Data and knowledge modeling: the key to integration
Genostar’s software is integrated. This means that the user can focus on the analysis process itself, rather than having to deal with the management of data between the many different methods for analysis, the visualizers and the data repositories.
The software efficiently and automatically handles data compliance, conversion and transfer. All the data are explicitly represented in an object-oriented model. Organisms, chromosomes, sequences, and sequence features such as CDS, signals, classification nodes, reactions, pathways, and so on are represented as objects. These objects are connected by relationships to form a large data web. For instance, a CDS is located on a sequence, is translated in a polypeptide, which is known to have an enzymatic activity and to catalyze a reaction that occurs in a metabolic pathway… These objects and relationships are created when data are read from files or produced by methods. For instance, when enzymatic activity is predicted for a polypeptide, a relationship is created between the polypeptide and one or several nodes of the EC classification.
Since the software recognizes methods as objects with typed input and ouput arguments, all necessary information is available for very thorough data checking and conversion. The software performs these tasks automatically.
The dataweb can be explored and queried. The user can either follow the links between the objects and thus discover their relationships, or express a query to retrieve all the objects which satisfy some constraints; for instance, all the metabolic reactions which are catalyzed by products of genes which have been identified to be specific to an organism. The most frequent queries are built in and can be easily run. The user can easily construct other queries, from simple to complex, with a graphical tool. These queries can then be saved for regular use.
Objects and relationships are mapped onto the tables that make up the structure of MicroB, so that their contents can be stored and integrated in this relational database, and retrieved as necessary.