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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 challenge1.
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 data2 3.
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 curation4.
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 community5 10.
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 usability6.
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 utility8 9.
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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Integrating biological databases
Recent years have seen an explosion in the amount of available biological data. More and more genomes are being sequenced and annotated, and protein and gene interaction data are accumulating. Biological databases have been invaluable for managing these data and for making them accessible. Depending on the data that they contain, the databases fulfil different functions. But, although they are architecturally similar, so far their integration has proved problematic.
Highly CitedThe Importance of Biological Databases in Biological Discovery
Biological databases play a central role in bioinformatics, providing scientists with access to sequence and structure data for tens of thousands of organisms.
The Importance of Biological Databases in Biological Discovery
Biological databases play a central role in bioinformatics, offering scientists access to a wide variety of biologically relevant data, including genomic sequences of an increasingly broad range of organisms.
Biological Databases for Human Research
Human-related biological databases are growing in number and volume, posing challenges in big data storage, processing, exchange, and curation.
Highly CitedThe BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions
The BioGRID database contains over 1,93 million curated protein and genetic interactions from various species, aiding in biomedical discoveries and cellular regulation.
Highly CitedTen Simple Rules for Developing Public Biological Databases
Follow these ten simple rules for creating and maintaining biological databases to ensure high-quality content and user-friendly functionality.
Databases of biological information
Genome projects generate a wealth of biological data, which can be interpreted from molecular interactions to organism interactions using database tools.
Database resources of the National Center for Biotechnology Information
NCBI's online resources for biological information and data, including GenBank and PubMed, have been updated and enhanced in the past year.
Highly CitedDatabase resources of the National Center for Biotechnology Information
NCBI provides online resources for biological information and data, including the GenBank nucleic acid sequence database and PubMed citations and abstracts, with new resources and updates released in the past year.
Highly CitedThe BioGRID interaction database: 2017 update
BioGRID now contains 1,072,173 genetic and protein interactions for 66 model organisms, with a 30% increase compared to the previous 2015 update, and now incorporates 27 501 chemical-protein interactions for human drug targets.
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