Human Phenotype Mode of Inheritance (HPMI).


An R object that contains information on Human Phenotype Mode of Inheritance 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.HPMI) onto.HPMI
An object of S4 class 'Onto' @adjMatrix: a direct matrix of 27 terms (parents/from) X 27 terms (children/to) @nodeInfo (InfoDataFrame) nodeNames: HP:0000005 HP:0003743 HP:0001466 ... HP:0001419 HP:0001475 (27 total) nodeAttr: term_id term_name term_namespace term_distance