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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Name of the species set e. Allows the storage of flat ensembk locations used to store large quanitities of data currently unsuitable in a traditional database table. Some ENSPs are associated with multiple closely related Swissprot entries which may both be associated with the same GO identifier but with different evidence tags. Used when more than one associated xref term must be used to describe a condition. This table contains details of the source from which a variation is derived.

Show columns [Back to top]. See below the command listing all the data sources in the human variation database: Table that links a regulatory build to the epigenomes that were used in it.

Homo sapiens Mus musculus. In peptide co-ordinates rather than contig co-ordinates. Transcript Consensus Web-based tool for visual comparison of alternative splicing isoforms Can draw from Ensembl annotation and sequence data OrthoMaM A database of alignments and trees based on orthologous exons and CDSs for mammalian species.


They are linked to primary external references instead. Text description, used in the z-menu that appears when hovering over the epigenome name.

Boolean value which defines whether this rank is used or not in the abbreviated lineage. See the explanation here. Represents what happened to all gene, transcript and translation stable IDs during a mapping session. Details of the “old” and “new” databases are stored. A small example, showing what it can do including coordinate transformation and reflecting on the types of associations for a given class can be found on the wiki page. The consequence s of the variant allele on this regulatory feature.

It has been initially developed for the gene tree view.

Ensembl Compara Schema Documentation

Stores the names of different genetic or radiation hybrid maps, for which there is marker map information. Foreign key, references to the phenotype table. List of the tables: This table stores the relationship between Ensembl’s internal coordinate system identifiers and traditional chromosome names.

In reality, however, we store this in the database like this: If set, this can be ‘genomic’ or ‘transcript’. Corresponds to original tag containing the full sequence. Some xref objects can be referred to by more than one name. A sample can be associated with a study. Describes sequence repeat regions.

Getting Genetics Done: Understanding the ENSEMBL Schema

This table stores the structure of the tree. Describes dependent external references which can’t be directly mapped to Ensembl entities. Length of the structural variant. This table stores information about structural variation.


Defines the zchema of structural variant. Further information about a group could be added here at a later date. Contains information defining an array or array set.

Used mainly inside pipeline. Hence the “biological roots” of the trees are the children nodes of the main clusterset root. Bos taurus Canis familiaris Danio rerio Drosophila melanogaster Equus caballus Gallus gallus Macaca mulatta Mus musculus Nomascus leucogenys Ornithorhynchus anatinus Ovis aries Pan troglodytes Pongo abelii Rattus norvegicus Saccharomyces cerevisiae Sus scrofa Taeniopygia guttata Tetraodon nigroviridis. This table contains descriptions of reasons for a variation being flagged as failed.

Variants from the Illumina Human v3. Several scores are stored per row.

Unlike other tables, data in the meta table is stored as key-value pairs. The data have been compressed to reduce table size and sxhema the speed of the web code when retrieving strain slices and LD data. We are working in getting IDs stable between releases. MySQL does not allow multiple autoincrement fields.

Each table file is gzipped so unpack the data into working directories, keeping separate directories for each database. Evidence tags unique key: Foreign key references to the allele table. Neanderthal Genome Browser Preliminary assembly of Homo sapiens neanderthalensis.