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monarch-initiative / monarch-ingest

Data ingest application for Monarch Initiative knowledge graph using Koza
https://monarchinitiative.org
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Add the Mouse Missense Mutation Library (MML) https://jcsmr.anu.edu.au/services/libraries-banking/missense-mutation-library #493

Open sierra-moxon opened 1 year ago

sierra-moxon commented 1 year ago

"This resource 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?"

Please see: https://github.com/monarch-initiative/helpdesk/issues/74 for more information.

sagehrke commented 1 year ago

@monarch-initiative/monarch-internal Please take a moment to review this proposed ingest, make comments, and ask questions.

Once reviewed, follow these directions to vote:

If you approve of moving forward with this ingest, mark this comment with a 👍 If you reject the proposal, mark this comment with a 👎 Voting is open to all Monarch Internal and ends on August 28, 2023.

joeflack4 commented 1 year ago

Just wondering how this would look in Mondo. Would we add/integrate info about all 10k genes as gene classes? Would we add all ~250k single nucleotide variants as some annotation property on those classes? Or their own classes? Probably not adding them ass classes, but FYI if we did, that sheer amount can cause memory issues with some of our tooling, like robot.

matentzn commented 1 year ago

This is for the Monarch KG, not Mondo!

sagehrke commented 1 year ago

@putmantime Can you please comment and make the final decision on this ingest proposal? From previous discussions, it seems like this is not currently in our scope, but I would like to have a more detailed explanation as to why that is for reference later. Thank you!