idMapping: Map IDs to Primary Uniprot or ChEBI IDs
Description
Unambiguously maps, e.g., HGNC gene symbols, NCBI Gene, RefSeq, ENS*, and
secondary UniProt identifiers to the primary UniProt accessions, or - ChEBI
and PubChem IDs to primary ChEBI. You can mix different standard ID types in
one query.
Usage
idMapping(ids, verbose = FALSE)
Arguments
ids
a vector of IDs
verbose
a boolean, display the command used to query Pathway Commons
Value
a list of where each entry is a HGNC symbol provided and the each
value is a primary UniProt or ChEBI ID.
concept
paxtoolsr
Details
This is a specific id-mapping (not general-purpose) for reference
proteins and small molecules; it was first designed for internal use, such
as to improve BioPAX data integration and allow for graph queries accept
not only URIs but also standard IDs. The mapping tables were derived
exclusively from Swiss-Prot (DR fields) and ChEBI data (manually created
tables and other mapping types and sources can be added in the future
versions if necessary).