WormBase-Caltech Weekly Calls
From WormBaseWiki
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2018 Meetings
June 7, 2018
Alliance literature pipeline working group
- Has anyone gotten back to Carol Bult about WB/Textpresso membership in the group? Not yet
- Paul & Kimberly can join; Kimberly will sit in on group meetings
SPELL migration
- SGD put SPELL into the cloud; will give us code to set up WB SPELL in cloud
- Want to have common interface but two instances (yeast & worm)
- Worm data in SPELL may be more complicated than the yeast data (different species, platforms, meta data, etc.)
- Mike Cherry proposed to use GTEx to replace SPELL. (www.gtexportal.org)
- Trying to get GTEX to have same functionality as SPELL
Progress report
- Wen can generate numbers of changes since last year
- 5-year progress report coming up (for funding agencies)
- Want a progress report-like document to give to SAB in July
- WS259 - WS265
Paper author name
- Jonathan Ewbank wrote in about an incorrect author name
- Issue for WBPaper00048704: https://wormbase.org/resources/paper/WBPaper00048704#0--10
- First author is "Li, C" as in PubMed (correct name) in WormBase as "Chun, L"
- Will make a GitHub ticket; web team may need to look at
Lab class
- Lab data is not clean/consistent; has gotten messy
- Cecilia trying to clean it up
- There is conflicting data from lab class, author class, and person class
- Currently there is a ~redundant curation pipeline; considering pulling person info into lab class
- When looking at lab page, if there is a problem with a person's info, changes would be made (requested) in the person class, not the lab class
- Cecilia will contact labs to ask about correctness of information
- Can have a discussion with Ann and Aric at CGC
How many C. elegans genes have "good" knockouts?
- Paul giving talk next week, wants to report
- Chris will look into
- Mitani did 1,000 deletions in last year
Server logs
- SimpleMine logs are all coming from Amazon; will need to ask Todd about SimpleMine usage (from AWS stats?)
Migration of lab data
- Data for labs was coming from Name Server (in Hinxton) - Comment:[PD] Not coming from the Nameserver, geneace was the only source of Lab data prior to handover.
- Now Paul D has stopped curating lab info - Comment:[PD] Build config has been updated to take the majority of lab data from citace rather than geneace
Database File Class remove/format ---------------------------------------------------------------------------------------------------------------- db=geneace file=geneace_Laboratory.ace class=Laboratory format="Alleles WBVar\d{8}" delete=Representative delete=Registered_lab_members delete=Past_lab_members delete=Allele_designation delete=Strain_designation delete=Address db=citace file=caltech_Laboratory.ace class=Laboratory delete=Alleles format="Representative WBPerson\d{1,5}" format="Registered_lab_members WBPerson\d{1,5}" format="Past_lab_members WBPerson\d{1,5}"
- Now that Cecilia is curating, will pull lab info from Postgres
June 21, 2018
SAB
- Lightning talks at project meeting
- 45 minutes curation talk to SAB
- What data types are being incorporated with the Alliance? What have we gained from those conversations?
- How have Alliance interactions benefited us?
- How does the Datomic migration affect our curation and data models?
- Alliance data models should be union of existing MOD data models, but does not require curation of all attributes at each MOD
- Do WB and our users benefit from creating a ?Genotype class?