{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T20:10:58Z","timestamp":1760213458757,"version":"build-2065373602"},"reference-count":25,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2016,9,29]],"date-time":"2016-09-29T00:00:00Z","timestamp":1475107200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"South African Research Chairs Initiative of the Department of Science and Technology and National Research Foundation of South Africa"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Data"],"abstract":"<jats:p>Procuring biomedical literature is a time-consuming process. The genomic sciences software solution described here indexes literature from Pubmed Central\u2019s 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\u2014called SNiPhunter\u2014is 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.<\/jats:p>","DOI":"10.3390\/data1030017","type":"journal-article","created":{"date-parts":[[2016,9,29]],"date-time":"2016-09-29T09:54:50Z","timestamp":1475142890000},"page":"17","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["SNiPhunter: A SNP-Based Search Engine"],"prefix":"10.3390","volume":"1","author":[{"given":"Werner","family":"Veldsman","sequence":"first","affiliation":[{"name":"South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alan","family":"Christoffels","sequence":"additional","affiliation":[{"name":"South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2016,9,29]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1093\/bib\/bbt079","article-title":"The semantic web in translational medicine: Current applications and future directions","volume":"16","author":"Machado","year":"2015","journal-title":"Brief. Bioinform."},{"key":"ref_3","first-page":"347","article-title":"Describing Black-Box Medicine","volume":"21","author":"Price","year":"2015","journal-title":"B.U. J. Sci. Tech. L."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Zhang, J., Baran, J., Cros, A., Guberman, J.M., Haider, S., Hsu, J., Liang, Y., Rivkin, E., Wang, J., and Whitty, B. (2011). International Cancer Genome Consortium Data Portal\u2014A one-stop shop for cancer genomics data. Database.","DOI":"10.1093\/database\/bar026"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1093\/nar\/29.1.308","article-title":"dbSNP: The NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"D1308","DOI":"10.1093\/nar\/gkr798","article-title":"SNPedia: A wiki supporting personal genome annotation, interpretation and analysis","volume":"40","author":"Cariaso","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_7","unstructured":"SNiPhunter. Available online: http:\/\/sniphunter.sanbi.ac.za."},{"key":"ref_8","unstructured":"(2016). Pubmed, Available online: http:\/\/www.ncbi.nlm.nih.gov\/pubmed."},{"key":"ref_9","unstructured":"Google form. Available online: https:\/\/goo.gl\/ccGgwb."},{"key":"ref_10","unstructured":"(2016). Pubmed Central open access initiative, Available online: https:\/\/www.ncbi.nlm.nih.gov\/pmc\/tools\/ftp\/."},{"key":"ref_11","unstructured":"Directory of Open Access Journals. Available online: http:\/\/doaj.org."},{"key":"ref_12","unstructured":"OpenDOAR. Available online: http:\/\/www.opendoar.org."},{"key":"ref_13","unstructured":"CiteSeerX. Available online: http:\/\/citeseerx.ist.psu.edu\/index."},{"key":"ref_14","doi-asserted-by":"crossref","unstructured":"Shah, P.K., Perez-Iratxeta, C., Bork, P., and Andrade, M.A. (2003). Information extraction from full text scientific articles: Where are the keywords?. 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Available online: https:\/\/github.com\/typicode\/lowdb."}],"container-title":["Data"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2306-5729\/1\/3\/17\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T19:32:06Z","timestamp":1760211126000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2306-5729\/1\/3\/17"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9,29]]},"references-count":25,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2016,12]]}},"alternative-id":["data1030017"],"URL":"https:\/\/doi.org\/10.3390\/data1030017","relation":{},"ISSN":["2306-5729"],"issn-type":[{"type":"electronic","value":"2306-5729"}],"subject":[],"published":{"date-parts":[[2016,9,29]]}}}