ensembl-glossary.owl
type: Ontology
version IRI: ensembl-glossary.owl
comment: ensembl-glossary

definition
type: AnnotationProperty

hasDbXref
type: AnnotationProperty

related
type: ObjectProperty

Genome annotation
type: Class
definition: A genomic locus that has been annotated.
hasDbXref: SO:0000001
has exact synonym: element
has exact synonym: Feature

Gene
type: Class
subclass of: Genome annotation
definition: Genomic locus where transcription occurs. A gene may have one or more transcripts, which may or may not encode proteins.
hasDbXref: SO:0000704
hasDbXref: https://en.wikipedia.org/wiki/Gene

Transcript
type: Class
subclass of: Gene
definition: A transcript is the operational unit of a gene. In a genomic context, transcripts consist of one or more exons, with adjoining exons being separated by introns. The exons/introns are transcribed and then the introns spliced out. Transcripts may or may not encode a protein
hasDbXref: SO:0000673
has exact synonym: isoform
has exact synonym: Splice variant

EST
type: Class
subclass of: Genome annotation
definition: Expressed Sequence Tag. Coarse sequence reads from flanking vector regions into the inserts of cDNA libraries. ESTs act as physical markers for cloning and full length sequencing of the cDNAs of expressed genes. Typically identified by purifying mRNAs, converting to cDNAs, and then sequencing a portion of the cDNAs. Usually short, single reads from a tissue or stage in development.
has exact synonym: Expressed sequence tag

Transcript support level
type: Class
subclass of: Transcript
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.
has exact synonym: TSL

TSL 1
type: Class
subclass of: Transcript support level
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: A transcript where all splice junctions are supported by at least one non-suspect mRNA.
has exact synonym: Transcript support level 1

TSL 2
type: Class
subclass of: Transcript support level
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: A transcript where the best supporting mRNA is flagged as suspect or the support is from multiple ESTs
has exact synonym: Transcript support level 2

TSL 3
type: Class
subclass of: Transcript support level
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: A transcript where the only support is from a single EST
has exact synonym: Transcript support level 3

TSL 4
type: Class
subclass of: Transcript support level
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: A transcript where the best supporting EST is flagged as suspect
has exact synonym: Transcript support level 4

TSL 5
type: Class
subclass of: Transcript support level
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: A transcript where no single transcript supports the model structure.
has exact synonym: Transcript support level 5

TSL NA
type: Class
subclass of: Transcript support level
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: A transcript that was not analysed for TSL.
has exact synonym: Transcript support level not applicable

APPRIS
type: Class
subclass of: Transcript
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods to identify the most functionally important transcript(s) of a gene.

APPRIS P1
type: Class
subclass of: APPRIS
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS.
has exact synonym: APPRIS Principal 1

APPRIS P2
type: Class
subclass of: APPRIS
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: Where the APPRIS core modules are unable to choose a clear principal variant (approximately 25% of human protein coding genes), the database chooses two or more of the CDS variants as "candidates" to be the principal variant.
has exact synonym: APPRIS Principal 2

APPRIS P3
type: Class
subclass of: APPRIS
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: Where the APPRIS core modules are unable to choose a clear principal variant and there more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated.
has exact synonym: APPRIS Principal 3

APPRIS P4
type: Class
subclass of: APPRIS
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: Where the APPRIS core modules are unable to choose a clear principal CDS and there is more than one variant with a distinct (but consecutive) CCDS identifiers, APPRIS selects the longest CCDS isoform as the principal variant.
has exact synonym: APPRIS Principal 4

APPRIS P5
type: Class
subclass of: APPRIS
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: Where the APPRIS core modules are unable to choose a clear principal variant and none of the candidate variants are annotated by CCDS, APPRIS selects the longest of the candidate isoforms as the principal variant.
has exact synonym: APPRIS Principal 5

APPRIS ALT1
type: Class
subclass of: APPRIS
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: For genes in which the APPRIS core modules are unable to choose a clear principal isoform, the ALT1 is the candidate transcript(s) models that is conserved in at least three tested species.
has exact synonym: APPRIS Alternative 1

APPRIS ALT2
type: Class
subclass of: APPRIS
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: For genes in which the APPRIS core modules are unable to choose a clear principal isoform, the ALT1 is the candidate transcript(s) models that appear to be conserved in fewer than three tested species.
has exact synonym: APPRIS Alternative 2

GENCODE Basic
type: Class
subclass of: Transcript
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts.

5' incomplete
type: Class
subclass of: Transcript
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: A protein-coding transcript which is missing the start codon due to incomplete evidence.
has exact synonym: five prime incomplete

3' incomplete
type: Class
subclass of: Transcript
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: A protein-coding transcript which is missing the stop codon due to incomplete evidence.
has exact synonym: three prime incomplete

Ensembl canonical
type: Class
subclass of: Transcript
documentation: http://www.ensembl.org/info/genome/genebuild/canonical.html
definition: A single transcript chosen for a gene which is the most conserved, most highly expressed, has the longest coding sequence and is represented in other key resources, such as NCBI and UniProt. This is defined in detail on http://www.ensembl.org/info/genome/genebuild/canonical.html
has exact synonym: canonical transcript
has exact synonym: Canonical

CCDS
type: Class
subclass of: Transcript
documentation: http://www.ensembl.org/info/genome/genebuild/ccds.html
definition: A coding sequence in the Consensus Coding Sequence Set is consistently annotated between Ensembl, MGI, HGNC and NCBI. The long term goal is to support convergence towards a standard set of gene annotations on the human genome.
hasDbXref: https://en.wikipedia.org/wiki/Consensus_CDS_Project
has exact synonym: Consensus Coding Sequence
has exact synonym: Consensus CDS

Biotype
type: Class
subclass of: Gene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: A gene or transcript classification.
has exact synonym: Gene type
has exact synonym: Transcript type
has exact synonym: Type

Protein coding
type: Class
subclass of: Biotype
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Gene/transcipt that contains an open reading frame (ORF).
hasDbXref: SO:0001217
hasDbXref: https://en.wikipedia.org/wiki/Gene
has exact synonym: Coding

Processed transcript
type: Class
subclass of: Biotype
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Gene/transcript that doesn't contain an open reading frame (ORF).
hasDbXref: https://en.wikipedia.org/wiki/Non-coding_RNA

Long non-coding RNA (lncRNA)
type: Class
subclass of: Processed transcript
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: A non-coding gene/transcript >200bp in length
hasDbXref: SO:0002127
hasDbXref: https://en.wikipedia.org/wiki/Long_non-coding_RNA
has exact synonym: Long non-coding RNA
has exact synonym: lncRNA

Non coding
type: Class
subclass of: Long non-coding RNA (lncRNA)
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Transcripts which are known from the literature to not be protein coding.
hasDbXref: SO:0001263
hasDbXref: https://en.wikipedia.org/wiki/Non-coding_RNA

3' overlapping ncRNA
type: Class
subclass of: Long non-coding RNA (lncRNA)
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Transcripts where ditag and/or published experimental data strongly supports the existence of long (>200bp) non-coding transcripts that overlap the 3'UTR of a protein-coding locus on the same strand.
has exact synonym: three prime overlapping ncRNA

Antisense
type: Class
subclass of: Long non-coding RNA (lncRNA)
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Transcripts that overlap the genomic span (i.e. exon or introns) of a protein-coding locus on the opposite strand.
hasDbXref: https://en.wikipedia.org/wiki/Antisense_RNA

lincRNA (long intergenic ncRNA)
type: Class
subclass of: Long non-coding RNA (lncRNA)
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Transcripts that are long intergenic non-coding RNA locus with a length >200bp. Requires lack of coding potential and may not be conserved between species.
hasDbXref: SO:0001641
hasDbXref: https://en.wikipedia.org/wiki/Long_non-coding_RNA#Long_intergenic_non-coding_RNAs_(lincRNA)
has exact synonym: Long intergenic RNA
has exact synonym: Long interspersed RNA
has exact synonym: lincRNA

Retained intron
type: Class
subclass of: Long non-coding RNA (lncRNA)
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.

Sense intronic
type: Class
subclass of: Long non-coding RNA (lncRNA)
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: A long non-coding transcript in introns of a coding gene that does not overlap any exons.
hasDbXref: SO:0002184

Sense overlapping
type: Class
subclass of: Long non-coding RNA (lncRNA)
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: A long non-coding transcript that contains a coding gene in its intron on the same strand.
hasDbXref: SO:0002183

Macro lncRNA
type: Class
subclass of: Long non-coding RNA (lncRNA)
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Unspliced lncRNAs that are several kb in size.

ncRNA
type: Class
subclass of: Processed transcript
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: A non-coding gene.

miRNA
type: Class
subclass of: ncRNA
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: A small RNA (~22bp) that silences the expression of target mRNA.
hasDbXref: SO:0001265
hasDbXref: https://en.wikipedia.org/wiki/MicroRNA
has exact synonym: micro RNA

piRNA
type: Class
subclass of: ncRNA
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: An RNA that interacts with piwi proteins involved in genetic silencing.
hasDbXref: SO:0001638
hasDbXref: https://en.wikipedia.org/wiki/Piwi-interacting_RNA
has exact synonym: piwi-interacting RNA

rRNA
type: Class
subclass of: ncRNA
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: The RNA component of a ribosome.
hasDbXref: SO:0001637
hasDbXref: https://en.wikipedia.org/wiki/Ribosomal_RNA
has exact synonym: ribsosomal RNA

siRNA
type: Class
subclass of: ncRNA
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: A small RNA (20-25bp) that silences the expression of target mRNA through the RNAi pathway.
hasDbXref: https://en.wikipedia.org/wiki/Small_interfering_RNA
has exact synonym: short interfering RNA
has exact synonym: silencing RNA
has exact synonym: small interfering RNA

snRNA
type: Class
subclass of: ncRNA
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Small RNA molecules that are found in the cell nucleus and are involved in the processing of pre messenger RNAs
hasDbXref: https://en.wikipedia.org/wiki/Small_nuclear_RNA
has exact synonym: U-RNA
has exact synonym: small nuclear RNA

snoRNA
type: Class
subclass of: ncRNA
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Small RNA molecules that are found in the cell nucleolus and are involved in the post-transcriptional modification of other RNAs.
hasDbXref: SO:0001272
hasDbXref: https://en.wikipedia.org/wiki/Small_nucleolar_RNA
has exact synonym: small nucleolar RNA

tRNA
type: Class
subclass of: ncRNA
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: A transfer RNA, which acts as an adaptor molecule for translation of mRNA.
hasDbXref: SO:0001272
hasDbXref: https://en.wikipedia.org/wiki/Transfer_RNA
has exact synonym: transfer RNA

vaultRNA
type: Class
subclass of: ncRNA
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Short non coding RNA genes that form part of the vault ribonucleoprotein complex.
hasDbXref: SO:0000404
hasDbXref: https://en.wikipedia.org/wiki/Vault_RNA

miscRNA
type: Class
subclass of: ncRNA
definition: Miscellaneous RNA. A non-coding RNA that cannot be classified.

Pseudogene
type: Class
subclass of: Biotype
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: A gene that has homology to known protein-coding genes but contain a frameshift and/or stop codon(s) which disrupts the ORF. Thought to have arisen through duplication followed by loss of function.
hasDbXref: SO:0000336
hasDbXref: https://en.wikipedia.org/wiki/Pseudogene

Processed pseudogene
type: Class
subclass of: Pseudogene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Pseudogene that lack introns and is thought to arise from reverse transcription of mRNA followed by reinsertion of DNA into the genome.
hasDbXref: SO:0000043
hasDbXref: https://en.wikipedia.org/wiki/Pseudogene#Processed

Unprocessed pseudogene
type: Class
subclass of: Pseudogene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Pseudogene that can contain introns since produced by gene duplication.
hasDbXref: SO:0001760
hasDbXref: https://en.wikipedia.org/wiki/Pseudogene#Non-processed
has exact synonym: Non-processed pseudogene

Transcribed pseudogene
type: Class
subclass of: Pseudogene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Pseudogene where protein homology or genomic structure indicates a pseudogene, but the presence of locus-specific transcripts indicates expression. These can be classified into 'Processed', 'Unprocessed' and 'Unitary'.
hasDbXref: SO:0002109, SO:0002107, SO:0002108

Translated pseudogene
type: Class
subclass of: Pseudogene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Pseudogenes that have mass spec data suggesting that they are also translated. These can be classified into 'Processed', 'Unprocessed'
hasDbXref: SO:0002105, SO:0002106

Polymorphic pseudogene
type: Class
subclass of: Pseudogene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Pseudogene owing to a SNP/indel but in other individuals/haplotypes/strains the gene is translated.

Unitary pseudogene
type: Class
subclass of: Pseudogene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species.
hasDbXref: SO:0001759
hasDbXref: https://en.wikipedia.org/wiki/Pseudogene#Unitary_pseudogenes

IG pseudogene
type: Class
subclass of: Pseudogene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Inactivated immunoglobulin gene.

IG gene
type: Class
subclass of: Biotype
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html, http://www.ensembl.org/info/genome/genebuild/ig_tcr.html
definition: Immunoglobulin gene that undergoes somatic recombination, annotated in collaboration with IMGT http://www.imgt.org/.
hasDbXref: SO:0002122
hasDbXref: https://en.wikipedia.org/wiki/V(D)J_recombination
has exact synonym: Immunoglobulin gene

TR gene
type: Class
subclass of: Biotype
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html, http://www.ensembl.org/info/genome/genebuild/ig_tcr.html
definition: T cell receptor gene that undergoes somatic recombination, annotated in collaboration with IMGT http://www.imgt.org/.
hasDbXref: SO:0002133
hasDbXref: https://en.wikipedia.org/wiki/V(D)J_recombination
has exact synonym: T cell receptor gene

TEC (To be Experimentally Confirmed)
type: Class
subclass of: Biotype
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Regions with EST clusters that have polyA features that could indicate the presence of protein coding genes. These require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies.

Readthrough
type: Class
subclass of: Biotype
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: A readthrough transcript has exons that overlap exons from transcripts belonging to two or more different loci (in addition to the locus to which the readthrough transcript itself belongs).
has exact synonym: read-through

IG V gene
type: Class
subclass of: IG gene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Variable chain immunoglobulin gene that undergoes somatic recombination before transcription
hasDbXref: SO:0002126
hasDbXref: https://en.wikipedia.org/wiki/V(D)J_recombination

IG D gene
type: Class
subclass of: IG gene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Diversity chain immunoglobulin gene that undergoes somatic recombination before transcription
hasDbXref: SO:0002124
hasDbXref: https://en.wikipedia.org/wiki/V(D)J_recombination

IG J gene
type: Class
subclass of: IG gene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Joining chain immunoglobulin gene that undergoes somatic recombination before transcription
hasDbXref: SO:0002125
hasDbXref: https://en.wikipedia.org/wiki/V(D)J_recombination

IG C gene
type: Class
subclass of: IG gene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Constant chain immunoglobulin gene that undergoes somatic recombination before transcription
hasDbXref: SO:0002123
hasDbXref: https://en.wikipedia.org/wiki/V(D)J_recombination

TR V gene
type: Class
subclass of: TR gene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Variable chain T cell receptor gene that undergoes somatic recombination before transcription
hasDbXref: SO:0002137
hasDbXref: https://en.wikipedia.org/wiki/V(D)J_recombination

TR D gene
type: Class
subclass of: TR gene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Diversity chain T cell receptor gene that undergoes somatic recombination before transcription
hasDbXref: SO:0002135
hasDbXref: https://en.wikipedia.org/wiki/V(D)J_recombination

TR J gene
type: Class
subclass of: TR gene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Joining chain T cell receptor gene that undergoes somatic recombination before transcription
hasDbXref: SO:0002136
hasDbXref: https://en.wikipedia.org/wiki/V(D)J_recombination

TR C gene
type: Class
subclass of: TR gene
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Constant chain T cell receptor gene that undergoes somatic recombination before transcription
hasDbXref: SO:0002134
hasDbXref: https://en.wikipedia.org/wiki/V(D)J_recombination

cDNA
type: Class
subclass of: Transcript
definition: The sequence of the spliced exons of a transcript expressed in DNA notation (T rather than U), representing the coding or sense strand. The cDNA contains the whole sequence of the RNA, including coding and untranslated sequence.
hasDbXref: SO:0000756
hasDbXref: https://en.wikipedia.org/wiki/Complementary_DNA
has exact synonym: complementary DNA

CDS
type: Class
subclass of: Transcript
definition: CoDing Sequence. The region of a cDNA which is translated. In Ensembl displays, the stop codon is included as part of the CDS sequence.
hasDbXref: SO:0000316
has exact synonym: ORF
has exact synonym: open reading frame
has exact synonym: translatable sequence
has exact synonym: translated sequence
has exact synonym: coding sequence

Peptide
type: Class
subclass of: Transcript
definition: A sequence of amino acids, translated from a CDS.
hasDbXref: https://en.wikipedia.org/wiki/Peptide
has exact synonym: Translation
has exact synonym: Protein

Protein domain
type: Class
subclass of: Peptide
definition: A region of special biological interest within a single protein sequence. However, a domain may also be defined as a region within the three-dimensional structure of a protein that may encompass regions of several distinct protein sequences that accomplishes a specific function. A domain class is a group of domains that share a common set of well-defined properties or characteristics.
hasDbXref: https://en.wikipedia.org/wiki/Protein_domain
has exact synonym: Domain

Exon
type: Class
subclass of: Transcript
definition: Transcribed genomic region that remains in the RNA after splicing, includes both the CDS and the UTRs.
hasDbXref: SO:0000147
hasDbXref: https://en.wikipedia.org/wiki/Exon

Intron
type: Class
subclass of: Transcript
definition: Transcribed genomic regions that is removed from the RNA by splicing.
hasDbXref: SO:0000188
hasDbXref: https://en.wikipedia.org/wiki/Intron

Codon
type: Class
subclass of: CDS
definition: Three base pairs in either DNA or RNA that code for an amino acid (or stop translation).
hasDbXref: SO:0000360
hasDbXref: https://en.wikipedia.org/wiki/Genetic_code

Constitutive exon
type: Class
subclass of: Exon
definition: Exons that are not spliced out, therefore present in all transcripts of a given gene.

Phase
type: Class
subclass of: Exon
definition: The position of an exon/intron boundary within a codon. A phase of zero means the boundary falls between codons, one means between the first and second base and two means between the second and third base. Exons have a start and end phase, whereas introns have just one phase. A boundary in a non-coding region has a phase of -1.

Flanking sequence
type: Class
subclass of: Genome annotation
definition: Sequence 5' or 3' to a DNA or RNA sequence of interest (for example gene, transcript, SNP or repeat).
hasDbXref: SO:0000239
has exact synonym: flank
has exact synonym: flanking region

Untranslated region
type: Class
subclass of: Transcript
definition: The region of a coding cDNA which is not translated.
hasDbXref: SO:0000203
hasDbXref: https://en.wikipedia.org/wiki/Untranslated_region
has exact synonym: UTR

5' UTR
type: Class
subclass of: Transcript
definition: The region of a coding cDNA upstream of the start codon which is not translated.
hasDbXref: SO:0000204
hasDbXref: https://en.wikipedia.org/wiki/Untranslated_region
has exact synonym: 5' untranslated region
has exact synonym: five prime untranslated region
has exact synonym: five prime UTR

3' UTR
type: Class
subclass of: Transcript
definition: The region of a coding cDNA downstream of the stop codon which is not translated.
hasDbXref: SO:0000205
hasDbXref: https://en.wikipedia.org/wiki/Untranslated_region
has exact synonym: 3' untranslated region
has exact synonym: three prime untranslated region
has exact synonym: three prime UTR

Homologues
type: Class
subclass of: Gene
documentation: http://www.ensembl.org/info/genome/compara/homologue_types.html
definition: Specific genes that are descended from the same common sequence in an ancestor.
hasDbXref: SO:0000853, FHOM_0000007
hasDbXref: https://en.wikipedia.org/wiki/Sequence_homology
has exact synonym: Homologs

Gene tree
type: Class
subclass of: Homologues
documentation: http://www.ensembl.org/info/genome/compara/homology_method.html
definition: A representation of the evolutionary relationship between homologues, constructed using the Ensembl gene tree pipeline.
hasDbXref: https://en.wikipedia.org/wiki/Phylogenetic_tree
has exact synonym: Protein tree

Orthologues
type: Class
subclass of: Homologues
documentation: http://www.ensembl.org/info/genome/compara/homologue_types.html
definition: Orthologues are genes derived from a common ancestor through vertical descent (or speciation) and can be thought of as the direct evolutionary counterpart.
hasDbXref: FHOM_0000017
hasDbXref: https://en.wikipedia.org/wiki/Sequence_homology#Orthology
has exact synonym: Orthologs

1-to-1 orthologues
type: Class
subclass of: Orthologues
documentation: http://www.ensembl.org/info/genome/compara/homologue_types.html
definition: A type of orthologue assigned for a pair of species where only one copy is found in each species.
hasDbXref: FHOM_0000020
has exact synonym: one-to-one orthologs
has exact synonym: one-to-one orthologues
has exact synonym: 1-to-1 orthologs

1-to-many orthologues
type: Class
subclass of: Orthologues
documentation: http://www.ensembl.org/info/genome/compara/homologue_types.html
definition: A type of orthologue assigned for a pair of species where one gene in one species is orthologous to multiple genes in the other species, due to (a) duplication event(s) in the second species.
hasDbXref: FHOM_0000034
has exact synonym: one-to-many orthologs
has exact synonym: one-to-many orthologues
has exact synonym: 1-to-many orthologs

Many-to-many orthologues
type: Class
subclass of: Orthologues
documentation: http://www.ensembl.org/info/genome/compara/homologue_types.html
definition: A type of orthologue assigned for a pair of species where multiple orthologues are found in both species, where the duplication events in both species occurred after the speciation event.
hasDbXref: FHOM_0000048
has exact synonym: many-to-many orthologs

Paralogues
type: Class
subclass of: Homologues
documentation: http://www.ensembl.org/info/genome/compara/homologue_types.html
definition: Genes (homologues) that have evolved by duplication.
hasDbXref: FHOM_0000011
hasDbXref: https://en.wikipedia.org/wiki/Sequence_homology#Paralogy
has exact synonym: Paralogs

Between species paralogues
type: Class
subclass of: Paralogues
documentation: http://www.ensembl.org/info/genome/compara/homologue_types.html
definition: Members of the same gene family in different species that are not direct orthologues. In a gene tree, these genes are separated by a duplication node.
hasDbXref: FHOM_0000050
has exact synonym: out paralogs
has exact synonym: out paralogues
has exact synonym: Between species paralogs

Gene split
type: Class
subclass of: Paralogues
documentation: http://www.ensembl.org/info/genome/compara/homologue_types.html
definition: Pairs of genes in a species that occur together in the same tree, but are actually two halves of the same gene split partway along.

Other paralogues
type: Class
subclass of: Paralogues
documentation: http://www.ensembl.org/info/genome/compara/homologue_types.html
definition: Paralogues which are very far away from the other members of a paralogue family. They are part of the same super-family, but the precise taxonomic relationship to other members is undefined, as the trees are too large to compute.
has exact synonym: Other paralogs

Within species paralogues
type: Class
subclass of: Paralogues
documentation: http://www.ensembl.org/info/genome/compara/homologue_types.html
definition: Two or more versions of a duplicated gene in a single species. In a gene tree, the genes are separated by a duplication node.
hasDbXref: FHOM_0000049
has exact synonym: In paralogs
has exact synonym: In paralogues
has exact synonym: Within species paralogs

Homoeologues
type: Class
subclass of: Homologues
definition: Pairs of genes in a polyploid genome that underwent (a) hybridisation event(s). The original genes were orthologues in the two (or more) species that hybridised, and now occur in the same species. Since they did not arise through a duplication event, they are not paralogues.
hasDbXref: FHOM_0000073
hasDbXref: https://en.wikipedia.org/wiki/Polyploid#Homoeologous

Variant
type: Class
subclass of: Genome annotation
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: Locus where the sequence differs between individuals of the same species
hasDbXref: SO:0001060
hasDbXref: https://en.wikipedia.org/wiki/Genetic_variation
has exact synonym: mutation
has exact synonym: variation
has exact synonym: Polymorphism

QTL
type: Class
subclass of: Variant
definition: Genetic loci where allelic variation is associated with variation in a quantitative trait (e.g. blood pressure).
hasDbXref: SO:0000771
hasDbXref: https://en.wikipedia.org/wiki/Quantitative_trait_locus
has exact synonym: Quantitative trait locus

eQTL
type: Class
subclass of: QTL
definition: Genetic loci where allelic variation is associated with expression levels of other genes.
hasDbXref: https://en.wikipedia.org/wiki/Expression_quantitative_trait_loci
has exact synonym: Expression quantitative trait locus

Evidence status
type: Class
subclass of: Variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html#evidence_status
definition: Codes that reflect the amount and type of evidence that supports the existence of a variant.

Sequence variant
type: Class
subclass of: Variant
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: Variant that only affects a small locus

Structural variant
type: Class
subclass of: Variant
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: Variant that affects a large locus
hasDbXref: SO:0001537

SNP
type: Class
subclass of: Sequence variant
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: Single Nucleotide Polymorphism, substitution of a single nucleotide for another nucleotide
hasDbXref: SO:0000694
hasDbXref: https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism
has exact synonym: SNV
has exact synonym: base-pair substitution
has exact synonym: point mutation
has exact synonym: single nucleotide variation
has exact synonym: Single nucleotide polymorphism

Insertion
type: Class
subclass of: Sequence variant
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: Insertion of one or more nucleotides
hasDbXref: SO:0000667
hasDbXref: https://en.wikipedia.org/wiki/Insertion_(genetics)

Deletion
type: Class
subclass of: Sequence variant
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: Deletion of one or more nucleotides
hasDbXref: SO:0000159
hasDbXref: https://en.wikipedia.org/wiki/Deletion_(genetics)

Indel
type: Class
subclass of: Sequence variant
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: An insertion and a deletion, affecting two or more nucleotides
hasDbXref: SO:1000032
hasDbXref: https://en.wikipedia.org/wiki/Indel

Substitution
type: Class
subclass of: Sequence variant
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: A sequence alteration where the length of the deleted sequence is the same as the length of the inserted sequence.
hasDbXref: SO:1000002

CNV
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: Copy Number Variation: increases or decreases the copy number of a given locus. Subcategorised into Loss and Gain compared to the reference.
hasDbXref: SO:0001019
hasDbXref: https://en.wikipedia.org/wiki/Copy-number_variation
has exact synonym: CNP
has exact synonym: copy number gain
has exact synonym: copy number loss
has exact synonym: copy number polymorphism
has exact synonym: deletion
has exact synonym: duplication
has exact synonym: Copy number variation

Inversion
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: A continuous nucleotide sequence is inverted in the same position
hasDbXref: SO:1000036
hasDbXref: https://en.wikipedia.org/wiki/Chromosomal_inversion

Translocation
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: A region of nucleotide sequence that has translocated to a new position
hasDbXref: SO:0000199
hasDbXref: https://en.wikipedia.org/wiki/Chromosomal_translocation
has exact synonym: chromosome rearrangement

Allele (variant)
type: Class
subclass of: Variant
documentation: http://www.ensembl.org/info/genome/variation/index.html
definition: One of a number of alternative forms of the same genetic locus/variant.
hasDbXref: SO:0001023

Allele (gene)
type: Class
subclass of: Gene
subclass of: Restriction
  on property: related
  some values from: Allele (variant)
documentation: http://www.ensembl.org/info/genome/genebuild/haplotypes_patches.html
definition: Different versions of a gene found between the primary assembly and a patch or genome haplotype.
has exact synonym: alternative sequence gene
has exact synonym: haplotype gene
has exact synonym: patch gene
has exact synonym: Alt gene

Reference allele
type: Class
subclass of: Allele (variant)
definition: The allele of a variant found in the reference genome currently being studied. The reference allele is not necessarily the major or ancestral allele.

Alternative allele
type: Class
subclass of: Allele (variant)
definition: Any allele of a variant which is not the in the reference genome currently being studied. The alternative allele is not necessarily the minor allele.

Major allele
type: Class
subclass of: Allele (variant)
documentation: http://www.ensembl.org/info/genome/variation/data_description.html#maf
definition: The allele which is most frequent in the global population, defined in human by the 1000 Genomes Project. The major allele may be the reference or the alternative allele, and may or may not be the ancestral allele.
hasDbXref: https://en.wikipedia.org/wiki/Allele_frequency

Minor allele
type: Class
subclass of: Allele (variant)
documentation: http://www.ensembl.org/info/genome/variation/data_description.html#maf
definition: The allele which is the second most frequent in the global population, defined in human by the 1000 Genomes Project. The minor allele may be the reference or the alternative allele, and may or may not be the ancestral allele.
hasDbXref: https://en.wikipedia.org/wiki/Allele_frequency

Private allele
type: Class
subclass of: Allele (variant)
definition: An allele which has only been identified in one individual or one family. A private allele may be the reference or the alternative allele, and may or may not be the ancestral allele.

Ancestral allele
type: Class
subclass of: Allele (variant)
definition: The allele which occurs at this locus in closely related species and is thought to reflect the allele present at the time of speciation. The ancestral allele may be the reference or the alternative allele, and the major or minor allele.

Minor allele frequency
type: Class
subclass of: Minor allele
documentation: http://www.ensembl.org/info/genome/variation/data_description.html#maf
definition: The frequency of the second most common allele in the specified population.
hasDbXref: https://en.wikipedia.org/wiki/Allele_frequency
has exact synonym: MAF

Highest population MAF
type: Class
subclass of: Minor allele frequency
documentation: http://www.ensembl.org/info/genome/variation/data_description.html#maf
definition: The highest minor allele frequency observed in any population typed for this variant. For human this includes the 1000 Genomes Project, gnomAD and UK10K.
hasDbXref: https://en.wikipedia.org/wiki/Allele_frequency
has exact synonym: Highest population minor allele frequency
has exact synonym: HPMAF

Global MAF
type: Class
subclass of: Minor allele frequency
documentation: http://www.ensembl.org/info/genome/variation/data_description.html#maf
definition: The frequency of the second most common allele in the global population, defined in human by the 1000 Genomes Project phase 3.

Genotype
type: Class
subclass of: Allele (variant)
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: The specific alleles that are present in an individual's genome. In diploid organisms two alleles make up the genotype (except for the sex chromosomes).
has exact synonym: Zygosity

Genetic marker
type: Class
subclass of: Variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A measurable locus that varies within a population.
hasDbXref: SO:0001645

Tandem repeat
type: Class
subclass of: Variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: Two or more adjacent copies of a region (of length greater than 1).
hasDbXref: SO:0000705

Alu insertion
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: An insertion of sequence from the Alu family of mobile elements.
hasDbXref: SO:0002063

Complex structural alteration
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A structural sequence alteration or rearrangement encompassing one or more genome fragments, with four or more breakpoints.
hasDbXref: SO:0001784

Complex substitution
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: When no simple or well defined DNA mutation event describes the observed DNA change, the keyword ""complex"" should be used. Usually there are multiple equally plausible explanations for the change.
hasDbXref: SO:1000005

Interchromosomal breakpoint
type: Class
subclass of: Translocation
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A rearrangement breakpoint between two different chromosomes.
hasDbXref: SO:0001873

Interchromosomal translocation
type: Class
subclass of: Translocation
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A translocation where the regions involved are from different chromosomes.
hasDbXref: SO:0002060

Intrachromosomal breakpoint
type: Class
subclass of: Translocation
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A rearrangement breakpoint within the same chromosome.
hasDbXref: SO:0001874

Intrachromosomal translocation
type: Class
subclass of: Translocation
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A translocation where the regions involved are from the same chromosome.
hasDbXref: SO:0002061

Loss of heterozygosity
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene.
hasDbXref: SO:0001786

Mobile element deletion
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element).
hasDbXref: SO:0002066

Mobile element insertion
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A kind of insertion where the inserted sequence is a mobile element.
hasDbXref: SO:0001837

Novel sequence insertion
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: An insertion the sequence of which cannot be mapped to the reference genome.
hasDbXref: SO:0001838

Short tandem repeat variant
type: Class
subclass of: Variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A variation that expands or contracts a tandem repeat with regard to a reference.
hasDbXref: SO:0002096

Tandem duplication
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A duplication consisting of 2 identical adjacent regions.
hasDbXref: SO:1000173

Probe
type: Class
subclass of: Structural variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html
definition: A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid.
hasDbXref: SO:0000051

Variant consequence
type: Class
subclass of: Variant
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: The effect that the variant has on each feature that it overlaps. A variant will have a consequence for each feature that it overlaps.

Variant impact
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A subjective classification of the severity of the variant consequence, based on agreement with SNPEff.

High impact variant consequence
type: Class
subclass of: Variant impact
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: The variant is assumed to have high (disruptive) impact in the protein, probably causing protein truncation, loss of function or triggering nonsense mediated decay.
has exact synonym: HIGH

Moderate impact variant consequence
type: Class
subclass of: Variant impact
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A non-disruptive variant that might change protein effectiveness.
has exact synonym: MODERATE

Low impact variant consequence
type: Class
subclass of: Variant impact
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A variant that is assumed to be mostly harmless or unlikely to change protein behaviour.
has exact synonym: LOW

Modifier impact variant consequence
type: Class
subclass of: Variant impact
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: Usually non-coding variants or variants affecting non-coding genes, where predictions are difficult or there is no evidence of impact.
has exact synonym: MODIFIER

Transcript ablation
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A feature ablation whereby the deleted region includes a transcript feature
hasDbXref: SO:0001893

Splice acceptor variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A splice variant that changes the 2 base region at the 3' end of an intron
hasDbXref: SO:0001574

Splice donor variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A splice variant that changes the 2 base region at the 5' end of an intron
hasDbXref: SO:0001575

Stop gained
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript
hasDbXref: SO:0001587

Frameshift variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three
hasDbXref: SO:0001589

Stop lost
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript
hasDbXref: SO:0001578

Start lost
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A codon variant that changes at least one base of the canonical start codo
hasDbXref: SO:0002012

Transcript amplification
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A feature amplification of a region containing a transcript
hasDbXref: SO:0001889

Inframe insertion
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: An inframe non synonymous variant that inserts bases into in the coding sequenc
hasDbXref: SO:0001821

Inframe deletion
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: An inframe non synonymous variant that deletes bases from the coding sequenc
hasDbXref: SO:0001822

Missense variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved
hasDbXref: SO:0001583

Protein altering variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence_variant which is predicted to change the protein encoded in the coding sequence
hasDbXref: SO:0001818

Splice region variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron
hasDbXref: SO:0001630

Incomplete terminal codon variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed
hasDbXref: SO:0001626

Stop retained variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant where at least one base in the terminator codon is changed, but the terminator remains
hasDbXref: SO:0001567

Synonymous variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant where there is no resulting change to the encoded amino acid
hasDbXref: SO:0001819

Coding sequence variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant that changes the coding sequence
hasDbXref: SO:0001580

Mature miRNA variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A transcript variant located with the sequence of the mature miRNA
hasDbXref: SO:0001620

5 prime UTR variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A UTR variant of the 5' UTR
hasDbXref: SO:0001623

3 prime UTR variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A UTR variant of the 3' UTR
hasDbXref: SO:0001624

Non coding transcript exon variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant that changes non-coding exon sequence in a non-coding transcript
hasDbXref: SO:0001792

Intron variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A transcript variant occurring within an intron
hasDbXref: SO:0001627

NMD transcript variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A variant in a transcript that is the target of NMD
hasDbXref: SO:0001621

Non coding transcript variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A transcript variant of a non coding RNA gene
hasDbXref: SO:0001619

Upstream gene variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant located 5' of a gene
hasDbXref: SO:0001631

Downstream gene variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant located 3' of a gene
hasDbXref: SO:0001632

TFBS ablation
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A feature ablation whereby the deleted region includes a transcription factor binding site
hasDbXref: SO:0001895

TFBS amplification
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A feature amplification of a region containing a transcription factor binding site
hasDbXref: SO:0001892

TF binding site variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant located within a transcription factor binding site
hasDbXref: SO:0001782

Regulatory region ablation
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A feature ablation whereby the deleted region includes a regulatory region
hasDbXref: SO:0001894

Regulatory region amplification
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A feature amplification of a region containing a regulatory region
hasDbXref: SO:0001891

Feature elongation
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant located within a regulatory region
hasDbXref: SO:0001907

Regulatory region variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant located within a regulatory region
hasDbXref: SO:0001566

Feature truncation
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence
hasDbXref: SO:0001906

Intergenic variant
type: Class
subclass of: Variant consequence
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html
definition: A sequence variant located in the intergenic region, between genes
hasDbXref: SO:0001628

Ambiguity code
type: Class
subclass of: Variant
definition: A single letter code that represents two or more possible nucleotides at a single base locus.
hasDbXref: https://en.wikipedia.org/wiki/International_Union_of_Pure_and_Applied_Chemistry#Amino_acid_and_nucleotide_base_codes

Flagged variant
type: Class
subclass of: Variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html#quality_control
definition: Variants that failed our quality control analyses, therefore they are flagged as suspicious.
has exact synonym: Failed variant

Clinical significance
type: Class
subclass of: Variant
documentation: http://www.ensembl.org/info/genome/variation/data_description.html#clin_significance
definition: A classification of a variant's impact on disease, taken from ClinVar.
has exact synonym: pathogenicity
has exact synonym: Clin sig

Linkage disequilibrium
type: Class
subclass of: Variant
documentation: https://en.wikipedia.org/wiki/Linkage_disequilibrium
definition: A measure of how often two variants or specific sequences are inherited together.
has exact synonym: Linkage
has exact synonym: LD

r2
type: Class
subclass of: Linkage disequilibrium
documentation: https://en.wikipedia.org/wiki/Linkage_disequilibrium
definition: The correlation between a pair of loci. It varies from 0 (loci are in complete linkage equilibrium) to 1 (loci are in complete linkage disequilibrium and coinherited).
has exact synonym: r squared

D'
type: Class
subclass of: Linkage disequilibrium
documentation: https://en.wikipedia.org/wiki/Linkage_disequilibrium
definition: The difference between the observed and the expected frequency of a given haplotype. If two loci are independent (i.e. in linkage equilibrium and therefore not coinherited at all), the D' value will be 0.
has exact synonym: D prime

Haplotype (variation)
type: Class
subclass of: Linkage disequilibrium
subclass of: Restriction
  on property: related
  some values from: Haplotype (genome)
documentation: https://en.wikipedia.org/wiki/Linkage_disequilibrium
definition: A set of variant alleles in a contiguous genomic region. A haplotype block describes a set of alleles which tend to be inherited together.
hasDbXref: SO:0001024

Transcript haplotype
type: Class
subclass of: Haplotype (variation)
definition: The transcript sequence derived from one copy of a gene in an individual, based on the phased 1000 Genomes genotype data. CDS and protein sequences are derived from this.

Genome
type: Class
definition: The complete set of DNA found in each cell.
hasDbXref: https://en.wikipedia.org/wiki/Genome

Genome assembly
type: Class
subclass of: Genome
documentation: http://www.ensembl.org/info/genome/genebuild/assembly.html
definition: A computational representation of the sequence of a haploid genome, representative of a species or strain.
hasDbXref: SO:0000353
hasDbXref: https://en.wikipedia.org/wiki/Sequence_assembly
has exact synonym: reference assembly
has exact synonym: assembly

Coverage
type: Class
subclass of: Genome assembly
documentation: http://www.ensembl.org/info/genome/genebuild/assembly.html
definition: Refers to the number of overlapping sequences used to build a region of the assembly. High coverage indicates a good amount of sequence information while low coverage reflects a low amount of sequence information.

Primary assembly
type: Class
subclass of: Genome assembly
documentation: https://www.ensembl.org/info/genome/genebuild/haplotypes_patches.html
definition: The underlying genome sequence, without alternative sequence included.
has exact synonym: reference sequence

Alternative sequence
type: Class
subclass of: Genome assembly
documentation: https://www.ensembl.org/info/genome/genebuild/haplotypes_patches.html
definition: Genomic sequence that differs from the genomic DNA on the primary assembly. These are represented as sequence on top of the primary assembly. Provided by the GRC for human and mouse.
has exact synonym: non-reference sequence

Patch
type: Class
subclass of: Alternative sequence
documentation: https://www.ensembl.org/info/genome/genebuild/haplotypes_patches.html
definition: New sequences that have been added to the genome assembly since its release. There are two types: fix and nove patches.

Haplotype (genome)
type: Class
subclass of: Alternative sequence
subclass of: Restriction
  on property: related
  some values from: Haplotype (variation)
documentation: https://www.ensembl.org/info/genome/genebuild/haplotypes_patches.html
definition: Known variations to the primary assembly, due to variability in the human genome sequence (eg. the highly variable MHC locus). These were included as part of the genome assembly when it was first produced.
hasDbXref: https://en.wikipedia.org/wiki/Major_histocompatibility_complex

Novel patch
type: Class
subclass of: Patch
documentation: https://www.ensembl.org/info/genome/genebuild/haplotypes_patches.html
definition: Novel patches represent new allelic loci. They can usually be considered as similar to haplotypes and are likely to be reclassified as such in the next genome assembly, but not necessarily.

Fix patch
type: Class
subclass of: Patch
documentation: https://www.ensembl.org/info/genome/genebuild/haplotypes_patches.html
definition: Fix patches are where the primary assembly was found to be incorrect, and the patch reflects the corrected sequence.

Contig
type: Class
subclass of: Genome assembly
documentation: https://www.ensembl.org/info/genome/genebuild/chromosomes_scaffolds_contigs.html
definition: A contig is a contiguous stretch of DNA sequence without gaps that has been assembled solely based on direct sequencing information.
hasDbXref: SO:0000149
hasDbXref: https://en.wikipedia.org/wiki/Contig

Scaffold
type: Class
subclass of: Genome assembly
documentation: https://www.ensembl.org/info/genome/genebuild/chromosomes_scaffolds_contigs.html
definition: Scaffolds are sets of ordered, oriented contigs, assembled by sequence overlap. They are longer sequences than contigs, but shorter than full chromosomes.
hasDbXref: SO:0000148
has exact synonym: Supercontig

Cytogenetic band
type: Class
subclass of: Genome assembly
definition: A banding pattern on a chromosome resulting from staining and examination by microscopy. These are named in terms of the chromosome arm they are found on, and are often used as a shorthand for describing the location of genomic features.
hasDbXref: https://en.wikipedia.org/wiki/Cytogenetics
has exact synonym: cytogenetic map
has exact synonym: chromosome band

Clone
type: Class
subclass of: Genome assembly
definition: A segment of DNA that has been inserted into a vector molecule, such as a plasmid, and then replicated to form many identical copies.

BAC
type: Class
subclass of: Clone
documentation: https://www.ensembl.org/info/genome/genebuild/chromosomes_scaffolds_contigs.html
definition: A vector used to clone DNA fragments (100 to 300-kb insert size; average, 150 kb) from another species so that it can be replicated in bacteria. Many genomes (such as human) were sequenced by cloning segments into BACs, amplifying and sequencing the clones.
hasDbXref: https://en.wikipedia.org/wiki/Bacterial_artificial_chromosome
has exact synonym: Bacterial artificial chromosome

YAC
type: Class
subclass of: Clone
definition: Originated from a bacterial plasmid, a YAC contains a yeast centromeric region, a yeast origin of DNA replication, a cluster of unique rectriction sites and a selectable marker and a telomere region at the en of each arm. YACs are capable of cloning extremely large segments of DNA (over 1 megabase long) into a host cell, where the DNA is propagated along with the other chromosomes of the yeast cell.
hasDbXref: https://en.wikipedia.org/wiki/Yeast_artificial_chromosome
has exact synonym: Yeast artificial chromosome

Cosmid
type: Class
subclass of: Clone
definition: DNA from a bacterial virus spliced with a small fragment of a genome (up to 50 kb) to be amplified and sequenced.
hasDbXref: https://en.wikipedia.org/wiki/Cosmid

Base pairs (genome size)
type: Class
subclass of: Genome assembly
definition: The actual number of bases of sequence we have for a full genome assembly, including alternative sequences and PARs, excluding gaps.

Golden path (genome size)
type: Class
subclass of: Genome assembly
definition: The golden path is the length of the non-redundant reference assembly. It excludes alternative sequences and PARs, but includes the estimated size of the gaps.
hasDbXref: SO:0000688

Coordinate system
type: Class
subclass of: Genome assembly
documentation: https://www.ensembl.org/info/genome/genebuild/chromosomes_scaffolds_contigs.html
definition: Which level of the assembly we are working on.
has exact synonym: coord_system

Karyotype
type: Class
subclass of: Genome assembly
definition: The number of chromosomes of a genome.

PAR
type: Class
subclass of: Genome assembly
documentation: https://www.ensembl.org/info/genome/genebuild/human_PARS.html
definition: Small regions of sequence identity located at the tips of the short and the long arms of the X and Y chromosomes where recombination and genetic exchange take place. Genes within the pseudoautosomal region are not sex linked.
has exact synonym: pseudoautosomal region

Slice
type: Class
subclass of: Genome assembly
documentation: http://www.ensembl.org/info/docs/api/core/core_tutorial.html#slices
definition: The term "slice" in Ensembl refers to a length of DNA sequence. A slice can be any length, from one base long to the entire length of a chromosome.

Toplevel
type: Class
subclass of: Genome assembly
documentation: https://www.ensembl.org/info/genome/genebuild/chromosomes_scaffolds_contigs.html
definition: The largest continuous sequence for an organism. The official technical definition for toplevel sequences are 'sequence regions in the genome assembly that are not a component of another sequence region'. For example, when a genome is assembled into chromosomes, toplevel sequences will be chromosomes and unplaced scaffolds. If a genome has only been assembled into scaffolds, then toplevel sequences are scaffolds and unplaced contigs.

Placed scaffold
type: Class
subclass of: Scaffold
documentation: https://www.ensembl.org/info/genome/genebuild/chromosomes_scaffolds_contigs.html
definition: A scaffold that can be positioned on a chromosome based on genetic mapping information.

Unplaced scaffold
type: Class
subclass of: Scaffold
documentation: https://www.ensembl.org/info/genome/genebuild/chromosomes_scaffolds_contigs.html
definition: A scaffold that cannot be positioned on a chromosome.
hasDbXref: SO:0001875
has exact synonym: unassigned supercontig
has exact synonym: unplaced supercontig
has exact synonym: Unassigned scaffold

Ensembl sources
type: Class
definition: Publicly available database that Ensembl imports data from.

Gene source database
type: Class
subclass of: Ensembl sources
definition: Database from which Ensembl imports cDNA or protein sequence for gene annotation, or gene names.

GENCODE
type: Class
subclass of: Gene source database
documentation: http://www.ensembl.org/info/genome/genebuild/annotation_merge.html
definition: The aim of GENCODE as a sub-project of the ENCODE scale-up project is to annotate all evidence-based gene features in the entire human and mouse genomes at a high accuracy. The GENCODE gene set is the default geneset in Ensembl and is equivalent to the Ensembl/HAVANA merged genes. https://www.gencodegenes.org/
hasDbXref: https://en.wikipedia.org/wiki/GENCODE

RefSeq
type: Class
subclass of: Gene source database
documentation: http://www.ensembl.org/info/genome/genebuild/annotation_sources.html
definition: NCBI's Reference Sequences (RefSeq) database is a curated database of Genbank's genomes, mRNAs and proteins. RefSeq attempts to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, tRNA, and protein products. https://www.ncbi.nlm.nih.gov/refseq/
hasDbXref: https://en.wikipedia.org/wiki/RefSeq

UniProt
type: Class
subclass of: Gene source database
documentation: http://www.ensembl.org/info/genome/genebuild/annotation_sources.html
definition: Database of protein sequence and functional information, based at European Bioinformatics Institute (EMBL-EBI), the SIB Swiss Institute of Bioinformatics and the Protein Information Resource (PIR). These sequences are used as evidence for annotating Ensembl genes. http://www.uniprot.org/
hasDbXref: https://en.wikipedia.org/wiki/UniProt
has exact synonym: UniProt Knowledgebase
has exact synonym: UniProtKB

IMGT
type: Class
subclass of: Gene source database
documentation: http://www.ensembl.org/info/genome/genebuild/ig_tcr.html
definition: International ImMunoGeneTics information system. Database of immunoglobulin and T-cell receptor annotation. We collaborate with IMGT on manual annotation of somatically recombined genes. http://www.imgt.org/
hasDbXref: https://en.wikipedia.org/wiki/HLA_Informatics_Group
has exact synonym: ImMunoGeneTics
has exact synonym: International ImMunoGeneTics information system

SwissProt
type: Class
subclass of: UniProt
documentation: http://www.ensembl.org/info/genome/genebuild/annotation_sources.html
definition: UniProt/Swiss-Prot is a curated protein sequence database that provides a high level of annotation, a minimal level of redundancy and high level of integration with other databases. These sequences are used as evidence for annotating Ensembl genes.
hasDbXref: https://en.wikipedia.org/wiki/UniProt#UniProtKB/Swiss-Prot
has exact synonym: UniProt/SwissProt

TrEMBL
type: Class
subclass of: UniProt
documentation: http://www.ensembl.org/info/genome/genebuild/annotation_sources.html
definition: A subset of TrEMBL (Translated EMBL database) containing the computer-annotated protein translations of all coding sequences (CDS) present in the ENA (formerly EMBL-bank) that are not yet incorporated into the UniProt/SwissProt database. These sequences are used as evidence for annotating Ensembl genes.
hasDbXref: https://en.wikipedia.org/wiki/UniProt#UniProtKB/TrEMBL
has exact synonym: UniProt/TrEMBL

INSDC
type: Class
subclass of: Gene source database
documentation: http://www.ensembl.org/info/genome/genebuild/annotation_sources.html
definition: An international consortium between the ENA, GenBank and DDBJ to share submissions of nucleotide sequence. These sequences are used as evidence for annotating Ensembl genes. http://www.insdc.org/
hasDbXref: https://en.wikipedia.org/wiki/International_Nucleotide_Sequence_Database_Collaboration
has exact synonym: International Nucleotide Sequence Database Collaboration

ENA
type: Class
subclass of: INSDC
documentation: http://www.ensembl.org/info/genome/genebuild/annotation_sources.html
definition: Europe's primary nucleotide sequence resource. The main sources of the DNA and RNA sequences in the database are submissions from individual researchers, genome sequencing projects and patent applications. https://www.ebi.ac.uk/ena
hasDbXref: https://en.wikipedia.org/wiki/European_Nucleotide_Archive
has exact synonym: European Nucleotide Archive

GenBank (database)
type: Class
subclass of: INSDC
subclass of: Restriction
  on property: related
  some values from: GenBank (file format)
documentation: http://www.ensembl.org/info/genome/genebuild/annotation_sources.html
definition: The US branch of INSDC. https://www.ncbi.nlm.nih.gov/genbank/
hasDbXref: https://en.wikipedia.org/wiki/GenBank

DDBJ
type: Class
subclass of: INSDC
documentation: http://www.ensembl.org/info/genome/genebuild/annotation_sources.html
definition: The Asian branch of INSDC. http://www.ddbj.nig.ac.jp/
hasDbXref: https://en.wikipedia.org/wiki/DNA_Data_Bank_of_Japan
has exact synonym: DNA Data Bank of Japan

Gene Ontology
type: Class
subclass of: Gene source database
definition: An organised hierarchy of terms produced by the Gene Ontology Consortium, used to describe the function of proteins. GO terms are split into three subcategories: biological processes (what the protein does), cellular component (where in the cell the protein is found), and molecular function (how the protein acts). http://www.geneontology.org/
hasDbXref: https://en.wikipedia.org/wiki/Gene_ontology
has exact synonym: GO terms
has exact synonym: GO

HGNC
type: Class
subclass of: Gene source database
documentation: http://www.ensembl.org/info/genome/genebuild/gene_names.html
definition: HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication. HGNC gene names are used for Ensembl human genes, where available, and for orthologous genes in other species. https://www.genenames.org/
hasDbXref: https://en.wikipedia.org/wiki/HUGO_Gene_Nomenclature_Committee
has exact synonym: HUGO gene nomenclature committee

Rfam
type: Class
subclass of: Gene source database
documentation: http://www.ensembl.org/info/genome/genebuild/annotation_sources.html
definition: The Rfam database is a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). These sequences are used as evidence for annotating Ensembl non-coding genes. http://rfam.xfam.org/
hasDbXref: https://en.wikipedia.org/wiki/Rfam

miRbase
type: Class
subclass of: Gene source database
documentation: http://www.ensembl.org/info/genome/genebuild/annotation_sources.html
definition: The miRBase database is a searchable database of published miRNA sequences and annotation. These sequences are used as evidence for annotating Ensembl miRNA genes. http://www.mirbase.org/
hasDbXref: https://en.wikipedia.org/wiki/MiRBase

MGI
type: Class
subclass of: Gene source database
documentation: http://www.ensembl.org/info/genome/genebuild/gene_names.html
definition: MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. MGI gene names are used for Ensembl mouse genes, where available. http://www.informatics.jax.org/
hasDbXref: https://en.wikipedia.org/wiki/Mouse_Genome_Informatics
has exact synonym: Mouse genome informatics

zFIN
type: Class
subclass of: Gene source database
documentation: http://www.ensembl.org/info/genome/genebuild/gene_names.html
definition: An online biological database of information about the zebrafish (Danio rerio). zFIN gene names are used for Ensembl zebrafish genes, where available. https://zfin.org/
hasDbXref: https://en.wikipedia.org/wiki/Zebrafish_Information_Network
has exact synonym: Zebrafish Information Network

SGD
type: Class
subclass of: Gene source database
definition: Canonical database for the molecular biology and genetics of Saccharomyces cerevisiae, source of the annotation seen in Ensembl. https://www.yeastgenome.org/
hasDbXref: https://en.wikipedia.org/wiki/Saccharomyces_Genome_Database
has exact synonym: Saccharomyces Genome Database

UCSC Genome Browser
type: Class
subclass of: Gene source database
definition: A genome browser hosted at the University of California Santa Cruz. Ensembl collaborates with UCSC in projects such as GENCODE, CCDS and TSL. https://genome.ucsc.edu/
hasDbXref: https://en.wikipedia.org/wiki/UCSC_Genome_Browser
has exact synonym: Genome Browser
has exact synonym: University of California Santa Cruz
has exact synonym: UCSC

Epigenome source database
type: Class
subclass of: Ensembl sources
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_sources.html
definition: Database from which Ensembl imports ChIP-seq, DNase-seq and other related datasets, which are used in the Ensembl regulatory build.

ENCODE
type: Class
subclass of: Epigenome source database
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_sources.html
definition: Project aiming to build a comprehensive parts list of functional elements in the human genome, including elements that act at the protein and RNA levels, and regulatory elements that control cells and circumstances in which a gene is active, by large scale functional analyses of laboratory cell lines. Used as a source for the Ensembl regulatory build. https://www.encodeproject.org/
hasDbXref: https://en.wikipedia.org/wiki/ENCODE
has exact synonym: ENCyclopedia Of DNA Elements

Blueprint Epigenomes
type: Class
subclass of: Epigenome source database
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_sources.html
definition: Project aiming to apply functional genomics analysis on primary cells of the haematopoietic cell lineage from healthy and diseased individuals, to produce lineage-specific epigenomes. Used as a source for the Ensembl regulatory build. http://www.blueprint-epigenome.eu/

Roadmap Epigenomics
type: Class
subclass of: Epigenome source database
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_sources.html
definition: Project aiming to develop publicly available reference epigenome maps from a variety of cell types. http://www.roadmapepigenomics.org/
hasDbXref: https://en.wikipedia.org/wiki/NCBI_Epigenomics#Roadmap_Epigenomics_Project

Variation source database
type: Class
subclass of: Ensembl sources
documentation: http://www.ensembl.org/info/genome/variation/sources_documentation.html
definition: Database from which Ensembl imports variation data, including loci, sample genotypes, population frequencies and phenotype associations.

dbSNP
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_documentation.html
definition: The Single Nucleotide Polymorphism database (dbSNP) is a public-domain archive for a broad collection of simple (short) genetic polymorphisms in human, maintained by NCBI. https://www.ncbi.nlm.nih.gov/projects/SNP/
hasDbXref: https://en.wikipedia.org/wiki/DbSNP
has exact synonym: Single Nucleotide Polymorphism database

EVA
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_documentation.html
definition: The European Variation Archive is an open-access database of all types of genetic variation data from all species. https://www.ebi.ac.uk/eva/
has exact synonym: European Variation Archive

dbVar
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_documentation.html
definition: dbVar is NCBI's database of human genomic structural variation — insertions, deletions, duplications, inversions, mobile elements, and translocations. https://www.ncbi.nlm.nih.gov/dbvar/

DGVa
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_documentation.html
definition: The Database of Genomic Variants archive (DGVa) is a repository that provides archiving, accessioning and distribution of publicly available genomic structural variants, in all species.https://www.ebi.ac.uk/dgva
has exact synonym: Database of Genomic Variants archive

1000 Genomes project
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_documentation.html
definition: The goal of the 1000 Genomes Project was to find most genetic variants with frequencies of at least 1% in the human populations studied. Ensembl display sample genotypes and population frequencies from the 1000 Genomes project. http://www.internationalgenome.org/
hasDbXref: https://en.wikipedia.org/wiki/1000_Genomes_Project
has exact synonym: 1000G
has exact synonym: 1kG

gnomAD
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_documentation.html
definition: An aggregation of publicly available whole genome and whole exome variant calling experiments in human. GnomAD was previously known as ExAC, when it contained only exome data. Ensembl display population frequencies from gnomAD. http://gnomad.broadinstitute.org/
has exact synonym: Exome Aggregation Consortium
has exact synonym: ExAC
has exact synonym: Genome Aggregation Database

TOPMed
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_documentation.html
definition: Whole genome variant calling data from humans worldwide with heart, lung, blood, and sleep disorders. Ensembl display population frequencies from TOPMed. https://www.nhlbi.nih.gov/science/trans-omics-precision-medicine-topmed-program
has exact synonym: Trans-Omics for Precision Medicine

UK10K
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_documentation.html
definition: Study comparing exomes of 6000 diseased individuals with 4000 healthy individuals in the UK in order to identify disease-causing variants. Ensembl display population frequencies from the control group. https://www.uk10k.org/

HapMap
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_documentation.html
definition: An international collaboration formed to develop a haplotype map of the human genome and thus describe the common patterns of human DNA sequence variation using genotyping. Ensembl display sample genotypes and population frequencies from the HapMap project. https://www.genome.gov/10001688/international-hapmap-project/
hasDbXref: https://en.wikipedia.org/wiki/International_HapMap_Project
has exact synonym: International HapMap Project

ClinVar
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_phenotype_documentation.html
definition: NCBI resource that aggregates information about genomic variation and its relationship to human health. Ensembl display clinical significance and phenotypes from ClinVar. https://www.ncbi.nlm.nih.gov/clinvar/

Phenotype source database
type: Class
subclass of: Ensembl sources
definition: Database from which Ensembl imports phenotype associations with genes and/or variants.

OMIM
type: Class
subclass of: Phenotype source database
documentation: http://www.ensembl.org/info/genome/variation/sources_phenotype_documentation.html
definition: An online database that describes the function and phenotypes associated with human genes. Ensembl display phenotypes from OMIM and MIM morbid. https://www.omim.org/
hasDbXref: https://en.wikipedia.org/wiki/Online_Mendelian_Inheritance_in_Man
has exact synonym: MIM morbid
has exact synonym: Mendelian Inheritance in Man
has exact synonym: Online Mendelian Inheritance in Man
has exact synonym: MIM

OMIA
type: Class
subclass of: Phenotype source database
documentation: http://www.ensembl.org/info/genome/variation/sources_phenotype_documentation.html
definition: An online database that describes the function and phenotypes associated with animal genes. Ensembl display phenotypes from OMIA. https://www.omia.org/
hasDbXref: https://en.wikipedia.org/wiki/Online_Mendelian_Inheritance_in_Animals
has exact synonym: Online Mendelian Inheritance in Animals

Orphanet
type: Class
subclass of: Phenotype source database
documentation: http://www.ensembl.org/info/genome/variation/sources_phenotype_documentation.html
definition: A catalogue of rare disease associations. Ensembl display phenotypes from Orphanet. http://www.orpha.net/
hasDbXref: https://en.wikipedia.org/wiki/Orphanet

GWAS catalog
type: Class
subclass of: Phenotype source database
documentation: http://www.ensembl.org/info/genome/variation/sources_phenotype_documentation.html
definition: A curated database that extracts associations between variants and genes from published genome-wide association studies in human. Ensembl display phenotypes from the GWAS catalog. https://www.ebi.ac.uk/gwas/
has exact synonym: NHGRI-EBI Genome-wide association study catalogue
has exact synonym: GWAS catalogue
has exact synonym: Genome-wide association study catalog
has exact synonym: Genome-wide association study catalogue
has exact synonym: NHGRI-EBI GWAS Catalogue
has exact synonym: NHGRI-EBI Genome-wide association study catalog
has exact synonym: NHGRI-EBI GWAS Catalog

IMPC
type: Class
subclass of: Phenotype source database
documentation: http://www.ensembl.org/info/genome/variation/sources_phenotype_documentation.html
definition: An international scientific endeavour to create and characterise the phenotype of 20,000 knockout mouse strains. Ensembl display phenotypes from the IMPC. http://www.mousephenotype.org/
hasDbXref: https://en.wikipedia.org/wiki/International_Mouse_Phenotyping_Consortium
has exact synonym: International Mouse Phenotyping Consortium

Animal QTLdb
type: Class
subclass of: Phenotype source database
documentation: http://www.ensembl.org/info/genome/variation/sources_phenotype_documentation.html
definition: Project aiming to house all publicly available QTL and association data on livestock animal species. Ensembl display phenotypes from the Animals QTLdb. https://www.animalgenome.org/cgi-bin/QTLdb/index
has exact synonym: Animal Quantitative Trait Loci Database

HGMD
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_phenotype_documentation.html
definition: Project aiming to collate all known (published) gene lesions responsible for human inherited disease. Full HGMD access is restricted to license holders so Ensembl supports the minimal public data release which consists of variant/mutation names and locations. http://www.hgmd.cf.ac.uk/ac/index.php
has exact synonym: Human Gene Mutation Database

COSMIC
type: Class
subclass of: Variation source database
documentation: http://www.ensembl.org/info/genome/variation/sources_documentation.html
definition: Database of somatic variants found in cancer. COSMIC licensing does not permit redistribution of the full dataset, but mutation identifiers, locations and tumour types are available in Ensembl. http://cancer.sanger.ac.uk/cosmic
hasDbXref: https://en.wikipedia.org/wiki/COSMIC_cancer_database
has exact synonym: Catalog Of Somatic Mutations In Cancer
has exact synonym: Catalogue Of Somatic Mutations In Cancer

Protein source database
type: Class
subclass of: Ensembl sources

PDB
type: Class
subclass of: Protein source database
definition: A repository for 3D biological macromolecular structure data. Ensembl provide links out to the PDB, and use structures to display the locations of variants in proteins. http://www.ebi.ac.uk/pdbe/
hasDbXref: https://en.wikipedia.org/wiki/Protein_Data_Bank
has exact synonym: Protein Data Bank

Algorithm
type: Class
definition: A sequence of computational tasks or actions that carry out a specific function.
hasDbXref: https://en.wikipedia.org/wiki/Algorithm

Ensembl Genebuild
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/genebuild/genome_annotation.html
definition: The automatic process by which Ensembl plot known RNA and protein sequence onto the genome, using sequence similarity.
has exact synonym: Ensembl Genes
has exact synonym: Ensembl annotation
has exact synonym: Genebuild

Ensembl Havana
type: Class
subclass of: Ensembl Genebuild
documentation: www.ensembl.org/info/genome/genebuild/manual_havana.html
definition: Human And Vertebrate ANalysis and Annotation. The team within Ensembl who manually annotate genes and transcripts for a subset of species.
has exact synonym: manual annotation
has exact synonym: Havana

Ensembl Regulatory Build
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_build.html
definition: The process by which Ensembl predict the location of regions that regulate gene expression using epigenomic evidence.

Ensembl gene tree pipeline
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/compara/homology_method.html
definition: The process by which Ensembl compare gene sequences in order to construct gene trees and predict homologues.

InterProScan
type: Class
subclass of: Algorithm
definition: InterPro is an integrated resource for protein families, domains and sites, combining information from several different protein signature databases, including PROSITE, PRINTS, Pfam, Seg, SignalP, Gene3D, SMART, TIGRFAMs, PIR SuperFamilies and SUPERFAMILY. Ensembl run InterProScan on all protein sequences, which uses these protein signatures to identify domains. https://www.ebi.ac.uk/interpro/
hasDbXref: https://en.wikipedia.org/wiki/InterPro

BLAST
type: Class
subclass of: Algorithm
definition: A sequence comparison algorithm optimised for speed which is used to search sequence databases for optimal local alignments to a query.
hasDbXref: https://en.wikipedia.org/wiki/BLAST
has exact synonym: Basic Local Alignment Search Tool

BLAT
type: Class
subclass of: Algorithm
definition: An mRNA/DNA and cross-species protein sequence analysis tool to quickly find sequences of 95% and greater similarity of length 40 bases or more.
hasDbXref: https://en.wikipedia.org/wiki/BLAT_(bioinformatics)
has exact synonym: BLAST-Like Alignment Tool

DUST
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: A standalone application that looks for low complexity sequences.

Eponine
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/genebuild/automatic_coding.html
definition: Eponine is a probabilistic method for detecting transcription start sites (TSS) in mammalian genomic sequence, with good specificity and excellent positional accuracy. Eponine models consist of a set of DNA weight matrices recognising specific sequence motifs. Each of these is associated with a position distribution relative to the TSS. http://www.sanger.ac.uk/science/tools/eponine

GeneWise
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/genebuild/automatic_coding.html
definition: GeneWise is a sequence analysis tool for comparing proteins to DNA sequences allowing for introns and frameshifts. It is used in the Targetted stage of the Ensembl GeneBuild. https://www.ebi.ac.uk/Tools/psa/genewise/

Exonerate
type: Class
subclass of: Algorithm
definition: A fast gapped DNA-DNA alignment algorithm. It can be used for aligning various types of sequences such as genomic DNA, cDNAs/ESTs, and proteins. It is used in the Targetted stage of the Ensembl GeneBuild. https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate

Projection build
type: Class
subclass of: Ensembl Genebuild
documentation: http://www.ensembl.org/info/genome/genebuild/2x_genomes.html
definition: A gene build method used by Ensembl for low coverage genomes, allowing genes to be annotated that span two scaffolds by mapping to the human gene.

GENSCAN
type: Class
subclass of: Algorithm
definition: An HMM-based ab initio gene prediction method, used to create a track of ab initio genes in Ensembl. http://genes.mit.edu/GENSCAN.html
hasDbXref: https://en.wikipedia.org/wiki/GENSCAN

SIFT
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html#sift
definition: A tool which predicts if missense variants are likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. http://sift.bii.a-star.edu.sg/

PolyPhen
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/variation/predicted_data.html#polyphen
definition: A tool which predicts if missense variants are likely to affect protein function based on physical and comparative considerations. http://genetics.bwh.harvard.edu/pph2/

RepeatMasker
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: The method by which repeated sequences and low-complexity regions are hidden, usually used in searches by alignment and homology-searching programs. http://www.repeatmasker.org/
hasDbXref: https://en.wikipedia.org/wiki/Repeated_sequence_(DNA)

BLOSUM 62
type: Class
subclass of: Algorithm
definition: A matrix that defines scores for amino acid substitutions, reflecting the similarity of physicochemical properties, and observed substitution frequencies. The BLOSUM 62 matrix is tailored using sequences sharing no more than 62% identity (sequences closer evolutionary, were represented by a single sequence in the alignment to avoid bias from using related family members).
hasDbXref: https://en.wikipedia.org/wiki/BLOSUM
has exact synonym: Blocks Substitution Matrix

VEP
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/docs/tools/vep/index.html
definition: The Variant Effect Predictor (VEP) is an Ensembl tool that predicts the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
hasDbXref: https://en.wikipedia.org/wiki/Ensembl_Genomes#Variant_Effect_Predictor
has exact synonym: Variant Effect Predictor

File formats
type: Class

HGVS nomenclature
type: Class
subclass of: File formats
definition: A set of recomendations for variant naming. The nomenclature describes the change a variant allele has on a named (genomic, transcript or protein) sequence. Can be used as an input for the VEP and displayed for known variants. http://varnomen.hgvs.org/
has exact synonym: HGVS
has exact synonym: Human Genome Variation Society
has exact synonym: Sequence Variant Nomenclature
has exact synonym: HGVS names

VCF
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#vcf
definition: VCF is a standard format for listing genetic variation, which is the output for many variant callers. It can be used as an input for the Ensembl VEP and is used to store and download variation data in Ensembl.
hasDbXref: https://en.wikipedia.org/wiki/Variant_Call_Format
has exact synonym: Variant Call Format

BED
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/website/upload/bed.html
definition: BED is a simple format for listing genomic loci. It can be used to upload data to view in Ensembl, as a custom file for additional VEP annotation and is used to store and download constrained elements in Ensembl.

FASTA
type: Class
subclass of: File formats
definition: FASTA is used to store finished nucleotide and peptide sequences. The Ensembl FTP site has genome, cDNA, CDS and peptide sequences in FASTA, and you can export FASTA from various webpages in Ensembl.
hasDbXref: https://en.wikipedia.org/wiki/FASTA_format

BAM/CRAM
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/website/upload/large.html#bam-format
definition: BAM and CRAM store alignments of NGS data to the genome. Ensembl allow attachment of BAM and CRAM files to view in against the gene, and store RNA-seq, ChIP-seq and DNase-seq in BAM.
hasDbXref: https://en.wikipedia.org/wiki/Binary_Alignment_Map
has exact synonym: BAM
has exact synonym: CRAM
has exact synonym: SAM
has exact synonym: Binary alignment map

BigBed
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/website/upload/large.html#bb-format
definition: BigBed is an indexed form of BED, which can be used to store larger scale data. Ensembl allow attachment of BigBed files to view against the genome and store peaks of regulatory evidence as BigBed.

Ensembl default (VEP)
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/docs/tools/vep/vep_formats.html#default
definition: Ensembl default is an input format for the VEP, used to describe the position and alleles of a variant.

BedGraph
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/website/upload/bed.html#bedGraph
definition: BedGraph allows you to store scores for loci in BED format, the loci can be of varying size. It can be uploaded to view in Ensembl.

GTF
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/website/upload/gff.html
definition: GTF is a tab-limited format that describes genomic features, such as genes and transcripts, and allows hierarchical linking of gene features. Ensembl store gene files as GTF, allow attachment of GTF files to view against the genome and allow custom annotation with the VEP using GTF files.
hasDbXref: https://en.wikipedia.org/wiki/Gene_transfer_format
has exact synonym: General transfer format
has exact synonym: Gene transfer format

GFF
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/website/upload/gff3.html
definition: GFF is a tab-limited format that describes genomic features, such as genes and transcripts, and allows hierarchical linking of gene features. Ensembl store gene files as GFF, allow attachment of GFF files to view against the genome and allow custom annotation with the VEP using GFF files.
hasDbXref: https://en.wikipedia.org/wiki/General_feature_format
has exact synonym: gene-finding format
has exact synonym: generic feature format
has exact synonym: General feature format

PSL
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/website/upload/psl.html
definition: PSL represents alignments and can be viewed in Ensembl.

Wiggle
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/website/upload/wig.html
definition: Wiggle format expresses scores across genomic loci, requiring fixed size bins for the scores. It can be uploaded to view in Ensembl.
has exact synonym: WIG

BigWig
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/website/upload/large.html#bw-format
definition: BigWig is an indexed form of wiggle and can be used to store larger scale data. Ensembl simplify NGS data, such as ChIP-seq and RNA-seq into BigWig to view in the browser. It can also be used to attach your own data to Ensembl.

Pairwise interactions (WashU)
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/website/upload/pairwise.html
definition: Pairwise interactions, such as those derived from Hi-C, can be stored in the WashU format and viewed in Ensembl.
hasDbXref: https://en.wikipedia.org/wiki/Chromosome_conformation_capture

chain
type: Class
subclass of: File formats
definition: Chain files describe the mapping between different genome assemblies. Ensembl store these on the FTP site.
has exact synonym: chain mapping
has exact synonym: mapping
has exact synonym: assembly chain

Newick
type: Class
subclass of: File formats
definition: Newick is a tree format. Ensembl gene trees can be downloaded in Newick and it is used to store Ensembl species trees.
hasDbXref: https://en.wikipedia.org/wiki/Newick_format
has exact synonym: New Hampshire tree format
has exact synonym: Newick format
has exact synonym: Newick notation
has exact synonym: Newick tree format

EMBL (file format)
type: Class
subclass of: File formats
definition: EMBL files store sequence and accompanying annotation for features across a genomic region. They can be exported from various webpages in Ensembl and are stored for 1Mb regions across the genome.

GenBank (file format)
type: Class
subclass of: File formats
subclass of: Restriction
  on property: related
  some values from: GenBank (database)
definition: GenBank files store sequence and accompanying annotation for features across a genomic region. They can be exported from various webpages in Ensembl and are stored for 1Mb regions across the genome.

EMF Alignment format
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/data/ftp/index.html
definition: Ensembl Multi Format (EMF) stores genomic alignments in Ensembl.
has exact synonym: Ensembl Multi Format

MAF
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/data/ftp/index.html
definition: Multiple alignment format (MAF) stores genomic alignments.
has exact synonym: Multiple alignment format

MySQL
type: Class
subclass of: File formats
documentation: http://www.ensembl.org/info/data/mysql.html
definition: MySQL is a database. All Ensembl data is stored in MySQL relational tables, which can be found on the FTP site and accessed directly by MySQL queries.
hasDbXref: https://en.wikipedia.org/wiki/MySQL

VEP cache
type: Class
subclass of: File formats
documentation: https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html
definition: A VEP cache contains all the gene and variant data needed to run a VEP query, and can be used to run large queries quickly on your own machine. These can be installed as part of your VEP installtion, or downloaded from the FTP site.

GVF
type: Class
subclass of: File formats
definition: Genome Variation Format (GVF) is used to store variation data. It can be found on the Ensembl FTP site.
has exact synonym: Genome Variation Format

PhyloXML
type: Class
subclass of: File formats
definition: PhyloXML is an XML language for the analysis, exchange, and storage of phylogenetic trees (or networks) and associated data. It is used to store Ensembl phylogenetic trees.
hasDbXref: https://en.wikipedia.org/wiki/PhyloXML

OrthoXML
type: Class
subclass of: File formats
definition: OrthoXML is an XML format to allow the storage and comparison of orthology data. It is used to store Ensembl homologues.

RDF
type: Class
subclass of: File formats
definition: Resource Description Framework (RDF) is used as a metadata data model. Ensembl use it to describe links from Ensembl annotations to those annotations in other databases.
hasDbXref: https://en.wikipedia.org/wiki/Resource_Description_Framework
has exact synonym: Resource Description Framework

AGP
type: Class
subclass of: File formats
definition: A golden path. A file provided to Ensembl that describes how the longer sequences in the genome assembly were assembled from shorter sequences. For example, an AGP file can describe how a chromosome is assembled from a collection of scaffolds or a collection of contigs. For an AGP file that describes how a scaffold is assembled from a collection of contigs, each contig will be listed on a separate line in the AGP file and the line will include information about where the contig lies within the scaffold and the orientation of the contig.
has exact synonym: A golden path

Repeat
type: Class
subclass of: Genome annotation
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
hasDbXref: https://en.wikipedia.org/wiki/Repeated_sequence_(DNA)

Repeat masking
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: The method by which repeated sequences and low-complexity regions are hidden, usually used in searches by alignment and homology-searching programs.
hasDbXref: https://en.wikipedia.org/wiki/Repeated_sequence_(DNA)

Hard masked
type: Class
subclass of: Repeat masking
definition: Hard masked sequence is repeat masked with the repeat sequences replaced by Ns. Hard masked sequence files on the Ensembl FTP site have "rm" in their file name.

Soft masked
type: Class
subclass of: Repeat masking
definition: Soft masked sequence is repeat masked with the repeat sequences in lower case. Soft masked sequence files on the Ensembl FTP site have "sm" in their file name.

Alu insertion
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: A dispersed intermediately repetitive DNA sequence found in the human genome in about one million copies. The sequence is about 300 bp long and is found commonly in introns, 3' untranslated regions of genes, and intergenic genomic regions. The name Alu comes from the a recognition site for the AluI endonuclease that cleaves it.
hasDbXref: SO:0002063
hasDbXref: https://en.wikipedia.org/wiki/Alu_element

Microsatellite
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: A region in the genomic sequence containing short tandem repeats of 2-10bp.
hasDbXref: SO:0000289
hasDbXref: https://en.wikipedia.org/wiki/Microsatellite

Centromere
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: The region of the chromosome at which the two sister chromatids are joined during mitosis and meiosis, mostly composed of satellite DNA.
hasDbXref: SO:0000577
hasDbXref: https://en.wikipedia.org/wiki/Centromere

Low complexity regions
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: Poly-purine or poly-pyrimidine stretches, or regions of extremely high AT or GC content.

RNA repeats
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: Non-functional copies of RNA genes which have been reintegrated into the genome with the assistance of a reverse transcriptase.

Satellite repeats
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: Multiple copies of the same base sequence on a DNA sequence. The repeated pattern can vary in length from a single base to several thousand bases long.
hasDbXref: SO:0000005
hasDbXref: https://en.wikipedia.org/wiki/Satellite_DNA

Simple repeats
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: Duplications of simple sets of DNA bases (typically 1-5bp) such as A, CA, CGG etc.

Tandem repeats
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: Typically found at the centromeres and telomeres of chromosomes these are duplications of more complex 100-200 base sequences.
hasDbXref: https://en.wikipedia.org/wiki/Tandem_repeat

LTRs
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: Long tandem repeats.
hasDbXref: https://en.wikipedia.org/wiki/Tandem_repeat

Type I Transposons/LINE
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: Long Interspersed Elements. Retrotransposed elements in the genome containing open reading frames encoding (often inactive) reverse transcription machinery.
hasDbXref: SO:0000194
hasDbXref: https://en.wikipedia.org/wiki/Long_interspersed_nuclear_element
has exact synonym: long interspersed nuclear element
has exact synonym: LINE

Type I Transposons/SINE
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: Short Interspersed Elements. Retrotransposed elements less than 500 bp that contain tRNA, snRNA and rRNA, which require other mobile elements to be transposed. Alu elements are a type of SINE.
hasDbXref: SO:0000206
hasDbXref: https://en.wikipedia.org/wiki/Short_interspersed_nuclear_element
has exact synonym: short interspersed nuclear element
has exact synonym: SINE

Type II Transposons
type: Class
subclass of: Repeat
documentation: http://www.ensembl.org/info/genome/genebuild/assembly_repeats.html
definition: Elements that have been transposed and duplicated around the genome by excision and ligation.
hasDbXref: SO:0000182
hasDbXref: https://en.wikipedia.org/wiki/Transposable_element#Classification
has exact synonym: DNA transposon

Unknown repeat
type: Class
subclass of: Repeat
definition: Repeats that cannot be classified.

Alignments
type: Class
subclass of: Genome annotation
definition: A comparison between two or more sequences by matching identical and/or similar residues/nucleotides and assigning a score to the match.
hasDbXref: https://en.wikipedia.org/wiki/Sequence_alignment

Whole genome alignment
type: Class
subclass of: Alignments
definition: An alignment carried out using the whole genome sequence.

Pairwise whole genome alignment
type: Class
subclass of: Whole genome alignment
documentation: http://www.ensembl.org/info/genome/compara/analyses.html
definition: An alignment between two whole genomes.
has exact synonym: Pairwise sequence alignment
has exact synonym: Pairwise alignment

Multiple whole genome alignment
type: Class
subclass of: Whole genome alignment
documentation: http://www.ensembl.org/info/genome/compara/multiple_genome_alignments.html
definition: An alignment between more than two whole genomes of a selected taxon.
has exact synonym: Multiple sequence alignment
has exact synonym: Multiple alignment

Synteny
type: Class
subclass of: Whole genome alignment
documentation: http://www.ensembl.org/info/genome/compara/synteny.html
definition: In a genomic context we refer to syntenic regions if the sequence is globally conserved between two species.
hasDbXref: https://en.wikipedia.org/wiki/Synteny

CIGAR
type: Class
subclass of: Alignments
definition: The cigar line defines the sequence of matches/mismatches and deletions (or gaps) in an alignment
hasDbXref: https://en.wikipedia.org/wiki/Sequence_alignment#Representations
has exact synonym: Compact Idiosyncratic Gapped Alignment Report

Identity
type: Class
subclass of: Alignments
definition: A measure of how similar two alignment sequences are, specifically, what percentage of amino acids or nucleotides are the same in type and position between the two sequences. The value is dependent on which sequence is used as the reference, since it is a percentage of that reference.
has exact synonym: %ID

Wasabi
type: Class
subclass of: Alignments
definition: An application for displaying sequence alignments with custom colour-annotation, which is used by Ensembl displaying gene tree and family alignments. http://wasabiapp.org/

Similarity
type: Class
subclass of: Alignments
definition: How well one sequence matches another determined by calculation by an alignment program of identical and conserved residues/nucleotides.

Pecan
type: Class
subclass of: Multiple whole genome alignment
documentation: http://www.ensembl.org/info/genome/compara/multiple_genome_alignments.html
definition: Pecan is a global multiple sequence alignment program that makes practical the probabilistic consistency methodology for significant numbers of sequences of practically arbitrary length.

EPO
type: Class
subclass of: Multiple whole genome alignment
documentation: http://www.ensembl.org/info/genome/compara/multiple_genome_alignments.html
definition: The EPO (Enredo, Pecan, Ortheus) pipeline is a three step pipeline for whole-genome multiple alignments, using Enredo segments, aligning them with Pecan and constructing ancestal sequences with Ortheus.
has exact synonym: Enredo Pecan Ortheus

Progressive cactus
type: Class
subclass of: Multiple whole genome alignment
documentation: http://www.ensembl.org/info/genome/compara/multiple_genome_alignments.html
definition: Progressive-Cactus is a next-generation aligner that stores whole-genome alignments in a graph structure.

LastZ
type: Class
subclass of: Pairwise whole genome alignment
documentation: http://www.ensembl.org/info/genome/compara/analyses.html
definition: LASTZ is a program for aligning DNA sequences in a pairwise manner. Its precedesessor is BlastZ.

BlastZ
type: Class
subclass of: Pairwise whole genome alignment
documentation: http://www.ensembl.org/info/genome/compara/analyses.html
definition: BlastZ is a program for aligning DNA sequences in a pairwise manner. It has been replaced by LASTZ.

Translated Blat
type: Class
subclass of: Pairwise whole genome alignment
definition: Translated Blat can be used for alignment of the coding regions of genomes only in a pairwise manner.
hasDbXref: https://en.wikipedia.org/wiki/BLAT_(bioinformatics)

Regulatory features
type: Class
subclass of: Genome annotation
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: Regions that are predicted to regulate the expression of genes, based on the Ensembl regulatory build.
has exact synonym: reg-feat

Promoters
type: Class
subclass of: Regulatory features
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: Regions at the 5' end of genes where transcription factors and RNA polymerase bind to initiate transcription.
hasDbXref: SO:0000167
hasDbXref: https://en.wikipedia.org/wiki/Promoter_(genetics)

Promoter flanking regions
type: Class
subclass of: Regulatory features
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: Transcription factor binding regions that flank promoters.
hasDbXref: SO:0001952
hasDbXref: https://en.wikipedia.org/wiki/Promoter_(genetics)

Enhancers
type: Class
subclass of: Regulatory features
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: Regions that bind transcription factors and interact with promoters to stimulate transcription of distant genes.
hasDbXref: SO:0000165
hasDbXref: https://en.wikipedia.org/wiki/Enhancer_(genetics)

CTCF binding sites
type: Class
subclass of: Regulatory features
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: Regions that bind CTCF, the insulator protein that demarcates open and closed chromatin.
hasDbXref: SO:0001974
hasDbXref: https://en.wikipedia.org/wiki/CTCF

Transcription factor binding sites
type: Class
subclass of: Regulatory features
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: Sites which bind transcription factors, for which no other role can be determined as yet.
hasDbXref: SO:0000235

Open chromatin regions
type: Class
subclass of: Regulatory features
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: Regions of spaced out histones, making them accessible to protein interactions.
hasDbXref: SO:0001747
hasDbXref: https://en.wikipedia.org/wiki/DNase_I_hypersensitive_site

Regulatory activity
type: Class
subclass of: Regulatory features
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: The activity state of a regulatory feature in a specific epigenome.

Active
type: Class
subclass of: Regulatory activity
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: When a regulatory feature displays an epigenetic signature which is consistent with it carrying out its named function, for example an active Promoter has an epigenetic signature consistent with initiating transcription, while an active CTCF binding site will bind CTCF. It is analogous to a sprinter running.

Poised
type: Class
subclass of: Regulatory activity
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: When a regulatory feature displays a epigenetic signature with the potential to be activated. It is analogous to a sprinter in the blocks.

Repressed
type: Class
subclass of: Regulatory activity
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: When a regulatory feature is epigenetically repressed, having an epigenetic signature that prevents it from being active.

Inactive
type: Class
subclass of: Regulatory activity
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: When a regulatory feature bears no epigenetic modifications from the ones included in the Regulatory Build.

NA
type: Class
subclass of: Regulatory activity
documentation: http://www.ensembl.org/info/genome/funcgen/regulatory_features.html
definition: When there is no available data in the cell type for this regulatory feature.

Epigenome evidence
type: Class
subclass of: Regulatory features
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_sources.html
definition: Experimental data that is used to construct and determine activity of regulatory features.

ChIP-seq
type: Class
subclass of: Epigenome evidence
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_sources.html
definition: A method to determine the genomic regions that proteins bind to.
hasDbXref: https://en.wikipedia.org/wiki/ChIP-sequencing
has exact synonym: Chromatin Immunoprecipitation Sequencing
has exact synonym: ChIPSeq

DNase sensitivity
type: Class
subclass of: Epigenome evidence
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_sources.html
definition: A method to determine regions of open and closed chromatin.
hasDbXref: https://en.wikipedia.org/wiki/DNase-Seq
has exact synonym: DNase hypersensitivity
has exact synonym: DNase-seq

Transcription factor
type: Class
subclass of: Epigenome evidence
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_sources.html
definition: A protein that binds to DNA and controls the rate of transcription.
hasDbXref: https://en.wikipedia.org/wiki/Transcription_factor
has exact synonym: TF

Histone modification
type: Class
subclass of: Epigenome evidence
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_sources.html
definition: Covalent modifications to the histone proteins that make up the nucleosome, which are known to regulate gene expression.
hasDbXref: SO:0001700
hasDbXref: https://en.wikipedia.org/wiki/Histone#Histone_modification
has exact synonym: histone acetylation
has exact synonym: histone methylation
has exact synonym: Histone mod

DNA methylation
type: Class
subclass of: Epigenome evidence
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_other.html
definition: Modification of cytosines in CpGs with methyl groups, which is known to repress gene expression.
hasDbXref: SO:0000114
hasDbXref: https://en.wikipedia.org/wiki/DNA_methylation
has exact synonym: CpG methylation

Bisulfite sequencing
type: Class
subclass of: Epigenome evidence
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_other.html
definition: A method to determine the methylation of genomic cytosines.
hasDbXref: https://en.wikipedia.org/wiki/Bisulfite_sequencing
has exact synonym: RRBS
has exact synonym: WGBS
has exact synonym: Bisulphite sequencing

Signal
type: Class
subclass of: Epigenome evidence
documentation: http://www.ensembl.org/info/genome/funcgen/peak_calling.html
definition: A count of the number of NGS reads from an epigenome experiment aligned to a locus, shown as a BigWig across the genome.

Peak
type: Class
subclass of: Epigenome evidence
documentation: http://www.ensembl.org/info/genome/funcgen/peak_calling.html
definition: Locus identified from epigenome signal as being having high signal, shown as a BigBed across the genome.

Transcription factor binding motif
type: Class
subclass of: Regulatory features
definition: Short genomic sequence that is known to bind to a particular transcription factor.
hasDbXref: https://en.wikipedia.org/wiki/DNA_binding_site
has exact synonym: Motif
has exact synonym: PWM
has exact synonym: Position weight matrices
has exact synonym: TFBM
has exact synonym: Position weight matrix

Epigenome
type: Class
subclass of: Regulatory activity
documentation: http://www.ensembl.org/info/genome/funcgen/regulation_sources.html
definition: A cell type, such as a primary tissue or lab cell line, for which we have epigenome evidence and can predict regulatory features.
has exact synonym: cell type
has exact synonym: tissue
has exact synonym: Cell line

Marker
type: Class
subclass of: Genome annotation
definition: A short sequence whose placement on the genome is known.

UniSTS
type: Class
subclass of: Marker
definition: UniSTS is a NCBI resource for non-redundant Sequence Tagged Sites (STS) markers. For each marker, UniSTS displays the primer sequences, product size, and mapping information, as well as cross references to dbSNP, RHdb, GDB, MGD, etc. The marker report also lists GenBank and RefSeq records that contain the primer sequences determined by ePCR.

External reference
type: Class
subclass of: Genome annotation
documentation: http://www.ensembl.org/info/genome/genebuild/xrefs.html
definition: Mapping between Ensembl genes, transcripts and proteins to the same features in other databases.
has exact synonym: general identifiers
has exact synonym: xref

CADD
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/variation/prediction/protein_function.html
definition: A tool that integrates multiple annotations into one metric for scoring the deleteriousness of single nucleotide variants.

REVEL
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/variation/prediction/protein_function.html
definition: A tool for predicting the pathogenicity of single nucleotide variants using an ensemble method.

MutationAssessor
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/variation/prediction/protein_function.html
definition: A tool for assessing the functional impact of single nucleotide variants based on evolutionary conservation of the affected amino acid in protein homologues.

MetaLR
type: Class
subclass of: Algorithm
documentation: http://www.ensembl.org/info/genome/variation/prediction/protein_function.html
definition: A tool for predicting the pathogenicity of single nucleotide variants using a logistic regression based ensemble method.

MANE
type: Class
subclass of: Transcript
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: The Matched Annotation from NCBI and EMBL-EBI is a collaboration between Ensembl/GENCODE and RefSeq to identify transcripts that match GRCh38 and are 100% identical between RefSeq and Ensembl/GENCODE for 5' UTR, CDS, splicing and 3'UTR.
has exact synonym: Matched Annotation between NCBI and EBI
has exact synonym: Matched Annotation from NCBI and EMBL-EBI
has exact synonym: Matched Annotation from NCBI and Ensembl
has exact synonym: MAIN

MANE Select
type: Class
subclass of: MANE
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: The Matched Annotation from NCBI and EMBL-EBI is a collaboration between Ensembl/GENCODE and RefSeq. The MANE Select is a default transcript per human gene that is representative of biology, well-supported, expressed and highly-conserved. This transcript set matches GRCh38 and is 100% identical between RefSeq and Ensembl/GENCODE for 5' UTR, CDS, splicing and 3'UTR.
has exact synonym: Matched Annotation from NCBI and EBI Select
has exact synonym: Matched Annotation from NCBI and EMBL-EBI Select
has exact synonym: Matched Annotation from NCBI and Ensembl Select
has exact synonym: MAIN Select

TAGENE
type: Class
subclass of: Transcript
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: Long-read sequence data is computationally processed into non-redundant transcript models which are manually appraised by the Ensembl-Havana annotation team.
has exact synonym: tagine

Stop codon readthrough
type: Class
subclass of: Biotype
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: The coding sequence contains a stop codon that is translated (as supported by experimental evidence), and termination occurs instead at a canonical stop codon further downstream. It is currently unknown which codon is used to replace the translated stop codon, hence it is represented by 'X' in the protein sequence
hasDbXref: https://en.wikipedia.org/wiki/Stop_codon#Translational_readthrough

Forward strand
type: Class
subclass of: Genome annotation
subclass of: Restriction
  on property: related
  some values from: Reverse strand
documentation: http://www.ensembl.org/Help/Faq
definition: DNA strand arbitrary defined as the strand with its 5' end at the tip of the short chromosome arm (p). If a gene is forward-stranded, its sense (sequence matching cDNA) is on the forward strand. Forward strand is reverse complementary to the reverse strand.
hasDbXref: SO:0001030
has exact synonym: + strand
has exact synonym: 1 strand
has exact synonym: positive strand
has exact synonym: Plus strand

Reverse strand
type: Class
subclass of: Genome annotation
subclass of: Restriction
  on property: related
  some values from: Forward strand
documentation: http://www.ensembl.org/Help/Faq
definition: DNA strand arbitrary defined as the strand with its 5' end at the tip of the long chromosome arm (q). If a gene is reverse-stranded, its sense (sequence matching cDNA) is on the reverse strand. Reverse strand is reverse complementary to the forward strand.
hasDbXref: SO:0001031
has exact synonym: - strand
has exact synonym: -1 strand
has exact synonym: negative strand
has exact synonym: Minus strand

RefSeq Match
type: Class
subclass of: MANE Select
documentation: http://www.ensembl.org/info/genome/genebuild/mane.html
definition: RefSeq transcripts that match 100% across the sequence, exon/intron structure and UTRs as part of the MANE project

UniProt Match
type: Class
subclass of: UniProt
definition: The UniProt identifier that matches to the Ensembl transcript. This may be a UniProt protein isoform and will have a number suffix, or may just refer to a UniProt entry.

Nonsense Mediated Decay
type: Class
subclass of: Biotype
definition: A transcript with a premature stop codon considered likely to be subjected to targeted degradation. Nonsense-Mediated Decay is predicted to be triggered where the in-frame termination codon is found more than 50bp upstream of the final splice junction.
hasDbXref: https://en.wikipedia.org/wiki/Nonsense-mediated_decay
has exact synonym: Nonsense-Mediated Decay
has exact synonym: NMD

Non-ATG start
type: Class
subclass of: Transcript
definition: A transcript with a non-ATG start codon but which still encodes a methionine since the ribosomal machinery allows non-AUG to translate as methionine in specific cases.
hasDbXref: https://en.wikipedia.org/wiki/Start_codon

MANE Plus Clinical
type: Class
subclass of: MANE
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: Transcripts in the MANE Plus Clinical set are additional transcripts per locus necessary to support clinical variant reporting, for example transcripts containing known Pathogenic or Likely Pathogenic clinical variants not reportable using the MANE Select set. Note there may be additional clinically relevant transcripts in the wider RefSeq and Ensembl/GENCODE sets but not yet in MANE.
has exact synonym: Matched Annotation from NCBI and EBI Plus Clinical
has exact synonym: Matched Annotation from NCBI and EMBL-EBI Plus Clinical
has exact synonym: Matched Annotation from NCBI and Ensembl Plus Clinical
has exact synonym: MAIN Plus Clinical

GENCODE Comprehensive
type: Class
subclass of: Transcript
documentation: http://www.ensembl.org/info/genome/genebuild/transcript_quality_tags.html
definition: The full GENCODE transcript set, containing both complete transcripts and 5' and 3' incomplete transcripts.

Protein coding CDS not defined
type: Class
subclass of: Biotype
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS.

Protein coding LOF
type: Class
subclass of: Biotype
documentation: http://www.ensembl.org/info/genome/genebuild/biotypes.html
definition: Not translated in the reference genome owing to a SNP/DIP but in other individuals/haplotypes/strains the transcript is translated. Replaces the polymorphic_pseudogene transcript biotype.