Attach robot template to GARD release - Githubissues

monarch-initiative / gard

GARD ingest.

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Attach robot template to GARD release #15

Closed matentzn closed 1 year ago

matentzn commented 1 year ago

We need a table (mondo-gard.robot.template.tsv) with the following data, attached to the GARD release:

mondo_id	type	gard_id	source_external	subset
ID	TYPE	A oboInOwl:hasDbXref	>A oboInOwl:source	AI oboInOwl:inSubset
MONDO:0011308	owl:Class	GARD:1	Orphanet:123	http://purl.obolibrary.org/obo/mondo#gard_rare
MONDO:0011801	owl:Class	GARD:10000	OMIM:321	http://purl.obolibrary.org/obo/mondo#gard_rare

The value in the subset column is always the same (http://purl.obolibrary.org/obo/mondo#gard_rare).
The source_external has the ID GARD was sourced from (OMIM, OMIMPS, GARD)
The source_type is always MONDO:equivalentTo (I will update the value of this dynamically on the Mondo side to obsoleteEquivalent). EDIT: THIS COLUMN NOW REMOVED IGNORE
The type column is always owl:Class.

I think you almost have this table, just attach it to the release and lemme know :)

joeflack4 commented 1 year ago

Completed! Thanks for the detailed issue.

You can find the template in the new release here. Here's a snippet:

mondo_id	type	gard_id	source_external	subset
ID	TYPE	A oboInOwl:hasDbXref	>A oboInOwl:source	AI oboInOwl:inSubset
MONDO:0000023	owl:Class	GARD:17820	Orphanet:464724	http://purl.obolibrary.org/obo/mondo#gard_rare
MONDO:0000208	owl:Class	GARD:18459	OMIM:616033	http://purl.obolibrary.org/obo/mondo#gard_rare
MONDO:0000209	owl:Class	GARD:17882	Orphanet:486811	http://purl.obolibrary.org/obo/mondo#gard_rare

More comments in the PR.