BioWare: A framework for bioinformatics data retrieval, annotation and publishing

Koh J. L., Krishnan S., Hong S. S., Tan P. T., Khan M. A., Lee M. L., ...More

27th Annual International ACM SIGIR Conference on Research and Development in IR, Sheffield, United Kingdom, 29 - 31 July 2004, pp.1-9

  • Publication Type: Conference Paper / Full Text
  • City: Sheffield
  • Country: United Kingdom
  • Page Numbers: pp.1-9
  • Bezmialem Vakıf University Affiliated: No


In-depth analysis about a specific subject in molecular biology, specifically those associated with the structural and functional properties of a particular group of sequences typically requires access to an extensive knowledge base. The knowledge base may take the form of a specialist database or subject-specific data warehouse (SSDW) to facilitate the organisation of specialized data and the extraction of new knowledge. These SSDWs are particularly useful for data mining or knowledge discovery processes which require the relevant information from multiple data sources. The construction of a specialist database is a multi- step process which typically involves enrichment of annotations (by domain experts), development and integration of analytical tools (by computer programmers), and construction of the system (by database experts). The SSDWs contain focused subsets of data compiled from multiple data sources and enriched with user annotations. In this article we present and describe the BioWare system which enables its users to collect, annotate, publish, and update specialized molecular data in personalized WWW- accessible databases. BioWare contains four data warehouse enabling components: (i) BioWare-Retrieve searches and extracts data from selected sources and integrates them into a standardized format, (ii) BioWare-Prep provides a semi-automated mechanism for user-driven cleaning, preliminary analysis and annotation of the data, (iii) TEMPLAR enables users to rapidly create searchable WWW-accessible SSDWs, and (iv) BioWare-Update enables incremental updating of the SSDWs with new data from the sources. We have used BioWare system for the creation and maintenance of several bioinformatic databases.