GOC 2017 meeting

June 1-3, 2017 | Draft Agenda | GOC

Detail agenda ref: http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda

or at the end of the s

Remote attendees call in via Bluejeans: https://bluejeans.com/993661940

Thursday June 1,

Venue: LaSells Stewart center (Map/Directions)

Room: Agriculture Science Room

  • 8:00am-9:00am Breakfast
  • 9:00am-12:00pm GOC: session-1
  • 12:00pm-1:00pm Lunch
  • 1:00pm-3:00pm GOC: session-2
  • 3:00pm-3:30pm snacks
  • 3:30pm-5:00pm GOC: session-3
  • 5:00pm onward mixer

Friday June 2

Venue: LaSells Stewart center (Map/Directions)

Room: Agriculture Science Room

  • 8:00am-9:00am Breakfast
  • 9:00am-12:00pm GOC: session-4
  • 12:00pm-1:00pm Lunch
  • 1:00pm-3:30pm GOC: session-5
  • 3:30pm pick snacks and go for recreation activity at Willamette Park (Transportation provided)
  • 6:00-8:00pm onward Dinner at at Willamette Park

Saturday June 3

Venue: CH2M Hill Alumni Center (MAP/directions)

Room: Willamette A-B

  • 8:00am-9:00am Breakfast
  • 9:00am-12:00pm GOC: session-6
  • 12:00pm-1:00pm Lunch
  • 1:00pm-3:00pm GOC: session-7
  • 3:00pm-5:30pm Walk to MU Basement for recreation activity
  • 5:30pm Start walking back to the meeting venue CH2M Hill Alumni Center (Willamette Room)
  • 6:00pm onward Poster Session and Mixer at CH2M Hill Alumni Center (Willamette Room)

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Thursday June 1

8-9am Breakfast and setup

Welcome, schedule and logistics

Overview of Objectives for Upcoming Year

  • Aim1: Provide a comprehensive model of biological knowledge focused on human biology
    • Ontology
      • MF refactoring completed
      • BP refactoring underway, including annotation qualifiers
    • Annotation
      • N# of pathways annotated according to prioritized list (Paul S to provide)
      • Complete the incorporation of new annotation groups/sources: SynGO, SIGNOR
  • Aim 2: Provide the “hub” for a broad community of scientists to extend and modify the GO
    • Pipeline transition completed (**almost** -- chris)
    • Noctua rolled out to all GO curation groups
      • Evidence issues resolved in Noctua
    • Documentation for ontology request guidelines completed
  • Aim 3: Apply biological knowledge obtained in model organisms to human biology
    • PAINT annotations going directly into GO database (not via MODs)
    • PAINT annotation completed for all families with experimental annotations
    • Established alert system for ongoing review of annotated families
  • Aim 4: Maintain the integrity and quality of new and existing annotations
    • Ongoing annotation consistency exercises (conference calls and github) will now include a write-up (or blog) as case studies to be published on the web site.
    • An automated rule-based annotation QA system will be put into place that will be refined/extended based on input from the consistency exercises and PAINT curators
    • Establishment of an agreed upon policy for when annotations will be removed (and put this policy into action)
  • Am 5: Enable the scientific community to make full use of the GO data resources
    • Fixed existing problems with enrichment analysis
    • Website?
    • Outreach?

Infrastructure (Aim 2—Provide a “hub”)

Pipeline Migration (Seth & Chris 20 mins) (Goal 2.a)

New APIs (Seth & Chris 10 mins)

TermGenie replacement* (Dan, Chris 20 mins)

12-1pm Lunch

Graph Store update (Eric 10 mins)

Licensing and GO (Seth 20 mins)

  • Where we currently stand with licensing and possible issues
  • What others do with our data

GO and Related Projects

3-3:30pm snacks

Identifiers (Chris) [WILL PROBABLY MOVE TO IDENTIFIERS SECTION IN AGR ABOVE]

Ontology (Aim 1—a comprehensive model of biological knowledge)

Update on Ontology Editing: David + Chris 20min

MF refactoring (Paul, DavidOS 30 mins) (Goal 1.a.i)

ECO

Noctua and SIGNOR2 (Chris & Paul T)

Straw man BP refactor Chris (Goal 1.a.ii)

6:00pm onwards mixer

Friday June 2

8-9am Breakfast

Ontology continued…

The fate of simple processes

Annotation (Aims 1, 3, & 4—integrity and quality)

Noctua Update (Seth & Chris 10 mins)

Noctua rollout to curation groups (Goal 2.b)

  • Current plan:
    • SGD (June, July)
    • WormBase (August, September)
    • Swiss-Prot (October)
    • Others? Issues?

GAFs and GPADs from Noctua models (David and Seth(?), 30 mins)

  • Where do we stand?
    • https://github.com/geneontology/noctua/issues/418
    • Challenges with complex models (evidence) (Goal 2.b.i)
    • All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly (PRO to supply a GPI file).
    • GP-CC Should we allow direct GO part_of CC assertion (rather than via GO <-- enabled_by MF occurs_in --> CC). This is more accurate in some cases e.g. for membrane components.

Use of Qualifiers in Legacy Annotations (needs to come before pipeline??)

  • RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)
  • New qualifiers for biological processes
  • Incorporate expanded list of GP-GO term relations into annotation tools and files
  • Regulation and causality

12-1pm Lunch

Focused Pathway annotation (Goal 1.b.i)

Contacts for Curation Groups (Pascale & David)

Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?

PAINT update (Chris, Karen, Suzi, Pascale and Huaiyu)

  • Analysis of the PAINT annotations (Karen and Huaiyu).
  • Plan for production services/pipeline for PAINT annotations (Chris)
  • Reverse flow (Goal 3.a)
  • Completion of all families with exp. evidence (Goal 3.b)
  • Initial implementation of alert system: what are the requirements? (Goal 3.c)

Annotation QC issues

Consistency exercises (written case studies - Goal 4.a)

GO Rules System (Eric) (Goal 4.b)

QA from PAINT - automated rule-based annotation QA (Pascale) (Goal 4.b)

How do annotation groups handle obsoleting/deprecating GO annotations? (led by someone from SGD or Val?) (Goal 4.c)

Consistent use of the type field in GAFs and GPAD (Chris)

3:30pm Networking and Recreational outing

6:00pm — Dinner

Saturday June 3

8-9am Breakfast

Annotation continued…

Annotation QC issues continued…

HTP papers (Helen, Pascale & Sylvain)

  • See notes /list of papers:

Transcription-Factor decision tree (Ruth - 20 mins)

Modified protein binding (Pascale & Sylvain)

Annotation of Viral Processes

  • 13214
  • Taxon restriction?
  • Annotation of host proteins involved in, or co-opted for, viral reproduction
  • Transcription, translation of viral genome
  • DOS proposal for multi-organism annotation (reviving old proposal) - poss allowing non-canonical function to be separable

12-1pm Lunch

Community relations (Aim 5—enabling the community)

Enrichment Analysis (Val & Seth) (Goal 5.a)

Website? (Goal 5.b)

Outreach? (Goal 5.c)

3-5:30-pm Networking and Recreation

5:30pm POSTERS and mixer