SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-accessible

database In computing, a database is an organized collection of data stored and accessed electronically. Small databases can be stored on a file system, while large databases are hosted on computer clusters or cloud storage. The design of databases sp ...

storing information about biochemical

reactions Reaction may refer to a process or to a response to an action, event, or exposure: Physics and chemistry *Chemical reaction *Nuclear reaction *Reaction (physics), as defined by Newton's third law *Chain reaction (disambiguation). Biology and me ...

and their

kinetic Kinetic (Ancient Greek: κίνησις “kinesis”, movement or to move) may refer to: * Kinetic theory of gases, Kinetic theory, describing a gas as particles in random motion * Kinetic energy, the energy of an object that it possesses due to i ...

properties. SABIO-RK comprises a reaction-oriented representation of quantitative information on reaction dynamics based on a given selected publication. This comprises all available kinetic parameters together with their corresponding

rate equation In chemistry, the rate law or rate equation for a reaction is an equation that links the initial or forward reaction rate with the concentrations or pressures of the reactants and constant parameters (normally rate coefficients and partial reacti ...

s, as well as kinetic law and parameter types and experimental and environmental conditions under which the kinetic data were determined. Additionally, SABIO-RK contains information about the underlying biochemical reactions and pathways including their reaction participants,

cellular Cellular may refer to: *Cellular automaton, a model in discrete mathematics * Cell biology, the evaluation of cells work and more * ''Cellular'' (film), a 2004 movie *Cellular frequencies, assigned to networks operating in cellular RF bands *Cell ...

location and detailed information about the

enzymes Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different molecule ...

catalysing the reactions.

SABIO-RK Database Content

The data stored in SABIO-RK in a comprehensive manner is mainly extracted manually from literature. This includes reactions, their participants (substrates, products), modifiers ( inhibitors, activators,

cofactors Cofactor may also refer to: * Cofactor (biochemistry), a substance that needs to be present in addition to an enzyme for a certain reaction to be catalysed * A domain parameter in elliptic curve cryptography, defined as the ratio between the order ...

catalyst Catalysis () is the process of increasing the rate of a chemical reaction by adding a substance known as a catalyst (). Catalysts are not consumed in the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recyc ...

details (e.g. EC enzyme classification, protein complex composition,

wild type The wild type (WT) is the phenotype of the typical form of a species as it occurs in nature. Originally, the wild type was conceptualized as a product of the standard "normal" allele at a locus, in contrast to that produced by a non-standard, "m ...

mutant In biology, and especially in genetics, a mutant is an organism or a new genetic character arising or resulting from an instance of mutation, which is generally an alteration of the DNA sequence of the genome or chromosome of an organism. It ...

information), kinetic parameters together with corresponding rate equation, biological sources (

organism In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and ...

, tissue, cellular location), environmental conditions ( pH, temperature, buffer) and reference details. Data are adapted, normalized and annotated to controlled vocabularies,

ontologies 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 ...

and external data sources including

KEGG KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances. KEGG is utilized for bioinformatics research and education, including data analysis i ...

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 ...

ChEBI Chemical Entities of Biological Interest, also known as ChEBI, is a chemical database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies (OBO) effort at the European Bioinform ...

PubChem PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which is part of ...

NCBI The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The ...

Reactome Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome. It is au ...

BRENDA Brenda is a feminine given name in the English language. Origin The overall accepted origin for the female name Brenda is the Old Nordic male name ''Brandr'' meaning both ''torch'' and ''sword'': evidently the male name Brandr took root in areas ...

MetaCyc The MetaCyc database is one of the largest metabolic pathways and enzymes databases currently available. The data in the database is manually curated from the scientific literature, and covers all domains of life. MetaCyc has extensive information ...

BioModels BioModels is a free and open-source repository for storing, exchanging and retrieving quantitative models of biological interest created in 2006. All the models in the curated section of BioModels Database have been described in peer-reviewed scie ...

, and

PubMed PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintain the ...

.
As of October 2021 SABIO-RK contains about 71.000 curated single entries extracted from more than 7.300 publications.
Several tools, databases and workflows in

Systems Biology Systems biology is the computational modeling, computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological syst ...

make use of SABIO-RK biochemical reaction data by integration into their framework including SYCAMORE, MeMo-RK, CellDesigner, PeroxisomeDB,

Taverna A taverna (Greek: ταβέρνα) is a small Greek restaurant that serves Greek cuisine. The taverna is an integral part of Greek culture and has become familiar to people from other countries who visit Greece, as well as through the establishmen ...

workflows or tools like KineticsWizard software for data capture and analysis. Additionally, SABIO-RK is part of

MIRIAM Miriam ( he, מִרְיָם ''Mīryām'', lit. 'Rebellion') is described in the Hebrew Bible as the daughter of Amram and Jochebed, and the older sister of Moses and Aaron. She was a prophetess and first appears in the Book of Exodus. The Tor ...

registry, a set of guidelines for the annotation and curation of

computational models A computational model uses computer programs to simulate and study complex systems using an algorithmic or mechanistic approach and is widely used in a diverse range of fields spanning from physics, chemistry and biology to economics, psychology, ...

SABIO-RK as part of MIRIAM Registry
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SABIO-RK Database Access

The usage of SABIO-RK is free of charge. Commercial users need a license. SABIO-RK offers several ways for data access: * a browser-based interface *

REST Rest or REST may refer to: Relief from activity * Sleep ** Bed rest * Kneeling * Lying (position) * Sitting * Squatting position Structural support * Structural support ** Rest (cue sports) ** Armrest ** Headrest ** Footrest Arts and entert ...

ful-based web services for programmatic access Result data sets can be exported in different formats including

SBML The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of use ...

BioPAX BioPAX (Biological Pathway Exchange) is a RDF/OWL-based standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data. Pathway data captures our understanding of ...

SBPAX BioPAX (Biological Pathway Exchange) is a RDF/OWL-based standard language to represent biological pathways at the molecular and cellular level. Its major use is to facilitate the exchange of pathway data. Pathway data captures our understanding of ...

, and table format.

References

External References

SABIO-RK homepage
{{DEFAULTSORT:SABIO-RK Database Systems biology Biochemistry Molecular biology Proteins Biological databases