ENSEMBL SCHEMA PDF

Tables are grouped into logical groups, 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. Typically this contains how chromosomes are made of contigs, clones out of contigs, and chromosomes out of supercontigs. It allows you to artificially chunk chromosome sequence into smaller parts. The data in this table defines the "static golden path", i. Each row represents a component, e.

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Tables are grouped into logical groups, 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.

Typically this contains how chromosomes are made of contigs, clones out of contigs, and chromosomes out of supercontigs.

It allows you to artificially chunk chromosome sequence into smaller parts. The data in this table defines the "static golden path", i.

Each row represents a component, e. Allows multiple sequence regions to point to the same sequence, analogous to a symbolic link in a filesystem pointing to the actual file. This mechanism has been implemented specifically to support haplotypes and PARs, but may be useful for other similar structures in the future. List of species with populated data: Show species. Allows the storage of flat file locations used to store large quanitities of data currently unsuitable in a traditional database table.

Contains DNA sequence. Contains genome and assembly related statistics These include but are not limited to: feature counts, sequence lengths. Stores data about the data in the current schema. Taxonomy information, version information and the default value for the type column in the assembly table are stored here.

Unlike other tables, data in the meta table is stored as key-value pairs. Also stores via assembly. Describes which co-ordinate systems the different feature tables use. Stores information about sequence regions. Contigs are stored with the co-ordinate system 'contig'. The relationship between contigs and clones is stored in the assembly table. The relationships between contigs and chromosomes, and between contigs and supercontigs, are stored in the assembly table.

Groups together xref associations under a single description. Used when more than one associated xref term must be used to describe a condition. This table associates extra associated annotations with a given ontology xref evidence and source under a specific condition. Describes dependent external references which can't be directly mapped to Ensembl entities. They are linked to primary external references instead. Stores data about the external databases in which the objects described in the xref table are stored.

Some xref objects can be referred to by more than one name. This table relates names to xref IDs. Allows storage of links to the InterPro database.

InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to unknown protein sequences. InterPro - The InterPro website. Some ENSPs are associated with multiple closely related Swissprot entries which may both be associated with the same GO identifier but with different evidence tags.

Describes why a particular external entity was not mapped to an ensembl one. Describes features representing a density, or precentage coverage etc. Describes type representing a density, or percentage coverage etc. Corresponds to original tag containing the full sequence. Describes where ditags hit on the genome. These are the original tags separated into start "L" and end "R" parts if applicable, successfully aligned to the genome.

Two DitagFeatures usually relate to one parent Ditag. Alternatively there are CAGE tags e. Provides the evidence which we have used to declare an intronic region.

Stores the names of different genetic or radiation hybrid maps, for which there is marker map information. Stores data about the marker itself. A marker in Ensembl consists of a pair of primer sequences, an expected product size and a set of associated identifiers known as synonyms. Used to describe positions of markers on the assembly. Markers are placed on the genome electronically using an analysis program. Stores map locations genetic, radiation hybrid and in situ hybridization for markers obtained from experimental evidence.

Stores exons that are predicted by ab initio gene finder programs. Stores transcripts that are predicted by ab initio gene finder programs e. Stores consensus sequences obtained from analysing repeat features. Describes general genomic features that don't fit into any of the more specific feature tables. Links intronic evidence to a pair of exons used within a transcript and to resolve the m:m relationship between introns and transcripts.

Stores information about genes on haplotypes that may be orthologous. MySQL does not allow multiple autoincrement fields. Further information about a group could be added here at a later date. Usually describes a program and some database that together are used to create a feature on a piece of sequence. The module column tells the pipeline which Perl module does the whole analysis, typically a RunnableDB module.

Allows the storage of a textual description of the analysis, as well as a "display label", primarily for the EnsEMBL web site. Enables storage of attributes that relate to DNA sequence alignments. Stores data about exons. Relationship table linking exons with transcripts. The rank column indicates the 5' to 3' position of the exon within the transcript, i. Stores translation alignments generated from Blast or Blast-like comparisons. Describes features on the translations as opposed to the DNA sequence itself , i.

In peptide co-ordinates rather than contig co-ordinates. Describes the exon prediction process by linking exons to DNA or protein alignment features. Stores information about transcripts.

Note that a transcript is usually associated with a translation, but may not be, e. Describes the exon prediction process by linking transcripts to DNA or protein alignment features. Search terms. Search all species. Search Ensembl genomes. Search Vega. Search Sanger. In this section. The overall diagram can be found here. List of the tables:. Show columns [Back to top]. Primary key, internal identifier.

Danio rerio Homo sapiens Mus musculus. Describes bands that can be stained on the chromosome. Drosophila melanogaster Homo sapiens Mus musculus Rattus norvegicus. Allows for storing multiple names for sequence regions. Saccharomyces cerevisiae. Stores data about the biotypes and mappings to Sequence Ontology.

Foreign key references to the xref table. Describes the reason why a mapping failed. Mus musculus. Canis lupus familiaris Homo sapiens Mus musculus Ovis aries Rattus norvegicus. Canis lupus familiaris Gasterosteus aculeatus Homo sapiens Mus musculus Ovis aries Rattus norvegicus.

Stores alternative names for markers, as well as their sources. Homo sapiens Mus musculus Ovis aries. Allows for storage of arbitrary features.

This table classifies features into distinct sets. Describes sequence repeat regions. Homo sapiens Mus musculus. Holds all the different attributes assigned to individual alleles. Used mainly inside pipeline.

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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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Ensembl Core - Schema documentation

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.

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