2017 Corvallis GOC Meeting Agenda

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Contents

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
      • Annotation metrics: for EXP: number of publications, not annotations
  • 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
    • Increase the number of contributing groups
  • 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)
  • Aim 5: Enable the scientific community to make full use of the GO data resources
    • Fixed existing problems with enrichment analysis
    • Website?
    • Outreach?

Provide a 'hub' (Aim 2)

Infrastructure

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

  • Migration from SVN
  • QC checks
  • New APIs (Seth & Chris 10 mins)
  • Graph Store update (Eric 10 mins)

Annotation

Increase the number of contributing groups


Ontology (Aim 1 comprehensive model of biological knowledge)

Update on Ontology Editing (David, Chris, Moni, Kimberly ~40min)

12-1pm Lunch

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

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

The fate of simple processes

3-3:30pm snacks

Annotation (Aim 1 comprehensive model of biological knowledge)

TermGenie replacement (Dan, Chris 20 mins)

HTP papers (Helen, Pascale & Sylvain)

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

Use of Qualifiers in Legacy Annotations (Pascale)

  • 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

ECO

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 - GOC will add itself as an admin on these annotations to update and remove them as necessary.


6:00pm onwards mixer

Friday June 2

8-9am Breakfast

PAINT update (Aim 3:Apply biological knowledge obtained in model organisms to human biology)

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)

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)


12-1pm Lunch

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.


3:30pm Networking and Recreational outing

6:00pm — Dinner

Saturday June 3

8-9am Breakfast

Community relations (Aim 5—enabling the community)

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

Licensing and GO (Seth 20 mins)

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

AGR update

  • Other Projects
    • BioCaddie and db-xrefs.yaml (Chris)
    • Monarch (Chris)
    • Panther?

Website? (Goal 5.b)

Outreach? (Goal 5.c)

12-1pm Lunch

3-5:30-pm Networking and Recreation

5:30pm POSTERS and mixer

Attendees

Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!

Name Organization Are you planning to attend the GOC meeting Are you planning to attend the GOC dinner Are you bringing a poster? how many? Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th? Are you planning to attend the Reactome workshop on Monday, June 5th?
Giulia Antonazzo FlyBase Y Y N N
Helen Attrill FlyBase Y Y N N
Judy Blake MGI Y Y Y-1 N N
Seth Carbon Berkeley/LBL Y Y Y
Mike Cherry SGD Y Y N N N
Paul Thomas USC Y Y Y Y
Laurel Cooper Jaiswal Group/Oregon State Y Y Y
Stacia Engel SGD Y N N N N
Priyanka Garg Y Y Y
Parul Gupta Jaiswal Group/Oregon State Y Y Y
Tom Hayman RGD Y Y Y Y
Emily Heald SGD Y Y N Y N
David Hill MGI Y Y N Y N
Doug Howe ZFIN Y maybe N Y N
Sridhar Ramachandran ZFIN N N N Y N
David Fashena ZFIN N N N Y N
Leyla Ruzica ZFIN N N N Y N
Pankaj Jaiswal Reactome/Oregon State Y Y Y
Stan Laulederkind RGD Y Y Y Y
Suzi Lewis Berkeley/LBL Y Y N Y N
Ruth Lovering UCL Y Y Y-3 Y Y
Austin Meier Jaiswal Group/Oregon State Y Y N
Moni Munoz-Torres Berkeley/LBL Y Y Y N
Sushma Naithani Jaiswal Group/Oregon State Y Y Y
Darren Natale PRO Y N N
Sabrina Toro Zfin Y maybe N Y Y
Kimberly Van Auken WB Y Y Y (1) Y Y
Edith Wong SGD Y Y N Y N
Huaiyu Mi USC Y Y N
Chris Mungall LBL Y Y Y Y
Peter D'Eustachio Reactome Y Y N? Y Y
Maria Martin EMBL-EBI Y Y Y(1) N N
Tony Sawford EMBL-EBI Y Y N N N
Alice Shypitsyna EMBL-EBI Y Y Y(1) Y Y
George Georghiou EMBL-EBI Y Y Y(1) Y Y
Pascale Gaudet GOC/SIB Swiss Institute of Bioinformtaics Y Y  ? Y Y
David OS EBI Y Y N AM N
Malcolm Fisher Xenbase Y Y N Y Y
  • NOT ATTENDING:Remote: Bluejeans
Name Organization
Harold Drabkin MGI
Mary Dolan MGI
Li Ni MGI
Karen Christie MGI
Dmitry Sitnikov MGI
Leonore Reiser TAIR
Tanya Berardini TAIR