VarfromPDB: Disease-Gene-Variant Relations Mining from the Public Databases and Literature
Version 2.2.7

Captures and compiles the genes and variants related to a disease, a phenotype or a clinical feature from the public databases including HPO (Human Phenotype Ontology, ), Orphanet , OMIM (Online Mendelian Inheritance in Man, ), ClinVar , and UniProt (Universal Protein Resource, ) and PubMed abstracts. HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. HPO currently contains approximately 11,000 terms and over 115,000 annotations to hereditary diseases. Orphanet is the reference portal for information on rare diseases and orphan drugs, whose aim is to help improve the diagnosis, care and treatment of patients with rare diseases. OMIM is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. UniProt focuses on amino acid altering variants imported from Ensembl Variation databases. For Homo sapiens, the variants including human polymorphisms and disease mutations in the UniProt are manually curated from UniProtKB/Swiss-Prot. Additionally, PubMed provides the primary and latest source of the information. Text mining was employed to capture the information from PubMed abstracts.

Browse man pages Browse package API and functions Browse package files

AuthorZongfu Cao <caozongfu@gmail.com>; Lei Wang <isan.wong@gmail.com>
Bioconductor views Software
Date of publication2017-05-06 05:18:57 UTC
MaintainerZongfu Cao <caozongfu@gmail.com>
LicenseGPL-2
Version2.2.7
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("VarfromPDB")

Man pages

aa: a table of Codon-Amino Acid Abbreviations
extract_clinvar: Extract the genes and variants related to a genetic disorder...
extract_genes_orphanet: Extract the genes related to a genetic disorder from Orphanet
extract_omim: Extract the genes and variants related to a genetic disorder...
extract_pubmed: Extract the genes and variants related to a genetic disorder...
extract_uniprot: Extract the genes and variants related to a genetic disorder...
genes_add_pubmed: Compile the disease-related genes from PubMed abstracts into...
genes_compile: Compile the disease-related genes from multiple public...
grep_split: Extention for grep function
localPDB: Localize the public databases including HPO, MedGen,...
pheno_extract_HPO: Extract the genes related to a disease or disease alias from...
variants_compile: Compile the disease-related variants from multiple public...

Functions

aa Man page
extract_clinvar Man page Source code
extract_genes_orphanet Man page Source code
extract_omim Man page Source code
extract_pubmed Man page Source code
extract_uniprot Man page Source code
genes_add_pubmed Man page Source code
genes_compile Man page Source code
grep_split Man page Source code
localPDB Man page Source code
pheno_extract_HPO Man page Source code
variants_compile Man page Source code

Files

inst
inst/doc
inst/doc/VarfromPDB.R
inst/doc/VarfromPDB.html
inst/doc/VarfromPDB.Rmd
NAMESPACE
data
data/aa.rda
R
R/extract_pubmed.R
R/grep_split.R
R/sysdata.rda
R/pheno_extract_HPO.R
R/extract_genes_orphanet.R
R/variants_compile.R
R/extract_clinvar.R
R/extract_uniprot.R
R/genes_add_pubmed.R
R/localPDB.R
R/genes_compile.R
R/extract_omim.R
vignettes
vignettes/VarfromPDB.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/genes_add_pubmed.Rd
man/grep_split.Rd
man/extract_omim.Rd
man/aa.Rd
man/localPDB.Rd
man/extract_uniprot.Rd
man/variants_compile.Rd
man/extract_pubmed.Rd
man/extract_clinvar.Rd
man/genes_compile.Rd
man/pheno_extract_HPO.Rd
man/extract_genes_orphanet.Rd
VarfromPDB documentation built on May 19, 2017, 6:04 p.m.