Description

An R object that contains information on Gene Ontology Biological Process 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/HumanDO.obo.

Usage

data(onto.DO)

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

Schriml et al. (2012) Disease Ontology: a backbone for disease semantic integration. Nucleic Acids Res, 40:D940-946.

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.DO)
onto.DO

An object of S4 class 'Onto'
@adjMatrix: a direct matrix of 6352 terms (parents/from) X 6352 terms (children/to) 
@nodeInfo (InfoDataFrame)
  nodeNames: DOID:4 DOID:630 DOID:7 ... DOID:5746 DOID:7438 (6352
    total)
  nodeAttr: term_id term_name term_namespace term_distance