Add protein binding information from the String database

Bertinus / FLeCS

Flexible and Learnable Cell Simulator

MIT License

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Add protein binding information from the String database #9

Closed Bertinus closed 2 years ago

josephdviviano commented 2 years ago

E.g.,: https://stringdb-static.org/download/protein.physical.links.detailed.v11.5/9606.protein.physical.links.detailed.v11.5.txt.gz

from https://string-db.org/cgi/download?sessionId=byMHyfAaukUX&species_text=Homo+sapiens

Bertinus commented 2 years ago

Idea: Add an option in the load_interaction_data method (see link) to get a graph containing:

protein nodes and gene nodes
protein-protein edges are derived from StringDB
edge (gene -> protein) are derived from a gene-prot mapping database (already provided by String? Otherwise check https://www.uniprot.org/help/gene_name).
edge protein -> gene derived from Fantom5 (already available in FLeCS)

Bertinus commented 2 years ago

Optional: download protein sequences from StringDB and make it part of FleCS. That way, protein sequences will be readily available in case people want to use this information to perform simulations

Bertinus commented 2 years ago

Could be 2 steps: 1/ Add an option to load String on its own 2/ Work on the pairing of String with one the GRNs already available (e.g. Fantom5)

Bertinus commented 2 years ago

I'll start working on step 2 ("Work on the pairing of String with one the GRNs already available")

Bertinus commented 2 years ago

Step 2 is handled now.