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SNiPhunter: A SNP-Based Search Engine

Author

Listed:
  • 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)

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.

Suggested Citation

  • Werner P. Veldsman & Alan Christoffels, 2016. "SNiPhunter: A SNP-Based Search Engine," Data, MDPI, vol. 1(3), pages 1-8, September.
    • Handle: RePEc:gam:jdataj:v:1:y:2016:i:3:p:17-:d:79458
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