HGNC robot template #559

joeflack4 · 2024-06-06T21:01:49Z

Addresses sub-tasks in:

HGNC robot template #558

Update mondo_genes.csv to be a proper ROBOT template, and ties into pipeline for externally managed content.

Pre-merge checklist

Documentation

Was the documentation added/updated under docs/?

Yes
No, updates to the docs were not necessary after careful consideration

QC

Was the full pipeline run before submitting this PR using sh run.sh make build-mondo-ingest on this branch (after
docker pull obolibrary/odkfull:dev), and no errors occurred?

Yes
No, there are no functional (code-related) changes to the pipeline in the PR, so no re-run is necessary

Build PR:

HGNC ROBOT template - build #564

New Packages

Were any new Python packages added?

Yes, requirements.txt.full was updated and an ODK issue submitted
No

Were any other non-Python packages added?

Yes, Dockerfile updated and an ODK issue submitted
No

PR Review and Conversations Resolved

Has the PR been sufficiently reviewed by at least 1 team member of the Mondo Technical team and all threads resolved?

Yes

CC: @souzadevinicius Thought this would be a good one for you to review

src/ontology/mondo-ingest.Makefile

joeflack4 · 2024-06-06T22:55:22Z

src/ontology/external/mondo_genes.robot.tsv

Add: external/mondo_genes.robot.tsv

Pulls from latest release, e.g.:

https://github.com/monarch-initiative/omim/releases/tag/2024-06-06

src/ontology/mondo-ingest.Makefile

matentzn

Nice work!

twhetzel · 2024-06-13T19:11:27Z

@matentzn In the file https://github.com/monarch-initiative/mondo-ingest/blob/hgnc-template/src/ontology/external/mondo_genes.robot.tsv for MONDO_0000208 I see the source is the OMIM record. This seems a better option that what is currently in Mondo as the source, e.g. MONDO:mim2gene_medgen.

However,

was this change discussed with curators?
is there a check in place after this robot template is merged into mondo-edit.obo to make sure there are not any classes with the has material basis in germline mutation in that have the old source annotation (MONDO:mim2gene_medgen)?

twhetzel

A few comments from yesterday that I can now submit after restoring my internet.

src/ontology/mondo-ingest.Makefile

sabrinatoro · 2024-06-13T20:04:13Z

MONDO:mim2gene_medgen

I do not know what this MONDO:mim2gene_medgen source refers to. It looks like a way to say that we are getting this information from the omim-gene file that somehow involves medgen?
@nicolevasilevsky do you remember anything about this?

I think it is ok to remove the MONDO:mim2gene_medgen sources and replace them with OMIM identifier.
However, it would not hurt to keep something like MONDO:mim2gene as a source to indicate that this annotation was made via a specific pipeline (similar to the "MONDO:MEDGE" source on the UMLS x-ref- image below for illustration).

We would therefore have the source be:

OMIM:1234
MONDO:OMIM2GENE

twhetzel · 2024-06-13T20:37:24Z

MONDO:mim2gene_medgen is documented on the Entities page as "This indicates the gene relationship came from MedGen.".
@joeflack4 can you remind me whether these mappings originally were from the MedGen mappings file?
@sabrinatoro do you want a different annotation used for the source still given the definition and pending Joe's answer for the question above?

twhetzel

I think regardless of which other source annotation should be added, an additional source annotation is needed in the ROBOT template.

src/ontology/external/mondo_genes.robot.tsv

sabrinatoro · 2024-06-13T23:52:28Z

@sabrinatoro do you want a different annotation used for the source still given the definition and pending Joe's answer for the question above?

I feel like I don't have enough information to give a clear answer, but I will try.
Where is the information coming from?

if we still get information from MedGen, then absolutely yes, we need to keep MONDO:mim2gene_medgen (and make sure to associate it with the correct annotations).
if we get the information directly from OMIM, then we can use something like "MONDO:OMIM" (or whatever source we have to say that something comes from OMIM; I don't have a strong opinion about what to name it, but I can make a name up).
if we get information from both, then we need to use both sources, associated to annotations appropriately.

My GUESS is that we were using the gene annotation from medgen at one point and medgen got this gene to disease annotation from omim (ie the MONDO:mim2gene_medgen source). It makes sense that we would switch to getting this information directly from omim now.

, then there is no point in keeping it. I am assuming (again assuming, please someone confirm)

twhetzel · 2024-06-14T01:47:39Z

Looking at the Monarch omim repo, I see references to the OMIM API and this download OMIM page so I guess the data in this HGNC ROBOT template is only coming from OMIM. That's the first thing for @joeflack4 or @matentzn to confirm.

If the data in this HGNC ROBOT file is only from OMIM, then we can go with Sabrina's comment:
if we get the information directly from OMIM, then we can use something like "MONDO:OMIM" (or whatever source we have to say that something comes from OMIM; I don't have a strong opinion about what to name it, but I can make a name up).
(from Trish - MONDO:OMIM fits the pattern I see for GARD and NORD so +1 from me)

The last thing that I do not know is where did the data (see example below) that is currently in Mondo with has material basis in germline mutation in come from and more importantly do we need to do anything about it.
For example, MONDO:0000208 and 'has material basis in germline mutation in' some TRMT10A with source MONDO:mim2gene_medgen.
I don't know if this HGNC template data in this PR is in addition to or intended to replace the existing data and if both the data in this ROBOT template and the existing data are from the same source and therefore should have the same source annotation. @matentzn do you know the answer to this?

joeflack4 · 2024-06-14T02:50:24Z

src/ontology/external/mondo_genes.robot.tsv

Duplicative sources?: MONDO:mim2gene_medgen

A / TLDR: I'm in favor of keeping as-is and merging for now if we need more time to think about this. But as we spend more time looking into this, I'm thinking we may drop MONDO:mim2gene_medgen in favor of MONDO:OMIM.

Man, sorry I could have provided some valuable information earlier, but I had some loose ends and wanted to collect my thoughts.

I decided to put this in a thread, if you guys don't mind responding further in this thread, to keep the related comments neatly together.

Some decisions / tasks

1. @twhetzel (or @matentzn) decide if this ROBOT template should be changed in any way based on this

e.g. additional source column

2. @twhetzel (or @matentzn) decide if existing MONDO:mim2gene_medgen source annotation should now be removed or kept

Some Q&A

1. Does the omim repo utilize any other sources, or just OMIM itself?

Trish:

Looking at the Monarch omim repo, I see references to the OMIM API and this download OMIM page so I guess the data in this HGNC ROBOT template is only coming from OMIM. That's the first thing for @joeflack4 or @matentzn to confirm.

Just OMIM itself! We're pulling data files just from the OMIM API, and that's it.

2. Where MONDO:mim2gene_medgen is coming from

Trish wrote:

@joeflack4 can you remind me whether these mappings originally were from the MedGen mappings file?

No, they're not coming from the medgen repo, or from ftp.ncbi.nlm.nih.gov/pub/medgen/MedGenIDMappings.txt.

I looked into it. They're being fetched in the mondo repo, from https://ftp.ncbi.nih.gov/gene/DATA/mim2gene_medgen. There is a mim2gene_medgen goal that Chris wrote in 2017 that fetches this, and it's also referenced in a Perl script he wrote a few years later, and some other places; I'm not yet entirely sure how it's all put together in `mondo.

Comments

1. MONDO:OMIM usage

Trish:

If the data in this HGNC ROBOT file is only from OMIM... then we can use something like "MONDO:OMIM"

As stated above, it is. And currently, there is a column source_code in the ROBOT template set to >A oboInOwl:source, and all the values are MONDO:OMIM.

2. Thoughts: Keep both OMIM & MedGen sources, or just 1?

A / TLDR: I lean towards keeping both for now, and merging this PR now. But we can investigate further and, if MedGen is just getting these from OMIM behind the scenes, then perhaps it is redundant and we should just fetch from OMIM as Trish is considering.

Further thoughts / responses

Trish:

I don't know if this HGNC template data in this PR is in addition to or intended to replace the existing data

That's for @matentzn to answer but my guess is that he either forgot about the mim2gene_medgen source, or maybe he thought this was intended to be in addition.

Trish:

if both the data in this ROBOT template and the existing data are from the same source and therefore should have the same source annotation. @matentzn do you know the answer to this?

We are fetching them from 2 different source files (one from OMIM, and one from MedGen), but as I contemplated above, it could be that MedGen sources this info from OMIM behind the scene.

I was at first confused by @sabrinatoro's comment. I read her say that she thinks we should keep both, but then keep just the new OMIM one. But I think that @sabrinatoro, @twhetzel , and I are mulling the same thing: that maybe MedGen is just sourcing these from OMIM, so we might be best to replace the old MONDO:mim2gene_medgen source with the new MONDO:OMIM one.

@matentzn responded on slack (thank you!).

Basically I think the 4 of us are in the same place on this. We will keep both sources for now, the one from OMIM (w/ MONDO:OMIM) and the one from MedGen (w/ MONDO:mim2gene_medgen), but we could consider removing the latter.

Where we left off:

Nico:

I think the missing piece in the thought process was that we decided to erase all existing gene links, and make OMIM (for now) the only source (even if once upon a time the mim2gene_medgen was a source). See you on Monday!

src/ontology/external/mondo_genes.robot.tsv

twhetzel · 2024-06-18T22:46:02Z

src/ontology/external/mondo-omim-genes.robot.tsv

@@ -0,0 +1,3366 @@
+mondo_id	hgnc_id	omim_disease_xref	source_code	omim_gene
+ID	SC 'has material basis in germline mutation in' some %	>A oboInOwl:source	>A oboInOwl:source	
+http://purl.obolibrary.org/obo/MONDO_0000208	https://identifiers.org/hgnc/28403	OMIM:616033	MONDO:OMIM	https://omim.org/entry/616013


I thought we decided yesterday to not include a column with MONDO:OMIM.

Yep, already done, see:

This comment about that thing being done: HGNC robot template omim#113 (comment)

This comment about the need to update mondo-ingest (by that, I meant this PR): HGNC robot template omim#113 (comment)

@twhetzel Review and approve

Now these files are also up-to-date in this PR as well:

external/mondo-omim-genes.robot.tsv

external/mondo-omim-genes.robot.owl

twhetzel

See comment inline

- Add: Goals for external/mondo_genes.robot.tsv - Add: external/mondo_genes.robot.tsv - Add: external/mondo_genes.robot.owl General - Update: Reorganized external/ goals a bit.

joeflack4 marked this pull request as draft June 6, 2024 21:01

joeflack4 self-assigned this Jun 6, 2024

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HGNC robot template monarch-initiative/omim#113

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HGNC ROBOT template - build #564

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This was referenced Jun 14, 2024

Update Genes from OMIM (do not merge) monarch-initiative/mondo#7806

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Remove mim2gene_medgen source annotations monarch-initiative/mondo#7821

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HGNC ROBOT template

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- Add: Goals for external/mondo_genes.robot.tsv - Add: external/mondo_genes.robot.tsv - Add: external/mondo_genes.robot.owl General - Update: Reorganized external/ goals a bit.

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joeflack4 merged commit 41ff1e2 into develop Jun 26, 2024

joeflack4 deleted the hgnc-template branch June 26, 2024 03:35

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HGNC robot template #559

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HGNC robot template #559

HGNC robot template #559

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Overview

Pre-merge checklist

Documentation

QC

New Packages

PR Review and Conversations Resolved

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Add: external/mondo_genes.robot.tsv

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Duplicative sources?: MONDO:mim2gene_medgen

Some decisions / tasks

Some Q&A

1. Does the omim repo utilize any other sources, or just OMIM itself?

2. Where MONDO:mim2gene_medgen is coming from

Comments

1. MONDO:OMIM usage

2. Thoughts: Keep both OMIM & MedGen sources, or just 1?

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Add: `external/mondo_genes.robot.tsv`

twhetzel commented Jun 13, 2024 •

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Duplicative sources?: `MONDO:mim2gene_medgen`

1. Does the `omim` repo utilize any other sources, or just OMIM itself?

2. Where `MONDO:mim2gene_medgen` is coming from

1. `MONDO:OMIM` usage

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