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Exploring the fantastic world of biological data: Why does every life form have its own database?
In today's scientific research, biological databases are like a treasure trove of countless knowledge, allowing people to deeply understand the diversity of various life forms. These databases bring together our biological data from experiments, literature, and computational analyses, providing a rich resource for research areas such as genomics, proteomics, and metabolomics.
The content of biological databases includes gene function, structure, location (including cells and chromosomes), clinical impact of mutations, and similarities in biological sequences and structures.
Biological databases can be classified according to the type of data collected. Classification in a broad sense includes molecular databases (such as sequences and molecules), functional databases (related to physiology, enzyme activity, phenotypes, etc.), taxonomic databases (related to species classification, etc.), images and other media, and even specimen libraries (such as museums) collection). These databases not only help scientists analyze biological phenomena, but also play an important role in fighting diseases, developing drugs, and predicting certain genetic diseases.
Technical basis and theoretical concepts
Understanding biological databases requires mastering the concept of relational databases in computer science and the concept of information retrieval in digital libraries. The design, development and long-term management of biological databases is one of the core areas in bioinformatics. The content of these data usually includes gene sequences, text descriptions, attribute and ontology classifications, citations and tabular data, which are generally considered semi-structured data.
Access method
Most biological databases are accessible through websites that aggregate data for easy online browsing. Additionally, the underlying data is often available for download in multiple formats. Biological data comes in a variety of formats, including text, sequence data, protein structures, and links. For example, PubMed and OMIM provide text formats, and GenBank and UniProt provide sequence data for DNA and proteins.
Problems and Challenges
Biological knowledge is scattered in countless databases, making it sometimes difficult to ensure the consistency of information. Since different databases may use different species names, this makes interoperability a challenge in information exchange. One potential solution is to cross-reference the access numbers of other databases so that the link remains stable even if species names change.
Model organism database
Special databases exist for some species commonly used for research. For example, EcoCyc is a database specific to E. coli. Other well-known model organism databases include Mouse Genome Informatics, Rat Genome Database, and Drosophila Database.
Biodiversity and species database
Many databases are devoted to documenting the diversity of life on Earth, such as the Catalog of Life. This is a collaborative project that aims to document the current classification of all recognized species and provide a unified database that researchers and policy makers can refer to.
Medical database
Medical databases are a specific biomedical data resource, ranging from literature such as PubMed to imaging databases for AI diagnosis. For example, WoundsDB is an imaging database designed to help facilitate the development of wound monitoring algorithms.
Nucleic Acids Research database issues
Another great resource for finding biological databases is the special annual issue of the journal Nucleic Acids Research, which is freely available and catalogs many public biological databases. As a supplement to the journal, a repository called the Networked Molecular Biology Database Collection lists 1,380 online databases.
As technology continues to advance, biological databases continue to evolve and adapt to new challenges. For future biological research, how will these databases affect our understanding and application of life?
