Network Databases¶
Database downloads.
MAGINE downloads network information from * Reactome Functional Interactions * HMDB * BioGrid * KEGG * Signor With the exception of KEGG and HMDB, all databases are downloaded and processed with pandas. KEGG is downloaded using Bioservices. HMDB is download in xml format and processed using lxml parser.
- magine.networks.databases.download_reactome_fi()[source]¶
Downloads reactome functional interaction network
- magine.networks.databases.load_biogrid_network(fresh_download=False)[source]¶
- Parameters
- fresh_downloadbool
Download a fresh copy from biogrid
- Returns
- nx.DiGraph
- magine.networks.databases.load_hmdb_network(fresh_download=False)[source]¶
Create HMDB network containing all metabolite-protein interactions
- Parameters
- fresh_downloadbool
Download fresh copy from HMDB
- verbosebool
- Returns
- nx.DiGraph
- magine.networks.databases.load_kegg(species='hsa', fresh_download=False)[source]¶
Loads all KEGG pathways as a single network
- Parameters
- speciesspecies
Default ‘hsa’
- fresh_downloadbool
Download kegg new
- Returns
- nx.DiGraph
- magine.networks.databases.load_kegg_mappings(species, fresh_download=False)[source]¶
Load mappings of kegg_pathway_id to nodes and nodes to kegg_pathway_id
- Parameters
- speciesstr
Species type, currently ‘hsa’ is the only species with automatic name conversion
- fresh_downloadbool
Download KEGG fresh
- Returns
- dict, dict