Difference between revisions of "2016 Geneva GOC Meeting Agenda"

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==Suggested Agenda Items==
 
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.
 
===List of suggested items===
 
* Annotation of protein complexes, Sandra Orchard, 15 min talk, 15 min discussion, Friday.
 
* InterPro2GO, Amaia Sangrador, 15 min talk, 5 min discussion, Friday.
 
 
 
 
==Planned Schedule for the Week of the Meeting==  
 
==Planned Schedule for the Week of the Meeting==  
  
 
===GOC-Geneva-2016 Meeting schedule===
 
===GOC-Geneva-2016 Meeting schedule===
* '''Friday April 15 and Saturday April 16 - GOC Meeting''':  
+
* '''Friday April 15 and Saturday April 16 - GOC Meeting''':
:* Meeting location:
+
:* April 15: 9am to 5pm, Campus Biotech room H8
:* April 15: 9am to 5pm
+
:**https://bluejeans.com/109819476/
:* April 16: 9am to 1pm
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:* April 16: 9am to noon, CMU
  
 
*'''Saturday April 16 - GOC Steering Committee Meeting''':  
 
*'''Saturday April 16 - GOC Steering Committee Meeting''':  
:* Meeting location:
+
:* Meeting location: CMU
  
 
===GOC-Geneva-2016 Meeting Dinner===
 
===GOC-Geneva-2016 Meeting Dinner===
Line 24: Line 17:
 
== Minutes ==
 
== Minutes ==
 
The Minutes of the GOC-Geneva-2016 Meeting are recorded here.
 
The Minutes of the GOC-Geneva-2016 Meeting are recorded here.
 
+
[https://docs.google.com/document/d/12CDf4s8YsylPMNHM3UuPis9NyVQ9WFpBpNYTFYAH7kc/edit?usp=sharing Minutes Google Doc]
  
 
=Agenda=
 
=Agenda=
  
Please ensure that all outstanding items from the Trello board are covered here and under the appropriate heading.
+
=Day 1 (Friday)=
 
 
  
=Day 1=
+
==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
 +
**what terms in GO and what terms in PRO
 +
**ontology of complexes including macromolecular complexes
 +
**reduce redundancy of annotation efforts for complexes
 +
***(http://jira.geneontology.org/browse/GO-1131) (Val?)
 +
* InterPro2GO, Amaia Sangrador.
 +
* Discussion InterPro2GO
 +
*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**Out-of-date JCVI annotations (https://trello.com/c/YRSPkeJb/157-out-of-date-jcvi-annotations).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?
  
==Session name (approx. times)==
 
* Item (speaker) (approx time)
 
  
 +
==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:
 +
****[http://www.ncbi.nlm.nih.gov/pubmed/24768165 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) - not presented in Geneva; will be discussed on one of the weekly LEGO calls
 +
** Protein2GO updates and LEGO/Noctua bridging (Aleksandra)
 +
** LEGO/Reactome bridging (Seth) [https://docs.google.com/presentation/d/1SM0rdMrXjDwtesY2EYdyBU793I2PD2Tx5r3ScbQeB6s/edit?usp=sharing slide]
  
==Group Photo==
+
=Day 2 (Saturday)=
=Day 2=
 
  
 +
==Community facing items==
 +
* Flash update on GO Website, Community feedback and outreach. (Moni) [http://www.slideshare.net/MonicaMunozTorres/gene-ontology-consortium-website-community Slides]
 +
* 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/presentation/d/17Myvef4sDgz20GTz_VipqEpXPSOdboD2jr3ycj0kaRs/edit?usp=sharing Slides]
  
==Session name (approx. times)==
+
==Ontology Development==
* Item (speaker) (approx time)
+
* Flash updates on ontology stats and ontology focused projects (Paola) https://www.dropbox.com/s/u5l8v3dyietdau2/Paola_GOC_mtg_Geneva.pptx?dl=0
 
+
* Synapse project update (David OS, Paul T, Ruth L-[https://docs.google.com/presentation/d/1d5caZQVFoI0hktsg-mnZI7CCwQTUQ1u4cFP2sXq3ZIs/edit?usp=sharing RLslides])
 +
* Making automation automatic - rationalising the inference pipeline (David OS)
  
 
==Wrap-up==
 
==Wrap-up==
 
* Review action items
 
* Review action items
 +
* Next GO Meeting
  
 
+
==Group photo==
 +
[[image:GO_2016_Geneva_meeting.JPG|800px|thumb|left|2016 GOC Group Photo in Campus Biotech, Geneva]]
  
  
 
[[Category: GO Consortium Meetings]]
 
[[Category: GO Consortium Meetings]]

Latest revision as of 02:35, 16 April 2016

Planned Schedule for the Week of the Meeting

GOC-Geneva-2016 Meeting schedule

  • Friday April 15 and Saturday April 16 - GOC Meeting:
  • 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)


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) - not presented in Geneva; will be discussed on one of the weekly LEGO calls
    • Protein2GO updates and LEGO/Noctua bridging (Aleksandra)
    • LEGO/Reactome bridging (Seth) slide

Day 2 (Saturday)

Community facing items

  • Flash update on GO Website, Community feedback and outreach. (Moni) Slides
  • 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

Wrap-up

  • Review action items
  • Next GO Meeting

Group photo

2016 GOC Group Photo in Campus Biotech, Geneva