transGeneIDKEGG2Cyc: Transfer KEGG ID to BioCyc ID.

In YulongNiu/KEGG_BioCyc_API: A package for providing KEGG and BioCyc databases API in R

Description

Translate KEGG ID to BioCyc ID.

Usage

transGeneIDKEGG2Cyc(KEGGID, speKEGGID, speCycID, type = "gene")

Arguments

KEGGID	Only one KEGG ID
speKEGGID	Species BioCyc ID.
speCycID	Species KEGG ID
type	'gene' or 'protein'

Details

Translate the KEGG gene ID to BioCyc gene ID is tricky. In BioCyc, the gene names is not in a uniform; some of them use symbol like 'dnaK', but some use the KEGGID. For genes, if symbol is given, we use 'http://biocyc.org/xmlquery?query=[x:x<-ECOLI^^genes,x^name="atpA"]&detail=full'. There are two circumstances that will return "0": one is that BioCyc database may marker some genes as "Pseudo-Genes", and the other is different gene symbols in KEGG and BioCyc. For proteins, we at first transfer KEGG gene IDs to UniProt IDs, and then to BioCyc gene IDs.

Value

The BioCyc gene ID or "0", if gene is not found.

Author(s)

Yulong Niu [e-mail]

Examples

# symbol is "atpD"
transGeneIDKEGG2Cyc('b3732', 'eco', 'ECOLI')

# symbol is "SMU_408" but the first annotation word is "permease"
transGeneIDKEGG2Cyc('SMU_408', 'smu', 'SMUT210007')

# It will return "0" because of the symbol 'atpE_H' from KEGG.
# The symbol in BioCyc is 'atpE/H'.
transGeneIDKEGG2Cyc('Bd0010', 'bba', 'BBAC264462')

# retrieve protein
transGeneIDKEGG2Cyc('b0001', 'eco', 'ECOLI', type = 'protein')

YulongNiu/KEGG_BioCyc_API documentation built on May 10, 2019, 1:13 a.m.