Disease Ontology (DO).

Description

An R object that contains information on Disease Ontology 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?format=raw.

Usage

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

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

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

Examples

ig.DO <- dRDataLoader(RData='ig.DO')
'ig.DO' (from https://github.com/hfang-bristol/RDataCentre/blob/master/dnet/1.0.7/ig.DO.RData?raw=true) has been loaded into the working environment (at 2017-03-27 19:58:49)
ig.DO
IGRAPH DN-- 6576 6923 -- + attr: name (v/c), term_id (v/c), term_name (v/c), term_distance | (v/n), relation (e/c) + edges (vertex names): [1] DOID:0001816->DOID:265 DOID:0001816->DOID:268 [3] DOID:0001816->DOID:4505 DOID:0001816->DOID:4512 [5] DOID:0001816->DOID:4513 DOID:0001816->DOID:4522 [7] DOID:0001816->DOID:4524 DOID:0001816->DOID:4525 [9] DOID:0001816->DOID:4527 DOID:0002116->DOID:10525 [11] DOID:0002116->DOID:10526 DOID:0014667->DOID:0060158 [13] DOID:0014667->DOID:655 DOID:0050013->DOID:4194 + ... omitted several edges