getSrcBuilt {AnnBuilder}R Documentation

Functions that get the built date or number of the source data used for annotation

Description

Given a data source name and organism, the built date or number of the annotation source data will be returned. The built date or number is provided by the data source through its web site.

Usage

getSrcBuilt(src = "LL", organism = "Homo sapiens")
getLLBuilt(url = "http://www.ncbi.nlm.nih.gov/LocusLink/statistics.html")
getUGBuilt(organism, url = "ftp://ftp.ncbi.nih.gov/repository/UniGene")
getUCSCBuilt(organism)
getGOBuilt(url = "http://www.godatabase.org/dev/database/archive/latest")
getKEGGBuilt(url = "http://www.genome.ad.jp/kegg/kegg2.html")
getYGBuilt()
getHGBuilt()
getRefSeqBuilt(organism)
getRefSeqBuilt()

Arguments

src A character string for name of the data source. See details for valid names
organism A character string for the name of the organism of interests. See details for valid names
url A character string for the url from which built information can be obtained

Details

getLLBuilt finds the built data for LocusLink from the statistics page.

getUGBuilt finds the built data for UniGene from the Xx.info file, where Xx is the short organism name (e.g. Hs for human)

getUCSCBuilt finds the built data for the Human Genome Project from the folder for the latest release.

getGOBuilt finds the built data for Gene Ontology from the timestamp for the -ont.xml.gz file.

getKEGGBuilt finds the built data for KEGG from kegg2.html page (Release version and date)

YGBuilt gets built information for Yeast Genome data.

Valid data source names include LL - LocusLink, UG - UniGene, UCSC - the Human Genome Project, GO - Gene Ontology, KEGG - KEGG, YG - Yeast Genome.

Valid organism name include human, mouse, rat, and yeast at this time.

Value

All functions return a string for the built information

Note

The functions are part of the Bioconductor project at Dana-Farber Cancer Institute to provide Bioinformatics functionalities through R

Author(s)

Jianhua Zhang

References

http://www.ncbi.nlm.nih.gov/LocusLink/statistics.html, ftp://ftp.ncbi.nih.gov/repository/UniGene, http://www.godatabase.org/dev/database/archive/latest, http://www.genome.ad.jp/kegg/kegg2.html, ftp://ftp.ncbi.nih.gov/refseq/LocusLink/, http://www.yeastgenome.org

See Also

getSrcUrl

Examples

# Get built information for LocusLink
ll <- getSrcBuilt(src = "LL")
ug <- getSrcBuilt(src = "UG", organism = "Homo sapiens")
yg <- getYGBuilt()
ll
ug
yg

[Package AnnBuilder version 1.4.21 Index]