Annotation Conf. Call 2018-04-24
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Agenda
GOC Meeting, NYU, New York, NY, May 12-14th
- Reminder to register, and reserve your hotel room before April 6th if staying at the Shelburne NYC
- Logistics
- Agenda
20th Anniversary GO Meeting, Montreal, Canada
- Dates set for Oct 17-19
Annotation Survey
- We are conducting a survey on annotation practices across the GOC
- This will allow us to have a better overall view of different group's workflows, pipelines
- Only need one response per annotation group
- Would like results before the GOC meeting in NY
- Please could each group respond by May 1st
Ontology Development and Annotation Review
Transcription factor refactoring
- Slides: summary of work so far: http://wiki.geneontology.org/images/1/18/Transcription-overhaul-STATUS-2018-04-24.pptx
- Remove the 'transcription factor activity, protein binding' branch
- https://github.com/geneontology/go-ontology/issues/15535
- Obsoletion notice: Some children of GO:0000988 transcription factor activity, protein binding’
- https://github.com/geneontology/go-ontology/issues/15538
Annotation Review requests
- GO:0000989 'transcription factor activity, transcription factor binding'
- GO:0001076 'transcription factor activity, RNA polymerase II transcription factor binding'
- There will be more annotations reviews to come in the upcoming days/weeks. For most the work load is expected to be small, a few proteins per group at the most.
- Please let Pascale know if you are trying to annotate a function and cannot find the term - this will help decide whether some terms are missing or if we need to improve some term labels/definitions.
Updates on Projects
MAPK Cascade
Extracellular Matrix
Canonical Wnt Signaling Pathway
- Working on compiling annotations to review
- Main issues:
- Distinguishing gene products that are involved in canonical Wnt signaling vs +/- regulation of canonical Wnt signaling
- Annotating to more granular child of Wnt signaling pathway when appropriate
- Annotation of downstream targets to the canonical Wnt signaling pathway
Infrastructure
References
- Proposal to change the cardinality of the reference field to be 1.
- MOD paper IDs would only be used if there is no PMID, doi, GO_REF, etc.
GO-CAM/Noctua
- Next call tomorrow, Wednesday, April 25th at 11:00am EDT (see Google calendar)
users.yaml
- As part of cleaning up the users.yaml file and setting Noctua editing permissions, we have added a new tag, previous_groups, to the users.yaml schema
- This tag will allow us to keep track of affiliations accurately
Protein Complexes Working Group
- Birgit will send around a Doodle poll for the next call.
Minutes
- On call: Chris, Dustin, Edith, George, Giulia, Harold, Karen, Kevin, Kimberly, Liz, Midori, Mila, Patrick, Pascale, Paul T. (?), Penelope, Petra, Rachael, Ruth, Sage, Sandra, Shur-Jen, Stacia, Stan, Suzi L., Tanya, Val
GOC Meeting
- Please check the agenda and contact the consortium if you have any questions/concerns
Annotation Survey
- Five groups have responded:
- dictyBase
- FlyBase
- MGI
- TAIR
- Zfin
- Please respond by May 1st so we can collate the results in time for the consortium meeting
Transcription - Ontology Updates
- Discussion:
- Meaning of gene-specific transcription factor activity (possible new name for DNA-binding transcription factor activity)
- Does this indicate a different mechanism of action than other (i.e. more general) transcription factors?
- Strong objection from Karen, Stacia to the gene-specific vs general terms - how would these terms actually be defined?
- What level of specificity is helpful/needed wrt the ontology terms?
- Users often want to retrieve lists of transcription factors; what classification is most helpful for this? This can actually be much more difficult to do than might be expected.
- Biological process?
- Can we define in GO the beginning and end of the transcription process?
- Yes, but we'd need to be aware that there might be substantial re-annotation as many genes are annotated to regulation of transcription-type terms.
- Complex membership?
- Is doing this via MF too hard, i.e. hard to uniquely distinguish functions for all the gene products involved in transcription?
- Biological process?
- What type of query would be most helpful to users?
- Meaning of gene-specific transcription factor activity (possible new name for DNA-binding transcription factor activity)
- ACTION ITEM:Curators please address the high priority annotation review tickets as soon as possible.