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Practical Innovation at BioCon 2003


MetaGraph Framework: A Knowledge Storage Platform That Breaks Out of the Relational Paradigm
John McNeil, Isis Pharmaceuticals
Alan Goates, Isis Pharmaceuticals

Track: Toolkits
Date: Tuesday, February 04
Time: 10:45am - 11:30am
Location: California Ballroom A & B

Biological data (functional, experimental, and modeling) do not easily fit into a relational schema. One problem is capturing ambiguity and multiple hypotheses in the model. A classical object-relational model must be revised and retested to keep up with advancement of the science being modeled. This can cause software development to be rate-limiting in drug discovery.

The MetaGraph Framework was built to solve this problem by supporting a very granular graph-like data structure by using a fixed number of types of relationships (edges) that can link any two data elements (nodes). Edge types represent concepts like ownership, description, equality, and temporal order. There are also a fixed number of root node types that are sub-classed to represent specific types of data. Edges are a subclass of nodes, allowing edges to point to other edges. A piece of data, and the reason that a relationship exists between two pieces of data, can be documented.

McNeil’s group developed an open source Java toolkit in three layers. The base layer provides persistence; SQL persistence is currently implemented (through JDBC), and XML persistence and temporary persistence (in memory) are also implemented. Using the layer above the persistence layer one can individually find and manipulate the node and edge objects. The top level supports "clusters," which are used to find and manipulate functional groups of nodes and edges. This Framework has been deployed for several internal projects, and as the basis of the GeneTrove functional genomics database.

You can reach John at: jmcneil@isisph.com

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