Issues in developing integrated genomic databases and application to the human X chromosome

Abstract

Motivation: In the past decade, a vast amount of mapping data has been generated on the human X chromosome, without a mechanism which would provide a global view of exactly what has been achieved. Large datasets are available electronically, but in heterogenous formate and with incompatible access modes. In addition, relationships between objects in different datasets are often not specified. Results: We discuss the problem of integrating these data into one database and define a number of requirements that are vital for any integration approach. We have developed IXDB, the Integrated X chromosome database, which fulfils those requirements and aims at providing a global view on genomic data at a chromosomal level. IXDB represents a conceptual framework based on identifying, storing and analysing relationships between biological objects, and includes a series of tools to automate the integration of such information. It currently focuses on physical mapping data, as a starting point towards a map of the human X chromosome that should provide a uniform and global research resource for ongoing and future sequencing and functional studies. Availability: IXDB is available at http://ixdb.mpimg-berlin-dahlem.mpg.de. The iace2ixdb software and a description of the lace data format are available from the authors. Contact: hrc@@@genoscope.cns.fr.