Adding mouse missense data resource to Monarch

cameron-jack commented 1 year ago

Hi, we have a mouse genomic resource that may be of interest to Monarch users wishing to develop mouse model lines in their own studies. It's called the Missense Mutation Library (MML) https://jcsmr.anu.edu.au/services/libraries-banking/missense-mutation-library, and consists of mouse sperm lines for ENU-induced single-SNV mutations across more than 10,000 genes. In total there are over 250,000 SNVs that have been computationally predicted for effect and are available for study. Is this something that Monarch would be interested in having available to users?

The standard interface (for the variant 'node' for instance) doesn't present a lot of information to viewers, and would likely make it very difficult to chose a particular variant or line of interest to "click through" to the main MML site. We'd probably be best served creating a new 'node' resource and providing a much expanded set of information about each available site, so that users could directly search for potential lines for their genes/pathways of interest.

Please let us know this is an appropriate resource to have available at the top level (monarchinitiative.org), or whether we should be forking and building our own hosted instance. Thanks in advance.

sagehrke commented 1 year ago

Hi @cameron-jack Thank you for submitting a question to the Monarch HelpDesk! We sincerely appreciate you taking the time to reach out and are working on an answer to share with you soon.

sierra-moxon commented 1 year ago

Hi @cameron-jack - thanks for reaching out! Monarch uses a couple of different tools to help coordinate ingests: 1) a proposal mechanism: https://monarch-initiative.github.io/monarch-ingest/Create-an-Ingest/1.%20Propose/

I went ahead and made a ticket there, following the ingest proposal mechanism here: https://github.com/monarch-initiative/monarch-ingest/issues/493. Any additional information you can provide about the shape of the data to ingest, the relationships to other data in Monarch that these could relate to, or if you wanted to go a step further and analyze which components of the Biolink Model would be represented by the data, that would be very helpful! 2) a declarative ingest framework: https://koza.monarchinitiative.org/
this is the code Monarch works with to ingest data sources.

monarch-initiative / helpdesk

Adding mouse missense data resource to Monarch #74