WormBase-Caltech Weekly Calls

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GoToMeeting link: https://www.gotomeet.me/wormbase1

2019 Meetings










October 3, 2019

SObA comparison graphs

  • What information does a user most care about?
  1. What terms (nodes) are annotated to gene 1 and what terms to gene 2
  2. For a given term, what is the relative number of annotations between gene 1 and gene 2.
  3. For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
  • # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.

Germ line discussion

  • Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
  • Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"

Script to remove blank entries from Postgres

  • Chris stumbled across several entries in the OA that were blank (empty strings ) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
  • Juancarlos has written a script to look for all such entries; 66 on sandbox (likely same on live OA)
  • Does anyone object to removing these entries throughout Postgres?