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 stores a variation’s name commonly an ID of the form e. The data have been compressed to reduce table size and increase the speed of the web code when retrieving strain slices and LD data.
Encoded representation of the genotype data: This table relates names to xref IDs. Some of these tables have been omitted from the schema diagram. Some contain extra fields or different enum values to support the funcgen schema.
Male Female Unknown ‘Unknown’ The sex of this individual. Allows for storage of arbitrary features. A set of clinical significance classes assigned to the ebsembl.
The table contains imports from externally curated resources e. A sample belongs to an individual. This table represents mappings of variations to genomic locations. Represents what happened to all gene, transcript and translation stable IDs during a mapping session.
The consequence s of the variant allele on this regulatory feature. Describes links between Ensembl objects and objects held in external databases. Used to describe positions of markers on the assembly.
Ensembl Regulation (Funcgen) Schema Documentation
The rank column indicates the 5′ to 3′ position of the exon within the transcript, i. This document gives a high-level description of the tables that make up the Ensembl variation schema. This document refers to version 91 of the Ensembl Regulation schema. The percentage of identity between the two members. Unique stable id of related transcript. Describes general genomic features that don’t fit into any of the more specific feature tables. We shall treat empty strings as NULLs.
Links intronic evidence to a pair of exons used within a transcript and to resolve the m: The numeric identifier of the codon-table that applies to this dnafrag https: 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 endembl regions of enesmbl human genome.
Allows transcripts to be related to genes.
User-contributed code Whilst we have developed a comprehensive Perl API in-house, we welcome contributions in other programming languages from the community. This table is optimised for retrieval from variation.
Installing the Ensembl Data
Foreign key references to the sample table. Ensembll species Mus musculus. This browser can be used to inspect the reference assemblies of human, mouse and zebrafish being created by the Scbema.
There are two genomic regions for every synteny relationship. List of the tables: May be 0 when the sequence is not available in the sequence table, e. Used mainly inside pipeline. Name of the collection this row of statistics refers to usual values are “ensembl”, “mouse”, etc.
Describes features on the translations as opposed to the DNA sequence itselfi. This table maps probe sets to transcripts.
Getting Genetics Done: Understanding the ENSEMBL Schema
Enables storage of attributes that relate to transcripts. Consortium or laboratory that produced sequencing experiments see experiment.
The FTP site will ideally be laid out as described. It contains the consequence of the allele. See below the query to display a subset of the attrib entries: Bos taurus Canis familiaris 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.
This table contains the coordinates and all the information needed to rebuild genomic alignments. This table defines the genomic sequences used in the comparative genomics analyisis.
Table that links a regulatory build to the epigenomes that were used in it. Groups together xref associations under a single description. 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. Foreign key references attrib table, describes the attribute.
Defines the individual or sample name. Short name of the individual type. This table contains the genomic regions corresponding to every synteny relationship found.
Enables storage of attributes that relate to translations. Foreign key to exon indicating the right hand flanking exon of the intron assume forward strand. Foreign key references to the transcript table.