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.

Usage

ig.GOBP <- dRDataLoader(RData = "ig.GOBP")

Value

an object of class "igraph". As a direct graph, it has attributes to vertices/nodes and edges:

  • vertex attributes: "name" (i.e. "Term ID"), "term_id" (i.e. "Term ID"), "term_name" (i.e "Term Name") and "term_distance" (i.e. Term Distance: the distance to the root; always 0 for the root itself)
  • edge attributes: "relation" (either 'is_a' or 'part_of')

References

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

Examples

ig.GOBP <- dRDataLoader(RData='ig.GOBP')
'ig.GOBP' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/ig.GOBP.RData?raw=true) has been loaded into the working environment (at 2017-03-27 19:58:52)
ig.GOBP
IGRAPH DN-- 27685 58979 -- + attr: name (v/c), term_id (v/c), term_name (v/c), term_distance | (v/n), relation (e/c) + edges (vertex names): [1] GO:0000002->GO:0032042 GO:0000002->GO:0033955 GO:0000003->GO:0019953 [4] GO:0000003->GO:0019954 GO:0000003->GO:0032504 GO:0000003->GO:0032505 [7] GO:0000003->GO:0051321 GO:0000012->GO:1903823 GO:0000012->GO:1990396 [10] GO:0000018->GO:0000019 GO:0000018->GO:0000337 GO:0000018->GO:0010520 [13] GO:0000018->GO:0010569 GO:0000018->GO:0045191 GO:0000018->GO:0045910 [16] GO:0000018->GO:0045911 GO:0000018->GO:0060542 GO:0000018->GO:0072695 [19] GO:0000018->GO:1903110 GO:0000019->GO:0032207 GO:0000019->GO:0045950 + ... omitted several edges