Izrada SQL upita za analizu bioloških podataka

master's thesis

• Title (english): Building SQL queries for biological data analysis
• Author: Andrea Plec
• Mentor: Janko Diminić (mentor)
• Granter: University of Zagreb; Faculty of Food Technology and Biotechnology; (Department of Biochemical Engineering); (Section for Bioinformatics); Zagreb
• Defense date and country: 2019-12-12, Croatia
• Scientific / art field, discipline and subdiscipline: BIOTECHNICAL SCIENCES; Biotechnology

Abstract

Zahvaljujući mnogim istraživanjima, crijevna mikrobiota se pokazala kao važna komponenta fiziologije čovjeka s kojim živi u mutualističkom odnosu. S obzirom da je riječ o kompleksnoj zajednici mikroorganizama na čiji sastav utječu mnogobrojni unutarnji i vanjski čimbenici, svaki pojedinac posjeduje jedinstveni sastav crijevne mikrobiote. Disbioza crijevne mikrobiote može dovesti do raznih upalnih i metaboličkih poremećaja, što može rezultirati bolestima. Utvrđivanje sličnosti i razlika među zdravim i bolesnim skupinama pojedinaca pruža mogućnost određivanja povezanosti sastava crijevne mikrobiote s tim poremećajima i bolestima. U tu svrhu se provodi sekvenciranje mnogobrojnih uzoraka crijevne mikrobiote, a dobivena očitanja se zatim bioinformatički obrađuju te se rezultati pohranjuju u baze podataka. U ovom radu je u sklopu računalnog paketa MySQL korištena baza podataka koja sadrži brojnosti pojedinih taksona za 1639 uzoraka crijevne mikrobiote. Korištenjem računalnog jezika SQL izrađeni su pohranjeni postupci za analizu raznolikosti sastava pojedinih uzoraka i procjenu prosječnog sastava za sve uzorke.

Abstract (english)

According to numerous studies, gut microbiota lives in a mutualistically beneficial relationship with humans and has proven to be an important component of their physiology. Each individual has a unique gut microbiota composition, given that it’s a complex community of microorganisms whose composition is affected by many internal and external factors. Dysbiosis of the gut microbiota can lead to various inflammatory and metabolic disorders, which can result in illness. Determining similarities and differences among healthy and affected cohorts provides an opportunity to establish correlations between gut microbiota composition and various afflictions. Such research requires sequencing of numerous intestinal microbiota samples. The acquired sequence reads are then bioinformatically processed and the results are stored in databases. In order to build several stored procedures using SQL, a database containing taxa abundance of 1639 gut microbiota samples was used. The stored procedures were built within MySQL database management system, and used to analyze the composition diversity of individual samples and to estimate the average composition for all samples.

• Keywords: bioinformatika; baza podataka; SQL; crijevna mikrobiota; bioraznolikost
• Keywords (english): bioinformatics; database; SQL; gut microbiota; biodiversity
• Language: croatian
• URN:NBN: urn:nbn:hr:159:087957
• Study programme: Title: Molecular Biotechnology; Study programme type: university; Study level: graduate; Academic / professional title: magistar/magistra inženjer/inženjerka molekularne biotehnologije (magistar/magistra inženjer/inženjerka molekularne biotehnologije)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Open access
• Created on: 2020-01-28 12:06:09