The System for the Analysis of Biochemical Pathways-Reaction Kinetics (SABIO-RK) like other databases such as BIND is used to represent data describing biochemical reactions and pathways. It is a web –based database accessed in net enabled servers. It is mainly used by modelers and wet-lab scientists to get detailed facts through integration of data from various origins. It differs from many biochemical databases as it entails Reaction Kinetics which represents the kinetic data acquired after a series of experiments. Parameters are also included with a list of conditions from which these parameters were measured. It also provides analytical essays which describes the parameters and the results (Krebs et al, 2007).
Funahash et al (2007) observe that SABIO-RK data model is used to store and represent information concerning the biochemical reactions of molecules, their kinetic equations and their parameters. The stored data are different but conceptually similar. The database is divided into two; the SABIO and RK. SABIO is used to represent data associated with biochemical reactions and pathways. This component shows detailed features of reaction equations together with associated molecules and it is able to store information about genes and proteins applied in the database’ user interface. While on other hand, RK, Reaction Kinematics extends the features of SABIO by representing the most related information on kinetics of biochemical reactions which are solely obtained through experiments. Mathematical formulas are mainly stored here with parameters such as PH, temperature changes, and molarities of reactants among others.
The objective of this model is to give support to scientists engaged in modeling of biochemical networks. The model derives its data from stored reaction results, their associations with pathways and enzymatic classes retrieved from other publicly available biological databases such as Kyoto Encyclopedia of Genes and Genomes (KEGG). It can also offer data extracted manually from publications and literature. Facts on kinetics are presented in relation with reactions, living organisms, organs, tissues or even cellular positions (Wittig, 2009).
Kinetic reactions constitute a greater percentage in SABIO-RK data model as the kinetic mechanisms and their corresponding rates of reactions are depicted alongside parameters and conditions under which the laboratories analyses were done (Rohwer, 2007). Likewise, data is represented in form of graphs which shows mechanisms and single stepwise reactions represented together with their relevant kinetic data. The models are presented with simulated Biomodels which provide links to the original sources and the created database which contain comprehensive information about such reactions, their rates, laws and the parameters.
SABO-RK is a suitable information system to store, distribute and provide better management of data and facts relating or about biochemical reactions and their associated kinetic properties. It can easily and efficiently used by researchers to obtain and carry out comparison on kinetic data. It is the only known system which can be used to integrate data into models of biochemical networks (Swainston, 2009).
The database is also highly recognized as being professional. The reason behind these attributes is because the integrated data is curated by biological experts, annotated by controlled vocabularies and is made consistent by avoiding too much verbosity and redundancy. SABIO-RK obtains its data from multiple sources hence it is enrich with information
SABIO-KR is known to provide models simulating biochemical reactions with their parameters but it is criticized for failing to provide documentation on the environmental conditions subjected to model for them to hold. This is attributed to insufficiency of relevant information in the literal publications and the publicly available biochemical databases. Researcher can overcome this weakness by ensuring a total comparison and combination of facts retrieved from experimental and model databases. This is implemented by successfully naming and relating data to traditional ontology, common vocabularies and the external databases (Wittig, 2009).
Krebs et al (2007), state that like other biological databases, SABIO-RK provides user interfaces where the user can interact with it. It uses scientific principles and formulas, professional terms like other databases. The only difference is its incorporated knowledge of kinetics of biochemical reactions.
Having studied the two databases in relation with the other biological databases, it is worth noting that they rely on information obtained from traditional literature. Therefore, any research and studies using these databases should go hand in hand with information found in literature and publications. it also recommendable that any successful study using these databases should try as much as possible to merge most if not all of them.