onto.UP: UniProtKB UniPathway (UP).

In hfang-bristol/dcGOR: Analysis of Ontologies and Protein Domain Annotations

UniProtKB UniPathway (UP).

Description

An R object that contains information on UniProtKB UniPathway 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 UniPathway (UP) is a fully manually curated resource for the representation and annotation of metabolic pathways, being used as a controlled vocabulary for pathway annotation in UniProtKB.

Usage

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

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

Morgat et al. (2006) UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res, 40:D761-9.
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.UP <- dcRDataLoader(RData='onto.UP')
onto.UP

hfang-bristol/dcGOR documentation built on July 16, 2022, 6:43 p.m.