Difference between revisions of "WBConfCall 2018.05.17-Agenda and Minutes"
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==Minutes== | ==Minutes== | ||
− | *On call: Adam, Cecilia, Chris, Daniela, Juancarlos, Karen, Kimberly, Raymond, Scott, Sibyl, Todd, Valerio, Wen, Kevin, Paul D, Gary, Matt, Paul K | + | *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 - Kimberly=== | ||
Line 28: | Line 28: | ||
**Resolution: for next release, provide intervening genomic sequence but make it clear that it's predicted from genomic. | **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. | **Chris will check and close the original ticket, if the changes Adam pushed are okay. | ||
+ | |||
+ | *[https://github.com/WormBase/website/issues/6391 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. | ||
+ | |||
+ | ===WBStrainIDs=== | ||
+ | *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 | ||
+ | **Reference? | ||
+ | **Genotype? | ||
+ | **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. |
Latest revision as of 16:43, 17 May 2018
Contents
Agenda
HelpDesk - Kimberly
Helpdesk Issues Still Open
WBStrain ids
- 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
AGR
Minutes
- 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.
WBStrainIDs
- 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
- Reference?
- Genotype?
- 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.