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.
Highlights
Procuring biomedical literature is a time-consuming process
NoSQL database search engine is that it returns results to the user ordered according to the amount of times a Reference single nucleotide polymorphism (refSNP) has appeared in an article, thereby allowing the user to make a quantitative estimate as to the relevance of an article
A representational state transfer (REST) protocol was used for interaction between the web application and the database, while calls to the database are initiated with asynchronous javascript and XML (AJAX)
Summary
Reference single nucleotide polymorphism (refSNP) identifiers are used to earmark SNPs in the human genome. RefSNPs identifiers can be useful to include as terms in query constructs submitted to search engines when sourcing biomedical literature. Central resource repositories), relevant results are returned for a plethora of information, after which data in related NCBI databases can be retrieved by selecting a database from a drop-down list. Searching for the SNP by its identifier in non-institutionalized databases such as SNPedia [6] returns results that point the user to literature relevant to the SNP, with an indication of whether this literature is provided under open access agreements, but the order in which the results are listed does not give the user an indication of how the ranking was determined. Specific literature ordered by quantified relevance is not supplied by SNPedia, and bulk querying using reference SNP identifiers is not available as part of its user interface
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