2017 Corvallis GOC Meeting Agenda: Difference between revisions
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==3-3:30pm snacks== | ==3-3:30pm snacks== | ||
==Annotation== | ==Annotation== | ||
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*Incorporate expanded list of GP-GO term relations into annotation tools and files | *Incorporate expanded list of GP-GO term relations into annotation tools and files | ||
*Regulation and causality | *Regulation and causality | ||
===ECO=== | ===ECO=== | ||
*Mapping to classic GO evidence codes. The official mapping of IMP to ECO is insufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological). | *Mapping to classic GO evidence codes (DOS). | ||
*The official mapping of IMP to ECO is insufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological). | |||
**https://github.com/evidenceontology/evidenceontology/issues/117 | **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. | *There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g. |
Revision as of 20:57, 31 May 2017
Thursday June 1
8-9am Breakfast and setup
Welcome, schedule and logistics
- Remote attendees call in via Bluejeans: https://bluejeans.com/993661940
- Introductions
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
- Ontology
- Aim 2: Provide the “hub” for a broad community of scientists to extend and modify the GO
- Annotation
- Facilitating and encouraging annotation submission for the community
- e.g. Xenbase (need action item to come out of this)
- Facilitating and encouraging annotation submission for the community
- Pipeline transition completed (**almost** -- chris)
- Noctua rolled out to all GO curation groups
- Evidence issues resolved in Noctua
- Documentation for ontology request guidelines completed
- Annotation
- 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?
Infrastructure (Aim 2—Provide a “hub”)
Pipeline Migration (Seth & Chris 20 mins) (Goal 2.a)
New APIs (Seth & Chris 10 mins)
Graph Store update (Eric 10 mins)
12-1pm Lunch
Ontology (Aim 1—a comprehensive model of biological knowledge)
Update on Ontology Editing: David + Chris 20min
- Design Pattern Updates: David OS + Chris 20 mins
- Ontology Documentation: Moni 10 mins (Goal 2.c)
- Curator notes and propagation
- Proposal: text mining github tickets for ontology terms (Chris, Kimberley)
MF refactoring (Paul, DavidOS 30 mins) (Goal 1.a.i)
- Issues: https://github.com/geneontology/molecular_function_refactoring/issues
- Emphasis on practical implications for LEGO curation (templates).
Straw man BP refactor Chris (Goal 1.a.ii)
- The distinction between cellular processes and processes, do we need it?
- GH ticket about cellular processes: https://github.com/geneontology/go-ontology/issues/12849
The fate of simple processes
- What do we consider a single-step process and what is their future?
- GH ticket about single step processes https://github.com/geneontology/go-ontology/issues/12859
- Is this a single step process? https://github.com/geneontology/go-ontology/issues/13012
3-3:30pm snacks
Annotation
TermGenie replacement (Dan, Chris 20 mins)
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
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
- Mapping to classic GO evidence codes (DOS).
- The official mapping of IMP to ECO is insufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).
- There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g.
6:00pm onwards mixer
Friday June 2
8-9am Breakfast
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.
12-1pm Lunch
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
12-1pm Lunch
Community relations (Aim 5—enabling the community)
Enrichment Analysis (Val & Seth) (Goal 5.a)
- 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
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
- Planteome (Chris, Seth, and Pankaj): How GO and Planteome contribute to one another
- AGR
- Parts of GO infrastructure being re-used by AGR (Chris)
- db-xrefs.yaml
- Data Formats (Chris)
- BGI and GPI
- Gene association JSON
- Ribbon demo (Suzi)
- Identifiers (Chris) [WILL PROBABLY MOVE TO IDENTIFIERS SECTION IN AGR ABOVE]**
- Replacing double MGI (Chris)
- Parts of GO infrastructure being re-used by AGR (Chris)
- Other Projects
- BioCaddie and db-xrefs.yaml (Chris)
- Monarch (Chris)
- Panther?
Website? (Goal 5.b)
Outreach? (Goal 5.c)
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 |