Journal: BMC Bioinformatics

Article Title: Ranked retrieval of Computational Biology models

doi: 10.1186/1471-2105-11-423

Figure Lengend Snippet: Growing number of Computational Biology models and their components in BioModels Database . Upper chart: Numbers of models in BioModels Database, as of January 2010. Lower chart: Number of species (black bar) and reactions (gray bar) in BioModels Database, as of January 2010. BioModels Database started with 20 models and a total of 322 species when it was launched in April 2005. In 2007 it already reached almost 200 models and 10482 species. The release in January 2010 recorded 453 models with 33702 species and 41069 reactions.

Article Snippet: We extend the current BioModels Database search engine by including a greater number of features in the search process, by weighting different information, and by ranking the results according to the user query.

Techniques:

Journal: BMC Bioinformatics

Article Title: Ranked retrieval of Computational Biology models

doi: 10.1186/1471-2105-11-423

Figure Lengend Snippet: Conceptual architecture . Overview of the conceptual architecture of the proposed ranking- and retrieval system. A version has been implemented in BioModels Database. The architecture shows the process of transforming a user given query by creating sub-queries, which are then assembled by enrichment of structural information and semantic indexing (see also Figure 3). The re-assembled query is then sent to the retrieval and ranking module, which makes use of the Extended Boolean Model to retrieve a list of matching models, and the Vector Space Model to rank the list of retrieved models. To determine the ranking, different weight information is used. Those are, however, not shown in the given Figure.

Article Snippet: We extend the current BioModels Database search engine by including a greater number of features in the search process, by weighting different information, and by ranking the results according to the user query.

Techniques: Plasmid Preparation

Journal: BMC Bioinformatics

Article Title: Ranked retrieval of Computational Biology models

doi: 10.1186/1471-2105-11-423

Figure Lengend Snippet: Sample query on the new BioModels Database search interface . Screenshot of a part of the new search interface of BioModels Database. The interface allows to search for Persons, SBML elements, Resources , and allows to restrict the search terms to particular features using a single qualifier. Models may only be considered for a certain range of dates . The sample search correspond to recent models by non-bogus authors describing the effect of caffeine in human's digestive tract when drinking coffee .

Article Snippet: We extend the current BioModels Database search engine by including a greater number of features in the search process, by weighting different information, and by ranking the results according to the user query.

Techniques:

Journal: BMC Bioinformatics

Article Title: Ranked retrieval of Computational Biology models

doi: 10.1186/1471-2105-11-423

Figure Lengend Snippet: Ranked results . Search result obtained on BioModels Database with the given sample query (see Figure 3). The upper panel shows the enriched query. Due to the precise formulation of the query, and the requirement that caffeine must occur and additionally must be qualified with is , the result contains only three hits. (1) This model matches the top two constituents resolved by the semantic index, and additionally the term gut in the compartment feature. (2) The model matches the constituent ranked third by the semantic index. (3) The lowest ranked model only matches one constituent ranked eight by the semantic index - this is a very weak relation resulting in a very low rank.

Article Snippet: We extend the current BioModels Database search engine by including a greater number of features in the search process, by weighting different information, and by ranking the results according to the user query.

Techniques: Formulation