Open joeflack4 opened 3 weeks ago
@matentzn RE: filename. I think you said robot.tsv
, which I've also seen recently, but I thought we were doing robot.template.tsv
. Has that changed?
@matentzn Just to clarify--you mentioned that we are aware that the prefixes and URI prefixes are in flux (e.g. MIM). But I think the determination was that we would keep the values the same? E.g. omim_disease_xref
entries will stay as OMIM:12345
, and the omim_gene
field (ignored by robot) will stay as-is, etc?
@joeflack4 for the robot file, I think the filename should be the same format as before, but it should be a .tsv
file instead of a .csv
file.
@matentzn Just to clarify--you mentioned that we are aware that the prefixes and URI prefixes are in flux (e.g. MIM). But I think the determination was that we would keep the values the same? E.g. omim_disease_xref entries will stay as OMIM:12345, and the omim_gene field (ignored by robot) will stay as-is, etc?
The world seems to be moving to "MIM" as a prefix. I am against such changes, but the the overwhelming majority is for it, so it should be on your radar somewhere - not in this issue though. you can leave everything as is!
Yep, on my radar!:
Removed myself as assignee, as my part is done.
Also, at the time I created this I didn't realize that these 2 were highly related / the same thing in other words, otherwise I might have not made this issue:
Overview
There is an OMIM release artefact
mondo_genes.csv
. It needs to be changed into a ROBOT template.Sub-tasks
I.
omim
@joeflack4SC 'has germline mutation in' some %
to the correct valuemondo_genes.robot.tsv
source_code
with valuesMONDO:OMIM
<
and>
around URIs?
from the front of each fieldII.
mondo-ingest
@joeflack4omim
: Joe to create PR in mondo ingest, to pull the released file from omim release intosrc/ontology/external
(remember namingrobot.tsv
, testing run) - Nico can do this as well in case Joe is already off.$(EXTERNAL_CONTENT_DIR)/mondo_genes.robot.owl
runs successfullyIII.
mondo
(@matentzn & @twhetzel)mondo-ingest
: @matentzn to add pipeline to Mondo to update gene links in MondoSub-task details
omim
1. Set a ROBOT subheaderAdditional details
Context: Tech meeting notes, 2024/06/05
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