Human Phenotype ONset and clinical course (HPON).


An R object that contains information on Human Phenotype ONset and clinical course terms. These terms are organised as a direct acyclic graph (DAG), which is further stored as an object of the class 'igraph' (see This data is prepared based on




an object of S4 class Onto. It has slots for "nodeInfo" and "adjMatrix"

  • nodeInfo: an object of S4 class InfoDataFrame, describing information on nodes/terms including: "term_id" (i.e. Term ID), "term_name" (i.e. Term Name), "term_namespace" (i.e. Term Namespace), and "term_distance" (i.e. Term Distance: the distance to the root; always 0 for the root itself)
  • adjMatrix: an object of S4 class AdjData, containing adjacency data matrix, with rows for parent (arrow-outbound) and columns for children (arrow-inbound)


Robinson et al. (2012) The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. Am J Hum Genet, 83:610-615.

Fang H and Gough J. (2013) dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res, 41(Database issue):D536-44.


data(onto.HPON) onto.HPON
An object of S4 class 'Onto' @adjMatrix: a direct matrix of 37 terms (parents/from) X 37 terms (children/to) @nodeInfo (InfoDataFrame) nodeNames: HP:0000004 HP:0003674 HP:0003812 ... HP:0003596 HP:0011460 (37 total) nodeAttr: term_id term_name term_namespace term_distance