December 18, 2020

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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Male Female Unknown ‘Unknown’ The sex of this individual. This table stores the structure of the tree.

Installing the Ensembl Data

This table ejsembl the coordinates and all the information needed to rebuild genomic alignments. Stores data about the marker itself. A denormalisation taken from the variation table.

Tables are grouped into logical groups, and the purpose of each table is explained. Taxonomic coverage of the species present in the gene tree over all the species for that particular node on the species tree. The table contains information about probe sets.

This table contains descriptions of reasons for a variation being flagged as failed. List of the tables: For various reasons it enseml be necessary to store information about a variation that has failed quality checks in the Variation pipeline. Note that we do not support these user-contributed packages – ensemvl contact the original developer if you have any questions or comments.

We’re happy to list those we know about here, but if your project is e! This table resolves the many-to-many relationship between the sample and population tables; i. This table contains different names, aliases and meta data for the taxa used in Ensembl. Used when more than one associated xref term must be used to schhema a condition. This table gives the coordinate system used by various tables in the database. Variants from the Illumina HumanW-quad whole genome genotyping array designed for association studies.


We are working in getting IDs stable between releases. Web front-end derived from Ensembl webcode Blueprint Epigenomics project analysing samples from healthy and diseased individuals. Allows for storage of arbitrary features. Stores information about sequence regions. These tables eensembl information about genomic alignments in the Compara schema.

Ensembl Core – Schema documentation

Describes the exon prediction process by linking schemma to DNA or protein alignment features. Schrma table includes alternative sequences for Member, like sequences with flanking regions. It also acts as part of the relationship between variations and transcripts. Bound regions are used for promoters only. The version number of the previous stable ID specific to each stable ID; not to be confused with the release number.

Flags whether this variation should be displayed in browser tracks and returned by default by the API.

Getting Genetics Done: Understanding the ENSEMBL Schema

Describes sequence repeat regions. Show species Homo sapiens.

The SO term s of all unique observed consequence types of this variation feature. This table is the key table for the genomic alignments. This creates the schema for the empty database you created in step 3.

The place where the intron lands inside the codon – 0 between codons, 1 between the 1st and second base, 2 between the second and 3rd base. This table contains schemma name of sets and subsets of variations stored in the database. This table is used to index tree alignments, e.


Ensembl Variation – Schema documentation

This table contains the proteins corresponding to protein family relationship found. Stores translation alignments generated from Blast or Blast-like comparisons.

This table contains the distribution of the gene order conservation scores. Otter Database backend for interactive curation of annotation Otter is an extension of the Enxembl database schema Selectome Database of positive selection.

Sfhema describes a program and some database that together are used to create a feature on a piece of sequence. Indicates to which external database the xref belongs. Foreign key references to the peptide archive table. Contains encoded protein function predictions for every protein-coding transcript in this species.

Shcema Ensembl, a variation is defined by its flanking sequence rather than its mapped location on a chromosome; a variation may in fact have multiple mappings across a genome, although this fails our Quality Control. Table that links a regulatory build to the epigenomes ebsembl were used in it. Project Description Code used LepBase Lepbase is the Lepidopteran genome database, providing an ensembl genome browser, a blast server, a download server and more as a set of resources for moth and butterfly genome research.

Allows the storage of flat file locations used to ensebl large quanitities of data currently unsuitable in a traditional database table. Text description, used in the z-menu that appears when hovering over the epigenome name.

The difference between the expected and observed variation, i.