The SABIO-Reaction Kinetics database (SABIO-RK) has as objective to provide data about the kinetics of biochemical reactions in different organisms, tissues and determined for or under diverse experimental conditions.The database builds on top of the database developed for the Mycoplasma pneumoniae database (http://sabio.eml.org/mycoplasma/testframe.html) concentrating mainly on the querying of reactions and their kinetic data. The database contains information about biochemical reactions, their compounds, their kinetics, and the pathways in which they participate. All this is related to information on enzymes, and organisms. The database allows the storage of multiple kinetic descriptions for the same reaction, according to factors such as the organism in which they were measured (or for which they were estimated), the environmental conditions under which the experiments were done, or even the experimental methods used.
The reactions included in the database have been mainly obtained from the KEGG (http://www.genome.jp/kegg/) database and from literature. Compounds in the database are classified based on functional groups, this allows the definition and querying of reactions at different levels of detail. For example one can query for a reaction having NTP as a substrate, which will result in querying for all reactions having ATP, UTP, GTP, etc. as a substrate.
TOPIn order to find a set of
reactions the user can specify the characteristics of the reaction(s)
searched.
These characteristics can comprise: the pathways in which the reaction
participates,
reactants of the reactions (substrates and products), organisms in
which the
reaction takes place, the enzyme classifications of the enzymes
catalysing the
reaction,
tissues and cellular locations in
which the reaction can take place, and publications in which kinetic data for
the reaction were reported (see figure 1). The user cn also specify the experimental
conditions (currently only pH and temperature) under which kinetic data has been reported.
The user can also choose to view only those results for which there is kinetic data associated with the
reactions found satisfying the search criteria, or leave this option out and view all reactions satisfaying the search criteria, even
if there is no kinetic data in the database associated some of these reactions.
To specify the search characteristics (apart from the experimental condition) the user must use the selection frames (clicking on the respective select link)
and select the elements desired.
From the list of reactions, the
user can
view the details of the reaction, by clicking on its respective
stochiometric
equation, mark the desired reactions in order to include them into an
SBML
file, or view the kinetic data associated with the reaction
or with its related enzyme(s) by cklicking on the respective
square.
The reactions details screen shows
apart from the reactants of the reaction, the enzymes that are known
(from literature data) to catalyse and in which organism, giving the
PubMedID associated with this information. A link to the
SwissProt/UnitPro database is also provided by using the enzyme
classification number and the organism name.
Figure 3.- Reaction details
By cliking in the results screen
the square (green or yellow) associated with a reaction, the system
will present all the kinetic data available for the given reaction,
presenting first the information matching the criteria defined
(organism, tissue/cell type, cellular location and experimental
conditions). First a summary view will be presented, which can be
expanded completely , showing the details of all the entries, or
partially, only expanding selected entries.
Figure 5.- Kinetic
data entry
