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Molecular biological databases: evolutionary history, data modeling, implementation and ethical background

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Author(s): MPNS Cooray

Journal: Sri Lanka Journal of Bio-Medical Informatics
ISSN 2012-6077

Volume: 3;
Issue: 1;
Start page: 2;
Date: 2013;
Original page

Keywords: Protein Data Bank | Electronic Data Publishing | GenBank | Biological Databases

ABSTRACT
Influence from the rapidly growing fields of computer and information sciences in early 1970s was one of the major factors leading to the development of computer based repositories for biological data. Since the emergence of the first ever computer based molecular biological database ‘Protein Data Bank’ in 1971, biological database domain has grown rapidly in the areas of information content and volume, database modeling, implementation and integration. Key driving forces of this growth are: the amount and diversity of data generated from advancing biological research technologies, the challenges imposed on data modeling by the inherent properties of biological data and the concept of ‘Electronic Data Publishing’ introduced in early 1990s. According to the database release of ‘Nucleic Acid Research’ in 2010, biological database number increased in about 5% during the year of 2009-2010 and in major databases like ‘GenBank’ data volume doubles approximately every 18 months.Due to the data modeling challenges driven by inherent properties of biological data, multiple modeling tools such as ‘Enhanced Entity Relationship’ diagrams and ‘Unified Modeling Language’ are used to model biological mini worlds. To be compatible with diverse data models, multiple implementation approaches are also used by the biological database developers, namely ‘Flat files’, ‘XML’, ‘Relational databases’, ‘Object oriented databases’, ‘ASN.1’ and etc. Adherence to simplicity and conservative technology provides a better practical approach to biological database modeling and implementation.Even though the biological databases differ in their internal data model, implementation approach and biological scope, almost all of them share similar 3 tier web architecture. This similarity is the basis of the current three major strategies used for database integration namely ‘Link/hypertext integration’, ‘View integration’ and ‘Data warehousing’.Ethical framework governing the molecular biological research and databases, need to be re-engineered to accommodate the demands imposed by this rapidly growing scientific field.
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