Fig 1.
Example output of the query investigating whether the reaction ATP:D-glucose 6-phosphotransferase occurs in Escherichia coli K-12. Neo4j provides a user-friendly web interface allowing relationships to be queried via CYPHER and results visually displayed as a graph that can be further explored interactively. Different types of data are shown (pink: Organism, red: Enzyme, blue: Reaction and green: Chemical). Relationships are displayed with their Types. In this example, the Organism Escherichia coli K-12 expresses the Enzyme Glucokinase, and Reaction R00299 has a relationship catalysed_by Glucokinase. Reaction R00299 has_reactants D-glycopyranose and D-glucopyranose-6-phosphate and has_cofactors ATP(4-) and ADP(3-). Additional relationships are shown: E. coli K-12 is_a Bacillus coli Migula 1895, and relationships between Chemicals are present, indicating that D-glucopyranose-6-phosphate has_functional_parent D-glucopyranose. This example indicates some of the relationships that exist between Organisms, Enzymes, Reactions and Chemicals, and an idea of the kind of queries that can be performed across them.
Table 1.
List of node types and their properties.
Table 2.
List of relationships between nodes.
Table 3.
Numbers of nodes and relationships.