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

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 heterogeneous formats 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 Iace data format are available from the authors. CONTACT hrc@genoscope.cns.fr

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