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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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NCBI to Dictybase Gene Mapping #283

Closed putmantime closed 2 years ago

putmantime commented 2 years ago

It is not obvious where to find these mappings. @pfey03 do you have any suggestions for where we could find these mappings?

pfey03 commented 2 years ago

@putmantime This is the NCBI link to the D. discoideum AX4 which is the the first sequenced and underlying genome of dictyBase https://www.ncbi.nlm.nih.gov/data-hub/gene/table/taxon/352472/

putmantime commented 2 years ago

We have code for this in the monarch-gene-mapping repo that transforms source mapping files to our gene sssom file.

https://github.com/monarch-initiative/monarch-gene-mapping/blob/main/monarch_gene_mapping/gene_mapping.py

RichardBruskiewich commented 2 years ago

@putmantime This is the NCBI link to the D. discoideum AX4 which is the the first sequenced and underlying genome of dictyBase https://www.ncbi.nlm.nih.gov/data-hub/gene/table/taxon/352472/

This link is not a direct downloading URL, but it does have a 'download table' link that gives a TSV file. Not sure where we should archive this (or do we just document it?)

I guess, @putmantime, that you are wanting us to adapt the gene_mapping.py script to this particular use case?