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

Database : the Journal of Biological Databases and Curation
Ron HenkelDagmar Waltemath

Abstract

Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems. However, their storage concepts support only restricted types of queries and not all data inside the repositories can be retrieved. In this article we present a storage concept that meets this challenge. It grounds on a graph database, reflects the models' structure, incorporates semantic annotations and simulation descriptions and ultimately connects different types of model-related data. The connections between heterogeneous model-related data and bio-ontologies enable efficient search via biological facts and grant access to new model features. 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. We show how these models can be linked via annotations and queried. Database URL: https://sems.uni-rostock.de/projects/masymos/

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Citations

Apr 24, 2015·Journal of Biomedical Semantics·Rebekka AlmRon Henkel
Sep 15, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Irina BalaurCharles Auffray
Jun 14, 2016·IEEE Transactions on Bio-medical Engineering·Dagmar Waltemath, Olaf Wolkenhauer
Oct 16, 2016·Briefings in Bioinformatics·Ron HenkelDagmar Waltemath
Apr 19, 2017·Genomics & Informatics·Byoung-Ha YoonSeon-Young Kim
Dec 7, 2016·BMC Bioinformatics·Vasundra TouréCharles Auffray
Jul 12, 2018·Database : the Journal of Biological Databases and Curation·Fabienne LambuschRon Henkel
Nov 22, 2018·Briefings in Bioinformatics·Maxwell Lewis NealDagmar Waltemath
Nov 28, 2017·Journal of Bioinformatics and Computational Biology·Fedor KazantsevVitaly Likhoshvai
Aug 28, 2020·Molecular Systems Biology·Sarah M KeatingUNKNOWN SBML Level 3 Community members
Mar 25, 2021·Briefings in Bioinformatics·Adrien RougnyAlexander Mazein
May 19, 2021·Database : the Journal of Biological Databases and Curation·Santiago Timón-ReinaRafael Martínez-Tomás

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Software Mentioned

SBML Biology Graphical Notations ( SBGN
BioPortal
Neo4J
Cypher
NuML
SPARQL
NeuroML
SIMULATION
Windows7
MATLAB

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