VarfromPDB

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

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, <http://human-phenotype-ontology.github.io/about.html>), Orphanet <http://www.orpha.net/consor/cgi-bin/index.php>, OMIM (Online Mendelian Inheritance in Man, <http://www.omim.org>), ClinVar <http://www.ncbi.nlm.nih.gov/clinvar>, and UniProt (Universal Protein Resource, <http://www.uniprot.org>) 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.

Total

6,361

Last month

256

Last week

64

Average per day

9

Daily downloads

Total downloads

Description file content

Package
VarfromPDB
Type
Package
Title
Disease-Gene-Variant Relations Mining from the Public Databases and Literature
Version
2.2.10
Depends
R (>= 3.4.0), XML, XML2R, curl, stringr
Imports
stringi, RISmed, utils
Suggests
tools,knitr,rmarkdown
LazyData
true
biocViews
Software
Date
2018-9-7
Author
Zongfu Cao ; Lei Wang
Maintainer
Zongfu Cao
Description
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.
License
GPL-2
NeedsCompilation
no
VignetteBuilder
knitr
Packaged
2018-09-07 06:21:14 UTC; john
Repository
CRAN
Date/Publication
2018-09-13 07:30:03 UTC

install.packages('VarfromPDB')

2.2.10

2 months ago

Zongfu Cao

GPL-2

Depends on

R (>= 3.4.0), XML, XML2R, curl, stringr

Imports

stringi, RISmed, utils

Suggests

tools,knitr,rmarkdown

Discussions