config.txt

PATH_SWISSPROT  data/UniProt/
FILE_SWISSPROT_PROTEINS swissprot_human_proteins.tab
URL_SWISSPROT_PROTEINS  https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:9606
PATH_BIOGRID    data/Biogrid/
URL_BIOGRID_ALL https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.175/BIOGRID-ALL-3.5.175.tab2.zip
BIOGRID_ALL BIOGRID-ALL-3.5.175.tab2.zip
BIOGRID_GGIS    BIOGRID-ORGANISM-Homo_sapiens-3.5.175.tab2
BIOGRID_PPIS    human_protein_interactions.tab
BIOGRID_ENTREZ_TO_UNIPROT   entrez_to_uniprot.tab
ID_MAPPING_BATCH_SIZE 1000
PATH_REACTOME   data/Reactome/
REACTOME_INTERNAL_EDGES proteinInternalEdges.tsv
REACTOME_PPIS   ppis.tsv
PATH_TOOLS  tools/
FILE_PATHWAYMATCHER PathwayMatcher.jar
URL_PATHWAYMATCHER  https://github.com/PathwayAnalysisPlatform/PathwayMatcher/releases/latest/download/PathwayMatcher.jar
PATH_STRING data/String/
STRING_PROTEIN_NETWORK  9606.protein.actions.v11.0.txt
URL_STRING_PROTEIN_NETWORK  https://stringdb-static.org/download/protein.actions.v11.0/9606.protein.actions.v11.0.txt.gz
STRING_ID_MAP   human.uniprot_2_string.2018.tsv
URL_STRING_ID_MAP   https://string-db.org/mapping_files/uniprot/human.uniprot_2_string.2018.tsv.gz
STRING_FEATURES string_features.csv
STRING_INTERACTIONS string_interactions.csv
STRING_TARGETS  string_targets.csv