Summary
Objectives: The increasing production of molecular biology data in the post-genomic era, and
the proliferation of databases that store it, require the development of an integrative
layer in database services to facilitate the synthesis of related information. The
solution of this problem is made more difficult by the absence of universal identifiers
for biological entities, and the breadth and variety of available data. Methods: Integr8 was modelled using UML (Universal Modelling Language). Integr8 is being implemented
as an n-tier system using a modern object-oriented programming language (Java). An
object-relational mapping tool, OJB, is being used to specify the interface between
the upper layers and an underlying relational database.
Results: The European Bioinformatics Institute is launching the Integr8 project. Integr8 will
be an automatically populated database in which we will maintain stable identifiers
for biological entities, describe their relationships with each other (in accordance
with the central dogma of biology), and store equivalences between identified entities
in the source databases. Only core data will be stored in Integr8, with web links
to the source databases providing further information.
Conclusions: Integr8 will provide the integrative layer of the next generation of bioinformatics
services from the EBI. Web-based interfaces will be developed to offer gene-centric
views of the integrated data, presenting (where known) the links between genome, proteome
and phenotype.
Keywords
Bioinformatics - databases – nucleic acid - databases – protein - genomics - proteomes
