|Version 38 (modified by anonymous, 8 years ago)|
Towards integrated web service in life science with Open Bio* libraries.
The number of web service providers in bioinformatics field is increasing year by year. In theory, these services are interoperable and independent from computer langugages. However, each service uses their own definition of the data types and naming convensions for the methods. Moreover, these services are often not usable by specific languages (partly, due to the lack of compliance of the SOAP/WSDL specification in the langauge's library).
This situation prevents these services to be popularized for and used in combination by end users as a infrastructure of the daily research. The BioMOBY project has been tried to overcome the circumstances by defining ontologies for data types and methods used in the services. However, there are many major service providers are not yet participated in the BioMOBY framework. Especially, there are several web service providers in Japan such as DDBJ, KEGG, PDBj and CBRC but none of them are not integrated in any context.
Thus, at DBCLS, we started to develop a new proxy server which translates user's request for the appropriate web service provider. If all Open Bio* libraries support BioMOBY and other service providers, interoperability of these services can be significantly improved. Here, we need agreement for the future web services with every web service providers and client developers.
We believe gathering all web service providers to disucuss about the standardization of objects and methods among web services, and Open Bio* library developers from different programming languages ( BioPerl, BioPython, BioRuby, and BioJava) to discuss about the implementation of the common infrastructure, must benefit usability and interoperability for the life science in the next era.
For this purpose, we hope to organize a BioHackathon specialized for the web services in 2008.
- Encourage independent service providers to join the movement of integration and interoperability
- How to increase the number of SOAP compliant services (tools/databases)
- Utilizing every bioinformatics web services by 4 major computer languages (Perl, Python, Ruby, Java)
- Creating compatible classes for sequences, expressions, pathways etc. among Open Bio* libraries
- Providing various clients to create and execute bioinformatics workflows
- Connecting seamlessly: Web service - Grid, Remote - Local, SOAP/WSDL - REST, Async - Sync
- Standardizing the objects and methods in bioinformatics web services (BioMOBY)
- Discuss about the best solution of the framework and ontologies for the life science
List of tentative meeting topics for the web service providers, the Open Bio* developers, the workflow client developers, and the BioMOBY project:
DBCLS and CBRC will provide ideal environment for discussions and developments.
- Roppongi Academy Hills (Roppongi, Central Tokyo)
- CBRC Computatonal Biology Research Cener (Odaiba, Tokyo Bay Area)
We will prepare KML file for Google Earth.
- 2008/2/10 (Sun) - Arrival ( Narita airport, Japan)
- 2008/2/11 (Mon) - Presentations & discussions (Roppongi Academy Hills)
- 2008/2/12 (Tue) - Hack, hack, hack (CBRC)
- 2008/2/13 (Wed) - Hack, hack, hack (CBRC)
- 2008/2/14 (Thr) - Hack, hack, hack (CBRC)
- 2008/2/15 (Fri) - Hack, hack, hack (CBRC)
- 2008/2/16 (Sat) - Depature
If you could recommend any appropriate persons from the following groups, please let me know:
- NCBI web service developers
- BioPerl, BioPython, and BioJava developers
- TracGuide -- Built-in Documentation
- The Trac project -- Trac Open Source Project
- Trac FAQ -- Frequently Asked Questions
- TracSupport -- Trac Support
For a complete list of local wiki pages, see TitleIndex.
- BioHackathon2008Tokyo.kmz (4.1 KB) - added by anonymous 8 years ago.
(212.0 KB) - added by yy
8 years ago.
Map of CBRC (venue after the 2nd day) and spots to visit nearby.
- CBRCMap.ppt (361.0 KB) - added by atsuko 8 years ago.
(52.9 KB) - added by atsuko
7 years ago.
(8.4 KB) - added by atsuko
7 years ago.
Adaptor plug left behind