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Ground entities in a backend's namespaces

convert_ids.Rd

Fills in namespace, entity_id, and entity_name from each row's id (parent_id for ptm_site rows), read as the identifier system in id_type. Rows that don't ground are left NA. backend_capabilities(backend)$id_conversions lists the (entity type, identifier system) pairs a backend can convert.

Usage

convert_ids(backend, entities, ...)

# S4 method for class 'NetworkBackend'
convert_ids(backend, entities, ...)

# S4 method for class 'IndraBackend'
convert_ids(backend, entities, ...)

Arguments

backend

a NetworkBackend, e.g. from indra_backend()

entities

entity table from prepare_entities()

...

passed to methods

Value

entities with the grounding columns filled in

Details

Ground the full results table, not only the significant rows, so that get_network() can recognize every node that is in the input.

For INDRA, UniProt IDs and mnemonics are mapped through CoGEx, and gene symbols and chemical names are grounded with Gilda. When an identifier is a protein group ("P1;P2") or a name with several candidates, the groundings are ";"-joined and positionally aligned.

See also

get_entity_properties()

Examples

df <- data.frame(Protein = c("P04637", "Q00610"))
entities <- prepare_entities(df, entity_type = "protein",
                             id_type = "uniprot")
convert_ids(indra_backend(), entities)
#>       id entity_type id_type namespace entity_id entity_name included_in_query
#> 1 P04637     protein uniprot      HGNC     11998        TP53              TRUE
#> 2 Q00610     protein uniprot      HGNC      2092        CLTC              TRUE
#>   site parent_id organism
#> 1 <NA>      <NA>     9606
#> 2 <NA>      <NA>     9606