genes_add_pubmed: Compile the disease-related genes from PubMed abstracts into...

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

Description

To compile the genes related to a disease especially for a rare disease from PubMed abstracts into the gene set from the public databases, including HPO, orphanet, omim, clinvar and uniprot.

Usage

genes_add_pubmed(keyword,genepdb, pubmed, 
             localPDB.path = paste(getwd(), "localPDB", sep = "/"))

Arguments

keyword	character string: keyword, to search the disease, clinical feature, or phenotype.
genepdb	the object from function genes_compiled.
pubmed	the object from function extract_pubmed. The object need to be checked mannually.
localPDB.path	the path of localized public databases.

Details

The relationships between genes and a phenotype are compared with those from public databases, then the additional relationships can be merged together. For the object from function extract_pubmed maybe have noise, we strongly recommend that the additional relationships between genes and phenotypes should be pay more attention and checked mannually.

Value

A matrix containing the following information

GeneSymbol	gene symbols from HGNC.
chr	chorosomes of the genes.
strand	strands of the genes.
start	start positions (hg19) of the genes.
end	end positions (hg19) of the genes.
EntrezGeneID	Entrez GeneID
ApprovedName	Approved gene name from HGNC.
Synonyms	gene Synonyms.
HPO	the phenotypes from HPO.
Orphanet	the phenotypes from orphanet.
OMIM	the phenotypes from OMIM.
ClinVar	the phenotypes from ClinVar.
Uniprot	the phenotypes from Uniprot.
pubmed	the phenotypes from PubMed.

Author(s)

Zongfu Cao ([e-mail])

See Also

extract_pubmed, genes_compile

Examples

## add the relationships between genes and phenotypes into those from 
## the public databases. 
#geneAll <- genes_add_pubmed(genepdb= genesPDB, pubmed=genes.pubmed)

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