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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This table is used to index tree alignments, e. The version number of the previous stable ID specific to each stable ID; not to be confused with the release number. This table contains information about the version of the genome assemblies used in this database. This table stores information linking entities variants, genes, QTLs and phenotypes. The tree required to index these sequences is stored in this table. Used mainly inside pipeline.
Foreign key linked to the xref table. Canis familiaris Gallus gallus Mus musculus Rattus norvegicus. 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.
The type of condition this link occurs in e. Length of the structural variant. This table stores genotypes and frequencies for variations in given populations.
MySQL does not allow multiple autoincrement fields. Danio rerio Homo sapiens Mus musculus.
Projects using Ensembl
It has been initially developed for the gene tree view. Some xref objects can be referred to by more than one name. Xref which is source of this association. This includes which IDs where deleted, created and related to each other. This table stores sample and strain information for structural variants and their supporting evidences. See below the list of the descriptions available in the Ensembl variation databases: This table contains all the group homologies found.
Maps a hex MD5 hash of a translation sequence to an ID used for the protein function predictions.
The deviation from the score that is enswmbl from alignment software e. 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 table gives a detailed description for each of the possible individual types: InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences.
The code has been designed to be version-aware a single installation works against current and previous releases and is hosted, together with documentationexamples and contact information for the Roslin groupat SourceForge.
This table stores accessions of phenotype ontology terms which have been linked to phenotype. This is the name or identifier that is used for displaying the feature. Represents a sequencing experiment. It contains the consequence of the allele e. This allows the user to also access the tree alignments as normal multiple alignments.
Projects using Ensembl
Alternatively there are CAGE tags e. These are almost exact clones of the corresponding core schema tables. Web tool to show the presence or absence of certain genes or proteins in a set of eukaryote species.
List of the tables: Variants from the Illumina Human v3. 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.
Foreign key references to the translation table. This table acts as a flag for such failures. GenomicAlignBlock is visible when you have more than 1 block covering the same region. Unique, stable ID for the tree follows the pattern: Define the numeric zygosity of the structural variant for the sample, when available.
This table contains the distribution of the gene order conservation scores. List of species with populated data: A set of clinical significance classes assigned to the structural variant. This creates the schema for the empty database you created in step 3.
Xref which is source of this association. Male Female Unknown ‘Unknown’ The sex of this individual.
Ensembl Variation – Schema documentation
The relationships between contigs and chromosomes, and between contigs and supercontigs, are stored in the assembly table. Tables are listed grouped in different categories, and the purpose of each table is explained.
Foreign key references to the population table. Source of the data. Describes features representing a density, or precentage coverage etc.