SNP based literature and data retrieval

>Magister Scientiae - MScReference 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.National Research Foundation (NRF) /The South African Research Chairs Initiative (SARChI

Drawing Database Schemas

A wide number of practical applications would benefit from automatically generated graphical representations of database schemas, in which tables are represented by boxes, and table attributes correspond to distinct stripes inside each table. Links, connecting attributes of two different tables, represent referential constraints or join relationships, and may attach arbitrarily to the left- or to the right hand side of the stripes representing the attributes. To our knowledge no drawing technique is available to automatically produce diagrams in such a strongly constrained drawing convention. In this paper we provide a polynomial time algorithm for solving this problem, and test its efficiency and effectiveness against a large test suite. Also, we describe an implementation of a system that uses such an algorithm and we study the main methodological problems we faced in developing such a technology

Drawing Database Schemas with DBdraw

DBdraw is an application that allows the user to automatically produce drawings of database schemas according to a drawing standard that is well accepted by the database community. The drawing engine of DBdraw is based on the GDToolkit library