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Evidence sources of INDRA

indra_evidence_sources.Rd

The names INDRA gives its evidence sources, in two groups: INDRA_DATABASE_SOURCES for curated databases (e.g. SIGNOR, BioGRID, PhosphoSitePlus) and INDRA_TEXT_MINED_SOURCES for the text-mining systems that read the literature (e.g. REACH, Sparser). Pass one to get_network(evidence_sources = ) to keep only the edges with evidence from a curated database, or only those with text-mined evidence.

Usage

INDRA_DATABASE_SOURCES

INDRA_TEXT_MINED_SOURCES

Format

character vectors

Source

db_sources and reader_sources in INDRA's indra.util.statement_presentation module (INDRA 1.23.0), which INDRA CoGEx uses for its own source lists. "bel" is added to the databases, as CoGEx does.

Details

These are the names INDRA uses internally, which are the ones in edges$evidence_sources, and some differ from the full source names: "psp" (PhosphoSitePlus), "pc" (Pathway Commons), "pe" (Phospho.ELM), "vhn" (VirHostNet), and "bel_lc" (BEL large corpus).

See also

get_network(), backend_capabilities()

Examples

INDRA_DATABASE_SOURCES
#>  [1] "acsn"       "bel"        "bel_lc"     "biogrid"    "cbn"       
#>  [6] "conib"      "creeds"     "crog"       "ctd"        "dgi"       
#> [11] "drugbank"   "hprd"       "minerva"    "omnipath"   "pc"        
#> [16] "pe"         "psp"        "signor"     "tas"        "trrust"    
#> [21] "ubibrowser" "vhn"       
INDRA_TEXT_MINED_SOURCES
#>  [1] "eidos"    "geneways" "gnbr"     "isi"      "medscan"  "reach"   
#>  [7] "rlimsp"   "semrep"   "sparser"  "tees"     "trips"   
# \donttest{
input <- data.table::fread(system.file(
    "extdata/groupComparisonModel.csv",
    package = "MSstatsBioNet"
))
indra <- indra_backend()
entities <- prepare_entities(input, entity_type = "protein",
                             id_type = "uniprot")
entities <- convert_ids(indra, entities)
entities <- select_entities(entities, pvalue_cutoff = 0.05)
curated <- get_network(indra, entities,
                       evidence_sources = INDRA_DATABASE_SOURCES)
#> INDRA subnetwork: how are 10 selected proteins connected to each other, with no other nodes added?
head(curated$edges$evidence_sources)
#> [1] "{\"biogrid\": 1}"                  "{\"biogrid\": 1}"                 
#> [3] "{\"biogrid\": 1}"                  "{\"sparser\": 21, \"biogrid\": 2}"
#> [5] "{\"biogrid\": 1}"                  "{\"sparser\": 21, \"biogrid\": 2}"
# }