WormBase-Caltech Weekly Calls
From WormBaseWiki
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2018 Meetings
March 1, 2018
Elsevier paper-linking through Scholix
- Bidirectional linking in place with ScienceDirect, Elsevier
- We link to their papers via DOI
- They link papers to WB
- Scholix
- http://www.scholix.org
- Scholix becoming a standard platform for linking to DB websites
- WB would need to establish Scholix integration?
- Daniela to check in with the Alliance to see what the other groups are doing
- Would Caltech library need to establish a pipeline or would WB do it?
- Would be good to revisit the paper page display for what is referenced in the paper
- GO terms are not showing currently
- Would be good to assess what else is not showing currently
Upstate NY Worm Meeting
- Confirmation from organizers?
- Kimberly and Wen reached out to organizers about WB presentation
- 20-30 minute time slot for talk
- What are most important topics to bring up?
- Ask authors to submit sequence for sequence features, etc.
- Micropublications
- Would be good to have answers to common questions about micropublications (how we get reviewers, etc.)
- Alliance of Genome Resources
- Help Desk/ Online chat service
- Organizers want WB to have table at meeting
- Meeting in Syracuse
Midwest Worm Meeting
- Organizers asked for $50-$100 sponsorship
We can pay for registration but we are not a company to sponsor events.
Metrics
- How do DBs help research?
- How much time do MODs/Alliance etc. databases save researchers?
March 8, 2018
SimpleMine interactions
- Wen considering adding interaction data to SimpleMine
- Should we add a single column listing interacting genes with types in parentheses
- Wouldn't want to add too many columns
- Want to indicate, for a query gene, genes for which multiple interaction types have been observed
- Once interaction data is in WormMine, we can omit it from SimpleMine
- SimpleMine is not too difficult to develop or maintain as long as data models don't change
SimpleMine preserving input list
- Adding functionality to WormMine that preserves original gene list
- Some input genes return multiple hits/rows
- We need to recognize these entries and deposit extra rows separately
Alliance working group project plans
- Interactions
- What are prioritized deliverables?
- Predicted (physical) interactions: Interologs, Inter-species extrapolations
- (Automated) gene descriptions
- Ranjana and Ceri have added content to project plan
- Add phenotype data to description for information-poor genes (currently last on priority list)
- Disease/phenotypes
- Cindy et al. producing project plan documents for disease and phenotype separately
March 15, 2018
HTTP vs HTTPS
- Plan to move to https site-wide as a standard
- Google site ranking includes metric for https security
- All pieces in place on main site; just a few small things at Caltech to resolve
- What services are having problems?
- Raymond: Don't know the SSL details; has made Caltech machines using SSL layer
- Todd: Not needed; should be handled by proxy
- Todd needs to just know what are problematic URLs; should all be handled by main URL www.wormbase.org
- Ontology Browser broke, Juancarlos went to fix then had problem with https
- Todd: haven't setup https for all development sites yet, but will do that
- Gene Set Enrichment Tool: redirects to local/Caltech site that serves the page
- Todd & Sibyl looking at; one possible solution is to get the recent code on staging and replace it (tool breaks on staging)
- Juancarlos, Raymond, Sibyl, and Todd will discuss later (Slack channel?)
Disease model annotation class display
- Ranjana has two GitHub tickets open
- Data has gone into ACEDB, but no display is configured yet
- Ranjana would like to Skype with Sibyl to explain
- Bypass ACEDB altogether? Go right into Datomic? Need to check, but will probably pull into ACEDB and do the conversion to Datomic at the same time?
Baltimore Area Worm Meeting
- Chris presenting tomorrow at the meeting
- Will cover data mining tools, new data and displays
Alliance
- Paul S: Work on Alliance plans; important
Citace upload
- Next Tuesday (March 20th) at 10am Pacific
