WormBase-Caltech Weekly Calls

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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



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.


  • 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


  • 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


  • Paul S: Work on Alliance plans; important

Citace upload

  • Next Tuesday (March 20th) at 10am Pacific

March 22, 2018

WB grant critique

  • Great comments
  • Skeptical that community curation will take off (or that it will get all curation done)
  • Positive reviews of Alliance interactions with WB

New York worm meeting

  • Kimberly and Wen will head to local worm meeting to present on WB

Human Genetics meeting

  • Meeting in October
  • Will have Alliance presence there


  • How important is it to have the MOD?
  • What is the added value of the Alliance portal?
  • What are the use cases that can be uniquely handled by the Alliance website/portal? MOD site?
  • Something to think about; send thoughts and ideas to Paul S.
  • Parallel development pipelines?
    • Valerio discussing with AGR developers tomorrow
    • So far, AGR development has been centralized; may need to allow parallel development for efficiency/efficacy
    • Example: development of automated gene descriptions
    • JBrowse and GO Ribbon currently developed independently

Person curation

  • Cecilia had looked at how other MODs/groups curate authors/persons? Interact with community?
  • How can the Alliance do the same (union of all approaches)?
  • ZFIN has person page

Variant graphical viewer

  • As requested by Andy Golden and others
  • Hope to have a mockup by April
  • Use synteny viewer/browser? Long evolutionary distances (human-worm) may be tricky

Baltimore Area Worm Meeting

  • Chris' slides
  • Enthusiasm for Micropublications
  • Enthusiasm for the Alliance of Genome Resources
  • Questions:
    • How to download RNASeq data values from gene page?
    • What does "WS" mean?
    • WormBase provides protein-coding gene exon expression evidence, what about small, non-coding RNAs?
    • How are micropublication reviewers selected?
      • Authors suggest reviewers; uP team suggest reviewers
      • PIs, post-docs and senior grad students (vetted; already have published papers)
    • Are phenotypes included in Ontology Browser also from genetic interactions? Answer: "No", response: "Good"
    • Are we going to lose WormBase and functionality?
  • 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
      • Would be good to have a simple document that outlines the best uses of each tool
      • How would we best provide such a document? Location? Versioning? Micropublication?
      • Create a one page PDF to print out and give out at meetings?
      • Update blogs (describing nature of updates to each tool)?
      • Existing FAQ Wiki?
      • Important to have a single place for documentation (to avoid denormalization)
  • 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
      • Probably worth considering; have heard from users before
      • Could also provide functionality in Phenotype Graph
    • Include BioRxiv papers in gene page References widget
      • Could provide links to BioRxiv (with relevant search results)?
      • Is there a way to link BioRxiv papers to the eventually published paper?
      • Are full texts indexed?

March 29, 2018

Gene Set Enrichment Analysis: duplicate entries

  • Although duplicate genes in an input list are not counted more than once, the output lists the valid gene list that includes duplicates

Interactions Venn Diagram

GO term and spatiotemporal expression comparison

GO enrichment analysis for interacting genes

Inclusion of negative GO annotations in Alliance GO ribbon

  • See cpx-1 gene page: http://www.alliancegenome.org/gene/WB:WBGene00022271
  • In the GO ribbon, the term "nucleus" is highlighted, yet this is only because of two negative annotations coming from mouse and rat
  • Do we want negative GO annotations included in the display by default? Shouldn't we alert users to this if we are going to do this?
  • Thoughts?

Upstate NY C elegans Meeting

  • Wen and Kimberly presented at the UNYCEM in Syracuse last Saturday (3/24)
  • Feedback:
    • WormMine is hard to learn (but performing operations on lists of genes is something people really want/need to do)
    • Video tutorials would be very helpful, especially for teaching students different WB functionality
    • Micropublications were well received
      • People were specifically interested in publishing negative results; maybe make that point even more prominent on the FAQs?
    • Downloading sequences that include coding and non-coding, it would be really helpful to have visual cues for coding vs non-coding
    • Should the C. elegans community consider moving towards more mammalian-centric gene names, even if that means changing current gene names?
    • A better mobile app would be great; people want to look up C. elegans info on their phones and the current view is cumbersome