WormBase-Caltech Weekly Calls

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2020 Meetings








July 9th, 2020

Gene names issue in SimpleMine and other mining tools

  • Wen: Last week, Jonathan Ewbank raised the issue of gene names that may refer to multiple objects.
  • this can be an issue for multiple data mining tools including WormMine, BioMart, and Gene Set Enrichment.
  • Perhaps have a standalone approach to check if any gene name among a list may refer to multiple objects (users check their name lists before submitting them to any data mining tool).
  • Jae: The public name issue has heterogeneous natures. That means there may be no single solution to solve all those problems.
  • Gene list curation from high-throughput studies, confusing usage of public names probably less than 2% (still cannot be ignored). See examples below--
    • single public name is assigned to multiple WBgene ID, Wen has a list of these genes
    • overlapped or dicistronic genes, ex. mrpl-44 and F02A9.10
    • overlapped or dicistronic, but has a single sequence name, examples:
   exos-4.1 and tin-9.2 (B0564.1)
   eat-18 and lev-10 (Y105E8A.7)
   cha-1 and unc-17 (ZC416.8)
    • simple confusion from authors, ex. mdh-1 and mdh-2
  • One of the most significant problems is a propagation to other DB and papers of these gene name issues.
  • We can make a special note for each gene page, but the people using batch analysis could not catch that easily.
  • Conclusion: Jae and Wen will work on a tool that lets Users "sanitize" their gene lists before submission to data mining tools. They will also write a microPub explaining this issue to the community.


  • Please test and leave any feedback on the word cloud tool (Wormicloud), https://wormicloud.textpressolab.com/
  • Valerio and Jae have worked on a tool that uses data in Textpresso; given a keyword, eg. "transposon", the tool generates a word cloud and word trend.
  • Any keyword can generate a graph that plots trends of occurence across the years in publication abstracts.

Noctua 2.0 form ready to use

  • Caltech summer student will try using Noctua initially for dauer (neuronal signaling) pathways

Nightly names service updates to postgres

  • Nightly using Matt's wb-names-export.jar to get full output of genes from datomic/names service, and updating postgres based on that.

July 16th, 2020

Citing ontologies and their versions

  • Came up in the context of the Alliance: It would be best practice to provide users with the list of ontologies used and their versions/date.
  • If WB ontology developers could make sure their ontology file headers (WB anatomy ontology, WB life stage, etc.) conformed to obo file header specifications, then it would be easy to pull in version and date information into the Alliance.
  • Some useful links
  • Chris worked with Nico yesterday to update the ODK version for WBbt and WBls; versioning should be fine now (once the OBO dashboard runs again (hasn't run since February))
  • Important point: the GitHub release version date tag (e.g. "v2020-06-30") needs to match the ODK release date (as stored in the OBO and OWL file headers)
    • There are some existing mismatches, Chris is cataloging them now

Gene Name Sanitizer

  • Would be good to always (when possible) make users aware of name ambiguities
  • Wen will keep the "Multiple Output" section at the bottom of SimpleMine output
  • The gene name sanitizer will be built as a stand alone tool
  • Important to include history of gene names

Tools linking to SimpleMine

  • Vennter and other tools link to SimpleMine with hard coded field/column names; we should have more dynamic/robust linking without relying on hard coded field names

July 23rd, 2020