A database system for the analysis of biochemical pathways.

Abstract (Expand)

To provide support for the analysis of biochemical pathways a database system based on a model that represents the characteristics of the domain is needed. This domain has proven to be difficult to … model by using conventional data modelling techniques. We are building an ontology for biochemical pathways, which acts as the basis for the generation of a database on the same domain, allowing the definition of complex queries and complex data representation. The ontology is used as a modelling and analysis tool which allows the expression of complex semantics based on a first-order logic representation language. The induction capabilities of the system can help the scientist in formulating and testing research hypotheses that are difficult to express with the standard relational database mechanisms. An ontology representing the shared formalisation of the knowledge in a scientific domain can also be used as data integration tool clarifying the mapping of concepts to the developers of different databases. In this paper we describe the general structure of our system, concentrating on the ontology-based database as the key component of the system.

Authors: I. Rojas, L. Bernardi, E. Ratsch, R. Kania, U. Wittig, J. Saric

Date Published: 18th Jun 2002

Publication Type: Journal

Notes on the use of ontologies in the biochemical domain.

Abstract (Expand)

In this paper we aim at presenting the main flavours and uses that are given to the term ontology in the bio-domains. The paper does not intend to be a thorough review of the existing work in the area. … It highlights the uses that are given to ontologies in the Scientific Databases and Visualisation Group at EML Research, in Heidelberg.

Authors: I. Rojas, E. Ratsch, J. Saric, U. Wittig

Date Published: 20th Apr 2004

Publication Type: Journal

Developing a protein-interactions ontology.

Abstract

Not specified

Authors: E. Ratsch, J. Schultz, J. Saric, P. C. Lavin, U. Wittig, U. Reyle, I. Rojas

Date Published: 17th Jul 2008

Publication Type: Journal

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