2018 Montreal GOC Meeting Agenda
Montreal meeting Milestones
New Pipeline & new pipeline documentation
Kimberly, Pascale, Chris, Seth, etc Must be completed (as much as possible) and announced
- Announcement: plan for migrating to GPAD (Seth)
- Manage migration of consortium members to use explicit snapshot PURLs :
- Excluding MOD-specific refs from the GO database: see
GO rules update, pipeline and error reports
Eric & Pascale
- Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928
- Current rules status & future priorities
- For MODs: where to find reports: http://snapshot.geneontology.org/reports/gorule-report.html
PAINT pipeline update
PAINT GAF file generation QC
Huaiyu and Pascale https://github.com/orgs/geneontology/projects/23
(can we do this at the same time as pipeline -- cjm?)
Kimberly Seth, etc https://github.com/orgs/geneontology/projects/19
GO website migration
Laurent-Philippe, Suzanna, Suzi, etc: https://github.com/orgs/geneontology/projects/22
Ontology and Annotation documentation update
David, Kimberly and Pascale (random thoughts:
- Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions
GO subsets update
- Deprecated a number of unused/unmaintained subsets
- Show subset yaml files and how they are used
- Each subset needs a maintainer
- Gene Product to terms relations: https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)
- Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?
- Signaling 2017 update
- ECM reviews
- Transcription reviews
- Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1
- MF refactor including transcription: https://github.com/orgs/geneontology/projects/25
- ECM update
- Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc
- Pathways2GO: https://github.com/orgs/geneontology/projects/24
- Ontology maintenance: https://github.com/orgs/geneontology/projects/14
- All synapse tickets are closed
Binding and Protein complexes
- Should these be separate branches of GO ?
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940
- Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.
Handling redundant information
- Define redundant information:
In AmiGO, we should be able to improve the display by removing redundant information. That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files.
Discussion points: Is redundant, non-experimental annotation ever useful?
- Are there any use cases where people have used these annotations for some type of analysis?
- Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced.
- Should all GOC members be handling redundancy in the same way?
- If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?
- If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered?
- Doubled up IBA+EXP annotations (from Karen Christie)
- Issue with GOC inference file (i) incorrect aspect reported
Representing complete proteomes in GO (added by Val, as suggested by Chris)
Datasets (obtaining/maintaining complete datasets with unique identifiers)
Overview. Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm
1. GO uses https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther. This reference proteome set represents each HGNC ID uniquely. This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?
- What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit
- Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between:
- (1) "not in the GO database (not found);
- (2) "unknown" (ND),
- (3) "unannotated" (no ND, and no annotation in Aspect of interest)
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)
Breakout sessions topics
- Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ?
- GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?
- Modeling transcription in GO-CAMs
- 'Response to' workshop (similar to the signaling WS)
- Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit
Product owners/tech leads discussion - lunch Thursday
- Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting