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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Stores data about the data in the current schema. The type of condition this link occurs in e.
Ensembl Variation – Schema documentation
Foreign key references to the translation table. This table stores hierarchical relationships between populations by relating them as populations and sub-populations. The minor allele is the second most frequent allele. Unique, stable ID for the tree follows the pattern: This table stores cross-references for gene members derived from the core databases. When this happens, the exon coordinates don’t match the transcript sequence. Used to describe positions of markers on the assembly.
Projects using Ensembl
Show species Mus musculus. See the evidence descriptions here. Enables storage of attributes that relate to genes. A sample can belong only to one individual.
This table stores the read coverage of resequenced samples.
Describes type representing a density, or percentage coverage etc. Stores information about a population.
This table contains the sequences corresponding to every genomic homology relationship found. String representing the allele.
Installing the Ensembl Data
If, however, for reasons of space or maintainability, files are not located as described then check the ftp site for README files which should explain where the data can be found.
HGVS representation of this allele with respect to the [coding or non-coding] transcript.
This table contains the distribution of the gene order conservation scores. Enables storage of attributes that relate to DNA sequence alignments. The numeric identifier of the codon-table that applies to this dnafrag https: Follow us Blog Twitter Facebook.
Usually describes a program and some database that together are used to create a feature on a piece of sequence. These tables define the sample, individual and population information.
Transcript Consensus Web-based tool for visual comparison of alternative splicing isoforms Can draw from Ensembl annotation and sequence data OrthoMaM A database of alignments schemaa trees based on orthologous exons and CDSs for mammalian species. This mechanism has been implemented specifically to support haplotypes and PARs, but may be useful for other similar structures in svhema future. Object xref schma this associated xref is linked to.
Here is an example on how to get the taxonomic ID for a species: Collaborations Ensembl are active collaborators in a number of projects, contributing code, know-how and a platform from which to distribute data.
Ensembl Regulation (Funcgen) Schema Documentation
Groups together xref associations under a single description. Go to the appropriate release directory and then to ‘mysql’. Contains all the syntenic relationships found and the relative orientation of both syntenic regions. Canis familiaris Gallus gallus Mus musculus Rattus norvegicus. It is used by Bio:: Currently either “ensembl” or “ucsc” if data were imported from UCSC. This table maps probes to transcripts. This creates the schema for schdma empty database you created in step 3.
Show species Canis familiaris Gallus gallus Mus musculus Rattus norvegicus. This table contains descriptions of group submitting data to public repositories such as ClinVar.
Typically this contains how chromosomes are made of contigs, schdma out of contigs, and chromosomes out of supercontigs. Coordinate system this file is linked to. Foreign key to exon indicating the left hand flanking exon of wchema intron assume forward strand. The minor allele frequency is the frequency of the second most frequent allele. Xref which is source of this association. The relation defining the association between the ontology term and the phenotype.
This table stores hierarchical relationships between variation sets by relating them as variation sets and variation subsets. Only data from resequenced samples are nesembl for LD calculations are included in this table. This table stores miscellaneous attributes associated with a variation entry.
It usually represents the name of the project or subproject where a group of variations has been identified. It is used to store options on clades and group of species. The GEnetic Factors for OSteoporosis Consortium international collaboration that seeks to identify common risk gene variants for osteoporosis.
The unpacked genotypes field then may contain the following elements: Foreign key references to the xref table. Various member gene and proteins related information stored in the database, either loaded from Core databases or aggregated from Compara analyses. These genotypes are mapped to particular genomic locations rather than variation objects.