'BMRB' File Downloader

Nuclear magnetic resonance (NMR) is a highly versatile analytical technique for studying molecular configuration, conformation, and dynamics, especially those of biomacromolecules such as proteins. Biological Magnetic Resonance Data Bank ('BMRB') is a repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules. Currently, 'BMRB' offers an R package 'RBMRB' to fetch data, however, it doesn't easily offer individual data file downloading and storing in a local directory. When using 'RBMRB', the data will stored as an R object, which fundamentally hinders the NMR researches to access the rich information from raw data, for example, the metadata. Here, 'BMRBr' File Downloader ('BMRBr') offers a more fundamental, low level downloader, which will download original deposited .str format file. This type of file contains information such as entry title, authors, citation, protein sequences, and so on. Many factors affect NMR experiment outputs, such as temperature, resonance sensitivity and etc., approximately 40% of the entries in the 'BMRB' have chemical shift accuracy problems [1,2] Unfortunately, current reference correction methods are heavily dependent on the availability of assigned protein chemical shifts or protein structure. This is my current research project is going to solve, which will be included in the future release of the package. The current version of the package is sufficient and robust enough for downloading individual 'BMRB' data file from the 'BMRB' database < http://www.bmrb.wisc.edu>. The functionalities of this package includes but not limited: * To simplifies NMR researches by combine data downloading and results analysis together. * To allows NMR data reaches a broader audience that could utilize more than just chemical shifts but also metadata. * To offer reference corrected data for entries without assignment or structure information (future release). Reference: [1] E.L. Ulrich, H. Akutsu, J.F. Doreleijers, Y. Harano, Y.E. Ioannidis, J. Lin, et al., BioMagResBank, Nucl. Acids Res. 36 (2008) D402–8. . [2] L. Wang, H.R. Eghbalnia, A. Bahrami, J.L. Markley, Linear analysis of carbon-13 chemical shift differences and its application to the detection and correction of errors in referencing and spin system identifications, J. Biomol. NMR. 32 (2005) 13–22. .


Author: Xi Chen Email: [email protected] Date: Jan 12, 2018 GitHub: github.com/billchenxi

Welcome!

BMRBr is a package that facilites R users to analyze data from BMRB data repo by simplifing the download procedure. Currently, the only way to download individual BMRB NMR-star file is to download manually or using shell code, this package frees R users by allowing users to enter only ID and store location.

Right now, the two function in this package is bmrb_download() and collect_ids(). In future, I will release more functionalities by adding more functions.

bmrb_download()

Required two input parameter: BMRB ID and storage path.

Example:

  • bmrb_download(956, "../store_location")

collect_ids()

No required parameter.

Example:

  • bmrb_download()

News

BMRBr Package News

Jan 13, 2018, resubmitting the package.

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("BMRBr")

0.2.0 by Xi Chen, 10 months ago


https://github.com/billchenxi/BMRBr


Report a bug at https://github.com/billchenxi/BMRBr/issues


Browse source code at https://github.com/cran/BMRBr


Authors: Xi Chen [aut, cre]


Documentation:   PDF Manual  


GPL-3 license


Depends on xml2, rvest, utils

Suggests knitr, rmarkdown, testthat


Imported by BaMORC.


See at CRAN