keggConv: Convert IDs

In VonWebEinstein/keggAPI: KEGG API

Description

Convert KEGG identifiers to/from outside identifiers.

Usage

keggConv(target_db, source_db)
keggConv(target_db, dbentries)

Arguments

target_db	string. The database convert to.
source-db	string. The database convert from.
dbentries	string/char array. The IDs of entry we want to convert.

Details

When converting from database to database, (target_db, source_db) = (kegg_db, outside_db) | (outside_db, kegg_db). For gene identifiers: kegg_db = org, org = KEGG organism code or T number, outside_db = ncbi-proteinid | ncbi-geneid | uniprot.

For chemical substance identifiers: kegg_db = drug | compound | glycan outside_db = pubchem | chebi.

When converting entries to target_db, For gene identifiers: <dbentries> = database entries involving the following <database>, <database> = <org> | genes | ncbi-proteinid | ncbi-geneid | uniprot, <org> = KEGG organism code or T number

For chemical substance identifiers: <dbentries> = database entries involving the following <database> <database> = drug | compound | glycan | pubchem | chebi

Note

The database name "genes" may be used only in the second form (convert entries to target_db).

Examples

# conversion from NCBI GeneID to KEGG ID for E. coli genes
gene_E.coli = keggConv('eco', 'ncbi-geneid')
# opposite direction
gene_E.coli = keggConv('ncbi-geneid', 'eco')

# conversion from KEGG ID to NCBI ProteinID
keggConv('ncbi-proteinid', 'hsa:10458+ece:Z5100')

# conversion from NCBI GeneID to KEGG ID when the organism code is not known
keggConv('genes', 'ncbi-geneid:19831932')
# same as above
keggConv('lpn', 'ncbi-geneid:19831932')

VonWebEinstein/keggAPI documentation built on May 9, 2019, 10:02 p.m.