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 or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...

storing information about biochemical reactions and their kinetic 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 equation (also known as the rate law or empirical differential rate equation) is an Empirical relationship, empirical Differential equation, differential Expression (mathematics), mathematical expression for the reaction rat ...

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 location and detailed information about the

enzymes An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as pro ...

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),

catalyst Catalysis () is the increase in rate of a chemical reaction due to an added substance known as a catalyst (). Catalysts are not consumed by the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recycles quick ...

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, " ...

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 i ...

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

organism An organism is any life, living thing that functions as an individual. Such a definition raises more problems than it solves, not least because the concept of an individual is also difficult. Many criteria, few of them widely accepted, have be ...

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

ontologies In information science, an ontology encompasses a representation, formal naming, and definitions of the categories, properties, and relations between the concepts, data, or entities that pertain to one, many, or all domains of discourse. More ...

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 ...

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 fro ...

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 Bioinfor ...

PubChem PubChem is a database of Chemistry, 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 ...

NCBI The National Center for Biotechnology Information (NCBI) is part of the 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 NCBI is loca ...

Reactome Reactome is a free online database of biological pathways. It is manually curated and authored by PhD-level biologists, in collaboration with Reactome editorial staff. The content is cross-referenced to many bioinformatics databases. The rationale ...

, BRENDA,

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, and

PubMed PubMed is an openly accessible, free database which includes 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 Institute ...

.
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 system ...

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

Taverna A taverna (; ) 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 establishment of tavernes ...

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

MIRIAM Miriam (, 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 Torah refers to her as "Miria ...

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, engineering, chemistry and biology to economics ...

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 (Representational State Transfer) is a software architectural style that was created to describe the design and guide the development of the architecture for the World Wide Web. REST defines a set of constraints for how the architecture of ...

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 us ...

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, and table format.

References

External References

SABIO-RK homepage
{{DEFAULTSORT:SABIO-RK Database Biochemistry databases