Open Access Highly Accessed Methodology article

Ranked retrieval of Computational Biology models

Ron Henkel12, Lukas Endler2, Andre Peters1, Nicolas Le Novère2 and Dagmar Waltemath1*

Author Affiliations

1 Database and Information Systems, University of Rostock, Rostock, Germany

2 Computational Neurobiology, European Bioinformatics Institute, Hinxton, UK

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BMC Bioinformatics 2010, 11:423  doi:10.1186/1471-2105-11-423

Published: 11 August 2010



The study of biological systems demands computational support. If targeting a biological problem, the reuse of existing computational models can save time and effort. Deciding for potentially suitable models, however, becomes more challenging with the increasing number of computational models available, and even more when considering the models' growing complexity. Firstly, among a set of potential model candidates it is difficult to decide for the model that best suits ones needs. Secondly, it is hard to grasp the nature of an unknown model listed in a search result set, and to judge how well it fits for the particular problem one has in mind.


Here we present an improved search approach for computational models of biological processes. It is based on existing retrieval and ranking methods from Information Retrieval. The approach incorporates annotations suggested by MIRIAM, and additional meta-information. It is now part of the search engine of BioModels Database, a standard repository for computational models.


The introduced concept and implementation are, to our knowledge, the first application of Information Retrieval techniques on model search in Computational Systems Biology. Using the example of BioModels Database, it was shown that the approach is feasible and extends the current possibilities to search for relevant models. The advantages of our system over existing solutions are that we incorporate a rich set of meta-information, and that we provide the user with a relevance ranking of the models found for a query. Better search capabilities in model databases are expected to have a positive effect on the reuse of existing models.