Difference between revisions of "2013 Cambridge GOC Meeting Agenda"

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The 2013 GO Consortium meeting will be held 11-13 April, in Cambridge, UK, immediately following [http://www.ebi.ac.uk/biocuration2013/home Biocuration 2013].
 
The 2013 GO Consortium meeting will be held 11-13 April, in Cambridge, UK, immediately following [http://www.ebi.ac.uk/biocuration2013/home Biocuration 2013].
  
= Agenda for Thursday=
+
=Thursday (starts at 8:30)=
*8:30AM MeetUp
 
*9:00AM Start
 
*10:30AM  break
 
*12:30PM lunch
 
*3:30PM afternoon break
 
*7PM Dinner at the Moller Centre (cash bar)
 
  
==Usability ==
+
==Usability==
 
GOAL:Provide community with ability to obtain and use GO resources
 
GOAL:Provide community with ability to obtain and use GO resources
* New Web Site http://beta.geneontology.org - drupal (Seth)
+
* Update on [http://galaxy.berkeleybop.org/ Galaxy] (Chris) (8:30-9)
 +
* New Web Site http://beta.geneontology.org - drupal (Seth) (9-9:30)
 
* [http://amigo2.berkeleybop.org/ AmiGO 2.0] (Seth & Chris)
 
* [http://amigo2.berkeleybop.org/ AmiGO 2.0] (Seth & Chris)
* Platinum standard data sets for enrichment analyses (Paul S, Rama)
+
* Platinum standard data sets for enrichment analyses (Paul S, Rama) (9:30-10:15)
* Update on [http://galaxy.berkeleybop.org/ Galaxy] (Chris)
+
==Coffee break (10:15-10:45)==
  
= Biological Knowledge =  
+
 
*[[Transition to OWL]] progress and status (Chris)
+
 
*Interaction between ontology development and annotation
+
== Comparative and Phylogenetic Annotations ==
 +
* PAINT progress, including overview of SOPs
 +
** PAINT progress overview (Paul T.) (10:45-11)
 +
** SOP overview plus example (Donghui) (11-11:20)
 +
** Examples of annotation issues in PAINT, plus discussion (11:20-12) (Paul T, Pascale)
 +
== Lunch (12-1) ==
 +
** Update on JsPAINT (Chris/Suzi) (1-1:15)
 +
* Jenkins for QC - http://build.berkeleybop.org/view/GAF/ (Heiko) (1:15-1:30)
 +
* ECO update (Chris) (1:30-1:40)
 +
* New rules for ISO mouse/human/rat when M:N gene sets (Judy) (1:40-2)
 +
 
 +
== Literature Annotation ==
 +
* apoptosis (re)annotation effort (Paola) [[File: GOC_2013_Cambridge.pdf]] (2-2:30)
 +
* production statistic reports (Paul S) (2:30-2:45)
 +
== Coffee break (2:45-3:15)
 +
* Curation tools: transition to Protein-GO, prospects for text-mining integratrion (3:15-4:15)
 +
 
 +
== Biological Knowledge ==
 +
*[[Transition to OWL]] progress and status (Chris) (4:15-4:45)
 +
*Interaction between ontology development and annotation (4:45-5:15)
 
**Current mechanisms: tracker, TG, Jira (Jane)
 
**Current mechanisms: tracker, TG, Jira (Jane)
 
**Update on existing TG templates, tree browser esp CHEBI, numbers of terms added (Jane) [[Media:TGreview_Cambridge_April13.pdf]]
 
**Update on existing TG templates, tree browser esp CHEBI, numbers of terms added (Jane) [[Media:TGreview_Cambridge_April13.pdf]]
 
**TermGenie freeform demo (Jane)
 
**TermGenie freeform demo (Jane)
*Cross-product status, inc cell type (David)
 
*Cell cycle report (Val)
 
*Annotation expressivity
 
**LEGO
 
***Test example: Wnt signaling (David)
 
***Implementation plan (Chris)
 
***Mapping to community representations, e.g. [http://www.biopax.org/ BioPAX], [http://www.sbgn.org/Main_Page SBGN] (Huaiyu)
 
**Annotation extensions (Rachael)
 
***Annotation relations
 
**GPAD status (Chris)
 
  
= Comparative and Phylogenetic Annotations =  
+
== Dinner at Moller Centre (7pm) ==
* PAINT progress, including overview of SOPs (Huaiyu)
+
 
** PAINT progress overview (Paul T.)
 
** SOP overview (Pascale)
 
** Example (Donghui)
 
** Update on JsPAINT (Chris/Suzi)
 
* Jenkins for QC - http://build.berkeleybop.org/view/GAF/ (Heiko)
 
* [http://code.google.com/p/evidenceontology ECO] update (Chris)
 
* New rules for ISO mouse/human/rat when M:N gene sets (Judy)
 
  
= Literature Annotation =
 
* apoptosis (re)annotation effort (Paola) [[File: GOC_2013_Cambridge.pdf]]
 
* production statistic reports (Paul S)
 
* Curation tools: transition to Protein-GO, prospects for text-mining integratrion
 
  
 
= Friday afternoon breakout sessions =
 
= Friday afternoon breakout sessions =
Line 70: Line 63:
  
 
  '''Interested in attending:''' Jane, Rachael, Susan, David, Tanya, Val, Paola, Rebecca, Prudence
 
  '''Interested in attending:''' Jane, Rachael, Susan, David, Tanya, Val, Paola, Rebecca, Prudence
 +
 +
= Saturday =
 +
== Biological Knowledge (continued) ==
 +
*Cross-product status, inc cell type (David) (8:30-9)
 +
*Cell cycle report (Val) (9-9:30)
 +
 +
*Annotation expressivity
 +
**LEGO
 +
***Test example: Wnt signaling (David) (9:30-10)
 +
***Implementation plan (Chris) (10-10:20)
 +
== Coffee break (10:20-10:45) ==
 +
***Mapping to community representations, e.g. [http://www.biopax.org/ BioPAX], [http://www.sbgn.org/Main_Page SBGN] (Huaiyu) (10:45-11:05)
 +
**Annotation extensions (Rachael) (11:05-11:30)
 +
***Annotation relations
 +
**GPAD status (Chris) (11:30-11:40)
 +
==Meeting wrap up and action item review (11:40-12:15) ==
  
 
= Action Item Review and Reports =
 
= Action Item Review and Reports =

Revision as of 07:58, 10 April 2013

The 2013 GO Consortium meeting will be held 11-13 April, in Cambridge, UK, immediately following Biocuration 2013.

Thursday (starts at 8:30)

Usability

GOAL:Provide community with ability to obtain and use GO resources

Coffee break (10:15-10:45)

Comparative and Phylogenetic Annotations

  • PAINT progress, including overview of SOPs
    • PAINT progress overview (Paul T.) (10:45-11)
    • SOP overview plus example (Donghui) (11-11:20)
    • Examples of annotation issues in PAINT, plus discussion (11:20-12) (Paul T, Pascale)

Lunch (12-1)

    • Update on JsPAINT (Chris/Suzi) (1-1:15)
  • Jenkins for QC - http://build.berkeleybop.org/view/GAF/ (Heiko) (1:15-1:30)
  • ECO update (Chris) (1:30-1:40)
  • New rules for ISO mouse/human/rat when M:N gene sets (Judy) (1:40-2)

Literature Annotation

== Coffee break (2:45-3:15)

  • Curation tools: transition to Protein-GO, prospects for text-mining integratrion (3:15-4:15)

Biological Knowledge

  • Transition to OWL progress and status (Chris) (4:15-4:45)
  • Interaction between ontology development and annotation (4:45-5:15)
    • Current mechanisms: tracker, TG, Jira (Jane)
    • Update on existing TG templates, tree browser esp CHEBI, numbers of terms added (Jane) Media:TGreview_Cambridge_April13.pdf
    • TermGenie freeform demo (Jane)

Dinner at Moller Centre (7pm)

Friday afternoon breakout sessions

1. Annotation Extension

Interested in attending: Jane, Rachael, Susan, Petra, Mary, David, Midori, Chris, Kimberly, Ruth, Donghui, Tanya, Val, Harold,
Rama, SGD curators, Rebecca, Li, Prudence

2. PAINT Meeting - Huaiyu

  • including ontology developers
  • Look at annotation consistency
Interested in attending: Jane, Susan, Ruth, Donghui,Val, Rama, Li

3. Cell cycle

  • WG to work through outstanding issues
Interested in attending: Jane, Rachael, Susan, David, Tanya, Val, Paola, Rebecca, Prudence

Saturday

Biological Knowledge (continued)

  • Cross-product status, inc cell type (David) (8:30-9)
  • Cell cycle report (Val) (9-9:30)
  • Annotation expressivity
    • LEGO
      • Test example: Wnt signaling (David) (9:30-10)
      • Implementation plan (Chris) (10-10:20)

Coffee break (10:20-10:45)

      • Mapping to community representations, e.g. BioPAX, SBGN (Huaiyu) (10:45-11:05)
    • Annotation extensions (Rachael) (11:05-11:30)
      • Annotation relations
    • GPAD status (Chris) (11:30-11:40)

Meeting wrap up and action item review (11:40-12:15)

Action Item Review and Reports

Caltech meeting minutes meeting minutes as a Google Doc

See also