Pathway and protein interaction data: From XML to FDM database

Abstract

This paper describes our experience with the first steps towards integrating pathway and protein interaction data with other data sets within the framework of a federated database system based on the functional data model. We have made use of DTD and XML files produced by the BIND project. The DTD provides a specification for information about biomolecular interactions, complexes and pathways, and can be translated semi-automatically to a database schema. The load utility uses metadata derived from this schema to help identify data items of interest when recursively traversing a Prolog tree structure representing the XML data. We also show how derived functions can be used to make explicit those relationships that are present in data sets but which are not fully described in DTD files. © Springer-Verlag 2004.