1. What is the Metabolic Framework

The Metabolic Framework uses the neo4j graph platform for the management of data on human metabolism. Specifically, it facilitates i) identification and ii) visualization of subnetworks of interest from the Human Metabolic Reconstruction (Recon2, Thiele et al., Nat Biotech, 2013) by using the powerful neo4j CYPHER query language and neo4j functionality, and iii) export in SBML standard and SIF formats in order to be integrated and shared among community using well-estabilished platforms (e.g. CellDesigner, yEd, Cytoscape, NDEx).

2. Graph database for human metabolic network

3. A quick overview

4. How to access the Metabolic Framework

The Metabolic Framework can be accessed online here.
A file with several Cypher query examples for the Metabolic Framework is available for download here. These queries can be extended to accommodate specific topics of interest.

For developers

The Metabolic Framework is freely available for non-commercial purposes and the java code used for i) data integration and mapping into the Metabolic Framework and ii) JSON Parser is available upon request by email to ibalaur@eisbm.org.

5. How to get Involved

We would be happy to hear from your experience and for feedback, any issues/ suggestions on this, please contact us by email to ibalaur@eisbm.org.

Please cite our paper on this work

Balaur I., Mazein A., Saqi M., Lysenko A., Rawlings C.J. and Auffray C. (2016), Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. Bioinformatics. 2016 Dec 19. pii: btw731. DOI: 10.1093/bioinformatics/btw731.