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Description

This page describes the relational database models used in the BioQ database documentation tools.

Contents

db_doc_model.mwb

A MySQL Workbench file containing the schema and ER diagrams. The diagrams below were taken directly from this file.

The core model

This entity-relationship (ER) diagram shows the core relational model for our database documentation (from subversion revision 70).

The BERT model

Our Biologic-Experiment-Results (BERT) relational model (from subversion revision 70).

The queries model

Our model for storing queries in the documentation database.  This information is used to populate the BioQ queries for each database.



The BioQ documentation database

The BioQ::Documentation (dbDoc) features, which allow investigators to browse genomic database documentation, are based on a single MySQL database (TODO: specify PHP variable name).  The current documentation database is bioq_dbdoc_1. Some ER diagrams for specific models in the database are shown above.

dbDoc Tables

db, tbl and col

These provide descriptions of database, tables and columns, respectively, in the BioQ genomic databases.

db_refs, tbl_refs and col_refs

Bibliographic references.

Web links.

To do: we should rename this to db_links, etc. They are probably not reference in code very much, if at all. See http://deku.psych.wucon.wustl.edu:8081/browse/BIOQ-21.

flow_group

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

The tables in a flow group.

flow_group_tags

Tags that describe a flow group. These are not the same as filters.

process

A process in the BERT model.

process_flow_group

A group of tables, columns and/or databases which are input/output for a process or experiment in the BERT model. It's possible to have multiple groups with the same name for different processes. Each process must have a group and groups may be singletons.



process_tags

Tags that describe a process. These can also be used as filters. No entries as of version 70.

query

A query used in the BioQ web application.



query_column

This is used in Process.pm to look up information about columns being queried.

It's actually not clear what the purpose of query_column is. Need to make sure this is actually being used, and for what.

reference

Reference table showing things like Subversion revision number.

relationships

For recording and describing relationships between tables in genomic databases. No entries as of version 70.

results_tables

For each table with table_type='result', determine if it can be traced to subjects and/or biologics.

search_terms

Items used in the the dbDoc autocomplete search tool.

Need to improve how this table is populated. See http://deku.psych.wucon.wustl.edu:8081/browse/BIOQ-18.

tags

Tags are used to group tables into categories. The 'tags' table contains names and descriptions of the tags.

tbl_tags

This records which tags go with which tables.

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