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Biological Database
Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including genomics, proteomics, metabolomics, microarray gene expression, and phylogenetics. Information contained in biological databases includes gene function, structure, localization (both cellular and chromosomal), clinical effects of mutations as well as similarities of biological sequences and structures. Biological databases can be classified by the kind of data they collect (see below). Broadly, there are molecular databases (for sequences, molecules, etc.), functional databases (for physiology, enzyme activities, phenotypes, ecology etc), taxonomic databases (for species and other taxonomic ranks), images and other media, or specimens (for museum collections etc.) Databases are important tools in assisting scientists to analyze and explain a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
String Home Page
String or strings may refer to: *String (structure), a long flexible structure made from threads twisted together, which is used to tie, bind, or hang other objects Arts, entertainment, and media Films * Strings (1991 film), ''Strings'' (1991 film), a Canadian animated short * Strings (2004 film), ''Strings'' (2004 film), a film directed by Anders Rønnow Klarlund * Strings (2011 film), ''Strings'' (2011 film), an American dramatic thriller film * Strings (2012 film), ''Strings'' (2012 film), a British film by Rob Savage * ''Bravetown'' (2015 film), an American drama film originally titled ''Strings'' * ''The String'' (2009), a French film Music Instruments * String (music), the flexible element that produces vibrations and sound in string instruments * String instrument, a musical instrument that produces sound through vibrating strings ** List of string instruments * String piano, a pianistic extended technique in which sound is produced by direct manipulation of the strings, r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ontology (information Science)
In computer science and information science, an ontology encompasses a representation, formal naming, and definition of the categories, properties, and relations between the concepts, data, and entities that substantiate one, many, or all domains of discourse. More simply, an ontology is a way of showing the properties of a subject area and how they are related, by defining a set of concepts and categories that represent the subject. Every academic discipline or field creates ontologies to limit complexity and organize data into information and knowledge. Each uses ontological assumptions to frame explicit theories, research and applications. New ontologies may improve problem solving within that domain. Translating research papers within every field is a problem made easier when experts from different countries maintain a controlled vocabulary of jargon between each of their languages. For instance, the definition and ontology of economics is a primary concern in Marxist econo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure Database
In biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way. Data included in protein structure databases often includes three-dimensional coordinates as well as experimental information, such as unit cell dimensions and angles for x-ray crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ... determined structures. Though most instances, in this case either proteins or a specific structure determinations of a protein, also contain sequence information and some databases even provide means for performing sequence based qu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Accession Number (bioinformatics)
An accession number, in bioinformatics, is a unique identifier given to a DNA or protein sequence record to allow for tracking of different versions of that sequence record and the associated sequence over time in a single data repository. Because of its relative stability, accession numbers can be utilized as foreign key A foreign key is a set of attributes in a table that refers to the primary key of another table. The foreign key links these two tables. Another way to put it: In the context of relational databases, a foreign key is a set of attributes subject to ...s for referring to a sequence object, but not necessarily to a unique sequence. All sequence information repositories implement the concept of "accession number" but might do so with subtle variations. LRG Locus Reference Genomic (LRG) records have unique accession numbers starting with LRG_ followed by a number. They are recommended in thHuman Genome Variation Society Nomenclature guidelinesas stable genomic ref ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cross-reference
The term cross-reference (abbreviation: xref) can refer to either: * An instance within a document which refers to related information elsewhere in the same document. In both printed and online dictionaries cross-references are important because they form a network structure of relations existing between different parts of data, dictionary-internal as well as dictionary external. * In an index, a cross-reference is often denoted by ''See also''. For example, under the term ''Albert Einstein'' in the index of a book about Nobel Laureates, there may be the cross-reference ''See also: Einstein, Albert''. * In hypertext, cross-referencing is maintained to a document with either in-context (XRIC) or out-of-context (''XROC'') cross-referencing. These are similar to KWIC and KWOC. * In programming, "cross-referencing" means the listing of every file name and line number where a given named identifier occurs within the program's source tree. * In a relational database management sy ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Integrative Bioinformatics
Integrative bioinformatics is a discipline of bioinformatics that focuses on problems of data integration for the life sciences. With the rise of high-throughput (HTP) technologies in the life sciences, particularly in molecular biology, the amount of collected data has grown in an exponential fashion. Furthermore, the data are scattered over a plethora of both public and private repositories, and are stored using a large number of different formats. This situation makes searching these data and performing the analysis necessary for the extraction of new knowledge from the complete set of available data very difficult. Integrative bioinformatics attempts to tackle this problem by providing unified access to life science data. Approaches Semantic web approaches In the Semantic Web approach, data from multiple websites or databases is searched via metadata. Metadata is machine-readable code, which defines the contents of the page for the program so that the comparisons between t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CATH
The CATH Protein Structure Classification database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains. It was created in the mid-1990s by Professor Christine Orengo and colleagues including Janet Thornton and David Jones, and continues to be developed by the Orengo group at University College London. CATH shares many broad features with the SCOP resource, however there are also many areas in which the detailed classification differs greatly. Hierarchical organization Experimentally-determined protein three-dimensional structures are obtained from the Protein Data Bank and split into their consecutive polypeptide chains, where applicable. Protein domains are identified within these chains using a mixture of automatic methods and manual curation. The domains are then classified within the CATH structural hierarchy: at the Class (C) level, domains are assigned according to their secondary structure content, i. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Structural Classification Of Proteins
The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. A motivation for this classification is to determine the evolutionary relationship between proteins. Proteins with the same shapes but having little sequence or functional similarity are placed in different superfamilies, and are assumed to have only a very distant common ancestor. Proteins having the same shape and some similarity of sequence and/or function are placed in "families", and are assumed to have a closer common ancestor. Similar to CATH and Pfam databases, SCOP provides a classification of individual structural domains of proteins, rather than a classification of the entire proteins which may include a significant number of different domains. The SCOP database is freely accessible on the internet. SCOP was created in 1994 in the Centre for Protein Engineering and the Labo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. History Two force ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UniProt
UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC, United States. The UniProt consortium The UniProt consortium comprises the European Bioinformatics Institute (EBI), the Swiss Institute of Bioinformatics (SIB), and the Protein Information Resource (PIR). EBI, located at the Wellcome Trust Genome Campus in Hinxton, UK, hosts a large resource of bioinformatics databases and services. SIB, located in Geneva, Switzerland, maintains the ExPASy (Expert Protein Analysis System) servers that are a central resource for proteomics tools and databases. PIR, hosted by the National Biomedical Research Foundation (NBRF) at the Geor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GenBank
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. It is produced and maintained by the National Center for Biotechnology Information (NCBI; a part of the National Institutes of Health in the United States) as part of the International Nucleotide Sequence Database Collaboration (INSDC). GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 500,000 formally described species. The database started in 1982 by Walter Goad and Los Alamos National Laboratory. GenBank has become an important database for research in biological fields and has grown in recent years at an exponential rate by doubling roughly every 18 months. Release 250.0, published in June 2022, contained over 17 trillion nucleotide bases in more than 2,45 billion sequences. GenBank is built by direct submissions from individual laboratories, as well as from bulk submis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OMIM
Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship. , approximately 9,000 of the over 25,000 entries in OMIM represented phenotypes; the rest represented genes, many of which were related to known phenotypes. Versions and history OMIM is the online continuation of Dr. Victor A. McKusick's ''Mendelian Inheritance in Man'' (MIM), which was published in 12 editions between 1966 and 1998.McKusick, V. A. ''Mendelian Inheritance in Man. Catalogs of Autosomal Dominant, Autosomal Recessive and X-Linked Phenotypes.'' Baltimore, MD: Johns Hopkins University Press, 1st ed, 1996; 2nd ed, 1969; 3rd ed, 1971; 4th ed, 1975; 5th ed, 1978; 6th ed, 1983; 7th ed, 1986; 8th ed, 1988; 9th ed, 1990; 10th ed, 1992. Nearly all of the 1,486 entries in the first edition of MIM discussed phenotypes. MIM/OMIM is produced and curated at the Johns Hopkins School of Medicine ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
