June 1-3, 2017 | Draft Agenda | GOC
Detail agenda ref: http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda
or at the end of the s
Remote attendees call in via Bluejeans: https://bluejeans.com/993661940
Room: Agriculture Science Room
- 8:00am-9:00am Breakfast
- 9:00am-12:00pm GOC: session-1
- 12:00pm-1:00pm Lunch
- 1:00pm-3:00pm GOC: session-2
- 3:00pm-3:30pm snacks
- 3:30pm-5:00pm GOC: session-3
- 5:00pm onward mixer
Room: Agriculture Science Room
- 8:00am-9:00am Breakfast
- 9:00am-12:00pm GOC: session-4
- 12:00pm-1:00pm Lunch
- 1:00pm-3:30pm GOC: session-5
- 3:30pm pick snacks and go for recreation activity at Willamette Park (Transportation provided)
- 6:00-8:00pm onward Dinner at at Willamette Park
- 8:00am-9:00am Breakfast
- 9:00am-12:00pm GOC: session-6
- 12:00pm-1:00pm Lunch
- 1:00pm-3:00pm GOC: session-7
- 3:00pm-5:30pm Walk to MU Basement for recreation activity
- 5:30pm Start walking back to the meeting venue CH2M Hill Alumni Center (Willamette Room)
- 6:00pm onward Poster Session and Mixer at CH2M Hill Alumni Center (Willamette Room)
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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
- N# of pathways annotated according to prioritized list (Paul S to provide)
- Complete the incorporation of new annotation groups/sources: SynGO, SIGNOR
- 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
- 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)
- Am 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)
TermGenie replacement* (Dan, Chris 20 mins)
Graph Store update (Eric 10 mins)
Licensing and GO (Seth 20 mins)
- Where we currently stand with licensing and possible issues
- What others do with our data
- Planteome (Chris, Seth, and Pankaj): How GO and Planteome contribute to one another
- SIGNOR (Chris and Paul T) and SynGO (Ruth?) annotation incorporation (Goal 1.b.ii)
- AGR
- Parts of GO infrastructure being re-used by AGR (Chris)
- Data Formats (Chris)
- BGI and GPI
- Gene association JSON
- Ribbon demo (Suzi)
- Other Projects
- BioCaddie and db-xrefs.yaml (Chris)
- Monarch (Chris)
- Panther?
Identifiers (Chris) [WILL PROBABLY MOVE TO IDENTIFIERS SECTION IN AGR ABOVE]
- Replacing double MGI (Chris)
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)
- Mapping to classic GO evidence codes. 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.
Noctua and SIGNOR2 (Chris & Paul T)
Straw man BP refactor Chris (Goal 1.a.ii)
The fate of simple processes
- What do we consider a single-step process and what is their future?
- The distinction between cellular processes and processes, do we need it?
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.
Use of Qualifiers in Legacy Annotations (needs to come before pipeline??)
- 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
Focused Pathway annotation (Goal 1.b.i)
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)
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
Annotation QC issues continued…
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
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)
3-5:30-pm Networking and Recreation