GOXMLParser {AnnBuilder}R Documentation

Parse the Gene Ontology OBO XML data file

Description

Generate R environment objects containing data parsed from the Gene Ontology (GO) XML data file. The GO data file is available from http://www.geneontology.org. This parser is designed to parse the go_YYYYMM-termdb.obo-xml file.

Usage

GOXMLParser(fileName)

Arguments

fileName Name of the XML file containing the GO source data in obo-xml format.

Value

A list of environment objects representing the GO data structures. The environments returned are:

TERM See GOTERM environment in the GO package
BPPARENTS See the GOBPPARENTS environment in the GO data packagey
MFPARENTS See the GOMFPARENTS environment in the GO data package
CCPARENTS See the GOCCPARENTS environment in the GO data package
BPCHILDREN See the GOBPCHILDREN environment in the GO data package
MFCHILDREN See the GOMFCHILDREN environment in the GO data package
CCCHILDREN See the GOCCCHILDREN environment in the GO data package
OBSOLETE See the GOOBSOLETE environment in the GO data package
BPOFFSPRING See the GOBPOFFSPRING environment in the GO data package
MFOFFSPRING See the GOMFOFFSPRING environment in the GO data package
CCOFFSPRING See the GOCCOFFSPRING environment in the GO data package
BPANCESTOR See the GOBPANCESTOR environment in the GO data package
MFANCESTOR See the GOMFANCESTOR environment in the GO data package
CCANCESTOR See the GOCCANCESTOR environment in the GO data package

Author(s)

Chenwei Lin, John Zhang, Seth Falcon


[Package AnnBuilder version 1.18.0 Index]