BOCK: Biological networks and Oligogenic Combinations as a Knowledge graph

BOCK is a knowledge graph integrating oligogenic disease information (originally from the Oligogenic Disease Database (Natchtegael et al. 2022)) together with multiple biological networks and ontologies.

Compared to more generic knowledge graphs, we selected specifically networks relevant to understand the molecular mechanisms of epistasis, placing genes as the central entities, and focused on trusted resources describing a large set of human genes and their interactions.

All entities in the KG are linked to their source database entry via an URI (Uniform Resource Identifier) to facilitate integrations within larger bioinformatics linked data repositories.

BOCK 2.0 integrates recent versions of the used ontologies and databases, as well as additional pathway-specific (The Reactome Pathway Knowledgebase 2024, Milacic et al.) and tissue-specific information (COXPRESdb v8, Obayashi et al.). Additionally the database used for the coexpression relation between genes, has been replaced by COXPRESdb v8.

We provide BOCK 2.0 in three formats:

GraphML (Graph Markup Language): a network format enabling the fast import of the KG by multiple libraries (e.g networkx) and tools (e.g Cytoscape).

XML (Extensible Markup Language): a text-encoding system that is human-readable and compatible with many systems.

Neo4J import files: tab-separated files that can be easily imported into Neo4J using the neo4j-admin utils.