26 research outputs found
Classification of Chemical Compounds to Support Complex Queries in a Pathway Database
Data quality in biological databases has become a topic of great discussion. To provide
high quality data and to deal with the vast amount of biochemical data, annotators
and curators need to be supported by software that carries out part of their work
in an (semi-) automatic manner. The detection of errors and inconsistencies is a part
that requires the knowledge of domain experts, thus in most cases it is done manually,
making it very expensive and time-consuming. This paper presents two tools to
partially support the curation of data on biochemical pathways. The tool enables the
automatic classification of chemical compounds based on their respective SMILES
strings. Such classification allows the querying and visualization of biochemical
reactions at different levels of abstraction, according to the level of detail at which the
reaction participants are described. Chemical compounds can be classified in a flexible
manner based on different criteria. The support of the process of data curation is
provided by facilitating the detection of compounds that are identified as different
but that are actually the same. This is also used to identify similar reactions and, in
turn, pathways
SABIO-RK: A data warehouse for biochemical reactions and their kinetics.
Systems biology is an emerging field that aims at obtaining a system-level understanding of biological processes. The modelling and simulation of networks of biochemical reactions have great and promising application potential but require reliable kinetic data. In order to support the systems biology community with such data we have developed SABIO-RK (System for the Analysis of Biochemical Pathways- Reaction Kinetics), a curated database with information about biochemical reactions and their kinetic properties, which allows researchers to obtain and compare kinetic data and to integrate them into models of biochemical networks. SABIO-RK is freely available for academic use a