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Change prefix of OMIM cross-references to MIM #1301
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A few thoughts:
Here's my own personal opinion:TL;DR - I wholly support this change and doing whatever work is needed to make it happen. Reasoning - The creator and maintainer of a resource should be the one to define it and it is best to ask that/those individual(s) when there is some decision on how their resource will be used. I believe some of the messiness in data and proliferation of competing resources exists because individuals do not think often enough about working together or are unwilling to do the work needed to discuss issues and come to a consensus. I see this as another unrecorded, aspect of FAIRness/TRUST-worthiness: users should communicate with the maintainers of a resource. If all OMIM users respected OMIM's desire to consolidate to the MIM prefix there would be only 1 prefix and no need for any programmatic efforts to correct them, making all data annotated with their identifiers more FAIR. |
Tagging @fschiettecatte so he's aware of this discussion and can chime in if needed (I hope you don't mind). |
@sbello what might the Alliance need to make this change? @lschriml, the only thing I can think of that we need to change, beyond the data in the ontology, is the loader that supports the tree views of the DO at https://disease-ontology.org/do. Can you help me identify other resources beyond the Alliance who might benefit from a heads up and help me set a timeframe for this change? |
@fschiettecatte does capitalization matter? Any preference for MIM vs mim? |
Do we want to change all references from OMIM to MIM? I'm wondering about the name of some files, e.g. DOreports/OMIMinDO.tsv, and references to OMIM in src/ontology/README_DO_Files. |
@allenbaron MGI and the Alliance and I suspect most other DO users would need to modify our loaders to recognize the new prefix. I don't think this would break the loads but it would mean that we would fail to load any OMIM IDs until the loader was updated so early warning would be good. |
Items to change in the DO files: On the DO website Code: OMIM susceptibility import File names: |
I agree that it's probably best to change only the prefixes.
Nothing needs to be done for the DO build files/make rules since we aren't changing file names.
This is one I'd forgotten about and it probably presents the biggest challenge because both the IDs and URIs are based on "OMIM" (e.g.
Neither of these is dependent on prefixes, so we shouldn't need any updates for them. I'll only have to check the example SPARQL query examples we provide with the sandbox. I decided to identify the use of "OMIM" for all non-OWL/OBO/JSON files in this repo (excluding files in the build, deprecated, and hidden directories). The files identified using this command are listed below along with the ontology edit/import files that need review/modification. find . ! -name "*.owl" ! -name "*.obo" ! -name "*.json*" ! -path "*build*" ! -path "*deprecated*" ! -path "./.*" -type f -print0 |
xargs -0 grep -c "OMIM" |
grep -E "[1-9]+$" Files in this repo:
Files outside this repo
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In preparation for change in DO outlined in DiseaseOntology/HumanDiseaseOntology#1301.
Apologies for the slow reply, I was out through today. We want upper case for 'MIM', see our linking help sections 1.8 and 1.9. |
I would prefer uppercase, as all other xrefs are uppercase.Sent from my iPhoneOn Feb 11, 2024, at 7:21 PM, François Schiettecatte ***@***.***> wrote:
@fschiettecatte does capitalization matter? Any preference for MIM vs mim?
Apologies for the slow reply, I was out through today.
We want upper case of the 'MIM', see our linking help sections 1.8 and 1.9.
—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>
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We've decided to push this change back one additional month to the April release to provide more time for the many resources using DO to prepare for this change. |
A test release, equivalent to official release Test files are available at https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/mim_test_release/src/ontology Please distribute this information as widely as possible so that all DO users are prepared for the April release in which this change will be implemented. Please reach out if you need any assistance. |
plot_xref_counts() and get_url() will now be able to use either "OMIM:" or "MIM:" input and still provide the expected output. inventory_omim() and generify_obo() will now forcibly convert "OMIM:" to the preferred "MIM:" prefix in their output. Changes prompted by DiseaseOntology/HumanDiseaseOntology#1301.
Will ensure compatibility with future inventories of OMIM in the DO, now that DO has moved to OMIM's preferred prefix. See DiseaseOntology/HumanDiseaseOntology#1301.
OMIM made a request that we use MIM as a prefix instead of OMIM:
I'm opening this issue so we can discuss and resolve this.
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