Query KEGG for pathways from KEGG Orthologs (KOs).
Eventually will allow more query types
There is a MUCH more robust Bioconducter packag called KEGGREST. However, I was too impatient to figure out how to query the actual pathway names for my KOs. So, based on the paste-in KEGG page, I created a few tools to use the exposed REST API that page uses.
Also, according to the KEGGREST docs,
NOTE: keggGet() can only return 10 result sets at once (this limitation is on the server side). If you supply more than 10 inputs to keggGet(), KEGGREST will warn that only the first 10 results will be returned.
I have found no such limitation in the REST API these tools use.
kegg_http_request = 'https://www.genome.jp/kegg-bin/search_pathway_object?org_name=ko&unclassified=K02078%20K00764%20K03657'
getPathwaysFromKEGGWebpage(kegg_http_request)
#> KO Pathway
#> 1 KO01100 Metabolic pathways
#> 2 KO01130 Biosynthesis of antibiotics
#> 3 KO00230 Purine metabolism
#> 4 KO00998 Biosynthesis of secondary metabolites - other antibiotics
#> 5 KO03420 Nucleotide excision repair
#> 6 KO01110 Biosynthesis of secondary metabolites
#> 7 KO00250 Alanine, aspartate and glutamate metabolism
#> 8 KO03430 Mismatch repair
kegg_http_request = createKeggHTTPRequest(c("K02078", "K00764", "K03657"))
print(kegg_http_request)
#> [1] "https://www.genome.jp/kegg-bin/search_pathway_object?org_name=ko&unclassified=K02078%20K00764%20K03657"
getPathwaysFromKEGGWebpage(kegg_http_request)
#> KO Pathway
#> 1 KO01100 Metabolic pathways
#> 2 KO01130 Biosynthesis of antibiotics
#> 3 KO03430 Mismatch repair
#> 4 KO00998 Biosynthesis of secondary metabolites - other antibiotics
#> 5 KO00250 Alanine, aspartate and glutamate metabolism
#> 6 KO01110 Biosynthesis of secondary metabolites
#> 7 KO00230 Purine metabolism
#> 8 KO03420 Nucleotide excision repair
getPathwaysFromKOList(c("K02078", "K00764", "K03657"))
#> [1] "https://www.genome.jp/kegg-bin/search_pathway_object?org_name=ko&unclassified=K02078%20K00764%20K03657"
#> KO Pathway
#> 1 KO01100 Metabolic pathways
#> 2 KO01130 Biosynthesis of antibiotics
#> 3 KO03420 Nucleotide excision repair
#> 4 KO00998 Biosynthesis of secondary metabolites - other antibiotics
#> 5 KO00230 Purine metabolism
#> 6 KO03430 Mismatch repair
#> 7 KO01110 Biosynthesis of secondary metabolites
#> 8 KO00250 Alanine, aspartate and glutamate metabolism
Created on 2019-11-05 by the reprex package (v0.3.0)
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