TogoWS

Integration of the bioinformatics web services

http://togows.dbcls.jp/entry/database/entry_id[,entry_id2,...]/field[.format]

Related resources

Status log of Japanese web services

Database of sample codes for Japanese web services (for Perl, Python, Ruby and Java)

Database of methods provided by EBI, NCBI, and Japanese web services

Integration with the TogoDB service, which we also provide as a repository for user driven database, enable users to combine their own data with public web services in the industry standard architectures such as Galaxy or GMOD/GBrowse.

Towards an integrated web service in life science

Summary of TogoWS service

To date, various databases have been made available through web services provided by major bioinformatics centers including NCBI, EBI, DDBJ, KEGG, PDBj, and CBRC. These web services are helpful especially for the high throughput analysis, however, there are no consistent way to utilize them uniformly. Our new web service, TogoWS, is designed to address several major issues for the improved usability and seamless integration.

(1) SOAP based web services are ideally follow the open standard and they should be independent from computer languages, however, many services still require language specific hacks in practice. TogoWS proxies these services to make them available in any programming language without difficulty.
(2) Query mechanism and syntax differs service to service that requires user to learn each usage beforehand. TogoWS provides a simple REST interface to query and retrieve in a unified manner.
(3) Entries obtained from databases are needed to be parsed by the client program to be fully utilized. TogoWS embeds open source bioinformatics libraries like BioPerl and BioRuby (which we also developed) to provide functionalities for parsing and conversion of various biological data formats without any installation on user side.

We, Database Center for Life Science (DBCLS), add a practical value which enable users to access and utilize any major biological databases without any additional software to create truly interoperable workflows with web services.

REST service: interoperable REST interface
SOAP service: integrated Japanese SOAP web services

Part of the concept of this work was emerged from the BioHackathon 2008, the international workshop entitled "Towards integrated web service in life science with Open Bio* libraries."

Reference

Toshiaki Katayama, Mitsuteru Nakao and Toshihisa Takagi (2010) TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services, Nucleic Acids Research, 2010, Vol. 38, No. suppl_2 W706-W711, doi:10.1093/nar/gkq386 (Web Server Issue 2010)