AMBOS is based on the methods and software developed under the ELSA project. It focuses on the development of methods and applications to support the integration and analysis of biochemical data. As ELSA it is aimed at data related to biochemical reactions; however the models and applications have been extended to support data related to regulation networks, experiments and general information related to simulation models for biochemical reactions.
Within the AMBOS project we have the following sub-projects:
- Expansion of the SABIO database: the SABIO database (core database of the ELSA project) is been extended to support the storage of data related to simulation of biochemical networks and wet-lab experiments. The extension of the database will allow, for example, a biochemical network modeller to query for reactions with certain characteristics (e.g. participating compounds, within a given pathways, catalysed by a certain enzyme, etc.) and to obtain experimental or simulation results that can be the basis for the definition of the parameters of his or her model.
- BioBrowser : A set of tools developed to query the SABIO database have been integrated into a Java-based platform termed Biobrowser. The current version of BiobBrowser runs as a client-server application and is currently in beta-testing. We are also developing a web-based access to the database, with a limited number of querying facilities. The ides of BioBrowser is that users can have the database on his or her own server and use it as a workbench for their data.
- Development of biological Ontologies: The development of biological ontologies is a core component of the groups activities. We are currently working on an ontology for protein interactions and of biochemical compounds. This last mainly as a taxonomy of biochemical compounds classified based on their functional groups and on the other hand on their biological functions. The classification criteria a made explicit within the ontology. The development of ontologies also plays an important role in the group’s activities in Information Extraction from Text (Genie).
