Description

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 http://igraph.org/r/doc/aaa-igraph-package.html). This data is prepared based on http://sourceforge.net/p/diseaseontology/code/HEAD/tree/trunk/HumanMP.obo.

Usage

data(onto.MP)

Value

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)

References

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.

Examples

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