chemistry

SABIO-Reaction Kinetics Database

SABIO-Reaction Kinetics Database is a chemistry topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand SABIO-Reaction Kinetics Database rather than just read about it. In short: SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-accessible database 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.

Key takeaways

SABIO-Reaction Kinetics Database belongs to chemistry; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect SABIO-Reaction Kinetics Database to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of SABIO-Reaction Kinetics Database from memory before moving on to harder problems.

Reference excerpt

SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-accessible database 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 equations, 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 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 details (e.g. EC enzyme classification, protein complex composition, wild type / mutant information), kinetic parameters together with corresponding rate equation, biological sources (organism, tissue, cellular location), environmental conditions (pH, temperature, buffer) and reference details. Data are adapted, normalized and annotated to controlled vocabularies, ontologies and external data sources including KEGG, UniProt, ChEBI, PubChem, NCBI, Reactome, BRENDA, MetaCyc, BioModels, and PubMed. 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 make use of SABIO-RK biochemical reaction data by integration into their framework including SYCAMORE, MeMo-RK, CellDesigner, PeroxisomeDB, Taverna workflows or tools like KineticsWizard software for data capture and analysis. Additionally, SABIO-RK is part of MIRIAM registry, a set of guidelines for the annotation and curation of computational models

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 RESTful-based web services for programmatic access Result data sets can be exported in different formats including SBML, BioPAX/SBPAX, and table format.

References

External References SABIO-RK homepage

Illustrations

Worked examples

Example 1 — a first encounter with SABIO-Reaction Kinetics Database

Start with the simplest possible case. Write down what SABIO-Reaction Kinetics Database claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In chemistry, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to SABIO-Reaction Kinetics Database before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about SABIO-Reaction Kinetics Database ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of SABIO-Reaction Kinetics Database

In research: SABIO-Reaction Kinetics Database appears in chemistry research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses SABIO-Reaction Kinetics Database in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: SABIO-Reaction Kinetics Database is common in secondary-school and first-year university syllabi. It links to neighbouring topics Biochemistry databases, so understanding it makes those chapters shorter.
In everyday life: Look for SABIO-Reaction Kinetics Database outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study SABIO-Reaction Kinetics Database in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what SABIO-Reaction Kinetics Database means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
Explain SABIO-Reaction Kinetics Database out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is SABIO-Reaction Kinetics Database in simple terms?

Why does SABIO-Reaction Kinetics Database matter?

Because it connects several chemistry ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study SABIO-Reaction Kinetics Database?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on SABIO-Reaction Kinetics Database.