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 2018-01-19 12:37:03)
ig.DO

IGRAPH cbe424f DN-- 6576 6923 -- 
+ attr: name (v/c), term_id (v/c), term_name (v/c), term_distance
| (v/n), relation (e/c)
+ edges from cbe424f (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