This document describes the tables that make up the Ensembl Regulation schema. Tables are grouped logically by their function, and the purpose of each table. Web front-end derived from Ensembl webcode, Ensembl schema databases. WormBase Parasite, Website presenting draft genome sequences for helminths. This creates the schema for the empty database you created in step 3. Note that we are using the example MySQL settings of /data/mysql as the install directory.

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The hits are actually stored in species-specific tables rather than in a single table. These have been omitted from the schema diagram.

Foreign key linked to the xref table. The goal of the NHLBI GO Exome Sequencing Project is to discover novel genes and mechanisms contributing to heart, lung and blood disorders by sequencing the protein coding regions of the human genome.

Show species Saccharomyces cerevisiae. This is a denormalisation as this particular feature is one example of a mapped location.

Primary key of linked entity e. Follow us Blog Twitter Facebook.


Show species Danio rerio Homo sapiens Mus musculus. A compressed binary string containing data relevant to the quality of the predictions. When this happens, the exon coordinates don’t match the transcript sequence. You can see the complete list, by species, here. Bos taurus Canis familiaris Capra hircus Danio rerio Drosophila melanogaster Equus caballus Gallus gallus Homo sapiens Macaca mulatta Monodelphis domestica Mus musculus Nomascus leucogenys Ornithorhynchus anatinus Ovis aries Pan troglodytes Pongo abelii Rattus norvegicus Saccharomyces cerevisiae Sus scrofa Taeniopygia guttata Tetraodon nigroviridis.

This can be used to limit the the features that come back from a query. The number of times that this variation has mapped to the genome.

Projects using Ensembl

Stores information about a population. We shall treat empty strings as NULLs. In reality, however, we store this in the database like this: Used to decipher the assembly version it was mapped to.

This table is optimised for retrieval from variation.

Homo sapiens Mus musculus. This table acts as a flag for such failures.

Schema Documentation

A set of clinical significance classes assigned to the variant. These data include details about the database, RegulatoryBuild and patches. This table associates extra associated annotations with a given ontology xref evidence and source under a specific condition. Stores data about the data in the current schema.


The list of consequence descriptions is available here. Whether there are SeqEdits that modify the transcript sequence. Used for the variants with a class “insertion”, when the size of the insertion is known.

This table stores the structure of the tree. This query defines which API version must be used to access this database. Unlike other tables, data in the meta table is stored as key-value pairs. Stores information about an identifiable individual, including gender and the identifiers of the individual’s parents if known.

This is set to 1 if the variant is flipped from the negative to the positive strand during import.

Ensembl Regulation (Funcgen) Schema Documentation

Not currently used for efg. Follow us Blog Twitter Facebook. Show species Homo sapiens Mus musculus Ovis aries. This table holds uncompressed genotypes for given variations.