WBConfCall 2020.10.01-Agenda and Minutes

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WormBase Webinars

Current Production Release on FTP is still WS276

WS280 Models

  • Kimberly/Paul - Species model additions
 > ?Species Evidence #Evidence                // Meta data for why the object was created
 >         References ?Paper     (optional XREF Species_in_paper)
 >         Remark ?Text #Evidence
  • SO_term
new tag "Sequence_comparison"

Adding Caltech designated WBIDs to the nameserver

added by Karen

  • Michael Paulini found that some Transgene IDs were missing in acedb from db to db
  • Caltech assigned IDs include, transgene, construct, molecule, others....
  • MP suggests using a centralized nameserver to keep track of ID history (merges, kills etc)
  • KY suggests alternative of added history to .ace files in citace upload

A dump of the merge information to Transgene Summary or Remark will get the info into WS. Karen will decide if a schema change is necessary.

Help Desk

  • Emails sent to help@wormbase.org did not generate github tickets.

* "phm-2 has been cloned. It is F32B4.4" help desk email from Jonathan Ewbank Sept 30 GitHub ticket #7905

  • "eiF3-L and dhs-6 confusion" help desk email from Mary-Anne Felix Sept 29 -- [PD I will look at this]

* "paper link missing to sax-1?" help desk email from Nathalie Pujol Sept 26
** all gene-paper links for that paper have been added to the paper object; responded to Nathalie (Kimberly)

  • Did anyone help Nathalie Pujol with this one: (PD will look at this)

I am working on COL-17 that was recently taken out of the collagen family (see Matrisome data). As it still have a weak homology to Briggsae COL-77 A, I wanted to check the prediction of the Briggsae protein with you. Cbr COL-77 in wormbase has 2 isoforms, A 351 aa and B 304 aa. It seems that the A long form is specific to Briggsae (and contain the very short homology domain with COL-17). The B form is shorter and produced after a frameshift after one or two base splice out, which is strange, but is 100 % identical to all other COL-77 protein in Caenorhabditis.

My question is then the following: Does the Cbr COL-77 A long isoform is real? I couldn’t have access to RNAseq or Est sequences.

New WormBase Tables

  • All New WormBase Tables Ready for Testing. Sibyl sent an email to the staff email list.

GAF file headers & column contents

  • We need files that are not GAF standard gene association files.
  • FTP site is organized is a way that a file can be accessed from different directories via symbolic links.
  • Not to make major changes to the file format. Change GAF2.1 file format.
  • GAF does not need column headers because there is a format specification. We are adding more headers.
  • Hinxton will generate both GAF and GAF-like files.