Difference between revisions of "2016 Geneva GOC Meeting Agenda"

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(Friday Morning)
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==Suggested Agenda Items==
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==Planned Schedule for the Week of the Meeting==
Please suggest Agenda items here, and these will later be arranged into the time slots below. Please list topic, name of speaker, estimated time for talk plus discussion, and requested day.
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===List of suggested items===
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===GOC-Geneva-2016 Meeting schedule===
====Friday Morning====
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* '''Friday April 15 and Saturday April 16 - GOC Meeting''':  
* Annotation  
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:* April 15: 9am to 5pm, Campus Biotech room H8
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:* April 16: 9am to noon, CMU
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*'''Saturday April 16 - GOC Steering Committee Meeting''':
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:* Meeting location: CMU
 +
 
 +
===GOC-Geneva-2016 Meeting Dinner===
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* April 15
 +
* Location:
 +
* Time:
 +
 
 +
== Minutes ==
 +
The Minutes of the GOC-Geneva-2016 Meeting are recorded here.
 +
 
 +
 
 +
=Agenda=
 +
 
 +
=Day 1 (Friday)=
 +
 
 +
==Friday Morning==
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===Annotation===
 
**GO annotation statistics - PaulT
 
**GO annotation statistics - PaulT
 
** InterPro2GO, Amaia Sangrador, 15 min talk, 5 min discussion, Friday.
 
** InterPro2GO, Amaia Sangrador, 15 min talk, 5 min discussion, Friday.
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***Out-of-date JCVI annotations (https://trello.com/c/YRSPkeJb/157-out-of-date-jcvi-annotations).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?
 
***Out-of-date JCVI annotations (https://trello.com/c/YRSPkeJb/157-out-of-date-jcvi-annotations).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?
  
====Friday Afternoon====
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==Group Photo==
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==Friday Afternoon==
 
*Noctua Workshop -  
 
*Noctua Workshop -  
 
** Protein2GO updates and LEGO/Noctua bridging (Aleksandra)
 
** Protein2GO updates and LEGO/Noctua bridging (Aleksandra)
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****Assessing direct vs indirect physical interactions
 
****Assessing direct vs indirect physical interactions
  
====Saturday Morning====
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=Day 2 (Saturday)=
* Community facing stuff
 
** Flash update on changes to Drupal website (Moni, PaulT)
 
** Flash update on AmiGO, including work on parallel projects, e.g. planteome (Seth) [https://docs.google.com/presentation/d/1qEQ9pzGwX6gtT_eCz2dNpuGTNi45W0OKATioX3uW69s/edit?usp=sharing 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?) https://docs.google.com/document/d/1mvMpW09kksDQ6QVpVf5O-0DOl9xbq_JaC4efOzogdus/edit?usp=sharing
 
 
 
* 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)
 
** Making automation automatic - rationalising the inference pipeline (David OS)
 
 
 
====Meeting Ends NoonTime====
 
 
 
==Planned Schedule for the Week of the Meeting==
 
 
 
===GOC-Geneva-2016 Meeting schedule===
 
* '''Friday April 15 and Saturday April 16 - GOC Meeting''':
 
:* Meeting location:
 
:* April 15: 9am to 5pm
 
:* April 16: 9am to 1pm
 
 
 
*'''Saturday April 16 - GOC Steering Committee Meeting''':
 
:* Meeting location:
 
 
 
===GOC-Geneva-2016 Meeting Dinner===
 
* April 15
 
* Location:
 
* Time:
 
 
 
== Minutes ==
 
The Minutes of the GOC-Geneva-2016 Meeting are recorded here.
 
 
 
 
 
=Agenda=
 
 
 
Please ensure that all outstanding items from the Trello board are covered here and under the appropriate heading.
 
 
 
 
 
=Day 1 (Friday)=
 
 
 
==Session name (approx. times)==
 
* Item (speaker) (approx time)
 
 
 
Protein Ontology representatives will be present
 
 
 
==Group Photo==
 
 
 
=Day 2=
 
 
 
  
==Session name (approx. times)==
+
==Community facing items==
* Item (speaker) (approx time)
+
* Flash update on changes to Drupal website (Moni, PaulT)
 +
* Flash update on AmiGO, including work on parallel projects, e.g. planteome (Seth) [https://docs.google.com/presentation/d/1qEQ9pzGwX6gtT_eCz2dNpuGTNi45W0OKATioX3uW69s/edit?usp=sharing 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?) https://docs.google.com/document/d/1mvMpW09kksDQ6QVpVf5O-0DOl9xbq_JaC4efOzogdus/edit?usp=sharing
  
 +
==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)
 +
* Making automation automatic - rationalising the inference pipeline (David OS)
  
 
==Wrap-up==
 
==Wrap-up==

Revision as of 03:56, 14 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.


Agenda

Day 1 (Friday)

Friday Morning

Annotation

    • GO annotation statistics - PaulT
    • InterPro2GO, Amaia Sangrador, 15 min talk, 5 min discussion, Friday.
    • Annotation of protein complexes, Sandra Orchard, IntACT, 10 min talk
    • Annotation of protein complexes, Ceci Arighi, PRO, 10 min talk
    • Discussion 1: 15 min
    • Discussion 2: (15 min)
      • Relations used for Biological Process annotations. In Barcelona, we proposed implementing an additional relation to capture the ambiguity of a gene's relation to a Biological Process. The implementation never happened, and with GAF outputs of LEGO models, the question becomes even more critical. It would be good to re-visit this issue, discuss the various proposals that have been made, and see if we still think it's appropriate to add this relation and if so, what steps need to be taken to do it. (Kimberly - 1 hour?)
      • 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

Friday Afternoon

  • Noctua Workshop -
    • Protein2GO updates and LEGO/Noctua bridging (Aleksandra)
    • I'd like to make some comments about "lossiness" and practicalities of LEGO here by showing a couple of Pombase examples (Val)
    • LEGO/Reactome bridging (Seth) slide
    • Noctua/LEGO workshop - Friday afternoon - 3 hours?
    • Introduction to the tool 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, 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
        • Assessing direct vs indirect physical interactions

Day 2 (Saturday)

Community facing items

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)
  • Making automation automatic - rationalising the inference pipeline (David OS)

Wrap-up

  • Review action items