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 alternative names for markers, as well as their sources. Stores data about the marker itself. A set of clinical significance classes assigned to the variant. These are our current entries: Stores consensus sequences obtained from analysing repeat features. Foreign key references to the marker table. The consequence s of the variant allele on this regulatory feature.
Contains a snapshot of the stable IDs associated with genes deleted or changed between releases. Description of the genomes assembly, sequences, genes, etc. Whether there are SeqEdits that modify the transcript sequence. A population may be an ethnic group e.
Further information about a group could be added here at a later date. Xref which is source of this association. The deviation from the score that is derived from alignment software e. This table stores data about projected transcripts in the gene-annotation processwhich is used to help the clustering.
Ensembl Variation – Schema documentation
Foreign key linked to the xref table key: This table contains descriptions of group submitting data to public repositories such as ClinVar. Text containing the reason why the Variation has been flagged as failed. Usually describes a program and some database that together are used to create a feature on a piece of sequence. Class of the variation, key in the attrib table.
Anolis carolinensis Astyanax mexicanus Bos taurus Callithrix jacchus Canis familiaris Carlito syrichta Cavia porcellus Choloepus hoffmanni Ciona intestinalis Ciona savignyi Danio rerio Dasypus novemcinctus Dipodomys ordii Echinops telfairi Equus caballus Erinaceus europaeus Felis catus Gallus gallus Gasterosteus aculeatus Gorilla gorilla Homo sapiens Ictidomys tridecemlineatus Latimeria chalumnae Loxodonta africana Macaca mulatta Meleagris gallopavo Microcebus murinus Monodelphis domestica Mus musculus Myotis lucifugus Nomascus leucogenys Notamacropus eugenii Ochotona princeps Ornithorhynchus anatinus Oryctolagus cuniculus Oryzias latipes Otolemur garnettii Pan troglodytes Papio anubis Poecilia formosa Pongo abelii Procavia capensis Pteropus vampyrus Rattus norvegicus Sorex araneus Sus scrofa Taeniopygia guttata Takifugu rubripes Tetraodon nigroviridis Tupaia cshema Tursiops truncatus Vicugna pacos Xenopus tropicalis Xiphophorus maculatus.
A resource for Schizosaccharomyces pombe ensebl includes structural and functional annotation, literature curation and access to large-scale data sets. The most common type is the single nucleotide variation SNP though the schema also accommodates copy number variations CNVs and structural variations SVs.
Bound regions are used for promoters only. A web browser and ftp sites are provided to access human genetic variation catalogued by the project.
Describes features on the translations as opposed to the DNA sequence itselfi. Show species Drosophila melanogaster Homo sapiens Mus musculus Rattus norvegicus. Canis familiaris Drosophila melanogaster Gallus gallus Mus musculus Rattus norvegicus.
Schema for Ensembl Genes – Ensembl Genes
Contains information defining an array or array set. Describes why a particular external entity was not mapped to an ensembl one. The following query refers to the members of the protein family PTHR The data have been compressed to reduce table size and increase the speed of the web code when retrieving strain slices and LD data.
These tables define the variation source and study information.
Defines the type of structural variant. This table stores the relationship between Ensembl’s internal coordinate system identifiers and traditional chromosome names. The compressed string using Perl’s pack method consisting of a repeating triplet of elements: See the examples below.
Stores data about the data in the current schema. An internal description of the alignment. Web tool to scehma the presence or absence of certain genes or proteins in a set of eukaryote species. Encoded representation of the genotype data: Bos taurus Canis familiaris Danio rerio Drosophila melanogaster Equus caballus Gallus enswmbl Macaca mulatta Mus musculus Nomascus leucogenys Ornithorhynchus anatinus Ovis aries Pan troglodytes Pongo abelii Rattus norvegicus Saccharomyces cerevisiae Sus scrofa Taeniopygia guttata Tetraodon nigroviridis.
Follow us Blog Twitter Facebook. These ensemnl define the genotype data at the sample and population levels.
This table stores genotypes and frequencies for variations in given populations. Note that a transcript is usually associated with a translation, but may not be, e. Contains the peptides for deleted or changed translations.
This table stores the raw local alignment results of peptide to peptide alignments returned by a BLAST run. A denormalisation taken from the variation table. Stores information about a population. Follow us Blog Twitter Facebook. Some of these tables have been omitted from the schema diagram.
Stores information about genes on haplotypes that may be orthologous. This prevents the date from chaging even if we accidentally remove the entry and have to re-load it.