,2 (MbN and DpN need to be component terms).<br />
|- <br />
| SLC22A<br />
| NT:positive regulation of olfactory learning<br />
| IMP<br />
| <br />
|<br />
| child of olfactory learning (GO:0008355). From fig 5c. Rate of learning is impaired in knockdown.<br />
|- <br />
| SLC22A<br />
| regulation of synaptic transmission, cholinergic (GO:0032222)<br />
| IMP<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| NT: choline uptake?<br />
| IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| dopamine uptake (GO:0015872)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| histamine uptake (GO:0051615)<br />
| IDA<br />
| <br />
| <br />
|<br />
|- <br />
| SLC22A<br />
| NT: amino-acid betaine uptake?<br />
| IDA<br />
| <br />
|<br />
|<br />
|-<br />
| Molecular Function<br />
|-<br />
| SLC22A<br />
| amino-acid betaine transmembrane transporter activity (GO:0015199)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity (GO:0005277)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| choline transmembrane transporter activity (GO:0015220)<br />
| IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| dopamine transmembrane transporter activity (GO:0005329)<br />
| IDA<br />
|<br />
|<br />
|<br />
|- <br />
| SLC22A<br />
| NT: histamine transmembrane transporter activity<br />
| IDA<br />
| <br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity (GO:0005277)<br />
| IDA/IMP<br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| choline transmembrane transporter activity<br />
| IDA <br />
|<br />
|<br />
|<br />
|-<br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity<br />
| IDA<br />
|<br />
| <br />
|<br />
|- <br />
| SLC22A<br />
| choline transmembrane transporter activity (GO:0015220)<br />
| IDA<br />
| <br />
| <br />
| <br />
|- <br />
| SLC22A<br />
| acetylcholine transmembrane transporter activity (GO:0005277)<br />
| IDA<br />
| <br />
|<br />
|<br />
|- <br />
| Cellular Component<br />
|-<br />
| SLC22A<br />
| dendrite (GO:0030425)<br />
| IDA<br />
| <br />
| part_of (calyx of adult mushroom body)<br />
|<br />
|- <br />
| SLC22A<br />
| plasma membrane (GO:0005886)<br />
| IDA<br />
|<br />
|<br />
| <br />
|-<br />
| SLC22A<br />
| dendrite (GO:0030425)<br />
| IDA<br />
|<br />
| part_of(cholinergic neuron), part_of (calyx of adult mushroom body)<br />
|<br />
|- <br />
| SLC22A<br />
| dendrite (GO:0030425)<br />
| IDA<br />
| <br />
| part_of(a/b MBn),part_of(a'/b' MBn)<br />
|<br />
|- <br />
| SLC22A<br />
| NT:dendrite plasma membrane<br />
| IC<br />
| GO:0030425,GO:0005277,GO:0051630<br />
| part_of(a/b MBn),part_of(a'/b' MBn)<br />
| Would need to use GO_REF:0000036<br />
|- <br />
|}<br />
<br />
*Other comments: "Not clear what the differences between memory retention and learning."<br />
I really don't understand the stuff about interference and forgetting.<br />
Overall I'm not fully convinced the set of memory BP annotations is self-consistent and sensible.<br />
Annotations like increased/decreased olfactory memory for RNAi and overexpressors should be phenotype annotation<br />
<br />
==Protein Binding Annotations==<br />
*Review [http://geneontology.org/page/go-annotation-conventions#binding Protein Binding Annotation Guidelines]<br />
*The following statement in our protein binding annotation guidelines does not hold for some annotation groups:<br />
The 'with' column (8) and the annotation extension column (16) should be used only for direct interactions and only when the binding <br />
relationship is not already included in the GO term and/or definition. See "column 16 documentation for relationship types to use when <br />
adding IDs in the annotation extension column (16). <br />
*Some groups do annotate protein binding from experiments that do not assess direct physical interactions, such as co-IP.<br />
*Proposal has been made to update documentation to be clearer about how the GOC members annotate protein binding.<br />
*Any objections to updating the documentation? Suggestions for clearer wording?<br />
<br />
=Minutes=<br />
*On call: Alice, Bob, David OS, Edith, Elena, Giulia, Helen, Kimberly, Li, Melanie, Midori, Paola, Petra, Rebecca, Sabrina, Shur-Jen, Stacia, Stan, Tanya<br />
<br />
==Annotation Consistency Exercise==<br />
*Molecular Function and Cellular Component annotations were all generally the same; no problems there<br />
*Biological Process annotations generated more discussion<br />
**Consensus seemed to be that this is an area of the ontology that would benefit from further development, with input from experts in the learning and memory field <br />
***There is a NeuroBehavior Ontology - who uses that ontology and would it be helpful for GO to work with that? <br />
**Paper raises the issue of what specific aspects of memory we want to capture in GO<br />
***Memory acquisition?<br />
***Memory retention?<br />
***Memory interference?<br />
**We also want to make sure we understand how the results of assays used to assess different aspects of learning and memory inform BP term choice<br />
**Tentative plan: compare learning and memory papers across organisms to find commonalities that could be used to develop GO BP<br />
<br />
==Protein Binding Documentation==<br />
*Review of different group's practices for capturing protein binding annotations indicates that there are still some differences with respect to what interactions groups capture<br />
*Some groups are more inclusive than others based largely on methodology and interpretation of author intent<br />
*Another contributing factor is whether or not groups have another mechanism in place, e.g. BioGrid or IntAct, to capture these physical interactions. Would be good to follow-up with IntAct to confirm what interactions they export to GOC and why.<br />
<br />
I asked Sandra for more details and she said:<br />
<br />
From http://www.ebi.ac.uk/intact/about/faq?conversationContext=5#8<br />
> How are binary interactions selected for export to UniProtKB/GOA records?<br />
><br />
> All binary interactions evidences in the IntAct database, including those generated by Spoke expansion of co-complex data, are clustered to produce a non- redundant set of protein pairs. Each binary pair is then scored, using a simple addition of the cumulated value of a weighted score for the interaction detection method and the interaction type for each interaction evidence associated with that binary pair. Only experimental data is scored, inferred interactions, for example, would not be scored, and any low confidence data, or data manually tagged by a curator for exclusion from the process, are also not scored. Isoforms and post-processed protein chains are regarded as individual proteins for scoring purposes. <br />
Score weightings were determined using the PSI-MI CV<br />
<br />
Once the interactions have been scored, a cut-off filter of 9 has been established, below which the interaction is not exported to UniProtKB and to the Gene Ontology annotation files. Additional rules ensure that any protein pair scoring above 9 must also include at least one evidence of a binary pair, excluding spoke expanded data, before export to UniProtKB/GOA.<br />
<br />
These criteria ensure that<br />
* Only experimental data is used for making the decision to export the protein pair to UniProtKB/GOA as a true binary interacting pair<br />
* The export decision is always based on at least two pieces of experimental data. A single evidence cannot score highly enough to trigger an export<br />
* An export cannot be triggered if the protein pair only ever co-occurs in larger complexes, there must be at least one evidence that the proteins are probably in physical contact.<br />
<br />
IMEx will only call an interaction 'direct' when performed with 2 purified molecules in vitro so any method using whole cells or cell lysates would not be regarded as direct. The described methodology will give you binary i.e. either direct or involved in the same small complex.<br />
<br />
*Consensus was, though, that this is an area of annotation where it is okay to have some differences but the documentation should reflect this<br />
*ACTION ITEM: Draft new statement explaining diverse GOC approach to protein binding annotations. Review at a future call to make sure everyone is okay with it.<br />
<br />
[[Category: Annotation Working Group]]</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2016-07-06&diff=61062Manager Call 2016-07-062016-06-24T10:48:43Z<p>MC: Created page with "Previous call minutes Category:GO Managers Meetings [http://wiki.geneontology.org/index.php/Manager_Call_2016-06-1 Minutes from the previous ..."</p>
<hr />
<div>[[Manager_Call_2016-06-15|Previous call minutes]]<br />
<br />
[[Category:GO Managers Meetings ]]<br />
[http://wiki.geneontology.org/index.php/Manager_Call_2016-06-1 Minutes from the previous GO Managers Meeting can be found here].<br />
GO Managers meet using the GO Phone Conference Line from Jackson Laboratory.<br />
<br />
= Agenda =<br />
==Identifier space in GO annotations (GAF, GPAD)==<br />
<br />
We discussed to allow all IDs to be used in AE, provided we can get GPIs from everyone, ticket filed: https://github.com/geneontology/go-site/issues/194<br />
<br />
I (Melanie) talked with Tony S., and as discussed during the data capture call our GPI files don't include cross-references (too many of them to do so). We could envision a solution if it were possible to get a list of those cross-references that are needed specifically, and create a GPI with only those.<br />
<br />
== Protein Complexes ==<br />
<br />
We discussed propagating functions, BP and CC annotations on a complex to the individual gene products, using the contibutes_to qualifier.<br />
<br />
I (Melanie) discussed this with Claire, Sandra and Birgit and there are concerns that while ok for BP and CC, the functions (using the contributes_to qualifier) could be confusing for users as a lot of people don't see these qualifiers - they'll only get as far a Protein X has a catalytic function associated with it and stop there. <br />
<br />
= Minutes =<br />
<br />
'''Attendees''':<br />
<br />
'''Regrets''': <br />
<br />
'''Agenda''': Moni | '''Minutes''':</div>MChttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-06-09&diff=60994Ontology meeting 2016-06-092016-06-10T08:26:09Z<p>MC: </p>
<hr />
<div>Attendees: Chris, Heiko, Tanya, Dvid OS, David H, Melanie<br />
Regrets: Paola<br />
Minutes: Melanie<br />
<br />
<br />
===ETINEs update===<br />
<br />
Chris, Heiko and David OS to report.<br />
<br />
===Minutes===<br />
<br />
==ETINES== <br />
A bit more work than planned but is happening. Inferred axioms would show in TG but would not actually be part of the commit. They'll be added in by the regular inference job.<br />
<br />
==Relations==<br />
GO rel should just be used for AE - no real pathway to keep relations in sync with RO_pending<br />
Chris: RO pending should go away, relations in the ontology should go into RO<br />
DOS: needs bit of work for sync with go rel<br />
<br />
=> RO should be primary space, with all axioms but for GO specific usage including local domain/range. May need to add an AP "GO usage" for some of those which could then live in RO<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>MChttps://wiki.geneontology.org/index.php?title=Manager_Call_2015-05-18&diff=60827Manager Call 2015-05-182016-05-17T10:19:13Z<p>MC: /* Agenda */</p>
<hr />
<div>=Agenda=<br />
<br />
==IDs in column 2 and 16==<br />
Progress on resolution still needed for what ID types we can use in AE for ‘regulation of transcription/translation/expression’ relation.<br />
After UCL/GOA discussion: Need to have motivation and impact detailed “Ruth can’t write on behalf of LEGO” before it be sent out to wider consortium. Need deadline (Ruth sent proposal a week ago)<br />
<br />
=Minutes=<br />
Text begins here.<br />
<br />
<br />
[[Category:GO Managers Meetings ]]</div>MC