dcGOR (version 1.0.0)

obo.GOBP: Gene Ontology Biological Process (GOBP).

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://www.geneontology.org/ontology/obo_format_1_2/gene_ontology.1_2.obo. Only the edges with the relation (either 'is_a' or 'part_of') are retained.

Usage

data(obo.GOBP)

Value

• an object of class "igraph". As a direct graph, it has attributes to vertices/nodes:
  • vertex attributes: "name" (i.e. Term ID), "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)

References

Ashburner et al. (2000) Gene ontology: tool for the unification of biology. Nat Genet, 25:25-29. 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(obo.GOBP)
obo.GOBP