bdbms -- A Database Management System for Biological Data

TL;DR

bdbms is an extensible database system tailored for biological data, integrating annotation, provenance, dependency tracking, content-based authorization, and specialized access methods to meet biological research needs.

Contribution

It introduces novel functionalities like annotation management, dependency tracking, and pattern matching support, extending current DBMS capabilities for biological data.

Findings

Supports annotation and provenance as first-class objects

Enables dependency tracking among data items

Provides pattern matching on compressed biological data

Abstract

Biologists are increasingly using databases for storing and managing their data. Biological databases typically consist of a mixture of raw data, metadata, sequences, annotations, and related data obtained from various sources. Current database technology lacks several functionalities that are needed by biological databases. In this paper, we introduce bdbms, an extensible prototype database management system for supporting biological data. bdbms extends the functionalities of current DBMSs to include: (1) Annotation and provenance management including storage, indexing, manipulation, and querying of annotation and provenance as first class objects in bdbms, (2) Local dependency tracking to track the dependencies and derivations among data items, (3) Update authorization to support data curation via content-based authorization, in contrast to identity-based authorization, and (4) New access methods and their supporting operators that support pattern matching on various types of compressed biological data types. This paper presents the design of bdbms along with the techniques proposed to support these functionalities including an extension to SQL. We also outline some open issues in building bdbms.