Description

An R object that contains information on Enzyme Commission 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). Enzyme Commission (EC) is a resource focused on enzyme nomenclature, which is a system of naming enzymes (protein catalysts) with Cross-references to UniProt sequences. It uses four-digit EC numbers to define the reaction catalysed. The first three digits are to define the reaction catalysed and the fourth for a unique identifier (serial number).

Usage

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

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

Fleischmann et al. (2004) IntEnz, the integrated relational enzyme database. Nucleic Acids Res, 32:D434-7.

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

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

An object of S4 class 'Onto'
@adjMatrix: a direct matrix of 5876 terms (parents/from) X 5876 terms (children/to) 
@nodeInfo (InfoDataFrame)
  nodeNames: root 4 5 ... 6.6.1.1 6.6.1.2 (5876 total)
  nodeAttr: term_id term_name term_namespace term_distance