kegg_pull: a software package for the RESTful access and pulling from the Kyoto Encyclopedia of Gene and Genomes

BMC Bioinformatics

Table 7 Entry fields that allow multiple entries to be pulled versus those that only allow one per request

Entry field	Can pull multiple entries in one request
aaseq	✓
ntseq	✓
mol	✓
kcf	✓
image	×
conf	×
kgml	×
json	×

One can pull up to 10 entries with a single request to the KEGG REST API. Pulling more entries per request can dramatically reduce pull time and increase the success percentage (see Table 6). However, this option is not available for all pulls. While this is not specified in the KEGG REST API documentation, nor do their requests fail if we request ten entries when only one is supported for a given entry field/database (they simply return the first entry in the request and exclude the other requested entries without any notification), we empirically determined which entry fields allow multiple entries per request and those that don’t. One can specify the field of an entry to pull rather than the standard “flat file format” (not available for Brite entries). While the flat file format pulls can pull multiple entries per request, some of the field entries can while others can’t. In addition to what’s displayed in this table, entries from the Brite database cannot be pulled more than one at a time per request, as Brite entries are not available in flat file format

ISSN: 1471-2105