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QUESTIONS
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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:2.7.2.4 1.1.1.3); K12524 bifunctional aspartokinase / homoserine
dehydrogenase 1 [EC:2.7.2.4 1.1.1.3] ".
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.