WBConfCall 2020.07.16-Agenda and Minutes

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Help Desk

HGNC IDs/name objects in WB

  • Have seen some e-mails/tickets about HGNC ID/names in WormMine and plans to have them in FTP orthology files
  • Are/will HGNC genes be made available as objects in WB so that we can refer to them in different datatype curations?
  • Use cases:
    • Formally refer to the standard HGNC human gene in disease model curation and other types of curation
    • Referencing human genes as expressed components in transgenes so we can link appropriately to human gene pages at the Alliance
    • All of the above will allow collection and display of this data on human gene pages at the Alliance (one of the future plans of the disease/pheno working group)


Protein Aligner

Problem occurs on some but not all examples, even after prefix are removed. Appears to be a database issue. Michael and Sibyl will work offline on this.

HGNC IDs/name objects in WB

  • Ranjana: Recalls the previously discussed plan to make HGNC genes WormBase entities. What's the status? Use case by Ranjana and Chris to curate onto HGNC ID
    • Kevin: we have had human genes, previously using Ensembl ID as primary identifier, and now using HGNC ID (HGNC:xxxx) same as AGR, coming in WS277 or WS278
    • Michael: due to feedback, the primary ID will be the HGNC ID in WS278, instead of HGNC symbol (as in WS277). The display name stays as HGNC symbol.
  • How would Caltech curate onto HGNC ID?
    • Kevin: Could do split object maintenance and are brought together in the build
    • Ranjana & Chris: Gene set version issue? Any mechanism to ensure WormBase internally use the same gene set?
    • Kevin: Name server? Is it possible? Maybe refreshed periodically, and Caltech can sync their database with the name server
      • Juancarlos: Caltech can sync nightly from Name Server
      • No objection from Caltech
      • Does HGNC provide files/logs to help update the Name Server? Needs looking into
  • Paul S: what do other groups do?
    • Ranjana: others at disease WG want to do this, but may not have done it yet
    • Paul S: Shall we have an AGR name server?
      • Sounds like a good idea.
      • We will just be pulling from AGR.
      • Could be a lot of work.
    • Kevin: Variant WG is having big discussions about human gene sets. Multiple sources of human gene set (Ensembl, HGNC, Uniprot, etc), all slightly different, are being used by different parts of the site, causing internal inconsistencies.
      • Paul S: why does this happen? historical? political? or technical?
      • Kevin: different groups having slightly different standards and funding source, and are slowly coming together
    • Karen: literature curation WG would be interested in having a central name server, looking for ideas
      • Ranjana: Do you mark up human genes?
      • Karen: Yes, doing this for micropublication
  • Sibyl: Is the conclusion that Hinxton will maintain the canonical human gene set for WormBase through name server, which Caltech will use to sync up their databases?
    • Kevin: generally the idea, but Hinxton needs to look into whether it would cause problem. Haven't used name server for human genes before. Needs to hear Matt's thought on this.