Abstract
AbstractIn this poster, we present our experience with techniques for the management of bio-models (i.e. XML-encoded computational models of biological systems) in repositories. These techniques support users to find, access, adapt and then re-submit models - tasks which are essential for the reuse of models in systems biology. Here, we focus on model retrieval, the ranking of search results and concepts to track the history of a model through version control. These concepts have so far not been sufficiently addressed in existing systems.To validate our techniques, we have been implemented a framework called Sombi. The underlying database called mDB is tailored towards a fine-grained storage of the model and its annotations. The design is applicable to different representation formats but, to begin with, has been tested with SBML models (Köhn et al., 2009).We furthermore present a retrieval algorithm for bio-model repositories (Henkel et al., 2010). The algorithm has been implemented and validated with mDB and the BioModels Database (www.ebi.ac.uk/biomodels-main/). The ranked retrieval enhances the result set by incorporating expert knowledge in the annotations. In contrast to existing systems, our approach provides a ranked result which is justified and explains the ordering of retrieved models to the users. The mDB design furthermore enables the application of structured queries on the stored model data.Finally, the poster proposes a solution to model version control. We introduce a library called BiVeS for tracking a model’s history in a diff tree; i.e. a tree-like storage of changes between model versions. These changes are additionally classified into modifications to XML structure, biology and mathematics. This information helps to understand existing models.All approaches are independent of the SBML format and can therefore be applied to other XML based exchange formats. All code is freely available on Sourceforge from http://bives.sourceforge.net/ and http://sombi.sourceforge.net/.
Highlights
Bio-models are made available through model repositories
The incorporation of Information Retrieval [2] techniques allows the advanced indexing of a set of bio-models in a repository [3]
We propose here a thorough versioning approach for biomodels that considers changes in the mathematics, in the biology and in the meta-information
Summary
Search results are ofen only presented to the user in an unsorted set. With high numbers of relevant models for a query, it becomes necessary to sort the results by relevance. Key Questions: How can search results be ranked according to their relevance? Which is the best applicable ranking function? Solutions: - ranking with a Vector Space Model - feature set partially derived from bio-model meta-information [1] - weight concept to satisfy diferent user requirements Key Questions: How can search results be ranked according to their relevance? What are the determining bio-model features? Which is the best applicable ranking function? Solutions: - ranking with a Vector Space Model - feature set partially derived from bio-model meta-information [1] - weight concept to satisfy diferent user requirements
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