Add mouse strain

[brianraymor]

Context

See cell-sci-data-wrangling.

References

• International Mouse Strain Resource (IMSR) - downloadable reports and format

There is no REST API, but the HTML has consistent anchor links for downloads which can be easily parsed:

<td>
--
  | <a id="textDownload" href="https://www.findmice.org/report.txt?repositories=JAX&results=12736"><img src="https://www.findmice.org/assets/images/text-document-icon.png" title="Download Text Report" /></a>&nbsp;
  | <a id="excelDownload" href="https://www.findmice.org/report.xlsx?repositories=JAX&results=12736"><img src="https://www.findmice.org/assets/images/Excel-icon.png" title="Download Excel Report" /></a>&nbsp;
  | 
</td>

Example processed output for report:

{'Nomenclature': '+',
 'Strain ID': 'JAX:005004',
 'Strain/Stock': 'ZRDCT Rax<ey1>/ChUmdJ',
 'Repository': 'JAX',
 'State': 'embryo',
 'Synonyms': 'ZRDCT Rax<ey1>/ChUmiJ',
 'Type': 'coisogenic strain',
 'Allele ID': 'MGI:1856862',
 'Allele Symbol': 'Rax<ey1>',
 'Allele Name': 'eyeless 1',
 'Gene ID': 'MGI:109632',
 'Gene Symbol': 'Rax',
 'Gene Name': 'retina and anterior neural fold homeobox',
 'URL': 'https://www.jax.org/strain/005004'}
{'Nomenclature': '+',
 'Strain ID': 'JAX:005004',
 'Strain/Stock': 'ZRDCT Rax<ey1>/ChUmdJ',
 'Repository': 'JAX',
 'State': 'embryo',
 'Synonyms': 'ZRDCT Rax<ey1>/ChUmiJ',
 'Type': 'mutant strain',
 'Allele ID': 'MGI:1856862',
 'Allele Symbol': 'Rax<ey1>',
 'Allele Name': 'eyeless 1',
 'Gene ID': 'MGI:109632',
 'Gene Symbol': 'Rax',
 'Gene Name': 'retina and anterior neural fold homeobox',
 'URL': 'https://www.jax.org/strain/005004'}

• Guidelines for Nomenclature of Mouse and Rat Strains
• Quick Guide to Mouse Nomenclature
• Mouse Strains in Mouse Phenome Database
• Mouse Genome Informatics strain report
• NCIT Mouse Strains - The Inbred Mouse terminology in NCI Thesaurus was based on Jax mice strains, hosted in International Mouse Strain Resource (IMSR). This terminology is provided to facilitate MMHCC and caMOD projects.
• EFO lists strains under the Taxonomy term

[jahilton]

Some notes from the scFAIR group...

• strains are not super well defined, and as with cell lines, there seems to be quite some drift in practice. This is a good caution piece by The Jackson Lab: https://www.jax.org/news-and-insights/jax-blog/2016/june/there-is-no-such-thing-as-a-b6-mouse
• bgee follow the UniProt controlled vocabulary for strain annotation it's basically the species code from here and lists available strains and their synonyms
• Uniprot solution seems reasonable. More lightweight than EFO and I think a flat list should be sufficient. It may be that EFO has some of these terms too. In that case we can check if they have a mapping to Uniprot terms and request that they fold one in if not.

[brianraymor]

There are Research Resource Identifiers for the mouse strains documented at IMSR.

For example, a JAX strain that references its RRID

Samples:

• JAX Mice and Services
• European Mouse Mutant Cell Repository