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 examples shows how to get the lineage for Homo sapiens: This table gives the coordinate system used by various tables in the database.
Ensembl Core – Schema documentation
Typically this will be the stable id of the transcript or the name of the sequence region. Foreign key references to the phenotype table. This table resolves the many-to-many relationship between the sample and population tables; i.
Quantomics Large-scale project to analyse sequence and variation in livestock genomes. Extended cigar line format representation of the alignment as defined here http: Class of the variation, key into the attrib table. Show species Drosophila melanogaster Homo sapiens Mus musculus Rattus norvegicus. A set of clinical significance classes assigned to the structural variant.
Used to decipher the assembly version it was mapped to.
Always set to 1 in ensembl dbs, but needed for otterlace dbs. A sample can belong only to one individual. Foreign schsma to regulation databases.
The AMD Gene consortium is an international collaboration that seeks to identify genetic loci associated with age-related macular degeneration. Install this if you want local GO information. If set, this can be ‘genomic’ or ‘transcript’.
This is the name or identifier that is used for displaying the feature e. This table contains the coordinates and all the information needed to rebuild genomic alignments. This table stores the structure of the tree. This table contains arbitrary data related to gene-trees. These contain data types which are used across many of the above tables and echema quite often denormalised to store generic associations to several table, this avoids the need for multiple sets of similar tables.
Each row represents a component, e. Length of the structural variant. The reference allele i. This table includes alternative sequences for Member, like sequences with flanking regions.
Installing the Ensembl Data
This table stores data about projected transcripts in the gene-annotation processwhich is used to help the clustering. Displays the type of the scuema e. Provides the evidence which we have used to declare an intronic region. Tables are listed by alphabetical order, and the purpose of each table is explained.
For every regulatory feature and epigenome that was a part of the regulatory build, this table links the regulatory feature to the predicted regulatory activity in ensembbl epigenome. This table has a 1: We’re happy to list those we know about here, but if your project is e!
You may optionally want to install the comparative genomics databases as well: It schma represents the name of the project or subproject where a group of variations has been identified. Xref which is the associated term.
Neanderthal Genome Browser Preliminary assembly of Homo sapiens neanderthalensis. List of the tables: