extract_pubmed: Extract the genes and variants related to a genetic disorder...

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

Description

extract_pubmed extracts the genes and variants related to a known genetic disorder or a clinical feature from NCBI PubMed.

Usage

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

Arguments

query	searching strategy in PubMed, such as "pubmed AND gene AND mutation AND chinese NOT meta analysis".
keyword	character string: keyword, to search the disease, clinical feature, or phenotype.
localPDB.path	the path of localized public data bases. The default value is set in the working directory.

Details

extract_pubmed extracts the phenotypes, genes and mutations from PubMed abstracts, and check the gene names to appoved symbol by HGNC. We recommend to check the searching strategy and the results carefully.

Value

A list containing two components:

pubmed_captures	the relationships among phenotypes, genes, and mutations captured from PubMed
abstracts	all the abstracts captured from PubMed.

Author(s)

Zongfu Cao ([e-mail])

Examples

## capture the genes and mutations related to cataract in Chinese populations 
## from PubMed
#cataract_pubmed <- extract_pubmed(
#    query = "cataract AND gene AND mutation AND chinese NOT meta analysis",
#               keyword="cataract",
#               localPDB="/public/home/czf/project/rare.disease/localPDB")
 

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