Varyasyon-Bazlı Kişisel Genetik Verilerin Doküman-Tabanlı No-Sql Veri Tabanı ile Organizasyonu

Year 2021, Volume: 14 Issue: 4, 391 - 402, 31.10.2021

Onur Çakırgöz , Süleyman Sevinç

Abstract

Varyasyon-bazlı kişisel genetik veriler çoğu klinik uygulamanın ve biyoinformatikteki çoğu çalışmanın merkezinde bulunmaktadır. Ne yazık ki, kişisel genetik verileri organize etmek için geliştirilen mevcut yöntemlerin neredeyse tamamı varyasyon-bazlı değildir ve bu yöntemler büyük miktardaki gerçek verilerle test edilmemiştir. Varyasyon-bazlı verilere ihtiyaç duyan uygulamalarda, bu mevcut yöntemler kullanıldığında, yoğun bir veri dönüştürme problemi ortaya çıkmaktadır. Öte yandan, az sayıdaki mevcut varyasyon-bazlı çözümler tamamıyla yapısal değildir ve günlük pratiğin gereksinimlerini karşılamamaktadır. Bu çalışmada, varyasyon-bazlı kişisel genetik verilerin organizasyonu için doküman-tabanlı No-SQL veri tabanı ve ilgili tasarımlar önerilmektedir. Yapısal çözümümüz çok sayıda sınıf, koleksiyon ve indeks içermektedir ve tüm varyasyon tiplerini (yapısal ve yapısal olmayan) desteklemektedir. Bu veri tabanında, 1000 Genom Projesi tarafından yayınlanan 2504 kişinin varyasyon verileri sorunsuz ve verimli bir şekilde depolanmıştır. Kişisel genetik verilerin ana bellek ve sabit diskte kapladığı alanlar incelenmiştir. Ayrıca, klinik uygulamaların sıklıkla kullanabileceği bazı sorgular çalıştırılmış ve veri tabanının yanıt süreleri hesaplanmıştır. Analizlerin sonuçları, önerilen yöntemin çok önemli kazanımlar sağladığını göstermektedir.

Keywords

no-sql veritabanı, kişisel genom veritabanı, kişisel genetik veriler, insan genomu varyasyonları, 1000 genom projesi

Organization of Variation-Based Personal Genetic Data with Document-Based No-Sql Database

Abstract

Variation-based personal genetic data are at the center of many clinical practices and many studies in bioinformatics. Unfortunately, almost all existing methods developed to organize personal genetic data are not variation-based and these methods have not been tested with a large amount of real data. In applications requiring variation-based data, an intense data conversion problem arises when these existing methods are used. On the other hand, the few solutions available that are variation-based are not entirely structural, and they do not meet the needs of daily practice. In this study, a document-based No-SQL database and related designs are proposed for the organization of variation-based personal genetic data. Our structural solution contains many classes, collections and indexes, and it supports all types of variations (both structural and non-structural). In this database, the variation data of 2504 people published by the 1000 Genomes Project were stored smoothly and efficiently. The spaces occupied by personal genetic data in primary memory and hard disk were analyzed. In addition, some queries that might be frequently used by clinical applications were run and the response times of the database was calculated. The results of the analyzes show that the proposed method provides very important gains.

Keywords

no-sql database, personal genome database, personal genetic data, human genome variations, 1000 genomes project

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