ENSEMBL SCHEMA PDF

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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Foreign key references to the peptide archive table. Used to store alternative names for populations when data comes from multiple sources. This table schemaa the raw local alignment results of peptide to peptide alignments returned by a BLAST run. This allows the user to also access the tree alignments as normal multiple alignments. Stores consensus sequences obtained from analysing repeat features. Needed for other species, but human, so keep it.

These tables store information linking entities variants, genes, QTLs with phenotypes and other annotations. Foreign key references to the marker table. Further information about a group could be added here at a later date. These tables define the variation source and study information. Some xref objects can be referred to by more than one name. This browser can be used to inspect the reference assemblies of human, mouse and zebrafish being created by the GRC.

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It contains the consequence of the allele e. Contains information defining an array or array set. Name of the collection this row of statistics refers to usual values are “ensembl”, “mouse”, etc.

For example, a given row may have a start position ofindicating the chromosomal position of the first rnsembl in this row. Normally, we use the date of creation of the mapping file being loaded.

Foreign key references to the translation table. The list of structural variation classes is available here. Two DitagFeatures usually relate to one parent Ditag. This document refers to version 91 of the Ensembl Regulation schema.

Installing the Ensembl Data

This table maps probes to transcripts. This table contains the name of sets and subsets of variations stored in the database.

Follow us Blog Twitter Facebook. For each database you have downloaded, cd into the database directory and perform steps Foreign schma linked to the xref table. Used to store alternative names for individuals when data comes from multiple sources. Represents a genomic segment feature as the result of an segmentation analysis i. Stores map locations genetic, radiation hybrid and in situ hybridization for markers obtained from experimental evidence.

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This table contains the sequences corresponding to every genomic homology relationship found.

Schema Documentation

These genotypes are mapped to particular genomic locations rather than variation objects. See below the command listing all the data sources in the human variation database: Represents the individual array chip design as part of an array or array set. This table stores the associations between structural variations and their supporting ehsembl. Various member gene and proteins related information stored in the database, either loaded from Core databases or aggregated from Compara analyses.

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