Next Article in Journal
Land Cover Data for the Mississippi–Alabama Barrier Islands, 2010–2011
Next Article in Special Issue
Application of Taxonomic Modeling to Microbiota Data Mining for Detection of Helminth Infection in Global Populations
Previous Article in Journal
Technical Guidelines to Extract and Analyze VGI from Different Platforms
Article Menu

Export Article

Open AccessData Descriptor
Data 2016, 1(3), 17; doi:10.3390/data1030017

SNiPhunter: A SNP-Based Search Engine

South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
*
Author to whom correspondence should be addressed.
Academic Editor: Vanathi Gopalakrishnan
Received: 10 June 2016 / Revised: 30 August 2016 / Accepted: 25 September 2016 / Published: 29 September 2016
(This article belongs to the Special Issue Biomedical Informatics)
View Full-Text   |   Download PDF [302 KB, uploaded 29 September 2016]   |  

Abstract

Procuring biomedical literature is a time-consuming process. The genomic sciences software solution described here indexes literature from Pubmed Central’s open access initiative, and makes it available as a web application and through an application programming interface (API). The purpose of this tertiary data artifact—called SNiPhunter—is to assist researchers in finding articles relevant to a reference single nucleotide polymorphism (SNP) identifier of interest. A novel feature of this NoSQL (not only structured query language) database search engine is that it returns results to the user ordered according to the amount of times a refSNP has appeared in an article, thereby allowing the user to make a quantitative estimate as to the relevance of an article. Queries can also be launched using author-defined keywords. Additional features include a variant call format (VCF) file parser and a multiple query file upload service. Software implementation in this project relied on Python and the NodeJS interpreter, as well as third party libraries retrieved from Github. View Full-Text
Keywords: search engine; reference SNP identifier; PMC-OAI; NoSQL; VCF search engine; reference SNP identifier; PMC-OAI; NoSQL; VCF
Figures

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Veldsman, W.P.; Christoffels, A. SNiPhunter: A SNP-Based Search Engine. Data 2016, 1, 17.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Data EISSN 2306-5729 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top