2017 Corvallis GOC Meeting Agenda

From GO Wiki
Jump to: navigation, search

DO NOT EDIT

Day 1

9am Welcome, schedule and logistics


Overview/Plan for Upcoming Year

  • GO PIs presentation
  • This year's goals

Pipeline Migration

Seth & Chris 20 mins

New APIs

Seth & Chris 20 mins

TermGenie replacement

https://github.com/geneontology/go-ontology/issues/13472 Chris 20 mins

Graph Store update

Eric 10 mins

GO and Related Projects

Licensing and GO

Seth 20 mins

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

AGR

  • What does GO need to do for AGR?
  • Is there anything that GO curators should do any differently for this?
  • Parts of GO infrastructure being re-used by AGR (Chris)
    • db-xrefs.yaml
  • Data Formats (Chris)
    • BGI and GPI
    • Gene association JSON

Planteome

  • How GO and Planteome contribute to one another Chris/Pankaj/Seth

Other Projects

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

Identifiers


Update on Ontology Editing

  • David + Chris 20min
  • Design Pattern Updates: David OS + Chris 20 mins
  • Ontology Documentation: Moni 10 mins
  • Curator notes and propagation
  • Proposal: text mining github tickets for ontology terms (Chris, Kimberly)

MF refactoring (Paul, DavidOS)

30 mins

Emphasis on practical implications for LEGO curation (templates).

ECO

Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).

IS THERE A TICKET FOR THIS ON THE ECO TRACKER?

I think it might be this one:

https://github.com/evidenceontology/evidenceontology/issues/117

There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g.:

https://github.com/evidenceontology/evidenceontology/issues/123#issuecomment-281041854

Noctua and SIGNOR2

Chris/PaulT

GAFs and GPADs from Noctua models

https://github.com/geneontology/noctua/issues/418

David + others? 30 min

  • Where do we stand?
  • Challenges with complex models (evidence)
  • 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); see GITHUB https://github.com/geneontology/noctua/issues/429
  • 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

(this should probably come before the go-cam->gaf pipeline above)

The fate of simple processes

The distinction between cellular processes and processes, do we need it?

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-cannonical function to be separable

Annotation QC issues

HTP papers

Helen, Pascale & Sylvain

See notes /list of papers:

Transcription-Factor decision tree (Breakout)

Ruth (20mins?)

https://github.com/geneontology/go-annotation/issues/1463

Modified protein binding

Pascale & Sylvain

https://github.com/geneontology/go-ontology/issues/12787

GO Rules System

Eric

Consistent use of the type field in GAFs/GPAD

Chris

Enrichment Analysis

Val & Seth

PAINT update

Pascale and Huaiyu

  • Analysis of the PAINT annotation.
  • Plan for production services/pipeline for PAINT annotations

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?

Community Relations

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
Ceri Van Slyke ZFIN N N 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 Y
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 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  ?
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: