EMBnet MCB, feb 2005 An introduction to biological databases Marie-Claude.Blatter@isb-sib.ch EMBnet MCB, feb 2005 What is a database ? Each biological database has a database accessor object in the system that handles the specific translations necessary to query that database. Databases are used to store and organize data in such a way that information can be retrieved easily via a variety of search criteria. One of the hallmarks of modern genomic research is the generation of enormous amounts of raw sequence data. However, UniProt also infers peptide sequences from genomic information, and it provides a wealth of additional information, some derived from automated annotation (TrEMBL), and even more from careful manual analysis (SwissProt). This database was updated and compiled by Dr. Carmen Ricos and colleagues, before the EFLM took the helm. Primary databases are also called as archieval database. https://www.ncbi.nlm.nih.gov/books/NBK44933/, Blood Cells- Definition and Types with Structure and Functions, Antimicrobial Susceptibility Testing (AST)- Types and Limitations, Hypersensitivity- Introduction, Causes, Mechanism and Types, Vaccines- Introduction and Types with Examples, Bone Marrow- Types, Structure and Functions, Widal Test- Objective, Principle, Procedure, Types, Results, Advantages and Limitations, DNA- Structure, Properties, Types and Functions, RNA- Properties, Structure, Types and Functions, Chromosome- Structure, Types and Functions, Centrifugation- Principle, Types and Applications, Linkage- Characteristics, Types and Significance, Extranuclear Inheritance- Cytoplasmic Factors and Types, Plastids- Definition, Structure, Types, Functions and Diagram, Vacuoles- Definition, Structure, Types, Functions and Diagram, Microbial interaction and its types with examples, Epidemiology- History, Objectives and Types, Endospore Staining- Types, principle, procedure and Interpretation, Endocytosis- Definition, Process and Types with Examples, Exocytosis- Definition, Process and Types with Examples, Types of PCR (Polymerase chain reaction) - definition and uses, Hemolysis of Streptococci- Types and Examples with Images, https://www.ebi.ac.uk/training/online/course/bioinformatics-terrified-2018/primary-and-secondary-databases, https://www.omicsonline.org/scholarly/bioinformatics-databases-journals-articles-ppts-list.php, Bioinformatics- Introduction and Applications, X-Ray Spectroscopy- Principle, Instrumentation and Applications. One solution is how biological databases cross-reference to other databases with accession numbers to link their related knowledge together. This sometimes makes it difficult to ensure the consistency of information. Biological databases can be broadly classified into sequence, structure and functional databases. Biological databases are stores of biological information. Secondary databases often draw upon information from numerous sources, including other databases (primary and secondary), controlled vocabularies and the scientific literature. These are often described as semi-structured data, and can be represented as tables, key delimited records, and XML structures. Data is seamless integration of biological applications within a database framework. The journal Nucleic Acids Research regularly publishes special issues on biological databases and has a list of such databases. Texas A & M University. The Database Issue of NAR is freely available, and categorizes many of the publicly available online databases related to biology and bioinformatics. For example, Flybase, HIV sequence database, and Ribosomal Database Project are databases that specialize in a particular organism or a particular type of data. WHAT IS A DATABASE? Bioinformatics is the application of Information technology to store, organize and analyze the vast amount of biological data which is available in the form of sequences and structures of proteins (the building blocks of organisms) and nucleic acids (the information carrier). © 2020 Microbe Notes. Thus, the very first challenge in the genomics era is to store and handle the staggering volume of information through the establishment and use of computer databases. New database design needed to be established to solve the problems that flat-file design created. Biological Data comes in many formats. Xiong J. However, over the time, database became a preferable term. It provides a homogeneous interface to over 80 biological databases (see SRS help at [25]). A database is a computerized archive used to store and organize data in such a way that information can be retrieved easily via a variety of search criteria. To assess the best way for reporting results 1.6. It includes databases of sequences, metabolic pathways, transcription factors, application results (like BLAST, SSEARCH, FASTA), protein 3-D structures, genomes, mappings, mutations, and locus specific mutations. Other popular model organism databases include Mouse Genome Informatics for the laboratory mouse, Mus musculus, the Rat Genome Database for Rattus, ZFIN for Danio Rerio (zebrafish), PomBase[7] for the fission yeast Schizosaccharomyces pombe, FlyBase for Drosophila, WormBase for the nematodes Caenorhabditis elegans and Caenorhabditis briggsae, and Xenbase for Xenopus tropicalis and Xenopus laevis frogs. 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