2017 Corvallis GOC Meeting Agenda: Difference between revisions
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Revision as of 12:44, 5 May 2017
Day 1
9am Welcome, schedule and logistics
- Remote attendees call in via Bluejeans: https://bluejeans.com/993661940
- Schedule
- Introductions
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 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
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?
- 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)
- RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)
The fate of simple processes
- What do we consider a single-step process and what is their future?
- GH ticket about single step processes
- Is this a single step process?
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
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
- by default have the enrichment tool run directly on the GO annotation dataset
- by default enable loading a background
- currently missing a substantial number of annotations (e.g. fission yeast)
- Via ontobio python library (Chris)
- Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb
PAINT update
Pascale and Huaiyu
- Analysis of the PAINT annotation.
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?
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 | Y-1 | 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 | N | |
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 |
- NOT ATTENDING: