1. What is the Protein Framework

The Protein Framework uses the neo4j graph platform for the integration of multiple heterogeneous biological data sources (such as protein-protein interactions, pathways, drug-target interactions, disease-gene interactions, sequence similarity relationships). The integrated network allows the biological context of disease associated genes to be explored through visualisation, and information can be retrieved using the powerful neo4j CYPHER query language.

2. The Data Model

3. A quick overview

4. How to access the Protein Framework

The Protein Framework addresses to several categories of users:
  1. General user (knowledgebase manager):
    2. The Protein Framework can be accessed online here.
    A file with several Cypher query examples for the Protein Framework is available for download here. These queries can be extended to accommodate specific topics of interest.
  2. Advanced biological queries:
    3. For more advanced biological queries and/or further exploration of the results, the Protein Framework can be interrogated directly using java and R. An example of running a simple Cypher query in the Protein Framework using directly R code (via the RNeo4j library): download it here.
  3. Developers:
    4. The Protein Framework is freely available for non-commercial purposes and the java code used to parse the data and populate the graph database is available here.

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 or msaqi@eisbm.org.

Please cite our paper on this work

Lysenko A.*, Roznovat I.A.*, Saqi M.*, Mazein A., Rawlings C.J. and Auffray C. (2016), Representing and querying disease networks using graph databases (* Contributed equally). BioData Mining, pp. 9:23. DOI: 10.1186/s13040-016-0102-8.