Data Models

We believe that it is important to keep the databases mostly unaware in which format the data was originally stored. A reference to this format will only be stored for specific purposes involving file transfers.

Data model for variants and alignments have been designed and implemented in Java. They explicitly specify the most commonly used fields, and at the same time provide mechanisms for preserving all the information of a certain format. For instance, the fields specified for a variant would be (among others) chromosome, position, reference and alternatives; if a VCF file is being stored, then columns such as INFO are also saved in a key-value data structure.

Implementation

Different data models from related projects such as CellBase or Biodata are used in OpenCGA, others such as Catalog have been implemented specifically for OpenCGA, these are:

• OpenCGA Catalog: these models represent all information about users, studies, files and samples among others, you can find a more detailed information at Catalog data models
• OpenCB Biodata: these models have been implemented in the Biodata project. Please visit its wiki for more detailed information.