ENSEMBL SCHEMA PDF

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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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Stores data about the data in the current schema. The compressed string using Perl’s pack method consisting of a repeating triplet of elements: Foreign key references to the ditag table. This table contains the proteins corresponding to protein family relationship found. It is styled as an attrib table to allow for a variety of fields to be populated across different object types. The compressed string using Perl’s pack method consisting of a repeating pair of elements: Name of the species set e.

An individual can have multiple samples. The list of reasons for a variation being flagged as failed is available in the Quality Control documentation. The number of samples the minor allele of this variant is found in. Class of the variation, key into the attrib table. Has a unique constraint on the first characters max allowed by MySQL.

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The scores are stored at different resolution levels. Uses Ensembl gene trees, gene data and xrefs extracted via the APIs. Follow us Blog Twitter Facebook.

Ensembl Core – Schema documentation

Stores data about the marker itself. Short name used for web purpose.

Stores map locations genetic, radiation hybrid and in situ hybridization for markers obtained from experimental evidence. This table stores information linking entities variants, genes, QTLs and phenotypes. The version number of achema previous stable ID specific to each stable ID; not to be confused with the release number. Follow us Blog Twitter Facebook.

Define the numeric zygosity of the structural variant for the sample, when ensemlb. Linking table to connect alignments to the reads that were aligned.

Installing the Ensembl Data

Taxonomy information, version information and the default value for the type column in the assembly table are stored here. Bos taurus Canis dnsembl 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.

Allows for storing multiple names for sequence regions. Whether there are SeqEdits that modify the protein sequence.

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. Brno nomenclature, Transcription Factor names etc.

Stores information about genes on haplotypes that may be orthologous.

Short name of the individual type. An internal description of the alignment.

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Installing the Ensembl Data

This table is only needed to create master schema when run healthcheck system. This table is optimised for retrieval from variation. Flag indicating if the structural variation is a supporting evidence 1 or not 0.

Shows the source enswmbl the projection key: Foreign key references to the source table. Foreign key references attrib table, describes the attribute. Groups together xref associations under a single description. Canis familiaris Drosophila melanogaster Gallus gallus Mus musculus Rattus norvegicus. The following query refers to the members of the protein family PTHR Represents a sequencing experiment.

Getting Genetics Done: Understanding the ENSEMBL Schema

Show columns [Back to top]. This document gives a high-level description of the tables that make up the Ensembl variation schema. Foreign key references to the transcript table.

Only data from resequenced samples are used for LD calculations are included in this table. Stores data about the external databases in which the objects described in the xref table are stored.

This table stores information about each of a variation’s alleles, along with population frequencies. List of the tables: Provides the evidence which we have used to declare an intronic region. Evidence tags unique key: This is a denormalised string taken from the alleles in the allele table associated with this variation.