[Biopython-dev] TogoWS in Biopython?

[Peter Cock]

Dear all,

Would someone like to review the TogoWS code I have written
to access the Togo Web Service's REST API please?

http://togows.dbcls.jp/
http://togows.dbcls.jp/site/en/rest.html
http://dx.doi.org/doi:10.1093/nar/gkq386

This provides a nice simple URL based API for fetching database
entries in various formats (XML, JSON, GenBank etc - even some
individual fields from some database records, e.g. the accession
of a GenBank record), searching, and even some file format
conversion (which uses a range of tools on their server, some
in BioRuby and others in BioPerl I believe).

The code is on this branch,
https://github.com/peterjc/biopython/tree/togows

See module Bio.TogoWS and its docstrings,
https://github.com/peterjc/biopython/blob/togows/Bio/TogoWS/__init__.py

Unit tests in Tests/test_TogoWS.py
https://github.com/peterjc/biopython/blob/togows/Tests/test_TogoWS.py

I have be guided by the naming we've used in Bio.Entrez
for accessing the NCBI Entrez API.

Note that in addition to major Japanese databases, TogoWS
also proxies and caches data from Europe (e.g. UniProt) and
America (e.g. GenBank and PubMed). It was very fast when
testing from Japan this summer - not quite so speedy from
the UK though ;)

Personally I found TogoWS much easier to use for searching
and retrieving batches of records than the NCBI Entrez API
with its complicated history requirement. I expect it to be
particularly popular with Biopython uses in Japan.

Thanks in advance,

Peter