WormBase-Caltech Weekly Calls

From WormBaseWiki
Revision as of 17:30, 22 March 2018 by Cgrove (talk | contribs)
Jump to navigationJump to search

Previous Years

2009 Meetings

2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings

2016 Meetings

2017 Meetings


GoToMeeting link: https://www.gotomeet.me/wormbase1


2018 Meetings

January

February


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

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


March 22, 2018

Baltimore Area Worm Meeting

  • Enthusiasm for Micropublications
  • Questions:
    • How to download RNASeq data values from gene page?
    • What does "WS" mean? (I don't know)
    • WormBase provides protein-coding gene exon expression evidence, what about small, non-coding RNAs?
  • Comments:
    • FTP README docs need work, updating
    • WormMine is not intuitive
    • It's hard to know what each data mining tool is good/best for
  • Requests:
    • Create simple Galaxy import of WB genome sequence
    • Display prevalence of splice junctions
    • Add README docs to FTP site (and/or update them)
    • Separate RNAi and allele based phenotypes
    • Include BioRxiv papers in gene page References widget