SNP based literature and data retrieval

dc.contributor.advisorChristoffels, Alan
dc.contributor.authorVeldsman, Werner Pieter
dc.date.accessioned2016-11-28T08:47:51Z
dc.date.accessioned2024-05-17T07:20:17Z
dc.date.available2016-11-28T08:47:51Z
dc.date.available2024-05-17T07:20:17Z
dc.date.issued2016
dc.description>Magister Scientiae - MScen_US
dc.description.abstractReference single nucleotide polymorphism (refSNP) identifiers are used to earmark SNPs in the human genome. These identifiers are often found in variant call format (VCF) files. RefSNPs can be useful to include as terms submitted to search engines when sourcing biomedical literature. In this thesis, the development of a bioinformatics software package is motivated, planned and implemented as a web application (http://sniphunter.sanbi.ac.za) with an application programming interface (API). The purpose is to allow scientists searching for relevant literature to query a database using refSNP identifiers and potential keywords assigned to scientific literature by the authors. Multiple queries can be simultaneously launched using either the web interface or the API. In addition, a VCF file parser was developed and packaged with the application to allow users to upload, extract and write information from VCF files to a file format that can be interpreted by the novel search engine created during this project. The parsing feature is seamlessly integrated with the web application's user interface, meaning there is no expectation on the user to learn a scripting language. This multi-faceted software system, called SNiPhunter, envisions saving researchers time during life sciences literature procurement, by suggesting articles based on the amount of times a reference SNP identifier has been mentioned in an article. This will allow the user to make a quantitative estimate as to the relevance of an article. A second novel feature is the inclusion of the email address of a correspondence author in the results returned to the user, which promotes communication between scientists. Moreover, links to external functional information are provided to allow researchers to examine annotations associated with their reference SNP identifier of interest. Standard information such as digital object identifiers and publishing dates, that are typically provided by other search engines, are also included in the results returned to the user.en_US
dc.description.sponsorshipNational Research Foundation (NRF) /The South African Research Chairs Initiative (SARChI)en_US
dc.identifier.urihttps://hdl.handle.net/10566/15253
dc.language.isoenen_US
dc.publisherUniversity of the Western Capeen_US
dc.rights.holderUniversity of the Western Capeen_US
dc.subjectAPI (Application Programming Interface)en_US
dc.subjectBioinformaticsen_US
dc.subjectData miningen_US
dc.subjectSNP (Single Nucleotide Polymorphism)en_US
dc.titleSNP based literature and data retrievalen_US
dc.typeThesisen_US

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