Difference between revisions of "WormBase-Caltech Weekly Calls"
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* 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" | * 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" | ||
** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request] | ** [https://github.com/obophenotype/c-elegans-gross-anatomy-ontology/pull/23 Made pull request] | ||
+ | |||
+ | === 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? |
Revision as of 15:03, 3 October 2019
Contents
Previous Years
GoToMeeting link: https://www.gotomeet.me/wormbase1
2019 Meetings
October 3, 2019
SObA comparison graphs
- Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
- Prototype 1
- Prototype 2
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?