ConvGeneKEGG2BioCyc: Transfer KEGG ID to BioCyc ID.
In YulongNiu/BioCyc_API: A package for providing BioCyc databases API in R

Description Usage Arguments Details Value Author(s) Examples

Convert KEGG ID to BioCyc ID.

1	ConvGeneKEGG2BioCyc(geneKEGG, speID, type = "gene")

`geneKEGG`	The gene symbol extract from KEGG.
`speID`	The BioCyc species ID, for example "ECOLI" is for "Escherichia coli K-12 substr. MG1655".
`type`	'gene' or 'protein'

Convert the KEGG gene ID to BioCyc gene ID is tricky. In BioCyc, the gene name is not in a uniform; some of them use symbol like "dnaK", but some use the KEGG ID. 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.

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

Yulong Niu yulong.niu@hotmail.com

## symbol is "atpD"
ConvGeneKEGG2BioCyc('eco:b3732', 'ECOLI')

## symbol is "SMU_408" but the first annotation word is "permease"
ConvGeneKEGG2BioCyc('smu:SMU_408', 'SMUT210007')

## It will return "0" because of the symbol 'atpE_H' from KEGG.
## The symbol in BioCyc is 'atpE/H'.
ConvGeneKEGG2BioCyc('bba:Bd0010', 'BBAC264462')

## retrieve protein
ConvGeneKEGG2BioCyc('eco:b0001', 'ECOLI', type = 'protein')