Seminar - Dr. Jacob Koehler

Speaker: Dr. Jacob Koehler (Rothamsted Research)
Title: The ONDEX Framework: Uniting Concept-based Data Integration, Text Mining, Biological Homology Searches and Data Analysis
Date: 2pm, 17th March, 2006
Location: Lecture Theatre E7, Renold Building (building 8 on the campus map)
Abstract: Biological information can be found in experimental results, in hundreds of scientific databases/ontologies and in millions of scientific publications. Furthermore, sequence analysis methods are commonly used to predict the functional and structural properties of genes and gene products. Extracting and combining information from these very different sources has many potential applications from Bioinformatics, for example: supporting i) database and ontology curation, ii) gene annotation, iii) analysis and interpretation of experimental results and iv) modelling and simulation of biological systems.

ONDEX is an integration framework which aims to address these, and similar applications by combining features of database integration, text mining and sequence analysis with methods for graph-based data analysis and visualisation. ONDEX is implemented using an ontology based data structure, which enables a coherent approach to the extraction, integration and analysis of data from heterogeneous sources at both the technical and the semantic levels. Although the ONDEX framework has been developed with biological applications in mind, the methods and systems architecture are developed in a generic way, which means that ONDEX can, in principle, also be applied in other domains.

This presentation gives an overview of the principles underlying the ONDEX framework, its ongoing development and future plans. Some example applications will also be presented. ONDEX can be found at

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