2017 Corvallis GOC Meeting Agenda
- 1 DO NOT EDIT
- 2 Day 1
- 2.1 9am Welcome, schedule and logistics
- 2.2 Overview/Plan for Upcoming Year
- 2.3 Pipeline Migration
- 2.4 New APIs
- 2.5 TermGenie replacement
- 2.6 Graph Store update
- 2.7 GO and Related Projects
- 2.8 Identifiers
- 2.9 Update on Ontology Editing
- 2.10 MF refactoring (Paul, DavidOS)
- 2.11 ECO
- 2.12 Noctua and SIGNOR2
- 2.13 GAFs and GPADs from Noctua models
- 2.14 Use of Qualifiers in Legacy Annotations
- 2.15 The fate of simple processes
- 2.16 The distinction between cellular processes and processes, do we need it?
- 2.17 Annotation of Viral Processes
- 2.18 Annotation QC issues
- 2.19 Enrichment Analysis
- 2.20 PAINT update
- 2.21 Contacts for Curation Groups
- 2.22 Community Relations
- 3 Attendees
DO NOT EDIT
9am Welcome, schedule and logistics
- Remote attendees call in via Bluejeans: https://bluejeans.com/993661940
Overview/Plan for Upcoming Year
- GO PIs presentation
- This year's goals
Seth & Chris 20 mins
Seth & Chris 20 mins
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
- 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)
- Data Formats (Chris)
- BGI and GPI
- Gene association JSON
- How GO and Planteome contribute to one another Chris/Pankaj/Seth
- BioCaddie and db-xrefs.yaml (Chris)
- Monarch (Chris)
- Replacing double MGI (Chris)
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)
Emphasis on practical implications for LEGO curation (templates).
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:
There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g.:
Noctua and SIGNOR2
GAFs and GPADs from Noctua models
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)
- 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
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
- 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
Helen, Pascale & Sylvain
See notes /list of papers:
Transcription-Factor decision tree (Breakout)
Modified protein binding
Pascale & Sylvain
GO Rules System
Consistent use of the type field in GAFs/GPAD
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
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?
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?|
|Laurel Cooper||Jaiswal Group/Oregon State||Y||Y||Y|
|Parul Gupta||Jaiswal Group/Oregon State||Y||Y||Y|
|Ceri Van Slyke||ZFIN||N||N||N||Y||N|
|Pankaj Jaiswal||Reactome/Oregon State||Y||Y||Y|
|Austin Meier||Jaiswal Group/Oregon State||Y||Y||N|
|Sushma Naithani||Jaiswal Group/Oregon State||Y||Y||Y|
|Kimberly Van Auken||WB||Y||Y||Y||Y|
|Pascale Gaudet||GOC/SIB Swiss Institute of Bioinformtaics||Y||Y||?||Y||Y|
- NOT ATTENDING: