Description

An R object that contains information on UniProtKB KeyWords 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). UniProtKB KeyWords (KW) controlled vocabulary provides a summary of the entry content and is used to index UniProtKB/Swiss-Prot entries based on 10 categories (the category "Technical term" being excluded here).

Usage

onto.KW <- dcRDataLoader(RData = "onto.KW")

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

Bairoch et al. (2005) The Universal Protein Resource (UniProt). Nucleic Acids Res, 33:D154-9.

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

onto.KW <- dcRDataLoader(RData='onto.KW')

'onto.KW' (from http://dcgor.r-forge.r-project.org/data/onto.KW.RData) has been loaded into the working environment
onto.KW

An object of S4 class 'Onto'
@adjMatrix: a direct matrix of 1169 terms (parents/from) X 1169 terms (children/to) 
@nodeInfo (InfoDataFrame)
  nodeNames: KW:0001 KW:0003 KW:0004 ... KW:9999 root (1169 total)
  nodeAttr: term_id term_name term_namespace term_distance