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This entity-relationship (ER) diagram shows the core relational model for our database documentation (from subversion revision 70).
The biologic-experiment-result (BERT) relational model
Our BERT relational model is designed to document a genomic database by tracing the experimental source of the data. The key entities in the models are the biologics, the experiments and the experimental results as illustrated in the following diagram.
In the model, the tables in a relational database are grouped into flow groups that can input, output or reference material for the various experiments and processes that determined the data. Here is an example from our BioQ web application of the BERT model being applied to linkage disequilibrium (LD) data from the HapMap database. In BioQ, the diagram is interactive and can be used to navigate documentation and query the actual data.
The following ER diagram shows the relational database implementation of the BERT model (from subversion revision 70, see the MySQL Workbench file ).
The queries model
This is our model for storing queries in the documentation database. This information is used to populate the BioQ queries for each database.
The features model
This is our model for querying genomic features such as genomic regions, gene transcripts, SNPs and other genetic variants. The way features are specified may depend on the database. For example, genes have different IDs in the NCBI, HUGO and Ensembl databases.
Features are specified in BioQ using keywords, such as SNP_ID and GENE_ID. There are usually defaults, such as a numeric feature being assumed to be a dbSNP rs ID and a alphanumeric string assumed to be a HUGO gene symbol.
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In the BERT model, a flow group is a group of tables that can be input or output for a specific process.
flow_group_tables
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A process in the BERT model.
process_flow_group
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