Difference between revisions of "April 2015 GOC Teleconference Agenda and Logistics"

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* Call-in information / screen sharing: We will use Bluejeans teleconferencing software for audio and video and WILL NOT use the GO conference line. We will use Bluejeans for screen sharing also. If attendees have a question they should post it on the chat window and they will answered in order.
 
* Call-in information / screen sharing: We will use Bluejeans teleconferencing software for audio and video and WILL NOT use the GO conference line. We will use Bluejeans for screen sharing also. If attendees have a question they should post it on the chat window and they will answered in order.
 
** Link for the Bluejeans meeting: https://bluejeans.com/626682538
 
** Link for the Bluejeans meeting: https://bluejeans.com/626682538
 +
* Minutes available on [https://docs.google.com/document/d/1ji04ZKPxRT9Do-PR52tAnD9pR_lMnP5FaRtYXpqvhaU/edit?usp=sharing Google Document here].
  
 
==Agenda==
 
==Agenda==
 
===Introduction (11:00 - 11:05) (GO PI's)===
 
===Introduction (11:00 - 11:05) (GO PI's)===
 
===Discussion of priorities for calendar year 2015 (11:05 - 11:30) (GO PI's)===
 
===Discussion of priorities for calendar year 2015 (11:05 - 11:30) (GO PI's)===
 +
*  Common Annotation Framework/Environment (CAF/E)
 +
** Goal: LEGO annotation and text mining support in production  (CAF/E)
 +
** Milestone 1: version of each component that can be used by curation test team
 +
** Milestone 2: Integration of components into Common Annotation Framework/Environment
 +
** Preliminary results on javascript PAINT as part of CAF/E
 +
* Phylogenetic annotation
 +
** meet production goals: annotate 1/3 of genes this grant year
 +
** software for updating annotations to reflect changes in gene sets, experimental annotations and ontology
 +
* Metrics for value/impact of GO data
 +
** Categorize and quantify usage of GO in published papers
 +
** Annotation quality metric and assessment
 +
* Monitoring and assessing our support for users
 +
** User survey
 +
** Website usability study
 +
** Enrichment Analysis: Documentation, UI improvement
  
===Talk by Paul Pavlidis, UBC (11:30 - 12:05)===
+
===Talk by Paul Pavlidis, UBC (11:30 - 12:15)===
 
====The use of GO in data analysis: can we raise the bar?====
 
====The use of GO in data analysis: can we raise the bar?====
 
* [http://pavlab.chibi.ubc.ca Paul Pavlidis's lab website]
 
* [http://pavlab.chibi.ubc.ca Paul Pavlidis's lab website]
  
===Other agenda items (12:05 - 12:30)===
+
===Other agenda items (12:15 - 12:30)===
 
* Update on AmiGO/GO website Behave testing framework (Mary/Seth/Chris)
 
* Update on AmiGO/GO website Behave testing framework (Mary/Seth/Chris)
* Annotating complexes as objects, producing a separate GAF for complexes, educating users about these annotations
+
** Mary slides [[File:AutomatedTestingAmiGO2.pdf]]
* Training curators on LEGO
+
* Upcoming Consortium meeting in Washington DC
  
 
==Attendees==
 
==Attendees==
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|The Jackson Laboratory, MGI
 
|The Jackson Laboratory, MGI
 
|-
 
|-
|Kimberly
+
|Harold Drabkin
 +
|The Jackson Laboratory, MGI
 +
|-
 +
|Judy Blake
 +
|The Jackson Laboratory
 +
|-
 +
|Mary Dolan
 +
|The Jackson Laboratory, MGI
 +
|-
 +
| Li Ni
 +
| The Jackson Laboratory, MGI
 +
|-
 +
| Dmitry Sitnikov
 +
| The Jackson Laboratory, MGI
 +
|-
 +
| Karen Christie
 +
| The Jackson Laboratory, MGI
 +
|-
 +
|Kimberly Van Auken
 
|Cal Tech, Wormbase
 
|Cal Tech, Wormbase
 
|-
 
|-
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|-
 
|-
 
| Eva Huala
 
| Eva Huala
 +
| Phoenix Bioinformatics, TAIR
 +
|-
 +
|Donghui Li
 
| Phoenix Bioinformatics, TAIR
 
| Phoenix Bioinformatics, TAIR
 
|-
 
|-
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| Pascale Gaudet
 
| Pascale Gaudet
 
| GOC / neXtProt
 
| GOC / neXtProt
 +
|-
 +
| Marc Feuermann
 +
| Swiss-Prot
 
|-
 
|-
 
| Birgit Meldal
 
| Birgit Meldal
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|-
 
|-
 
| Aleks Shypitsyna
 
| Aleks Shypitsyna
 +
| UniProt-GOA, EMBL-EBI
 +
|-
 +
| Penelope Garmiri
 
| UniProt-GOA, EMBL-EBI
 
| UniProt-GOA, EMBL-EBI
 
|-
 
|-
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| UCL
 
| UCL
 
|-
 
|-
|}
+
| Ruth Lovering
 +
| UCL
 +
|-
 +
| Rachael Huntley
 +
| UCL
 +
|-
 +
| Tom Hayman
 +
| RGD
 +
|-
 +
| Mary Shimoyama
 +
| RGD
 +
|-
 +
|Shur-Jen Wang
 +
|RGD
 +
|-
 +
|Stan Laulederkind
 +
|RGD
 +
|-
 +
| Helen Attrill
 +
| FlyBase
 +
|-
 +
| Midori Harris
 +
| PomBase
 +
|-
 +
| Val Wood
 +
| PomBase
 +
|-
 +
| Paola Roncaglia
 +
| EMBL-EBI
 +
|-}

Latest revision as of 12:28, 15 April 2015


Logistics

  • Call runs April 1, from 11am to 12:30pm EDT
  • Call-in information / screen sharing: We will use Bluejeans teleconferencing software for audio and video and WILL NOT use the GO conference line. We will use Bluejeans for screen sharing also. If attendees have a question they should post it on the chat window and they will answered in order.
  • Minutes available on Google Document here.

Agenda

Introduction (11:00 - 11:05) (GO PI's)

Discussion of priorities for calendar year 2015 (11:05 - 11:30) (GO PI's)

  • Common Annotation Framework/Environment (CAF/E)
    • Goal: LEGO annotation and text mining support in production (CAF/E)
    • Milestone 1: version of each component that can be used by curation test team
    • Milestone 2: Integration of components into Common Annotation Framework/Environment
    • Preliminary results on javascript PAINT as part of CAF/E
  • Phylogenetic annotation
    • meet production goals: annotate 1/3 of genes this grant year
    • software for updating annotations to reflect changes in gene sets, experimental annotations and ontology
  • Metrics for value/impact of GO data
    • Categorize and quantify usage of GO in published papers
    • Annotation quality metric and assessment
  • Monitoring and assessing our support for users
    • User survey
    • Website usability study
    • Enrichment Analysis: Documentation, UI improvement

Talk by Paul Pavlidis, UBC (11:30 - 12:15)

The use of GO in data analysis: can we raise the bar?

Other agenda items (12:15 - 12:30)

  • Update on AmiGO/GO website Behave testing framework (Mary/Seth/Chris)
  • Upcoming Consortium meeting in Washington DC

Attendees

Please sign up so we know who can attend.


Name Organization
Rama Balakrishnan Stanford University, SGD
David Hill The Jackson Laboratory, MGI
Harold Drabkin The Jackson Laboratory, MGI
Judy Blake The Jackson Laboratory
Mary Dolan The Jackson Laboratory, MGI
Li Ni The Jackson Laboratory, MGI
Dmitry Sitnikov The Jackson Laboratory, MGI
Karen Christie The Jackson Laboratory, MGI
Kimberly Van Auken Cal Tech, Wormbase
Paul Thomas USC
Huaiyu Mi USC
Moni Munoz-Torres Lawrence Berkeley National Lab, BBOP
Seth Carbon Lawrence Berkeley National Lab, BBOP
Chris Mungall Lawrence Berkeley National Lab, BBOP
Tanya Berardini Phoenix Bioinformatics, TAIR
Eva Huala Phoenix Bioinformatics, TAIR
Donghui Li Phoenix Bioinformatics, TAIR
Doug Howe ZFIN
Sabrina Toro ZFIN
Pascale Gaudet GOC / neXtProt
Marc Feuermann Swiss-Prot
Birgit Meldal IntAct / Complex Portal
Aleks Shypitsyna UniProt-GOA, EMBL-EBI
Penelope Garmiri UniProt-GOA, EMBL-EBI
Rebecca Foulger UCL
Ruth Lovering UCL
Rachael Huntley UCL
Tom Hayman RGD
Mary Shimoyama RGD
Shur-Jen Wang RGD
Stan Laulederkind RGD
Helen Attrill FlyBase
Midori Harris PomBase
Val Wood PomBase
Paola Roncaglia EMBL-EBI