PhenCode: Example of adding a new data source

In order to load the data into the Locus Variants track, it must be rearranged into tab-delimited files that match the track's table schema, with one file for each table.

• The main base table is called gv ("genome variation"). It contains one entry (row) for each mutation. Each mutation needs a unique identifier, which is created by concatenating the abbreviation for the database with the database's unique identifier for the mutation. If the database does not have unique identifiers for its mutations, then the HGVS-style names are used.

• The gvPos[Build] table stores the position fields that place each mutation onto the track. If the data is to appear on the Genome Browser for several assemblies (genome builds), then there will be a version of this table for each one, since the coordinates will likely be different.

• The gvLink table contains values for building links back to the data source and to other databases if available. The template describing how to build the links is stored in a flat file (links.ra) in the UCSC source code tree.

• The gvSrc table contains the full name of the data source, and also distinguishes between LSDBs and genome-wide data sets.

• The gvAttr table stores all the other data that is displayed on the details page for each mutation. This also opens up opportunities for querying across multiple data sources simultaneously, by using common attributes stored here. The attrType field is used to group similar types of data and to control how the attribute is displayed on the details page.

• The linkBuilder table stores the information on the base URL and information needed to generate links back to the LSDBs or other relevent data.
• The srcDetails table stores the details about the source such as the logo and names for credits.
• The gvAttributes table stores the categories, display order, and other information on how to display the attributes.

The precise schema definitions for these tables can be viewed here.

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