Tissue Network - serratus-bio/open-virome GitHub Wiki

Brenda Tissue Ontology

The Brenda Tissue Ontology (BTO) forms a monopartite network containing Tissue nodes and HAS_PARENT edges from a human curated ontology. This network forms a Directed Acyclic Graph (DAG). The nodes and edges are extracted from BTO OWL data.

A bipartite network can be formed with SRA Run nodes and their associated Tissue nodes via HAS_TISSUE_METADATA edges. These edges are mined from BioSample metadata associated to the run which is then mapped to a matching term in the BTO.

Summary stats

Total number of Tissue nodes: 6,569

Total number of HAS_PARENT relationships: 15,292

Total number of HAS_TISSUE_METADATA relationships: 6,869,797

Communities

In the monopartite tissue network, the majority of the tissue nodes (6511/6569) form a connected component and the remaining 58 tissues are isolated.

Visualizing the entire network with a force-directed layout shows naturally forming communities of closely related tissue terms. We can use hierarchical community detection algorithms to reduce the number of labels during a feature engineering step.