Difference between revisions of "WBConfCall 2020.01.16-Agenda and Minutes"

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*GitHub acts like a FAQ for mostly curators, not for Users
*GitHub acts like a FAQ for mostly curators, not for Users
*Does Google index GitHub repos?
*Does Google index GitHub repos?
*We agree to make it private
*The group agrees to make it private
*Todd will drop a summary of the requested

Revision as of 17:19, 16 January 2020


Allele / variation curation

  • Follow-up from Caltech call last week

Should the Issue Tracker be private?

Direct Message retention setting on Slack

Should we remove the ability to comment on pages?


  • upload is on the 31st of January (in two weeks)

Protein domains FTP file only has Interpro domains

  • The "protein_domains" file, for example here only has Interpro domains
  • Can we add all domains from all sources (e.g. PFAM, SUPERFAM, SMART etc.)?


Allele curation

  • Hinxton has made it a priority to get the Micropub alleles curated
  • Karen puts in alleles in the name server with paperID, these will be prioritized as well
  • AGR wide focus on allele curation, so give this high priority
  • Kevin is on the AGR Variation working group, WB are ahead in terms of sequence curation and have doing it for years
  • Use case is groups such as the UDN who come in with a human variant, we need to begin work on this. Need displays to map human variant to MOD variant
  • With data with co ordiantes, we have flanking sequences, we have the chromosome sequnce, WB has both
  • What is the backlog? Hinxton can allocate resources to this--Gary Williams can switch from gene to allele curation
  • Caltech system has papers flagged with variation, Hinxton has this as 'pending curation'
  • Karen enters allele data from papers that come through the GSA markup pipeline before publication, maybe display the notes from these on the website
  • Sometimes things get named on an unnamed assembly and detective work is required, authors don't give complete information
  • Have the allele author submission form, enough for Paul D., to convert to a variation with molecular change information
  • Action Item: Paul will report the priority backlog; Textpresso already flags alleles, runs once a month;not high volume, rungs on new papers, maybe run on whole corpus to address old papers

Should the Issue Tracker be private?

  • Should it be private? Reasons to make it private
    • Can discuss more freely
    • Prevents inadvertant leaking of unpublished data
    • We don't tell people that it goes on a public website
    • People don't really use the issue tracker
  • We have received a few complaints about this, need full disclosure or need to be made private
  • What is the workflow-might be made simpler if private, maybe simplify the process even more to avoid writing multiple e-mails
  • GitHub acts like a FAQ for mostly curators, not for Users
  • Does Google index GitHub repos?
  • The group agrees to make it private
  • Todd will drop a summary of the requested