Biopath
The Biopath database is a collection of molecular pathways, manually annotated from original scientific publications and comprising biological models and diagrams. It is developed by the Institute of Systems Biology, LLC in Novosibirsk, Russia.
The main goals of the Biopath project are:
- to describe formally the structure and function of complex biological systems and processes on different logical levels in the form of a set of complementary diagrams;
- to provide a formal description of the main properties of biological entities (genes, proteins, substances, and chemical reactions) that are components of these processes;
- to give possibility to simulate dynamic behaviour of the processes or their parts;
- to provide the user with an interface for access to the Biopath database and enable users to edit the information via the Internet.
To achieve these goals the BioUML framework is used for formal description of the structure and function of complex biological systems and processes and for building dynamic models of the biological systems internal Java simulation engine. The platform provides possibility to visualize and browse the diagrams and models from the Biopath database.
Data collected in Biopath were compiled from literature annotation and were imported from SBML model repository and CellML model repository.
Currently, Biopath focuses on description of the following biological processes:
- regulation of eukaryotic cell cycle and cancer,
- NF-kappaB pathway,
- inflammation,
- oxidative stress,
- nucleosomal regulation of gene expression,
- arterial hypertension.
The database can be found in the repository pane with read access only. The Diagrams subdirectory currently contains 571 diagrams, of which only 50 items are shown at a time in the repository tree. To find a certain model you can either scroll down and subsequently expand the subdirectory by clicking on the Load next 50 icon (
) as necessary or just run a text search through the database.
Diagram elements in the repository pane contain their components listed underneath as nodes (
), edges (
),or compartments (
), for which additional information can be retrieved in the same way as for the whole diagram.
