compressa

Poa compressa LinnaeusCanada bluegrass;flat-stemmed bluegrasspâturin comprimé;pâturin du Canadacompressaalong Ill. #1, about 3 miles north of AllendaleRoadside embankmen

mollis

Helianthus mollis Lamarckashy sunflowerhélianthe soyeuxHelianthus mollisopen field, along U.S. #50, about 2 miles west of Ottaw

fasciculatum

Aphyllon fasciculatum (Nutt.) Torr. & A.Grayorobanche fasciculéeclustered broomrapeMeadow S. of CorralsT. ChisholmE. of forest equestrian trail (orange markings) that joins with ATV trail1415Balsamorhiza saggitata, Delphinium bicolor, Castilleja hispida, Senecio integerrimus, Lithophragma parviflorum, Toxscordion venenosum, Lomatium triternatum, Amelanchier alnifolia>3

septentrionalis

Androsace septentrionalis Linnaeusnorthern fairy-candelabra;hairy northern fairy-candelabra;pygmyflower rock jasmine;northern androsace;northern pygmyflower;northern rock jasmine;pygmyflowerandrosace septentrionale;androsace du Nord;androsace septentrionalseptentrionalisSect. of Livingstone Range, W of AGT Util. Stn (N Burmis Road)Sheltered on E-side of 5 needle Pinus - high elevation5 needle pinu

Additional file 5: of Representing and querying disease networks using graph databases

Cypher query on the relationships between a) the O15534 protein (PER gene) and b) the P20393 protein (REV/ERBalpha gene) and the core clock genes, (Table 3). (DOCX 77 kb

Additional file 4: of Representing and querying disease networks using graph databases

Information on genes related to a simple disease only, as reported in [23]. (DOCX 120 kb

Additional file 1: of Representing and querying disease networks using graph databases

Disease-associated genes used in the study (from [23]). (DOCX 93 kb

Additional file 3: of Representing and querying disease networks using graph databases

Brief introduction to Cypher query language; for more details on the Cypher language, the reader is referred to the Neo4j website: http://neo4j.com/ . (DOCX 17 kb

STON.pdf

<b>STON, SBGN to Neo4j: using graph database technologies for storing disease-relevant biological pathways and networks</b> <p> Vasundra Touré¹, Alexander Mazein², Dagmar Waltemath¹, Irina Balaur², Ron Henkel¹, Mansoor Saqi², Johann Pellet² and Charles Auffray²</p> <p> <br> </p> <p> ¹Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany.</p> <p> ²European Institute for Systems Biology and Medicine (EISBM), Centre National de la Recherche Scientifique (CNRS), Campus Charles Mérieux - Université de Lyon - 50 Avenue Tony Garnier, 69007 Lyon, France; IMI-eTRIKS consortium.</p> <p> <br> </p> <p> Abstract <br></p> <p> <br> </p> <p> <b>Background: </b>Graph databases can be successfully applied in Systems Biology and in Systems Medicine for managing extensive and complex information. Ultimately, graphs are a natural way of representing biological networks. The use of graph databases enables efficient storing and processing of biological relationships, and it can lead to a better response time when querying the data.</p> <p> <br> </p> <p> <b>Objectives: </b>We would like to use graph databases structure to store and explore biological pathways and networks.</p> <p> <br> </p> <p> <b>Method:</b> Translation rules have been determined to represent biological reaction networks in a graph model, that is to say as nodes, relationships and properties. The reaction networks are provided in the graphical standard Systems Biology Graphical Notation (SBGN). The graph model is stored in a Neo4j database.</p> <p> <br> </p> <p> <b>Results: </b>We present the Java-based framework STON (SBGN TO Neo4j) to import and translate metabolic, signalling and gene regulatory pathways. On the poster, we show examples of networks representing parts of the Asthma Map, the iNOS pathway (a SBGN use case network).</p> <p> <br> </p> <p> <b>Conclusion: </b>STON exploits the power of a graph database for the search in complex biological pathways. Importing biological pathways in a graph database enables:</p> <p> 1) identification of functional sub-modules and comparing different networks in order to discover common patterns. </p> <p> 2) merging multiple diagrams for creating large comprehensive networks for empowering systems medicine approaches.</p> <p> <br> </p> <p> <b>Availability:</b> The STON framework is available here: <a href="http://sourceforge.net/projects/ston/">http</a><a href="http://sourceforge.net/projects/ston/">://</a><a href="http://sourceforge.net/projects/ston/">sourceforge</a><a href="http://sourceforge.net/projects/ston/">.</a><a href="http://sourceforge.net/projects/ston/">net</a><a href="http://sourceforge.net/projects/ston/">/</a><a href="http://sourceforge.net/projects/ston/">projects</a><a href="http://sourceforge.net/projects/ston/">/</a><a href="http://sourceforge.net/projects/ston/">ston</a><a href="http://sourceforge.net/projects/ston/">/</a>.</p> <p><br> </p