Questions for the KEGG team. ** No apparent replacement found for old APIs Is there a new programmatic way to call the old SOAP api "get_motifs_by_gene"? I know I can do it manually with a request like this: http://www.kegg.jp/ssdb-bin/ssdb_motif?kid=eco%3Ab0002&lib=pfam But then I have to scrape the page. I have a similar question about "get_genes_by_motifs", which I can also do manually from http://www.kegg.jp/kegg/ssdb/. Also, the SOAP API had "start" and "max_results" arguments; is there an equivalent? About the SOAP APIs "get_best_neighbors_by_gene" and "get_best_best_neighbors_by_gene"; it looks like similar functionality is provided by http://www.kegg.jp/kegg/ssdb/ but again, is there a more programmatic way to do it? I’d also like to replace the old API "get_paralogs_by_gene" which it seems like I can also do from the http://www.kegg.jp/kegg/ssdb/ page. With all of these SSDB functions, is there support for the "start" and "max_results" arguments? Although I can search compounds by mass, (example: http://rest.kegg.jp/find/compound/174.05/exact_mass/), I can’t seem to search glycans by mass as I could with the SOAP API "search_glycans_by_mass". Is there an equivalent function in the REST API? There does not seem to be an equivalent to the SOAP API "search_compounds_by_subcomp". Is there a replacement? What about "search_glycans_by_kcam" and the more general-purpose "bget"? Is there a way in the REST api to return flat-file records, similar to what "bget" did? Two other "missing" functions seem to be "get_ko_by_ko_class" and "get_genes_by_ko_class". Are there replacements for these? Is the SOAP function get_html_of_colored_pathway_by_elements any different from e.g. http://www.kegg.jp/kegg-bin/show_pathway?eco00260/b0002%09%23ff0000,%2300ff00/c00263%09%23ffff00,yellow ? Is there a REST implementation of the SOAP functions get_element_relations_by_pathway and get_elements_by_pathway? ** Results of new APIs differ from old Calling the SOAP api "get_enzymes_by_pathway" with "pathway_id" equal to "path:eco00020" yields a result of 14 enzymes; what seems to be the equivalent in REST, http://rest.kegg.jp/link/enzyme/path:eco00020 returns nothing. Is this expected? Have the data changed? Similarly, calling "get_compounds_by_pathway" with a "pathway_id" argument of "path:eco00020" returns 20 compounds in SOAP, but the REST equivalent (?), http://rest.kegg.jp/link/compound/path%3aeco00020 returns nothing. Calling this REST api with a different argument: http://rest.kegg.jp/link/compound/path:map00010 does return some results. Calling the SOAP api "get_kos_by_pathway" with a "pathway_id" argument of "path:hsa00010" returns 36 results, but the seeming REST equivalent, http://rest.kegg.jp/link/ko/path%3ahsa00010 returns nothing. ** Missing Arguments The SOAP API "get_genes_by_organism" has "start" and "max_results arguments. The REST equivalent, which seems to be, for example http://rest.kegg.jp/list/hsa does not appear to have such arguments. Is there a way to paginate results that come back from the REST server? It looks like I can call an equivalent of the old "get_genes_by_ko" API, as follows: http://rest.kegg.jp/link/genes/ko:K12524 But in the old API, I could filter by organism (e.g. "eco"). Also, the SOAP api would return annotations, for example, for eco:b0002 it would return "thrA; fused aspartokinase I and homoserine dehydrogenase I (EC:18.104.22.168 22.214.171.124); K12524 bifunctional aspartokinase / homoserine dehydrogenase 1 [EC:126.96.36.199 188.8.131.52] ". Is there a way I can get these annotations back in a REST query? It seems I only get two columns back, the ko ID and gene ID. Similarly, the SOAP API "get_pathways_by_kos" had an "org" argument to filter by "organism". The REST equivalent, for example http://rest.kegg.jp/link/pathway/ko:K00016+ko:K00382 oes not seem to have this option, and the results do not allow me to do my own filtering (that is, they do not have three-letter organism codes). Also, the results differ between SOAP and REST. In SOAP, calling "get_pathways_by_kos" with a "ko_id_list" argument of ko:K00016 and ko:K00382, and an "org" argument of "hsa", returns path:hsa00010 and path:hsa00620, but the results of http://rest.kegg.jp/link/pathway/ko:K00016+ko:K00382 do not include these items.