DODO

DODO provides a Neo4j-based graph database and accompanying R package to integrate and map disease and phenotype ontologies for cross-ontology mappings and integrated linkage of biomedical data.

Key Features:

• Graph Database Implementation: Implemented on Neo4j and using graph structures to identify indirect cross-references via transitive relationships.
• Meta-Database Construction: Integrates information from multiple publicly available disease ontologies to provide comprehensive cross-ontology mappings.
• R Package Integration: Offers functions for building disease networks, converting identifiers between ontologies, and exploring disease concepts.
• Facilitation of Data Integration: Enables linking information across drugs, drug targets, genetic variants, and literature without upfront harmonization of life science databases.
• Local Adaptation and Extension: Provides a workflow for local adaptation and extension of the database and a Docker image with a pre-configured instance.

Scientific Applications:

• Drug Discovery: Facilitates connections between disease ontologies and drug databases to support identification of potential therapeutic targets.
• Genomic Research: Enables linking of genetic variants to specific diseases through comprehensive phenotype and ontology mappings.
• Literature Mining: Supports extraction and standardization of disease identifiers from biomedical literature to enable consistent annotation.

Methodology:

Uses a Neo4j graph database to integrate multiple publicly available disease and phenotype ontologies, identifies indirect cross-references via transitive relationships, and provides an R package for network construction and identifier conversion; includes a workflow for local adaptation and a Docker image with a pre-configured instance.