ontology
Definition
An ontology is a structured, hierarchical framework that formally defines concepts, their properties, and relationships within a specific domain of knowledge. In life sciences, ontologies like Gene Ontology (GO), Disease Ontology (DO), and Cell Ontology provide standardized vocabularies and classifications for biological entities and processes. Ontologies enable consistent annotation of experimental data, facilitate computational analysis, and allow researchers to query relationships across different levels of biological organization. They organize knowledge as directed acyclic graphs where terms (nodes) are connected by defined relationships such as 'is-a' or 'part-of', enabling both human interpretation and machine-readable data integration across databases and studies.
Visualize ontology in Nodes Bio
Researchers can visualize ontology structures as hierarchical networks in Nodes Bio, exploring parent-child relationships between biological terms. By mapping experimental data onto ontology networks, users can identify enriched pathways, cluster functionally related genes, and trace how specific proteins or diseases connect through multiple ontological levels. This enables systematic interpretation of high-throughput data within established biological frameworks.
Visualization Ideas:
- Hierarchical ontology trees showing parent-child term relationships
- Gene-to-GO term bipartite networks mapping experimental data to functional categories
- Multi-level ontology networks integrating gene, disease, and phenotype ontologies
Example Use Case
A cancer genomics team identifies 500 differentially expressed genes from RNA-seq data. They map these genes to Gene Ontology terms and visualize the resulting network in Nodes Bio, revealing that upregulated genes cluster around 'cell cycle regulation' and 'DNA repair' processes, while downregulated genes associate with 'immune response' terms. By exploring the ontology hierarchy, they discover that several enriched terms share a common parent process, suggesting a coordinated transcriptional program driving tumor progression.