SABIO-RK
Category Cross-Omics>Knowledge Bases/Databases/Tools and Cross-Omics>Pathway Analysis/Tools
Abstract The SABIO-RK (System for the Analysis of Biochemical Pathways - Reaction Kinetics) is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.
It aims to support modelers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics.
Information about reactions and their kinetics can be exported in the Systems Biology Mark-Up Language (SBML) format.
SABIO-RK User interface --
Users can access the SABIO-RK database by a web-based interface that allows the search for biochemical reactions and their kinetics by specifying characteristics of the reactions of interest (such as reactants, enzymes or pathways) as well as the kinetic data searched (e.g. from a particular tissue, determined under certain experimental conditions or having a certain parameter type).
All reactions matching the search criteria are shown. Details about the reactions, catalyzing enzymes and the corresponding kinetic data can be displayed upon selection.
Links to several external databases enable the user to gather further information about compounds, enzymes and reactions, and to refer to the original publications.
These links together with the use of synonymic notations for compounds and enzymes, as well as with the use of controlled vocabularies and ontologies, facilitate the comparison and integration of the data.
Data about biochemical reactions and their kinetics (including parameters with their respective rate equations) can be exported in SBML format, allowing its import into simulation and modeling programs supporting SBML.
The SABIO-RK Web Service(s) --
You can also access The SABIO-RK Database programmatically using web services.
The SABIO-RK Web Service provides customizable points of entry into the SABIO-RK system in a language independent fashion.
Using this Web service, users can write their own clients to customize and automate access to SABIO-RK directly from their simulation software, tools or databases, thereby negating the need to manually parse information from Web pages.
SABIO-RK Data Source(s) --
The database is populated by merging data from several sources. The general information about the reactions is mainly obtained from external databases such as KEGG (Kyoto Encyclopedia of Genes and Genomes).
In contrast, the kinetic data along with the descriptions of the experimental conditions under which they were determined are primarily manually extracted from literature and curated by a team of scientists.
This is supported by a tailored input interface that has been adapted to allow external users to directly submit their information and results from their experiments to SABIO-RK, avoiding the possible loss of information during publication and information extraction.
The interface employs controlled vocabularies and ontologies to avoid the introduction of errors and duplications through misspelling or variants in spellings.
Other problems faced in the population process are the identification and unambiguous description of compounds (identification of synonyms), enzymes and reactions, as well as missing specifications of experimental conditions or the multiplicity of parameter units.
SABIO-RK Main features/capabilities include:
1) SABIO-RK allows the querying for reactions:
- a) Within pathway(s);
- b) Having certain reactant(s);
- c) Classified with an EC Number;
- d) Reported to occur in organism(s) -- from curated data;
- e) Reported to occur in tissue(s)/cell type(s) -- from curated data;
- f) Reported to occur in a cellular location -- from curated data;
- g) Reported to occur at a certain temperature/pH -- from curated data;
- h) Reported about in a certain publication -- giving PubMed ID.
2) Link to Swissprot and PubMed.
3) Generation of SBML format file, containing information about the reactions, their kinetic laws (if existing) and parameter definition and values.
NOTE: The SBML file generated needs to be edited before it can be used by most modeling tools supporting SBML, given that the system will create as many unit definitions as defined for the parameters.
Thus the user needs to perform the unit conversion in order to have all parameter values defined using the same basic units.
The manufacturer plans to include information about 'in vivo' compound concentrations in the near future, which can then be included in the SBML file.
Currently all ‘compound concentrations’ will be set to 1.
System Requirements
Web-based.
Manufacturer
- Scientific Databases and Visualization Group
- EML Research gGmbH
- Schloss-Wolfsbrunnenweg 31C
- D-69118 Heidelberg
- Germany
- E-mail: sabiork@eml-r.org
Manufacturer Web Site SABIO-RK
Price Contact manufacturer.
G6G Abstract Number 20459
G6G Manufacturer Number 104087