Difference between revisions of "2016 Geneva GOC Meeting Agenda"

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(Ontology Development)
 
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**Out-of-date JCVI annotations (https://trello.com/c/YRSPkeJb/157-out-of-date-jcvi-annotations).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**Out-of-date JCVI annotations (https://trello.com/c/YRSPkeJb/157-out-of-date-jcvi-annotations).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?
  
==Group Photo==
 
  
 
==Friday Afternoon==
 
==Friday Afternoon==
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***Introduction to Principles of LEGO Annotation - Paul T. (20 minutes)
 
***Introduction to Principles of LEGO Annotation - Paul T. (20 minutes)
 
***Hands-on Noctua using an annotation consistency exercise.  Paper for this exercise:
 
***Hands-on Noctua using an annotation consistency exercise.  Paper for this exercise:
****[http://www.ncbi.nlm.nih.gov/pubmed/26341465 WLS retrograde transport to the endoplasmic reticulum during Wnt secretion.]
+
****[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.
 
****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
 
*****Cellular component annotations - capturing where a gene product may be found vs. where a gene product is active
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***Discussion of GAF/GPAD output from Noctua/LEGO
 
***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?
 
****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)
+
** 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
****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)
 
** Protein2GO updates and LEGO/Noctua bridging (Aleksandra)
 
** LEGO/Reactome bridging (Seth) [https://docs.google.com/presentation/d/1SM0rdMrXjDwtesY2EYdyBU793I2PD2Tx5r3ScbQeB6s/edit?usp=sharing slide]
 
** LEGO/Reactome bridging (Seth) [https://docs.google.com/presentation/d/1SM0rdMrXjDwtesY2EYdyBU793I2PD2Tx5r3ScbQeB6s/edit?usp=sharing slide]
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==Community facing items==
 
==Community facing items==
* Flash update on changes to Drupal website (Moni, PaulT)
+
* 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 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
 
* Flash update on QuickGO (Tony) 10 min
 
* Set of files we produce and their format. Updated GPAD spec with extra columns (Tony)
 
* 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]
+
* 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]
  
 
==Ontology Development==
 
==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.
+
* 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])
 
* 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)
 
* Making automation automatic - rationalising the inference pipeline (David OS)
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==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