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Combining computational models, semantic annotations and simulation experiments in a graph database.

Henkel R, Wolkenhauer O, Waltemath D - Database (Oxford) (2015)

Bottom Line: The introduced concept notably improves the access of computational models and associated simulations in a model repository.This has positive effects on tasks such as model search, retrieval, ranking, matching and filtering.Furthermore, our work for the first time enables CellML- and Systems Biology Markup Language-encoded models to be effectively maintained in one database.

View Article: PubMed Central - PubMed

Affiliation: University of Rostock, Department of Computer Science, Albert-Einstein-Straße 22, D-18059 Rostock, Germany, Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, 18057 Rostock, Germany and Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa ron.henkel@uni-rostock.de.

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Results for Query BM3. The query output at the top of the figure restricts the species role to ‘modifier’. Three SED-ML files match. The first and second files belong to the same model and both observe the species Cdc25. The third query result is a SED-ML file observing four different species. The query output at the bottom of the figure shows the result of a similar query. Here the species must act as ‘reactants’. Only one SED-ML file is retrieved, namely the third result of the top query. All retrieved species (declared as observed by a SED-ML file) are annotated with a UniProt ID. The annotation is either P06652, the protein Cdc25 in yeast, or P20483, the protein Stg (Cdc25) in the fruit fly. Simulation files for CellML files are not retrieved, because CellML files are not yet fully annotated. If the CellML version of the Novak 1997 model had annotations corresponding to ‘m-phase inducer phosphatase’, the database would have also returned the simulation description for that model.
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bau130-F3: Results for Query BM3. The query output at the top of the figure restricts the species role to ‘modifier’. Three SED-ML files match. The first and second files belong to the same model and both observe the species Cdc25. The third query result is a SED-ML file observing four different species. The query output at the bottom of the figure shows the result of a similar query. Here the species must act as ‘reactants’. Only one SED-ML file is retrieved, namely the third result of the top query. All retrieved species (declared as observed by a SED-ML file) are annotated with a UniProt ID. The annotation is either P06652, the protein Cdc25 in yeast, or P20483, the protein Stg (Cdc25) in the fruit fly. Simulation files for CellML files are not retrieved, because CellML files are not yet fully annotated. If the CellML version of the Novak 1997 model had annotations corresponding to ‘m-phase inducer phosphatase’, the database would have also returned the simulation description for that model.

Mentions: Result 4: The result is shown and explained in Figure 3.


Combining computational models, semantic annotations and simulation experiments in a graph database.

Henkel R, Wolkenhauer O, Waltemath D - Database (Oxford) (2015)

Results for Query BM3. The query output at the top of the figure restricts the species role to ‘modifier’. Three SED-ML files match. The first and second files belong to the same model and both observe the species Cdc25. The third query result is a SED-ML file observing four different species. The query output at the bottom of the figure shows the result of a similar query. Here the species must act as ‘reactants’. Only one SED-ML file is retrieved, namely the third result of the top query. All retrieved species (declared as observed by a SED-ML file) are annotated with a UniProt ID. The annotation is either P06652, the protein Cdc25 in yeast, or P20483, the protein Stg (Cdc25) in the fruit fly. Simulation files for CellML files are not retrieved, because CellML files are not yet fully annotated. If the CellML version of the Novak 1997 model had annotations corresponding to ‘m-phase inducer phosphatase’, the database would have also returned the simulation description for that model.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4352687&req=5

bau130-F3: Results for Query BM3. The query output at the top of the figure restricts the species role to ‘modifier’. Three SED-ML files match. The first and second files belong to the same model and both observe the species Cdc25. The third query result is a SED-ML file observing four different species. The query output at the bottom of the figure shows the result of a similar query. Here the species must act as ‘reactants’. Only one SED-ML file is retrieved, namely the third result of the top query. All retrieved species (declared as observed by a SED-ML file) are annotated with a UniProt ID. The annotation is either P06652, the protein Cdc25 in yeast, or P20483, the protein Stg (Cdc25) in the fruit fly. Simulation files for CellML files are not retrieved, because CellML files are not yet fully annotated. If the CellML version of the Novak 1997 model had annotations corresponding to ‘m-phase inducer phosphatase’, the database would have also returned the simulation description for that model.
Mentions: Result 4: The result is shown and explained in Figure 3.

Bottom Line: The introduced concept notably improves the access of computational models and associated simulations in a model repository.This has positive effects on tasks such as model search, retrieval, ranking, matching and filtering.Furthermore, our work for the first time enables CellML- and Systems Biology Markup Language-encoded models to be effectively maintained in one database.

View Article: PubMed Central - PubMed

Affiliation: University of Rostock, Department of Computer Science, Albert-Einstein-Straße 22, D-18059 Rostock, Germany, Department of Systems Biology and Bioinformatics, University of Rostock, Ulmenstrasse 69, 18057 Rostock, Germany and Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch 7600, South Africa ron.henkel@uni-rostock.de.

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