localPDB: Localize the public databases including HPO, MedGen,...

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

Description

localPDB downloads the necessary files from the public databases including HPO, MedGen, GeneReview, HGNC, Orphanet, ClinVar and Uniprot.

Usage

localPDB(localPDB.path = paste(getwd(), "localPDB", sep = "/"), PDB = "all", 
         omim.url = NULL, download.method = "curl_fetch_disk")

Arguments

localPDB.path	the path to localize the public databases.
PDB	which database to localize. The value must be one of "all"(default), "HPO", "MedGen", "GeneReview", "HGNC", "Orphanet", "ClinVar" or "Uniprot".
omim.url	the FTP URL of OMIM.
download.method	the method for downloading files, including "curl_fetch_disk", "curl_download", "download.file".

Details

The function gets the necessary files from the public databases including HPO, MedGen, GeneReview, HGNC, OMIM, Orphanet, ClinVar and Uniprot.

For the omim.url, you shoul apply for an OMIM account from http://omim.org/downloads and get the FTP URL.

Author(s)

Zongfu Cao ([e-mail])

References

1.Sebastian Kohler, 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

2.Orphanet: an online rare disease and orphan drug data base. INSERM 1997. Available on http://www.orpha.net. Accessed [date accessed].

3.Orphadata: Free access data from Orphanet. INSERM 1997. Available on http://www.orphadata.org. Data version [XML]

4.Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014 Jan 1;42(1):D980-5. doi: 10.1093/nar/gkt1113. PubMed PMID: 24234437

5.The UniProt Consortium UniProt: a hub for protein information. Nucleic Acids Res. 43: D204-D212 (2015).

6.Amberger JS, Bocchini CA, Schiettecatte F, Scott AF, Hamosh A. OMIM.org: Online Mendelian Inheritance in Man (OMIM), an online catalog of human genes and genetic disorders. Nucleic Acids Res. 2015 Jan;43(Database issue):D789-98. doi:10.1093/nar/gku1205. Epub 2014 Nov 26. PubMed PMID: 25428349; PubMed Central PMCID: PMC4383985.

7.GeneReviews: http://www.ncbi.nlm.nih.gov/books/NBK1116/

8.MedGen: http://www.ncbi.nlm.nih.gov/medgen

9.OMIM:http://www.omim.org/

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