GenDBWiki/DataModel

The GenDB Data Model

Gen``DB is based on a data model with three core types of objects. Regions describe arbitrary (sub-) sequences. A region can be related to a parent region, e.g. a CDS is part of a contig. Observations correspond to information computed by various tools (e.g. Blast or Inter``Pro) for those regions. Annotations store the interpretation of a (human) annotator. They describe regions based on the evidence stored in the observations.

attachment:GenDB-UML-DataModel.jpg

The figure shown above illustrates the relationships between the different core objects. As can be seen, there is a clear distinction between the results from various bioinformatics tools (observations) and their interpretation (annotations) which was implemented in the data model. While this data model seems very generic, it represents a hierarchy of classes, including the complete EM``BL feature set for prokaryotes with several extensions as illustrated in the figure below.

attachment:GenDB-Regions.jpg

to be continued ...