WBConfCall 2018.05.17-Agenda and Minutes
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HelpDesk - Kimberly
Helpdesk Issues Still Open
- would be good to get a list of people who need to be able to create new strains
- will reside temporary in the old NameServer at Sanger and then move to the new Datomic one on AWS
SAB - Toronto, CA
- On call: Adam, Cecilia, Chris, Daniela, Juancarlos, Karen, Kimberly, Paulo, Raymond, Scott, Sibyl, Todd, Valerio, Wen, Kevin, Paul D, Gary, Matt, Paul K
HelpDesk - Kimberly
Helpdesk Issues Still Open
- I am trying to have access to fosmid ...
- On staging, we will begin providing the end sequences
- We've never had the full sequence, so if we were providing a "fosmid" sequence, it might have been the intervening genomic sequence
- What would users want?
- It seems we could provide the intervening sequence but we need to communicate with users about what they're actually getting, i.e. a prediction.
- Would this be a potential source of confusion to users, though, who may need to validate the sequence against a clone they order from Don Moerman's group?
- Resolution: for next release, provide intervening genomic sequence but make it clear that it's predicted from genomic.
- Chris will check and close the original ticket, if the changes Adam pushed are okay.
- I'm only filling this out because your "need help ...
- We can't really address every possible browser add-on issue
- Sibyl will respond and close.
- Bulk assigning strain IDs to existing strains is easy.
- How do we assign new strain IDs at the point of curation?
- Will treat similarly to variations, i.e. use a name service to check if an ID already exists; if not, can request a new strain ID to use in postgres curation database.
- Who needs access to the name server for this?
- Chris, Daniela, Karen, Ranjana
- Discussed institutional vs personal sign-on; personal is better, allows for assignment of WBPerson IDs
- What additional information will be solicited when requesting a new strain ID?
- Public name is most important
- This really is an issue of what gets curated where.
- Ideally, we'd have a central curation database (just saying) that would allow immediate entry of the data.
- Another option is that all strain information would come from Caltech curation.
- Would there be anything left for Hinxton to add or do wrt strain curation?
- One caveat: if author's potentially correct data in the paper when they submit the strain data to the CGC, how would we reconcile that?
- It would be good to have a shared data model with the CGC, maybe even share the same curation tool.
- Circling back, do we really need strain IDs?
- Are strain names unique?
- Karen has found some strain and clone names that are the same.
- Todd did some analysis several years ago to see how many classes have overlapping entity names.
- There were some wrt CDS and transcript; cell and cell group (no longer an issue), but overall the issue was not that bad.
- For AGR, Sibyl created an ID resolver page. Kevin tested and, so far, hasn't found any issues.
- There is also the issue of assigning unique IDs to genotypes. Should this issue be coordinated with assigning strain IDs?
- Raymond: can this change be coordinated with moving to the centralized curation database?
- Is use of the strain server an efficient way to curate?
- Would it be possible to create a strain in the OA during curation? Would this be more efficient?
- Strain IDs could be created during curation, added to postgres, and immediately available for curation, similarly to variation IDs.
- If there were conflicts with the information in the CGC, we would ask the CGC to correct it, so that the information in WB and the CGC is the same.
- What's the plan?
- Check which strain fields are free text vs controlled list in OA
- Possibley create a strain curation form that would allow curators to create WBStrain IDs and associated information that could be used immediately in the OA.
- AI:Kevin, Paul, Ranjana, Juancarlos will work on coming up with the most efficient way to handle strain curation.
- Discussion on creating genotypes in WB
- What is a 'relevant' genotype? This may depend on the organism.
- A 'relevant' genotype would be selected at the time of curation, and exported to AGR.
- The 'absolute' genotype could still be completely captured in WB.
- Can we move forward on creating a server/system for creating genotypes in WB?
- AI:Chris will report back about genotypes from the AGR phenotypes working group.
AGR All-Hands Meeting
- Anyone who wants to attend from WB can go.
- Schedule/agenda for meeting will be discussed further by the AGR PIs.