ontology mapping
Definition
Ontology mapping is the process of establishing semantic correspondences between concepts, terms, and relationships across different biological ontologies or controlled vocabularies. In life sciences, this technique enables integration of heterogeneous data sources by identifying equivalent or related entities across systems like Gene Ontology (GO), Disease Ontology (DO), and pathway databases. Ontology mapping addresses the challenge that different research communities often use distinct terminologies for similar biological concepts. It involves creating alignment rules, equivalence relationships, and hierarchical mappings that preserve semantic meaning while bridging vocabulary gaps. This methodology is essential for cross-database queries, meta-analyses, and comprehensive knowledge integration in systems biology and translational research.
Visualize ontology mapping in Nodes Bio
Researchers can visualize ontology mappings as bipartite networks connecting terms from different vocabularies, revealing conceptual overlaps and gaps. Nodes Bio enables exploration of how genes annotated in one ontology relate to disease terms or pathways in another system. Users can identify bridging concepts that link disparate data sources, facilitating integrated analyses across multiple biological databases and supporting hypothesis generation through cross-ontology network traversal.
Visualization Ideas:
- Bipartite networks showing term-to-term mappings between two ontologies with edge weights representing mapping confidence
- Multi-layer networks where each layer represents a different ontology and inter-layer edges show cross-ontology relationships
- Hierarchical tree comparisons displaying parallel ontology structures with highlighted equivalent or related concepts
Example Use Case
A pharmaceutical team investigating Alzheimer's disease needs to integrate data from multiple sources: gene expression datasets annotated with GO terms, patient phenotypes coded in Human Phenotype Ontology (HPO), and drug targets from ChEMBL. By creating ontology mappings between these vocabularies, they discover that genes associated with 'synaptic vesicle recycling' (GO) map to 'progressive memory impairment' (HPO) and identify existing compounds targeting these pathways. The mapping reveals previously overlooked therapeutic candidates by connecting concepts across traditionally siloed knowledge domains.