Develop a script to build a NGD Database

RTXteam / RTX

Software repo for Team Expander Agent (Oregon State U., Institute for Systems Biology, and Penn State U.)

https://arax.ncats.io/

MIT License

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Develop a script to build a NGD Database #2311

Closed mohsenht closed 1 month ago

dkoslicki commented 2 months ago

@chunyuma @amykglen don't we have an NGD/FastNGD database builder somewhere?

chunyuma commented 2 months ago

This script should be what you need. Correct me if I am wrong @amykglen.

chunyuma commented 2 months ago

But it seems like that script is not for building a database to store the NGD scores but for storing the PMID mapping only.

amykglen commented 2 months ago

yes, that's right - the script Chunyu shared is the one we use for building the curie_to_pmids.sqlite database - ARAX doesn't do any further precomputation for NGD scores than that (so far). FYI there is also a README with instructions on how to use that script: https://github.com/RTXteam/RTX/tree/master/code/ARAX/ARAXQuery/Overlay/ngd