Workflow Entry: KEGG Pathway Analysis

The KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes:

External database Database prefix ----------------- --------------- NCBI GI ncbi-gi:

NCBI GeneID ncbi-geneid:

GenBank genbank:

UniGene unigene:

UniProt uniprot:

It performs this using the web service bconv, provided by the KEGG database (Kanehisa et al., 2010), described in the KEGG API available at: http://www.genome.jp/kegg/docs/keggapi_manual.html#label:42. A list of KEGG Ids in a tabular format is produced, the first element contains the input ID, the second element is the KEGG ID and the third element is a string confirming the corresponding existence of the proteins in both databases used. This tabular format is then split into three segments using white-space as a regular expression. Each element from each line is then entered into a new separate list. The next step in the workflow is to remove the confirmation string and the NCBI-GI ID, leaving the KEGG ID of the proteins. This is done by using the regular expression: .{3}:.* The get_pathways_by_genes web service from the KEGG database then queries the KEGG database and retrieves the pathways the protein participates in. The mark_pathway_by_objects method is used to mark the input proteins from the filtered list in their respective KEGG pathways found by get_pathways_by_genes. This method then generates a list of URLs as an output. The URLs retrieved corresponds to the images of the KEGG pathways. In these images the target proteins are marked in orange. For this procedure the Get_Image_From_URL method is used. The final output is a list of images with the target proteins in their respective KEGG pathways highlighted in orange.