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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. 

Tables used for basic database documentation

db, tbl and col

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

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database_links, column_links, tbl_links

Web links.

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.

Tables related to the BERT model and experimental process flow

flow_group

In the BERT model, a flow group is a group of tables that can be input or output for a specific process.

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Tags that describe a process. These can also be used as filters. 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.

Tables related to BioQ queries

query

A query used in the BioQ web application.

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

Tables related to genomic features

When querying databases in BioQ you may limit the queries to certain genomic features such as regions, genes and specific genetic variants.  The way features are specified may depend on the database. For example, the same gene may have different IDs in the NCBI, HUGO and Ensembl databases.  BioQ allows you to specifiy genomic features in a variety of ways.  In some situations it will also add features automatically based on other features, such as finding all SNPs in a gene, and genes in a region, or all SNPs in a region. We are currently expanding this sytem to provider greater power in configuring how features are specified and how they relate to one another.

feat_keyword

A list of all the keywords and their aliases.

feat_table

The list of MySQL "feature tables" that contain feature data. 

Some example of feature tables:

• feat_dbsnp_snp: a list of SNPs in the dbSNP database. Some keywords used to populate this table are DBSNP_ID (single SNP) and REGION (all SNPs in a given genomic region)

feat_table_keyword

This describes how specific feature tables are built using keywords. The keyword/feature table association is very important. It represents a process used to populate a feature table from a feature query (a feature specified on the BioQ query page). The descriptions in this table describe this process.

feat_table_can_pop

This explains how feature tables relate and interact with other feature tables.  It contgains the other tables a feature table can populate.  For example, the feature table feat_region can populate the table feat_dbsnp_snp via the relationship of the coordinate of a SNP being with the boundaries of a genomic region.

query_feat_table_map

This explains how to use feature tables once they are created.  Specifically, it identifies the columns of a query that can be used to limit the query results by a feature table.  

Miscellaneous tables

reference

Reference table showing things like Subversion revision number.

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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.

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.

Updating the documentation schema

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