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What a backend supports

backend_capabilities.Rd

Lists the queries, identifier conversions, entity properties, and limits of a backend, so a choice can be checked before a query is sent.

Usage

backend_capabilities(backend)

# S4 method for class 'NetworkBackend'
backend_capabilities(backend)

# S4 method for class 'IndraBackend'
backend_capabilities(backend)

Arguments

backend

a NetworkBackend, e.g. from indra_backend()

Value

named list:

query_types

the query_type values of the queries the backend answers, e.g. "subnetwork" for subnetwork_query()

id_conversions

for each entity_type, the id_type values convert_ids() can convert

entity_properties

the properties get_entity_properties() can add

interaction_types

the edges$interaction values the backend returns

evidence_sources

the evidence_sources values get_network() filters on, as a list with database and text_mined elements, e.g. INDRA_DATABASE_SOURCES

max_nodes

for each query type, the largest number of groundings one query can take

See also

network_queries

Examples

backend_capabilities(indra_backend())
#> $query_types
#> [1] "subnetwork"
#> 
#> $id_conversions
#> $id_conversions$protein
#> [1] "uniprot"          "uniprot_mnemonic" "hgnc_symbol"     
#> 
#> $id_conversions$ptm_site
#> [1] "uniprot"          "uniprot_mnemonic" "hgnc_symbol"     
#> 
#> $id_conversions$metabolite
#> [1] "chemical_name"
#> 
#> $id_conversions$lipid
#> [1] "chemical_name"
#> 
#> $id_conversions$drug
#> [1] "chemical_name"
#> 
#> 
#> $entity_properties
#> [1] "is_transcription_factor" "is_kinase"              
#> [3] "is_phosphatase"         
#> 
#> $interaction_types
#>  [1] "Activation"            "Inhibition"            "IncreaseAmount"       
#>  [4] "DecreaseAmount"        "Regulation"            "Influence"            
#>  [7] "Gef"                   "Gap"                   "GtpActivation"        
#> [10] "Modification"          "Phosphorylation"       "Dephosphorylation"    
#> [13] "Autophosphorylation"   "Transphosphorylation"  "Ubiquitination"       
#> [16] "Deubiquitination"      "Sumoylation"           "Desumoylation"        
#> [19] "Hydroxylation"         "Dehydroxylation"       "Acetylation"          
#> [22] "Deacetylation"         "Glycosylation"         "Deglycosylation"      
#> [25] "Farnesylation"         "Defarnesylation"       "Geranylgeranylation"  
#> [28] "Degeranylgeranylation" "Palmitoylation"        "Depalmitoylation"     
#> [31] "Myristoylation"        "Demyristoylation"      "Ribosylation"         
#> [34] "Deribosylation"        "Methylation"           "Demethylation"        
#> [37] "Complex"               "Association"           "Conversion"           
#> [40] "Translocation"        
#> 
#> $evidence_sources
#> $evidence_sources$database
#>  [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"       
#> 
#> $evidence_sources$text_mined
#>  [1] "eidos"    "geneways" "gnbr"     "isi"      "medscan"  "reach"   
#>  [7] "rlimsp"   "semrep"   "sparser"  "tees"     "trips"   
#> 
#> 
#> $max_nodes
#> subnetwork 
#>        399 
#>