Mammalian Phenotype (MP).


An R object that contains information on Mammalian Phenotype 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)


Smith et al. (2009) The Mammalian Phenotype Ontology: enabling robust annotation and comparative analysis. Wiley Interdiscip Rev Syst Biol Med, 1:390-399.

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.MP) onto.MP
An object of S4 class 'Onto' @adjMatrix: a direct matrix of 10214 terms (parents/from) X 10214 terms (children/to) @nodeInfo (InfoDataFrame) nodeNames: MP:0000001 MP:0001186 MP:0002006 ... MP:0008360 MP:0008364 (10214 total) nodeAttr: term_id term_name term_namespace term_distance