Uniprot&metanetx #63
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Uniprot&metanetx #63
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Update to use ncbi_taxon input from kg-microbe
Update to ingest all uniprot/rhea relationships based on kg-microbe microbes - comment out all other code (for now)
Update to ingest all uniprot/rhea relationships based on kg-microbe microbes - Use kg-microbe NCBITaxon.json input rather than ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
Update to ingest all uniprot/rhea relationships based on kg-microbe microbes - output Enzyme_Reaction.tsv and Organism_Enzyme.tsv based on kg-microbe nodes --> UniProt enzymes --> Rhea reactions
Update to ingest all uniprot/rhea relationships based on kg-microbe microbes - Get Rhea reactions based on enzymes expressed by kg-microbe set of microbes from nbcbitaxon.json
Update to ingest all uniprot/rhea relationships based on kg-microbe microbes - query uniprot based on organism_ids, not enzyme_ids
Update to ingest all uniprot/rhea relationships based on kg-microbe microbes - query uniprot based on organism_ids, not enzyme_ids
Include enzyme to reaction, and reaction to chemical relationships
Include enzyme to reaction, and reaction to chemical relationships. Also include testing dataset
Include enzyme to reaction, and reaction to chemical relationships. Also include testing dataset
Include enzyme to reaction, and reaction to chemical relationships. Also include testing dataset
Include enzyme to reaction, and reaction to chemical relationships. Also include testing dataset
Include enzyme to reaction, and reaction to chemical relationships. Also include testing dataset
Include enzyme to reaction, and reaction to chemical relationships. Also include testing dataset
Include enzyme to reaction, and reaction to chemical relationships. Also include testing dataset
Include enzyme to reaction, and reaction to chemical relationships. Also include testing dataset
…esources to graph.
…esources to graph.
Adding code to create labels (combined_kgx_merged-kg_nodes.csv) and edges (combined_kg.csv) files for full graph.
Updated to use wget instead of url retrieve due to ftp issues
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Will be updating this code to introduce within transform framework of kg-microbe. |
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