Difference between revisions of "Managers 16Jan08"

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Minutes: Pascale
 
Minutes: Pascale
  
Present: Midori, Pascale, Jen, Midori, Chris,
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Present: Midori, Pascale, Jen, Chris.
Suzi, Judy, Michael
+
 
  
 
== Review Action Items from previous meeting ==
 
== Review Action Items from previous meeting ==
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# Tanya and managers: Schedule Webex/call for Tanya to present her annotation-acquisition talk.
 
# Tanya and managers: Schedule Webex/call for Tanya to present her annotation-acquisition talk.
 
# Midori: Follow up on fungal terms with Val and Maria for sensu work: [Done]
 
# Midori: Follow up on fungal terms with Val and Maria for sensu work: [Done]
 +
# Chris: Ask the wider group whether the ontology development wiki should be public. Maybe also there are better ways to link the two wikis?
  
 
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Chris
 
Chris
 
* Set up an instance of AmiGO at Berkeley running with all the IEAs to test what problems are in moving on with this
 
* Set up an instance of AmiGO at Berkeley running with all the IEAs to test what problems are in moving on with this
* Annotation cross products: extra column in annotation file: Evelyn sent some examples  
+
* Annotation cross products: (extra column in annotation file): Evelyn sent some examples  
(see wiki)
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see  
 +
http://gocwiki.geneontology.org/index.php/Annotation_Cross_products
 +
Chris would like some more examples
  
  
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==  Meetings ==  
 
==  Meetings ==  
 +
* Avian annotation workshop
 +
* ISAFG
 +
* PAG?
 +
*Jen gives a tutorial in Belgium (funded by EBI) Feb
 +
* Midori will give a talk at the London School of economics in march
 +
  
 
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==  Collaborations and Interactions, active and new ==  
 
==  Collaborations and Interactions, active and new ==  
 
# Report from Larry Hunter on Jan 11th meeting re NLP & ontology QA
 
# Report from Larry Hunter on Jan 11th meeting re NLP & ontology QA
 
+
Several people met in person and by webex/skype. Larry presented ways to use Natural Language Processing to use with ontology quality control.
 +
Jen thought it was helpful and would like more discussion. Chris suggest starting with a wiki page.
 +
Should this be on the public wiki ?
 
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==  Operations and Procedures ==  
 
==  Operations and Procedures ==  
  
 
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nothing
 
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==  Staffing and Personnel==  
 
==  Staffing and Personnel==  
  
 +
Nomi has accepted the position :)
 
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==  Budget issues ==  
 
==  Budget issues ==  
 +
nothing
  
 
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==  Publications ==  
 
==  Publications ==  
  
 +
* Erika and Jen wrote a paper about the muscle meeting; asked Genome Biology if they'd consider
 +
* Pascale sent a draft of reference genome paper to some people for help.
 
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==  Other Current Topics and Concerns ==  
 
==  Other Current Topics and Concerns ==  

Revision as of 09:00, 16 January 2008

GO Managers, Weds. Jan. 16, 2008 8a.m. PST, 9a.m. MST, 10a.m. CST, 11a.m. EST, 4p.m. GMT

Agenda/chair: Midori

Minutes: Pascale

Present: Midori, Pascale, Jen, Chris.


Review Action Items from previous meeting

  1. All: review document on regulation wiki page
  2. Chris: Draft proposal for GO slim maintenance. [in progress will send email to managers with the different options by the next meeting]
  3. Pascale, Jim et al.: Continue discussing wiki-based annotation tool.
  4. Jen: Organize conf call on gohelp technology. [Done; problem went away magically]
  5. Pascale (and rest of annotators): Continue improving annotation SOPs.
  6. Judy: Contact sea urchin db about doing GO annotation.
  7. See if we can collaborate with journals to obtain annotations from users. Responsible groups: managers, software group and annotators?: Test various methods of accepting user submissions for annotation; converge on best solution, and seek journal buy-in.
  8. Tanya and managers: Schedule Webex/call for Tanya to present her annotation-acquisition talk.
  9. Midori: Follow up on fungal terms with Val and Maria for sensu work: [Done]
  10. Chris: Ask the wider group whether the ontology development wiki should be public. Maybe also there are better ways to link the two wikis?

Individual Manager reports

Ontology Development

Regulation

many relationship fixes; ready to deploy 'regulates' relationship; draft announcement email on wiki: http://gocwiki.geneontology.org/index.php/Meeting_Minutes_3:Stanford

  • Chris: summary of achievements: repositioned many of the is_a relationships so that they are more accurate, ie structure of the graph is improved. This allows better statistical analyses using the GO. Would be nice to quantify this, for example by taking papers that used GO and repeat analyses and see if results are better. Added >900 relationships.
  • See wiki for all details

In progress

Transport, electron transport

Next priorities

Function- process links?


Outreach/User Advocacy

Jen

Avian annotation workshop

Fiona McCarthy is organizing an Avian annotation workshop (Miss. St University)

ISAFG

Fiona is giving a GO tutorial at the ISAFG - European Farm animal conference


Software

Chris

  • Set up an instance of AmiGO at Berkeley running with all the IEAs to test what problems are in moving on with this
  • Annotation cross products: (extra column in annotation file): Evelyn sent some examples

see http://gocwiki.geneontology.org/index.php/Annotation_Cross_products Chris would like some more examples



Reference Genomes


Meetings

  • Avian annotation workshop
  • ISAFG
  • PAG?
  • Jen gives a tutorial in Belgium (funded by EBI) Feb
  • Midori will give a talk at the London School of economics in march



Collaborations and Interactions, active and new

  1. Report from Larry Hunter on Jan 11th meeting re NLP & ontology QA

Several people met in person and by webex/skype. Larry presented ways to use Natural Language Processing to use with ontology quality control. Jen thought it was helpful and would like more discussion. Chris suggest starting with a wiki page. Should this be on the public wiki ?


Operations and Procedures

nothing


Staffing and Personnel

Nomi has accepted the position :)


Budget issues

nothing


Publications

  • Erika and Jen wrote a paper about the muscle meeting; asked Genome Biology if they'd consider
  • Pascale sent a draft of reference genome paper to some people for help.

Other Current Topics and Concerns

Back to minutes list