pheno_extract_HPO: Extract the genes related to a disease or disease alias from...

In VarfromPDB: Disease-Gene-Variant Relations Mining from the Public Databases and Literature

Description

Extract the genes associated to a disease or disease alias from the Human Phenotype Ontology (HPO) database. The keyword can also be a clinical feature. All the genes and alias of a disease here can be considered in other databases, including Ophanet, OMIM, ClinVar and Uniprot.

Usage

pheno_extract_HPO(keyword, localPDB.path = paste(getwd(),"localPDB",sep="/"))

Arguments

keyword	character string: keyword, to search a disease, a clinical feature, or a phenotype.
localPDB.path	the path of localized public data bases. The default value is set in the working directory.

Details

Many genetic diseases have multiple aliases, and for a clinical feature, there are many different disease names too. All he information can be gotten from HPO. More details about HPO, please see http://www.human-phenotype-ontology.org/.

The HPO files include phenotype_annotation.tab and diseases_to_genes, which can be downloaded automatically. However, the speed may depend on the network environment. So, we recommend to make the files ready locally before the jobs using localPDB().

Value

A list contains two complements

HPO	subset of HPO
diseases_to_genes	extract the genes and alias for a disease(phenotype), or a clinical feature.

Author(s)

Zongfu Cao ([e-mail])

References

1.Sebastian K?hler, Sandra C Doelken, Christopher J. Mungall, Sebastian Bauer, Helen V. Firth, et al. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data Nucl. Acids Res. (1 January 2014) 42 (D1): D966-D974 doi:10.1093/nar/gkt1026

See Also

extract_omim, extract_uniprot, extract_genes_orphanet, extract_clinvar

Examples

#extract the phenotypes and genes from HPO
#    HPO.phenotype = pheno_extract_HPO("retinoblastoma")

Example output

Loading required package: XML
Loading required package: XML2R
Loading required package: curl
Loading required package: stringr

VarfromPDB documentation built on May 2, 2019, 2:10 a.m.