Bio.KEGG.REST module

Provides code to access the REST-style KEGG online API.

This module aims to make the KEGG online REST-style API easier to use. See: https://www.kegg.jp/kegg/rest/keggapi.html

The KEGG REST-style API provides simple access to a range of KEGG databases. This works using simple URLs (which this module will construct for you), with any errors indicated via HTTP error levels.

The functionality is somewhat similar to Biopython’s Bio.TogoWS and Bio.Entrez modules.

Currently KEGG does not provide any usage guidelines (unlike the NCBI whose requirements are reasonably clear). To avoid risking overloading the service, Biopython will only allow three calls per second.

References: Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 29-34 (2000).

Bio.KEGG.REST.kegg_info(database)

KEGG info - Displays the current statistics of a given database.

db - database or organism (string)

The argument db can be a KEGG database name (e.g. ‘pathway’ or its official abbreviation, ‘path’), or a KEGG organism code or T number (e.g. ‘hsa’ or ‘T01001’ for human).

A valid list of organism codes and their T numbers can be obtained via kegg_info(‘organism’) or https://rest.kegg.jp/list/organism

Bio.KEGG.REST.kegg_list(database, org=None)

KEGG list - Entry list for database, or specified database entries.

db - database or organism (string) org - optional organism (string), see below.

For the pathway and module databases the optional organism can be used to restrict the results.

Bio.KEGG.REST.kegg_find(database, query, option=None)

KEGG find - Data search.

Finds entries with matching query keywords or other query data in a given database.

db - database or organism (string) query - search terms (string) option - search option (string), see below.

For the compound and drug database, set option to the string ‘formula’, ‘exact_mass’ or ‘mol_weight’ to search on that field only. The chemical formula search is a partial match irrespective of the order of atoms given. The exact mass (or molecular weight) is checked by rounding off to the same decimal place as the query data. A range of values may also be specified with the minus(-) sign.

Bio.KEGG.REST.kegg_get(dbentries, option=None)

KEGG get - Data retrieval.

dbentries - Identifiers (single string, or list of strings), see below. option - One of “aaseq”, “ntseq”, “mol”, “kcf”, “image”, “kgml” (string)

The input is limited up to 10 entries. The input is limited to one pathway entry with the image or kgml option. The input is limited to one compound/glycan/drug entry with the image option.

Returns a handle.

Bio.KEGG.REST.kegg_conv(target_db, source_db, option=None)

KEGG conv - convert KEGG identifiers to/from outside identifiers.

Arguments:

  • target_db - Target database

  • source_db_or_dbentries - source database or database entries

  • option - Can be “turtle” or “n-triple” (string).

KEGG link - find related entries by using database cross-references.

target_db - Target database source_db_or_dbentries - source database option - Can be “turtle” or “n-triple” (string).