ENSEMBL SCHEMA PDF

Use the search box at the top right of all Ensembl views to search for a gene, phenotype, sequence variant, and more. Touch the left menu icon or swipe right to open the side menu and touch anywhere outside the menu or touch the cross icon or swipe left to close. 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 is explained. This document refers to version 91 of the Ensembl Regulation schema. The table contains the features resulting from the regulatory build process.

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Use the search box at the top right of all Ensembl views to search for a gene, phenotype, sequence variant, and more. Touch the left menu icon or swipe right to open the side menu and touch anywhere outside the menu or touch the cross icon or swipe left to close. This document gives a high-level description of the tables that make up the Ensembl variation schema.

Tables are listed by alphabetical order, and the purpose of each table is explained. It is intended to allow people to familiarise themselves with the schema when encountering it for the first time, or when they need to use some tables that they've not used before.

This document refers to version of the Ensembl variation schema. List of species with populated data: Show species. Defines the set of possible attribute types used in the attrib table. The list of reasons for a variation being flagged as failed is available in the Quality Control documentation.

This table contains descriptions of reasons for a variation being flagged as failed. For various reasons it may be necessary to store information about a structural variation that has failed quality checks mappings in the Structural Variation pipeline.

This table acts as a flag for such failures. For various reasons it may be necessary to store information about a variation that has failed quality checks in the Variation pipeline. For various reasons it may be necessary to store information about a variation feature that has failed quality checks.

These tables define the genotype data at the sample and population levels. This table holds genotypes compressed using the pack method in Perl.

These genotypes are mapped to particular genomic locations rather than variation objects. The data have been compressed to reduce table size and increase the speed of the web code when retrieving strain slices and LD data.

Only data from resequenced samples are used for LD calculations are included in this table. These genotypes are mapped directly to variation objects. The data have been compressed to reduce table size. This table is optimised for retrieval from variation. This table stores genotypes and frequencies for variations in given populations.

This table stores the read coverage of resequenced samples. Each row contains sample ID, chromosomal coordinates and a read coverage level. This table is only needed to create master schema when run healthcheck system. Needed for other species, but human, so keep it. This table stores various metadata relating to the database, generally used by the Ensembl web code. This table gives the coordinate system used by various tables in the database.

These tables define the other data associated with a variation. This table stores the relationship between the internal allele identifiers and the alleles themselves. This table stores the relationship between Ensembl's internal coordinate system identifiers and traditional chromosome names.

These tables store information linking entities variants, genes, QTLs with phenotypes and other annotations. This table stores information linking entities variants, genes, QTLs and phenotypes. It is styled as an attrib table to allow for a variety of fields to be populated across different object types.

This table stores accessions of phenotype ontology terms which have been linked to phenotype. Contains encoded protein function predictions for every protein-coding transcript in this species. Contains information on the data use in protein function predictions. Maps a hex MD5 hash of a translation sequence to an ID used for the protein function predictions. These tables define the sample, individual and population information. Used to store groups of populations displayed separately on the Population Genetics page.

Stores information about an identifiable individual, including gender and the identifiers of the individual's parents if known. Used to store alternative names for individuals when data comes from multiple sources. Stores information about a population. A population may be an ethnic group e. Caucasian, Hispanic , assay group e. This table stores hierarchical relationships between populations by relating them as populations and sub-populations. Used to store alternative names for populations when data comes from multiple sources.

Stores information about a sample. A sample belongs to an individual. An individual can have multiple samples. A sample can belong only to one individual. A sample can be associated with a study. This table resolves the many-to-many relationship between the sample and population tables; i. Hence it is composed of rows of sample and population identifiers. Used to store alternative names for samples when data comes from multiple sources. These tables define the variation source and study information.

This table contains identifiers of associated studies e. This table contains details of publications citing variations. This table contains details of the source from which a variation is derived. You can see the complete list, by species, here.

This table contains details of the studies. This table contains descriptions of group submitting data to public repositories such as ClinVar. This table stores the associations between structural variations and their supporting evidences. This table stores information about structural variation features i. This table stores sample and strain information for structural variants and their supporting evidences.

These tables define the variation effect prediction data in different Ensembl features. It contains the consequence of the allele. It contains the consequence of the allele e. This table is used in web index creation. These tables define the variation and structural variation set data. The complete list of variation sets with their descriptions is available here.

This table contains the name of sets and subsets of variations stored in the database. It usually represents the name of the project or subproject where a group of variations has been identified.

This table stores hierarchical relationships between variation sets by relating them as variation sets and variation subsets. This table stores information about each of a variation's alleles, along with population frequencies. This table allows for the allele of a variant to have multiple IDs. This is the schema's generic representation of a variation, defined as a genetic feature that varies between individuals of the same species. The most common type is the single nucleotide variation SNP though the schema also accommodates copy number variations CNVs and structural variations SVs.

In 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. This table stores a variation's name commonly an ID of the form e. This table stores miscellaneous attributes associated with a variation entry. This table represents mappings of variations to genomic locations. It stores an allele string representing the different possible alleles that are found at that locus e.

It also acts as part of the relationship between variations and transcripts. This table allows for a variation to have multiple IDs, generally given by multiple sources. Search terms. Mouse Mus musculus. Ensembl Variation - Schema documentation This document gives a high-level description of the tables that make up the Ensembl variation schema. The variation database schema diagram PDF format is available here:. Show columns [Back to top].

Show query results. Homo sapiens. For example, a given row may have a start position of , indicating the chromosomal position of the first genotype in this row. The third genotype similarly has a position of , and so on.

Canis lupus familiaris Gallus gallus Mus musculus Rattus norvegicus. This table holds uncompressed genotypes for given variations. Foreign key references to the variation table. Bos taurus Gallus gallus Macaca mulatta Mus musculus Rattus norvegicus.

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Use the search box at the top right of all Ensembl views to search for a gene, phenotype, sequence variant, and more. Touch the left menu icon or swipe right to open the side menu and touch anywhere outside the menu or touch the cross icon or swipe left to close. The Ensembl project is both a source of genome sequence related data and an open source software system that can be used to organise any such data. Ensembl are active collaborators in a number of projects, contributing code, know-how and a platform from which to distribute data. Our open access data and open source code mean that many projects are able to make use of Ensembl data and software without our active involvement. We're happy to list those we know about here, but if your project is e!

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Use the search box at the top right of all Ensembl views to search for a gene, phenotype, sequence variant, and more. Touch the left menu icon or swipe right to open the side menu and touch anywhere outside the menu or touch the cross icon or swipe left to close. This document describes the tables that make up the Ensembl Compara schema. Tables are listed grouped in different categories, and the purpose of each table is explained. Several examples are also given. They are intended to allow people to familiarise themselves with the schema.

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MySQL databases are also used by the BioMart data warehouse interface, although we recommend that you use the web interface to access data in BioMart, as the mart schema contains many tables of denormalised data. Ensembl Genomes operates a MySQL server for public use which contains all databases from the last 10 Ensembl Genomes releases, including those used for the BioMart interface. This server can be used in conjuction with the Ensembl public MySQL servers though Ensembl Genomes do not currently offer any mirror servers. Details of Ensembl and Ensembl Genomes servers are shown below, and all servers can be accessed using the user 'anonymous' no password required :. Ensembl Genomes databases from all five divisions are located on the same server. Ensembl BioMart is on a different server.

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