MSD's API and WebAPI Development

MSD's Application Programing Interface Development

Database application program interface development to the EBI-PDBe is a part of: EU-TEMBLOR (New-generation bioinformatics) Project.

Prof Geoffrey J Barton

School of Life Sciences,
WTB/MSI Complex, University of Dundee
Dow St
Dundee    DD1 5EH
Scotland    UK
Email: g.j.barton@dundee.ac.uk
Tel: (+44 1382) 344880
Fax: (+44 1382) 322558

Dr Thomas W Hamelryck

Dept. Ultrastructuur, Vrije Universiteit Brussel
Paardenstraat 65
1640 Sint-Genesius-Rode
Brussels
Belgium
E-mail: thamelry@vub.ac.be
Tel: (+32 2) 3590267
Fax: (+32 2) 3590289

Description of Work

This WP will develop an Application Programming Interface (API) to the EBI-PDBe database. The API will consist of a series of functions that external 3rd party software can use to allow their systems to access the EBI-PDBe database independently. The API will be derived by defining, both, queries and event requests. The API will be tested with browsers that will carry the functionality for displaying co-ordinates and sequence information.

In order to allow a more general and database independent interoperation, alternative integration strategies will also be explored. Partner 1 in an earlier EU grant has developed a CORBA interface to the EMBL nucleotide sequence database. A similar interface will be developed for the EBI-PDBe database. This will enable software developers to code to a defined standard interface that is independent of the underlying database architecture. It is likely that during the course of the project the XML standard will be widely adopted for communication of documents. We will track these developments and, as appropriate, support XML as an interchange format. Partners 24 and 25 have developed software systems for the display and analysis of macromolecular sequences and structures. Work will be carried out to extend the data structures in these packages to give a formal representation of macromolecules that will allow the systems to interact directly with the EBI-PDBe database. These browsers will have a direct connection to the EBI-PDBe database via the internet using the API. The API will be developed in parallel with the browser work. The first stage of the development of the API and its testing will be prototyped with the extended 3D browsers. Further development will allow for a generalised API implementation that will be made available to all 3rd party software interests.

The next step is the development of an interactive 3D-database browser. In order to display query results graphically, one has to retrieve the co-ordinate entries, and start up a molecular graphics display program. The interactive browser will have a direct connection to the EBI/PDBe relational database via the Internet. The API will enable the user to generate sophisticated queries and the retrieved information would then be immediately displayed at a remote user's console. New algorithms for the analysis of macromolecular structure will be developed that exploit the simplification that is possible by direct access to the EBI/PDBe relational database via the API. A further aim of this WP is to make use of the training workshops in WP1 to assist groups in academia and industry in the efficient use of the resource.