2016 Geneva GOC Meeting Agenda: Difference between revisions

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* '''Friday April 15 and Saturday April 16 - GOC Meeting''':   
* '''Friday April 15 and Saturday April 16 - GOC Meeting''':   
:* April 15: 9am to 5pm, Campus Biotech room H8
:* April 15: 9am to 5pm, Campus Biotech room H8
:**https://bluejeans.com/109819476/
:* April 16: 9am to noon, CMU
:* April 16: 9am to noon, CMU


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== 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=
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==Friday Morning==
==Friday Morning==
===Annotation===  
===Annotation===  
**GO annotation statistics - PaulT
*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, Sandra Orchard, IntACT, 10 min talk
* Annotation of protein complexes, Sandra Orchard, IntACT, 10 min talk
** Annotation of protein complexes, Ceci Arighi, PRO, 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
**reduce redundancy of annotation efforts for complexes
***reduce redundancy of annotation efforts for complexes
***(http://jira.geneontology.org/browse/GO-1131) (Val?)
****(http://jira.geneontology.org/browse/GO-1131) (Val?)
* 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***Out-of-date JCVI annotations (https://trello.com/c/YRSPkeJb/157-out-of-date-jcvi-annotations).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**Out-of-date JCVI annotations (https://trello.com/c/YRSPkeJb/157-out-of-date-jcvi-annotations).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==


==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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*****Annotation of splice variants and proteoforms (secondary to model discussion)
*****Annotation of splice variants and proteoforms (secondary to model discussion)
***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?
** 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)
** 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) [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 05:35, 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