WormBase-Caltech Weekly Calls

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Nov 5th, 2020

WS279 GAF 2.0 and disease files

  • Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions
  • Valerio and Ranjana will probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
  • Will let Raymond know if the disease GAFs are okay after they test these for gene descriptions
  • Raymond needs the GAFs for WoBR

Experimenting with addeding new citace data to the current WS release

  • Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACeDB database. Then compare WS279.1 to WS279 by comparing the SimpleMine results generated from these two versions of ACeDB. The goal is to explore the possibility of notifying users some of the new curation since the data freeze for the WS build.

MicroPub user webinar on Nov 9th

  • Ranjana and Kimberly have conflicts--Alliance call and GO call. Anyway microPub team is running the show and they have other WormBasers to help as well.

WS280 deadlines

  • Caltech files due for citace: Dec 15th, 2020

Nov 12th, 2020

Cynthia Kenyon tool

  • developed a new tool for the worm, complete with very nice tutorials, for analyzing gene expression data using Gene Module analysis.
  • tool at http://genemodules.org
  • add link outs from the gene expression widget or add in general WB tools?

Graphical curation tool update

  • We will show a live demo on the current state of the graphical curation tool

Curating to human genes in ACEDB

  • Karen requested option to curate constructs with human genes
  • Would we need to change our human genes in ACEDB? For example, migrate from Ensembl IDs to HGNC IDs as primary keys?

GAF (and GAF-like) file headers

  • GO GAF files (on FTP, WS279) for WormBase now in 2.2 format with header like
!gaf-version: 2.2
!generated-by: WormBase
!date-generated: 2020-10-30
! WB annotations 00015014
  • For files that can migrate to 2.2 format (e.g. always require column 4 qualifier) we could adopt a similar header
  • For other files (that cannot always have a qualifier in column 4), we could stick to 2.0 format with a header like:
!gaf-version: 2.0
!generated-by: WormBase
!date-generated: 2020-10-30
  • Current need is to include information about format specification, possibly in addition to other extra header content.