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Update Genes from OMIM (do not merge) #7806

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Update Genes from OMIM (do not merge) #7806

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matentzn
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@matentzn matentzn commented Jun 14, 2024 •
edited by joeflack4
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This PR is a draft. The main issue is this:

[Term]
id: MONDO:0005575
name: colorectal cancer
def: "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." [NCIT:C4978]
comment: Editor note: some sources make distinct classes for colorectal vs large intestine. We follow NCIT and make these equivalent
...
is_a: MONDO:0005335 {source="MONDO:Redundant", source="NCIT:C4978"} ! colorectal neoplasm
is_a: MONDO:0005814 {source="DOID:5672", source="DOID:9256/inferred", source="MONDO:Redundant", source="NCIT:C4978"} ! intestinal cancer
intersection_of: MONDO:0004992 ! cancer
intersection_of: disease_has_location UBERON:0012652 ! colorectum
relationship: disease_has_location UBERON:0000059 {source="EFO:0000784"} ! large intestine
relationship: has_material_basis_in_germline_mutation_in https://identifiers.org/hgnc/11393 {source="MONDO:OMIM", source="OMIM:114500"}
relationship: has_material_basis_in_germline_mutation_in https://identifiers.org/hgnc/2897 {source="MONDO:OMIM", source="OMIM:114500"}
relationship: has_material_basis_in_germline_mutation_in https://identifiers.org/hgnc/6935 {source="MONDO:OMIM", source="OMIM:114500"}
relationship: has_material_basis_in_germline_mutation_in https://identifiers.org/hgnc/9031 {source="MONDO:OMIM", source="OMIM:114500"}
relationship: has_material_basis_in_germline_mutation_in https://identifiers.org/hgnc/9645 {source="MONDO:OMIM", source="OMIM:114500"}

How can we justify having so many gene links for colorectal cancer? they are certainly not all strictly causal?

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@matentzn
Add simple pipeline to update genes from OMIM
c9b1902 
The first draft of the pipeline basically removes _all_ "has germline mutation" relations and swaps in the new ones.
@matentzn
Draft update of mondo edit with new gene relations
803e0fa
@matentzn matentzn self-assigned this Jun 14, 2024
twhetzel
twhetzel reviewed Jun 14, 2024
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src/ontology/mondo.Makefile
@@ -963,6 +963,20 @@ update-%-mappings: $(TMPDIR)/new-exact-matches-%.owl
make NORM
mv NORM $(SRC)

$(TMPDIR)/mondo-omim-genes.robot.owl:
wget "https://raw.githubusercontent.com/monarch-initiative/mondo-ingest/hgnc-template/src/ontology/external/mondo_genes.robot.owl" -O $@
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I think you asked in the HGNC PRs to re-name this file.

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Yes thanks, we wont merge this before the mondo ingest pr is merged!

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@joeflack4 joeflack4 Jun 14, 2024 •
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  • @matentzn Update the wget w/ correct URL once Mondo PR has been merged (into main).

File has been renamed: mondo-omim-genes.robot.owl

I'm sure this is also on your radar to update it so it pulls from the main branch eventually.

Just thinking about this now, that necessitates that we merge that PR into main after merging it into develop, so I'll do the merging / build running a couple more times when we're ready for that.

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Hasn't been merged into main yet, but has been merged into develop.

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Once we hear from Sabrina when the alignment work is done, we can decide when to bring updates from mondo-ingest develop back into main and make sure the proper test builds are done.

joeflack4
joeflack4 reviewed Jun 14, 2024
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src/ontology/mondo.Makefile

.PHONY: update-omim-genes
update-omim-genes:
$(MAKE) $(TMPDIR)/mondo-omim-genes.robot.owl
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Does this need a -B at the end of it?
I could be having a brain blip, but I think it needs it, and that's the only reason I can think of for putting this in the body instead of in the prereqs in this case.

Other than this, I don't understand the rest of this robot-foo, but you know what you're doing it looks like what you did worked correctly.

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Good point about -B, thanks!

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sabrinatoro commented Jun 14, 2024 •
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We should not have more than 1 gene annotation per disease. In other words, we should only bring gene annotations when there is only 1 disease-1 gene.
Also, we need to have a QC to report when we have more than 1 gene per disease (if it is by design, ie a curator said both genes should be mutated to get the disease, the curator will add "exclude from QC") see QC requests here

Having more than 1 gene associated per disease is a bug in the pipeline.
(see here, and see also original document that Joe created sometime ago - I will update this comment once I found it)

Note that the rules for the gene to disease annotations we bring in the Monarch KG are different than what we bring in Mondo.

This was referenced Jun 18, 2024
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joeflack4
joeflack4 reviewed Jun 26, 2024
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src/ontology/mondo.Makefile
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FYI: Merged other PRs

@matentzn I've just merged the following PRs. Don't know if that means anything for this PR at all; just letting you know.

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