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monarch-initiative / monarch-legacy

Monarch web application and API
BSD 3-Clause "New" or "Revised" License
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Some MGI variant/allele symbols incomplete #1601

Open cindyJax opened 6 years ago

cindyJax commented 6 years ago

Some MGI symbols are not rendering correctly on the variant summary pages. For example:

https://monarchinitiative.org/phenotype/GO:0006915PHENOTYPE#variants

On the above page, there are a mix of MGI allele symbols, some of which are correct and hyperlinked, and many that are listing only the superscript portion of the allele symbol. For example, Kras is essentially correct (if you accept listing the superscript in angle brackets instead of actual superscripts), but in another line, tm2Jcbr is not listed correctly. The gene symbol part is missing. It should be Plrg1tm2Jcbr, which I found by tracing through the publication to MGI.

kshefchek commented 6 years ago

Plrg1tm2Jcbr is associated with two phenotypes in this table, but the fact that it's hard to find is a usability issue. We are working on these issues in the new monarch app, thank you for your feedback!

For the tm2Jcbr association, we split the sequence alteration tm2Jcbr and allele Plrg1tm2Jcbr into two separate ids, each with their own associations. I believe this is part of the geno spec but @mbrush can confirm.