Disease Knowledge Base

This activity in eTRIKS describes an effort to construct an integrated knowledge repository to provide biological context to data emerging from experimental studies for selected IMI projects. We envisage the disease areas to be respiratory, neurological and possibly rheumatoid arthritis. The project has three main aims:
  1. To construct networks that integrate multiple heterogeneous biological data sources to provide a database of background knowledge
  2. To construct detailed expert-verified metabolic and signalling pathways known to be involved in the disease condition
  3. To enable sharing and community curation of of these disease knowledge representations, using the NDex or other appropriate frameworks.
We anticipate that these research efforts will facilitate i) interpretation of new experimental data (such as differentially expressed genes) in the context of existing background knowledge such as pathways and protein interactions, ii) hypothesis generation by enabling mining of the complex networks to look for new unexpected relationships and iii) exploration of disease co-morbidity in terms of molecular mechanism.

Disease Networks

The Disease Networks module is been developed as a multi-scale framework (using the graph datagabse approach) to facilitate management (integration, exploration, visualisation, interpretation) of diverse types of biological and biomedical data. Disease Networks employ the popular graph database Neo4j, which provides a persistence mechanism that is robust and has powerful functionality (the Cypher query language) that allows the user to query networks, to find connections between particular data entries using graph traversal techniques.

Disease Maps

Disease map is a collection of interconnected signalling, metabolic and gene regulatory pathways relevant to a particular disease. Disease mechanisms are depicted on the level of molecular processes and represented in standard computer-readable formats.


Contact us!

We would be happy to hear from your experience and for feedback, any issues/ suggestions on this, please contact us by email to Mansoor Saqi at msaqi@eisbm.org, Irina Balaur at ibalaur@eisbm.org or Alexander Mazein at amazein@eisbm.org.


Authors would like to acknowledge for access to the Neo4j and to NDEx frameworks and for data resources within the databases interrogated: DisGeNET, DrugBank, Human Protein Atlas, IntAct, Reactome, UniProt, Human Metabolic Reconstruction (Recon2). Users of this resource should respect any restrictions of use associated with these component databases.


This eTRIKS Labs module is offered to the public as freely available resource, for non-commercial research use. Some aspects of this experimental module may still be under development, and there are no warranties about the completeness, reliability, accuracy, and security of the software package. Please bear this in mind, especially if you wish to analyse personal and/or confidential data.