Difference between revisions of "2016 Geneva GOC Meeting Agenda"

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(Friday Afternoon)
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==Friday Morning==
 
==Friday Morning==
 
===Annotation===  
 
===Annotation===  
**GO annotation statistics - PaulT
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*GO annotation statistics - PaulT
** InterPro2GO, Amaia Sangrador, 15 min talk, 5 min discussion, Friday.
+
*Annotation of protein complexes, Ceci Arighi, PRO, 10 min talk
**Annotation of protein complexes, Ceci Arighi, PRO, 10 min talk
+
* Annotation of protein complexes, Sandra Orchard, IntACT, 10 min talk
** Annotation of protein complexes, Sandra Orchard, IntACT, 10 min talk
+
* Discussion on protein complexes:  15 min
** Discussion 1:  15 min
+
**what terms in GO and what terms in PRO
***what terms in GO and what terms in PRO
+
**ontology of complexes including macromolecular complexes
***ontology of complexes including macromolecular complexes
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**reduce redundancy of annotation efforts for complexes
***reduce redundancy of annotation efforts for complexes
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***(http://jira.geneontology.org/browse/GO-1131) (Val?)
****(http://jira.geneontology.org/browse/GO-1131) (Val?)
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* InterPro2GO, Amaia Sangrador.
**Discussion 2:  (15 min)
+
* Discussion InterPro2GO
***Out-of-date JCVI annotations (https://trello.com/c/YRSPkeJb/157-out-of-date-jcvi-annotations). A proposal was made to retire JCVI files and make sure that as many of their experimental annotations as possible (41 in QuickGO) can consistently live on corresponding UniProt entries. Feedback?
+
*Discussion on stale annotations:  (15 min)
 +
**Out-of-date JCVI annotations (https://trello.com/c/YRSPkeJb/157-out-of-date-jcvi-annotations). A proposal was made to retire JCVI files and make sure that as many of their experimental annotations as possible (41 in QuickGO) can consistently live on corresponding UniProt entries. Feedback?
  
 
==Group Photo==
 
==Group Photo==

Revision as of 00:15, 15 April 2016

Planned Schedule for the Week of the Meeting

GOC-Geneva-2016 Meeting schedule

  • Friday April 15 and Saturday April 16 - GOC Meeting:
  • April 15: 9am to 5pm, Campus Biotech room H8
  • April 16: 9am to noon, CMU
  • Saturday April 16 - GOC Steering Committee Meeting:
  • Meeting location: CMU

GOC-Geneva-2016 Meeting Dinner

  • April 15
  • Location:
  • Time:

Minutes

The Minutes of the GOC-Geneva-2016 Meeting are recorded here. Minutes Google Doc

Agenda

Day 1 (Friday)

Friday Morning

Annotation

  • GO annotation statistics - PaulT
  • Annotation of protein complexes, Ceci Arighi, PRO, 10 min talk
  • Annotation of protein complexes, Sandra Orchard, IntACT, 10 min talk
  • Discussion on protein complexes: 15 min
  • InterPro2GO, Amaia Sangrador.
  • Discussion InterPro2GO
  • Discussion on stale annotations: (15 min)

Group Photo

Friday Afternoon

  • Noctua Workshop -
    • Noctua/LEGO workshop - Friday afternoon
      • Introduction to Principles of LEGO Annotation - Paul T. (20 minutes)
      • Hands-on Noctua using an annotation consistency exercise. Paper for this exercise:
        • WLS retrograde transport to the endoplasmic reticulum during Wnt secretion.
        • This paper addresses some common annotation scenarios that will be interesting to model in Noctua.
          • Cellular component annotations - capturing where a gene product may be found vs. where a gene product is active
          • How do the events of ligand processing, localization and transport, and secretion relate to a downstream signaling pathway and the organismal level processes controlled by that pathway?
          • When does an MF annotation represent activity vs a mechanism that is part of how the activity is executed?
          • Annotation of splice variants and proteoforms (secondary to model discussion)
      • Discussion of GAF/GPAD output from Noctua/LEGO
        • How far away do we want to make Biological Process annotations and how should they be expressed in GAF and GPAD?
    • I'd like to make some comments about "lossiness" and practicalities of LEGO here by showing a couple of Pombase examples (Val, some thoughts on the above item)
        • How do we want to handle reciprocal binding annotations when only one half of the binding is part of an activity?
    • Protein2GO updates and LEGO/Noctua bridging (Aleksandra)
    • LEGO/Reactome bridging (Seth) slide

Day 2 (Saturday)

Community facing items

  • Flash update on changes to Drupal website (Moni, PaulT)
  • Flash update on AmiGO, including work on parallel projects, e.g. planteome (Seth) slides
  • Flash update on QuickGO (Tony) 10 min
  • Set of files we produce and their format. Updated GPAD spec with extra columns (Tony)
  • GO website community annotation page and forms for contributors to complete (Ruth/Val 5 min presentation, 10 min discussion?) slides

Ontology Development

  • Flash updates on ontology stats and ontology focused projects, Melanie/David OS/Paola, 45 min talk total (among the 3 of us), 15 min discussion, Friday anytime or Saturday morning.
  • Synapse project update (David OS, Paul T, Ruth L-RLslides)
  • Making automation automatic - rationalising the inference pipeline (David OS)

Wrap-up

  • Review action items