Ontology

class chamois.ontology.Ontology(adjacency_matrix)

An ontology represented as a Directed Acyclic Graph.

The ontology is encoded using an adjacency matrix representing the graph of subclasses. It supports computing the similarity between terms or term groups based on the GOGO algorithm by Zhao and Wang.

adjacency_matrix

The adjacency matrix encoding the class hierarchy in the ontology.

Type:

AdjacencyMatrix

semantic_similarity

The semantic similarity of the ontology classes, which estimates the shared information between a class and its direct subclasses based on the number of total subclasses.

Type:

numpy.ndarray

References

Zhao, C., Wang, Z. “GOGO: An improved algorithm to measure the semantic similarity between gene ontology terms”. Sci Rep 8, 15107 (2018). doi:10.1038/s41598-018-33219-y

similarity(x, y)

Return the semantic similarity between two set of terms.