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Review of Recent Biological Databases
Explosion of Biological Data and Database Integration
In recent years, the volume of biological data has surged, driven by advancements in genome sequencing and annotation, as well as the accumulation of protein and gene interaction data. Biological databases have become essential tools for managing and accessing this vast amount of data. Despite their architectural similarities, integrating these databases remains a significant challenge.
Central Role of Biological Databases in Bioinformatics
Biological databases are pivotal in bioinformatics, providing access to sequence and structure data for numerous organisms. Key sequence databases include GenBank, UCSC Genome Browser, and Ensembl. Additionally, non-sequence-centric databases like OMIM, PDB, MetaCyc, and KEGG play crucial roles in storing diverse biological data .
Human-Related Biological Databases
The completion of the Human Genome Project has spurred the development of numerous databases focused on human-related research. These databases are categorized based on data types and are instrumental in studying the human genome, evolutionary history, and precision medicine. However, the rapid growth of these databases presents challenges in data storage, processing, exchange, and curation.
BioGRID: A Comprehensive Interaction Database
The BioGRID database is a comprehensive resource that curates protein, genetic, and chemical interactions from various species, including humans. It supports biomedical discoveries by providing access to a vast number of curated interactions, which can be used to build complex networks. BioGRID also includes a network visualization tool and captures data from CRISPR screens, making it a valuable resource for the research community .
Guidelines for Developing Public Biological Databases
Developing high-quality biological databases requires adherence to several key principles. These include ensuring data quality, avoiding redundancy, and maintaining clear data provenance. Primary databases collect unique content directly from experiments, while secondary databases aggregate data from other sources. Both types must follow best practices and standards to ensure data integrity and usability.
NCBI's Suite of Online Resources
The National Center for Biotechnology Information (NCBI) offers a comprehensive suite of online resources, including the GenBank nucleic acid sequence database and PubMed. The Entrez system facilitates search and retrieval operations across multiple databases, and new tools like PubMed Data Management and RefSeq Functional Elements enhance data accessibility and utility .
Conclusion
The landscape of biological databases is rapidly evolving, driven by the increasing volume of biological data and the need for efficient data management and accessibility. Key databases like GenBank, UCSC Genome Browser, Ensembl, and BioGRID play crucial roles in supporting biological research. As the field progresses, maintaining high data quality and integrating diverse data types will be essential for maximizing the utility of these invaluable resources.
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