title: STON: exploring biological pathways using the SBGN standard and graph databases.
abstract: BACKGROUND
  When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient storage and processing of the encoded biological relationships. They furthermore support queries on the structure of biological networks.
  
  
  RESULTS
  We present the Java-based framework STON (SBGN TO Neo4j). STON imports and translates metabolic, signalling and gene regulatory pathways represented in the Systems Biology Graphical Notation into a graph-oriented format compatible with the Neo4j graph database.
  
  
  CONCLUSIONS
  STON exploits the power of graph databases to store and query complex biological pathways. This advances the possibility of: i) identifying subnetworks in a given pathway; ii) linking networks across different levels of granularity to address difficulties related to incomplete knowledge representation at single level; and iii) identifying common patterns between pathways in the database.
authors.affiliation: Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, 18051, Germany. vasundra.toure@uni-rostock.de.|European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France. vasundra.toure@uni-rostock.de.
authors.forename: Vasundra
authors.identifier: http://orcid.org/0000-0003-4639-4431
authors.initials: V
authors.lastname: Touré
authors.affiliation: European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France.
authors.forename: Alexander
authors.initials: A
authors.lastname: Mazein
authors.affiliation: Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, 18051, Germany.
authors.forename: Dagmar
authors.initials: D
authors.lastname: Waltemath
authors.affiliation: European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France.
authors.forename: Irina
authors.initials: I
authors.lastname: Balaur
authors.affiliation: European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France.
authors.forename: Mansoor
authors.initials: M
authors.lastname: Saqi
authors.affiliation: Scientific Databases and Visualization, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.|Department of Business Information Systems, University of Rostock, Rostock, 18051, Germany.
authors.forename: Ron
authors.initials: R
authors.lastname: Henkel
authors.affiliation: European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France.
authors.forename: Johann
authors.initials: J
authors.lastname: Pellet
authors.affiliation: European Institute for Systems Biology and Medicine (EISBM), CIRI UMR 5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, Lyon, 69007, France.
authors.forename: Charles
authors.initials: C
authors.lastname: Auffray
mesh_terms: D016208:Databases, Factual; D053263:Gene Regulatory Networks; D006801:Humans; D053858:Metabolic Networks and Pathways; D015398:Signal Transduction; D012984:Software; D049490:Systems Biology / Q000379:methods*
keywords: Graph database; Neo4j; Systems biology; Systems biology graphical notation; Systems medicine