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124 add strain information linked with the species csv #126

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merged 4 commits into from
Jan 24, 2025

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@dbirman dbirman commented Jan 10, 2025

This is a draft PR looking at how to add strain information by adding a StrainModel and Strain class in the species.py file. I also had to add a new filter function to the generator.py file to allow for filtering a dataframe to get back only the unique rows -- this is needed to make the sets of Species unique, even though multiple strains might share a species.

The intention is to use this new feature to separately validate subject.json models to ensure that the species matches the species listed in the strain, when the strain is set.

We can't merge this PR until registry information is added for strains or we remove the registry fields from StrainModel.

@dbirman dbirman requested a review from saskiad January 10, 2025 04:55
@dbirman dbirman linked an issue Jan 10, 2025 that may be closed by this pull request
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saskiad commented Jan 17, 2025

MGI has strain info for mice:
https://www.informatics.jax.org/strain/MGI:3028467
https://www.informatics.jax.org/strain/MGI:2161072

The best way to find them is through this: https://phenome.jax.org/strains
which has a link to the MGI entry for each strain.
(you can also search in MGI and look in the strain list ... if you start with the exact strain name, you'll get it, if you trying something incomplete, you probably won't)

@dbirman dbirman marked this pull request as ready for review January 17, 2025 05:49
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I think this looks good

@saskiad saskiad merged commit aab568c into v1 Jan 24, 2025
@saskiad saskiad deleted the 124-add-strain-information-linked-with-the-species-csv branch January 24, 2025 06:01
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Add strain information linked with the species CSV
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