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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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Visualization of Query BM3. The centered node (purple) is the requested annotation GO:0005892 (acetylcholine-gated channel complex). This node is connected to the orange node representing the GO term within the GO. The green nodes represent the species linked to the GO:0005892 annotation, the blue nodes represent the models ‘Edelstein1996—EPSP ACh event’ (BIOMD0000000001) and ‘Edelstein1996—EPSP ACh species’ (BIOMD0000000002). Documents are displayed as yellow nodes. Nodes in gray represent annotation containers as stated in the SBML specification (4) and do not carry any meaning themselves.
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bau130-F4: Visualization of Query BM3. The centered node (purple) is the requested annotation GO:0005892 (acetylcholine-gated channel complex). This node is connected to the orange node representing the GO term within the GO. The green nodes represent the species linked to the GO:0005892 annotation, the blue nodes represent the models ‘Edelstein1996—EPSP ACh event’ (BIOMD0000000001) and ‘Edelstein1996—EPSP ACh species’ (BIOMD0000000002). Documents are displayed as yellow nodes. Nodes in gray represent annotation containers as stated in the SBML specification (4) and do not carry any meaning themselves.

Mentions: Recently, the European Bioinformatics Institute in Hinxton, UK, announced a SPARQL endpoint for BioModels Database. All SBML-encoded models in BioModels Database were converted into RDF representations and added to the EBI RDF Platform (60). For comparison of our concept against BioModels Database’s approach, we translated the query examples from the EBI web page (http://www.ebi.ac.uk/rdf/services/biomodels/) into queries against our graph database. The executed queries and retrieved results are shown in the following three listings. Additionally, Figure 4 shows a visualization for Query BM3.Figure 4.


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

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

Visualization of Query BM3. The centered node (purple) is the requested annotation GO:0005892 (acetylcholine-gated channel complex). This node is connected to the orange node representing the GO term within the GO. The green nodes represent the species linked to the GO:0005892 annotation, the blue nodes represent the models ‘Edelstein1996—EPSP ACh event’ (BIOMD0000000001) and ‘Edelstein1996—EPSP ACh species’ (BIOMD0000000002). Documents are displayed as yellow nodes. Nodes in gray represent annotation containers as stated in the SBML specification (4) and do not carry any meaning themselves.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

bau130-F4: Visualization of Query BM3. The centered node (purple) is the requested annotation GO:0005892 (acetylcholine-gated channel complex). This node is connected to the orange node representing the GO term within the GO. The green nodes represent the species linked to the GO:0005892 annotation, the blue nodes represent the models ‘Edelstein1996—EPSP ACh event’ (BIOMD0000000001) and ‘Edelstein1996—EPSP ACh species’ (BIOMD0000000002). Documents are displayed as yellow nodes. Nodes in gray represent annotation containers as stated in the SBML specification (4) and do not carry any meaning themselves.
Mentions: Recently, the European Bioinformatics Institute in Hinxton, UK, announced a SPARQL endpoint for BioModels Database. All SBML-encoded models in BioModels Database were converted into RDF representations and added to the EBI RDF Platform (60). For comparison of our concept against BioModels Database’s approach, we translated the query examples from the EBI web page (http://www.ebi.ac.uk/rdf/services/biomodels/) into queries against our graph database. The executed queries and retrieved results are shown in the following three listings. Additionally, Figure 4 shows a visualization for Query BM3.Figure 4.

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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