Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update Genes from OMIM (do not merge) #7806

Draft
wants to merge 2 commits into
base: master
Choose a base branch
from
Draft

Update Genes from OMIM (do not merge) #7806

wants to merge 2 commits into from

Conversation

matentzn
Copy link
Member

@matentzn matentzn commented Jun 14, 2024 •
edited by joeflack4
Loading

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?

Related

@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
View reviewed changes
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 $@
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think you asked in the HGNC PRs to re-name this file.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

Copy link
Collaborator

@joeflack4 joeflack4 Jun 14, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

  • @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.

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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
View reviewed changes
src/ontology/mondo.Makefile

.PHONY: update-omim-genes
update-omim-genes:
$(MAKE) $(TMPDIR)/mondo-omim-genes.robot.owl
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Good point about -B, thanks!

@sabrinatoro
Copy link
Collaborator

sabrinatoro commented Jun 14, 2024 •
edited
Loading

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
Merged
Merged
joeflack4
joeflack4 reviewed Jun 26, 2024
View reviewed changes
src/ontology/mondo.Makefile
Copy link
Collaborator

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@twhetzel twhetzel twhetzel left review comments

@sabrinatoro sabrinatoro sabrinatoro left review comments

@joeflack4 joeflack4 joeflack4 left review comments

At least 1 approving review is required to merge this pull request.

Assignees

@matentzn matentzn

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
4 participants
@matentzn @sabrinatoro @twhetzel @joeflack4