ENSEMBL SCHEMA PDF

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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Remember, you also need to download and install the multi-species databases. See the examples below. The complete list of variation sets with their descriptions is available here. The number of times that this variation has mapped to the genome.

Corresponds to original tag containing the full sequence. Defines the type of structural variant. This browser can be used to inspect the reference assemblies of human, mouse ensemhl zebrafish being created by the GRC. Stores information about genes on haplotypes that may be orthologous.

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Installing the Ensembl Data

Foreign key references to the exon table. Variants from the Illumina ImmunoChip genotyping array designed to target variants of interest for autoimmune and inflammatory diseases.

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If set, this can be ‘genomic’ or ‘transcript’. Used to store alternative names for samples when data comes from multiple sources. Shows the source of the projection key: Some contain extra fields or different enum values to support the funcgen schema. Represents a peak calling analysis. Unlike other tables, data in the meta table is stored as key-value pairs. This table stores the structure of the tree.

List of the tables: Variants from the Illumina Human1M-duo v3 whole genome genotyping array designed for association studies.

Installing the Ensembl Data

Stores data about the biotypes and mappings to Sequence Ontology. Describes where ditags hit on the genome. Stores translation alignments generated from Blast or Blast-like comparisons.

The consequence s of the variant allele on this regulatory feature. Anolis carolinensis Astyanax mexicanus Bos taurus Callithrix jacchus Canis familiaris Carlito syrichta Cavia porcellus Ciona intestinalis Ciona savignyi Danio rerio Dasypus novemcinctus Dipodomys ordii Echinops telfairi Equus caballus Erinaceus europaeus Felis catus Gallus gallus Gasterosteus aculeatus Gorilla gorilla Homo sapiens Ictidomys tridecemlineatus Latimeria chalumnae Loxodonta africana Macaca mulatta Meleagris gallopavo Microcebus murinus Monodelphis domestica Mus musculus Myotis lucifugus Nomascus leucogenys Ochotona princeps Enembl anatinus Oryctolagus cuniculus Oryzias latipes Otolemur garnettii Pan troglodytes Ennsembl anubis Poecilia formosa Pongo abelii Procavia capensis Pteropus vampyrus Rattus norvegicus Sorex araneus Sus scrofa Taeniopygia guttata Takifugu rubripes Tetraodon nigroviridis Tursiops truncatus Vicugna pacos Xenopus tropicalis Xiphophorus maculatus.

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Foreign key references to the source table. These genotypes are mapped directly to variation objects. Show species Homo sapiens Mus musculus Ovis aries.

The type of condition this link occurs in e. Foreign key references to the phenotype table. Foreign key, references to the phenotype table. Show species Mus musculus.

The relationship between contigs and clones is stored in the assembly table. It is used to store options on clades and group of species.

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Otter Database backend for interactive curation of annotation Otter is an extension of the Ensembl database schema Selectome Database of positive selection. Each row represents a component, e.

Describes which co-ordinate systems the different feature tables use.

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