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Dagmar Waltemath

last modified 2011-08-20 21:14

Title of PhD thesis:
Annotation-based storage and retrieval of models and simulation descriptions in computational biology


Andreas Heuer (Rostock, Germany)

Nicolas Le Novère (Cambridge, UK)

Ulf Leser (Berlin, Germany)


The purpose of this work was to enhance the reuse of computational biology models by iden- tifying and formalizing relevant meta-information, and to develop extended model storage and retrieval concepts. The work focussed on models in XML formats and annotated with RDF-encoded meta- information. One particular type of meta-information investigated in this thesis is experiment- related meta-information attached to a model, which is necessary to accurately recreate simulations. The implementations in this work were carried out using methods from the re- search area of ’Information Retrieval’, and proposed solutions were tested on the BioModels Database repository. The main results of the study are: a detailed concept for model annotation, a proposed format for the encoding of simulation experiment setups, a storage solution for standardized model representations, and the development of a retrieval concept. A model annotation strategy has been developed for the model representation format SBML. The proposed simulation experiment encoding is being considered by various groups within the computational biology arena, including the SBML, CellML and NeuroML working groups. It has been shown that a fine-grained storage approach enables model search and versioning across different model representation formats. The application of information retrieval techniques indicated how the model search process can be enhanced by considering meta-information and incorporating information from external resources. The principal conclusion was that a fine-grained encoding and storage of model meta-information enhances the retrieval process and thereby improves model reuse.

Important publications

  • Ron Henkel, Lukas Endler, Andre Peters, Nicolas Le Novère and Dagmar Waltemath (2010): Ranked retrieval of Computational Biology models. - BMC Bioinformatics, 11(423).
  • Dagmar Waltemath, Frank T Bergmann, Richard Adams and Nicolas Le Novère (2011): Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1. - Webpublished,
  • Dagmar Waltemath, Richard Adams, Daniel A Beard, Frank T Bergmann, Upinder S Bhalla, Randall Britten, Vijayalakshmi Chelliah, Michael T Cooling, Jonathan Cooper, Edmund Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter Hunter, Edda Klipp, Camille Laibe, Andrew MIller, Ion Moraru, David Nickerson, Poul Nielsen, Macha Nikolski, Sven Sahle, Herbert Sauro, Henning Schmidt, Jacky Snoep, Dominic Tolle, Olaf Wolkenhauer and Nicolas Le Novère (2011): Minimum Information About a Simulation Experiment (MIASE). - PLoS Computational Biology, 7(4).

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