HGNC robot template

[joeflack4]

Overview

There is an OMIM release artefact mondo_genes.csv. It needs to be changed into a ROBOT template.

Sub-tasks

I. omim @joeflack4

• 1. Set a ROBOT subheader
  • Set SC 'has germline mutation in' some % to the correct value
• 2. Change from CSV to TSV
• 3. Change filename to mondo_genes.robot.tsv
• 4. Add field source_code with values MONDO:OMIM
• 5. Remove < and > around URIs
• 6. Optional: Remove the ? from the front of each field

II. mondo-ingest @joeflack4

• 1. Pull from omim: Joe to create PR in mondo ingest, to pull the released file from omim release into src/ontology/external (remember naming robot.tsv, testing run) - Nico can do this as well in case Joe is already off.
• 2. Ensure that $(EXTERNAL_CONTENT_DIR)/mondo_genes.robot.owl runs successfully

III. mondo (@matentzn & @twhetzel)

• 1. Pull from mondo-ingest: @matentzn to add pipeline to Mondo to update gene links in Mondo
  • Report these are all the axioms that do not have OMIM support (and whether they have any support from anyone else, like Orphanet or Clingen or PMID)
    • Any disease that have more than one germline mutation link to gene
  • Add QC check to ensure that no disease has unverified multiple germline mutation links.
• 2. @matentzn After this is done:
  • Rerun SPARQL query to check overlap between relations with textual definitions
• 3. @twhetzel to update the LLM pipeline.

Sub-task details

omim 1. Set a ROBOT subheader

mondo_id	hgnc_id	omim_disease_xref	source_code	omim_gene
ID	SC 'has germline mutation in' some %	>A oboInOwl:source	>A oboInOwl:source
http://purl.obolibrary.org/obo/MONDO_0032710	https://identifiers.org/hgnc/7763	OMIM:618374	MONDO:OMIM	https://omim.org/entry/601725
http://purl.obolibrary.org/obo/MONDO_0044724	https://identifiers.org/hgnc/23656	OMIM:617698	MONDO:OMIM	https://omim.org/entry/607381

Additional details

Context: Tech meeting notes, 2024/06/05

Related

• Add pipeline to update gene links in Mondo #561
• Create synchronization pipeline for disease-gene in Mondo mondo#7229

[joeflack4]

@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?

[joeflack4]

@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?

[twhetzel]

@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]

@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!

[joeflack4]

Yep, on my radar!:

• OMIM prefix & URI prefix updates omim#111

[joeflack4]

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:

• Create synchronization pipeline for disease-gene in Mondo mondo#7229
• Add pipeline to update gene links in Mondo #561