2016 Geneva GOC Meeting Agenda: Difference between revisions

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==Friday Afternoon==
==Friday Afternoon==
*Noctua Workshop -  
*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/26341465 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
** Protein2GO updates and LEGO/Noctua bridging (Aleksandra)
** 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)
** 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) [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]
** Noctua/LEGO workshop  - Friday afternoon - 3 hours?
** Introduction to the tool 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.]
***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)=
=Day 2 (Saturday)=

Revision as of 13:29, 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)

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
    • 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

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