SNiPhunter: A SNP-Based Search Engine

Werner P. Veldsman and Alan Christoffels
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Werner P. Veldsman: South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa
Alan Christoffels: South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa

Data, 2016, vol. 1, issue 3, 1-8

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.

Keywords: search engine; reference SNP identifier; PMC-OAI; NoSQL; VCF (search for similar items in EconPapers)
JEL-codes: C8 C80 C81 C82 C83 (search for similar items in EconPapers)
Date: 2016
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