PREFIX glossary:
PREFIX rdf:
PREFIX rdfs:
PREFIX xsd:
glossary:ENSGLOSSARY_0000068 a rdfs:Class ;
rdfs:label "CDS" ;
rdfs:comment "CoDing Sequence. The region of a cDNA which is translated. In Ensembl displays, the stop codon is included as part of the CDS sequence." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000123 a rdfs:Class ;
rdfs:label "Interchromosomal breakpoint" ;
rdfs:comment "A rearrangement breakpoint between two different chromosomes." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000105 .
glossary:ENSGLOSSARY_0000265 a rdfs:Class ;
rdfs:label "Exonerate" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000362 a rdfs:Class ;
rdfs:label "MutationAssessor" ;
rdfs:comment "A tool for assessing the functional impact of single nucleotide variants based on evolutionary conservation of the affected amino acid in protein homologues." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000014 a rdfs:Class ;
rdfs:label "APPRIS P2" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000012 .
glossary:ENSGLOSSARY_0000169 a rdfs:Class ;
rdfs:label "Regulatory region ablation" ;
rdfs:comment "A feature ablation whereby the deleted region includes a regulatory region" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000343 a rdfs:Class ;
rdfs:label "Repressed" ;
rdfs:comment "When a regulatory feature is epigenetically repressed, having an epigenetic signature that prevents it from being active." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000340 .
glossary:ENSGLOSSARY_0000246 a rdfs:Class ;
rdfs:label "Orphanet" ;
rdfs:comment "A catalogue of rare disease associations. Ensembl display phenotypes from Orphanet. http://www.orpha.net/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000243 .
glossary:ENSGLOSSARY_0000290 a rdfs:Class ;
rdfs:label "EMBL (file format)" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000242 a rdfs:Class ;
rdfs:label "ClinVar" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000306 a rdfs:Class ;
rdfs:label "Microsatellite" ;
rdfs:comment "A region in the genomic sequence containing short tandem repeats of 2-10bp." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000007 a rdfs:Class ;
rdfs:label "TSL 2" ;
rdfs:comment "A transcript where the best supporting mRNA is flagged as suspect or the support is from multiple ESTs" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000005 .
glossary:ENSGLOSSARY_0000057 a rdfs:Class ;
rdfs:label "TEC (To be Experimentally Confirmed)" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000025 .
glossary:ENSGLOSSARY_0000252 a rdfs:Class ;
rdfs:label "Protein source database" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000208 .
glossary:ENSGLOSSARY_0000090 a rdfs:Class ;
rdfs:label "Within species paralogues" ;
rdfs:comment "Two or more versions of a duplicated gene in a single species. In a gene tree, the genes are separated by a duplication node." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000086 .
glossary:ENSGLOSSARY_0000379 a rdfs:Class ;
rdfs:label "Ensembl Canonical Extended" ;
rdfs:comment "Not part of the MANE transcript set but a version of a MANE Select or MANE Plus Clinical transcripts with maximal 3’ and/or 5’ UTR extension. The extension is added by the LEAP pipeline based on PacBio/Nanopore and PolyA/CAGE data or manually curated transcript termini." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000351 a rdfs:Class ;
rdfs:label "DNA methylation" ;
rdfs:comment "Modification of cytosines in CpGs with methyl groups, which is known to repress gene expression." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000346 .
glossary:ENSGLOSSARY_0000099 a rdfs:Class ;
rdfs:label "Insertion" ;
rdfs:comment "Insertion of one or more nucleotides" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000096 .
glossary:ENSGLOSSARY_0000231 a rdfs:Class ;
rdfs:label "Roadmap Epigenomics" ;
rdfs:comment "Project aiming to develop publicly available reference epigenome maps from a variety of cell types. http://www.roadmapepigenomics.org/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000228 .
glossary:ENSGLOSSARY_0000213 a rdfs:Class ;
rdfs:label "IMGT" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000276 a rdfs:Class ;
rdfs:label "BED" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000153 a rdfs:Class ;
rdfs:label "Incomplete terminal codon variant" ;
rdfs:comment "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000328 a rdfs:Class ;
rdfs:label "EPO" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000321 .
glossary:ENSGLOSSARY_0000182 a rdfs:Class ;
rdfs:label "Transcript haplotype" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000181 .
a rdf:Property ;
rdfs:label "related"@en ;
rdfs:range .
glossary:ENSGLOSSARY_0000220 a rdfs:Class ;
rdfs:label "Gene Ontology" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000336 a rdfs:Class ;
rdfs:label "Enhancers " ;
rdfs:comment "Regions that bind transcription factors and interact with promoters to stimulate transcription of distant genes." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000333 .
glossary:ENSGLOSSARY_0000158 a rdfs:Class ;
rdfs:label "5 prime UTR variant" ;
rdfs:comment "A UTR variant of the 5' UTR" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000340 a rdfs:Class ;
rdfs:label "Regulatory activity" ;
rdfs:comment "The activity state of a regulatory feature in a specific epigenome." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000333 .
glossary:ENSGLOSSARY_0000049 a rdfs:Class ;
rdfs:label "Unprocessed pseudogene" ;
rdfs:comment "Pseudogene that can contain introns since produced by gene duplication." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000047 .
glossary:ENSGLOSSARY_0000354 a rdfs:Class ;
rdfs:label "Peak" ;
rdfs:comment "Locus identified from epigenome signal as being having high signal, shown as a BigBed across the genome." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000346 .
glossary:ENSGLOSSARY_0000070 a rdfs:Class ;
rdfs:label "Protein domain" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000069 .
glossary:ENSGLOSSARY_0000038 a rdfs:Class ;
rdfs:label "miRNA" ;
rdfs:comment "A small RNA (~22bp) that silences the expression of target mRNA." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000037 .
glossary:ENSGLOSSARY_0000101 a rdfs:Class ;
rdfs:label "Indel" ;
rdfs:comment "An insertion and a deletion, affecting two or more nucleotides" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000096 .
glossary:ENSGLOSSARY_0000317 a rdfs:Class ;
rdfs:label "Unknown repeat" ;
rdfs:comment "Repeats that cannot be classified." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000160 a rdfs:Class ;
rdfs:label "Non coding transcript exon variant" ;
rdfs:comment "A sequence variant that changes non-coding exon sequence in a non-coding transcript" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000365 a rdfs:Class ;
rdfs:label "MANE Select" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000364 .
glossary:ENSGLOSSARY_0000147 a rdfs:Class ;
rdfs:label "Transcript amplification" ;
rdfs:comment "A feature amplification of a region containing a transcript" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000294 a rdfs:Class ;
rdfs:label "MySQL" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000081 a rdfs:Class ;
rdfs:label "Gene tree" ;
rdfs:comment "A representation of the evolutionary relationship between homologues, constructed using the Ensembl gene tree pipeline." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000080 .
glossary:ENSGLOSSARY_0000118 a rdfs:Class ;
rdfs:label "Genetic marker" ;
rdfs:comment "A measurable locus that varies within a population." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000017 a rdfs:Class ;
rdfs:label "APPRIS P5" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000012 .
glossary:ENSGLOSSARY_0000370 a rdfs:Class ;
rdfs:label "Reverse strand" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000001 .
glossary:ENSGLOSSARY_0000303 a rdfs:Class ;
rdfs:label "Hard masked" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000302 .
glossary:ENSGLOSSARY_0000310 a rdfs:Class ;
rdfs:label "Satellite repeats" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000067 a rdfs:Class ;
rdfs:label "cDNA" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000133 a rdfs:Class ;
rdfs:label "Probe" ;
rdfs:comment "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000358 a rdfs:Class ;
rdfs:label "UniSTS" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000357 .
glossary:ENSGLOSSARY_0000272 a rdfs:Class ;
rdfs:label "VEP" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000224 a rdfs:Class ;
rdfs:label "MGI" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000321 a rdfs:Class ;
rdfs:label "Multiple whole genome alignment" ;
rdfs:comment "An alignment between more than two whole genomes of a selected taxon." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000319 .
glossary:ENSGLOSSARY_0000369 a rdfs:Class ;
rdfs:label "Forward strand" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000001 .
glossary:ENSGLOSSARY_0000107 a rdfs:Class ;
rdfs:label "Allele (gene)" ;
rdfs:comment "Different versions of a gene found between the primary assembly and a patch or genome haplotype." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000002 .
glossary:ENSGLOSSARY_0000332 a rdfs:Class ;
rdfs:label "Translated Blat" ;
rdfs:comment "Translated Blat can be used for alignment of the coding regions of genomes only in a pairwise manner." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000320 .
glossary:ENSGLOSSARY_0000298 a rdfs:Class ;
rdfs:label "OrthoXML" ;
rdfs:comment "OrthoXML is an XML format to allow the storage and comparison of orthology data. It is used to store Ensembl homologues." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000035 a rdfs:Class ;
rdfs:label "Sense overlapping" ;
rdfs:comment "A long non-coding transcript that contains a coding gene in its intron on the same strand." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000028 .
glossary:ENSGLOSSARY_0000154 a rdfs:Class ;
rdfs:label "Stop retained variant" ;
rdfs:comment "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000171 a rdfs:Class ;
rdfs:label "Feature elongation" ;
rdfs:comment "A sequence variant located within a regulatory region" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000240 a rdfs:Class ;
rdfs:label "UK10K" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000129 a rdfs:Class ;
rdfs:label "Mobile element insertion" ;
rdfs:comment "A kind of insertion where the inserted sequence is a mobile element." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000288 a rdfs:Class ;
rdfs:label "chain" ;
rdfs:comment "Chain files describe the mapping between different genome assemblies. Ensembl store these on the FTP site." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000261 a rdfs:Class ;
rdfs:label "BLAT" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000347 a rdfs:Class ;
rdfs:label "ChIP-seq" ;
rdfs:comment "A method to determine the genomic regions that proteins bind to." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000346 .
glossary:ENSGLOSSARY_0000314 a rdfs:Class ;
rdfs:label "Type I Transposons/LINE" ;
rdfs:comment "Long Interspersed Elements. Retrotransposed elements in the genome containing open reading frames encoding (often inactive) reverse transcription machinery." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000143 a rdfs:Class ;
rdfs:label "Stop gained" ;
rdfs:comment "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000024 a rdfs:Class ;
rdfs:label "CCDS" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000202 a rdfs:Class ;
rdfs:label "Karyotype" ;
rdfs:comment "The number of chromosomes of a genome." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000096 a rdfs:Class ;
rdfs:label "Sequence variant" ;
rdfs:comment "Variant that only affects a small locus" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000339 a rdfs:Class ;
rdfs:label "Open chromatin regions " ;
rdfs:comment "Regions of spaced out histones, making them accessible to protein interactions." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000333 .
glossary:ENSGLOSSARY_0000209 a rdfs:Class ;
rdfs:label "Gene source database" ;
rdfs:comment "Database from which Ensembl imports cDNA or protein sequence for gene annotation, or gene names." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000208 .
glossary:ENSGLOSSARY_0000193 a rdfs:Class ;
rdfs:label "Scaffold" ;
rdfs:comment "Scaffolds are sets of ordered, oriented contigs, assembled by sequence overlap. They are longer sequences than contigs, but shorter than full chromosomes." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000137 a rdfs:Class ;
rdfs:label "Moderate impact variant consequence" ;
rdfs:comment "A non-disruptive variant that might change protein effectiveness." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000135 .
glossary:ENSGLOSSARY_0000027 a rdfs:Class ;
rdfs:label "Processed transcript" ;
rdfs:comment "Gene/transcript that doesn't contain an open reading frame (ORF)." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000025 .
glossary:ENSGLOSSARY_0000380 a rdfs:Class ;
rdfs:label "LEAP" ;
rdfs:comment "Long read Extension and Annotation Pipeline (LEAP) adds UTR extensions to transcripts based on PacBio/Nanopore and PolyA/CAGE data or manually curated transcript termini" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000046 a rdfs:Class ;
rdfs:label "miscRNA" ;
rdfs:comment "Miscellaneous RNA. A non-coding RNA that cannot be classified." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000037 .
glossary:ENSGLOSSARY_0000093 a rdfs:Class ;
rdfs:label "QTL" ;
rdfs:comment "Genetic loci where allelic variation is associated with variation in a quantitative trait (e.g. blood pressure)." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000219 a rdfs:Class ;
rdfs:label "DDBJ" ;
rdfs:comment "The Asian branch of INSDC. http://www.ddbj.nig.ac.jp/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000216 .
glossary:ENSGLOSSARY_0000120 a rdfs:Class ;
rdfs:label "Alu insertion" ;
rdfs:comment "An insertion of sequence from the Alu family of mobile elements." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000112 a rdfs:Class ;
rdfs:label "Private allele" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000106 .
glossary:ENSGLOSSARY_0000078 a rdfs:Class ;
rdfs:label "5' UTR" ;
rdfs:comment "The region of a coding cDNA upstream of the start codon which is not translated." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000256 a rdfs:Class ;
rdfs:label "Ensembl Havana" ;
rdfs:comment "Human And Vertebrate ANalysis and Annotation. The team within Ensembl who manually annotate genes and transcripts for a subset of species." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000255 .
glossary:ENSGLOSSARY_0000325 a rdfs:Class ;
rdfs:label "Wasabi" ;
rdfs:comment "An application for displaying sequence alignments with custom colour-annotation, which is used by Ensembl displaying gene tree and family alignments. http://wasabiapp.org/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000318 .
glossary:ENSGLOSSARY_0000283 a rdfs:Class ;
rdfs:label "GFF" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000089 a rdfs:Class ;
rdfs:label "Other paralogues" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000086 .
glossary:ENSGLOSSARY_0000235 a rdfs:Class ;
rdfs:label "dbVar" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000363 a rdfs:Class ;
rdfs:label "MetaLR" ;
rdfs:comment "A tool for predicting the pathogenicity of single nucleotide variants using a logistic regression based ensemble method." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000330 a rdfs:Class ;
rdfs:label "LastZ" ;
rdfs:comment "LASTZ is a program for aligning DNA sequences in a pairwise manner. Its precedesessor is BlastZ." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000320 .
glossary:ENSGLOSSARY_0000186 a rdfs:Class ;
rdfs:label "Primary assembly" ;
rdfs:comment "The underlying genome sequence, without alternative sequence included." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000197 a rdfs:Class ;
rdfs:label "YAC" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000195 .
glossary:ENSGLOSSARY_0000214 a rdfs:Class ;
rdfs:label "SwissProt" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000212 .
glossary:ENSGLOSSARY_0000338 a rdfs:Class ;
rdfs:label "Transcription factor binding sites " ;
rdfs:comment "Sites which bind transcription factors, for which no other role can be determined as yet." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000333 .
glossary:ENSGLOSSARY_0000020 a rdfs:Class ;
rdfs:label "GENCODE Basic" ;
rdfs:comment "A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000052 a rdfs:Class ;
rdfs:label "Polymorphic pseudogene" ;
rdfs:comment "Pseudogene owing to a SNP/indel but in other individuals/haplotypes/strains the gene is translated." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000047 .
glossary:ENSGLOSSARY_0000179 a rdfs:Class ;
rdfs:label "r2" ;
rdfs:comment "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)." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000178 .
glossary:ENSGLOSSARY_0000232 a rdfs:Class ;
rdfs:label "Variation source database" ;
rdfs:comment "Database from which Ensembl imports variation data, including loci, sample genotypes, population frequencies and phenotype associations." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000208 .
glossary:ENSGLOSSARY_0000004 a rdfs:Class ;
rdfs:label "EST" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000001 .
glossary:ENSGLOSSARY_0000378 a rdfs:Class ;
rdfs:label "Protein coding LOF" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000025 .
glossary:ENSGLOSSARY_0000305 a rdfs:Class ;
rdfs:label "Alu insertion" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000085 a rdfs:Class ;
rdfs:label "Many-to-many orthologues" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000082 .
glossary:ENSGLOSSARY_0000063 a rdfs:Class ;
rdfs:label "TR V gene" ;
rdfs:comment "Variable chain T cell receptor gene that undergoes somatic recombination before transcription" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000056 .
glossary:ENSGLOSSARY_0000344 a rdfs:Class ;
rdfs:label "Inactive" ;
rdfs:comment "When a regulatory feature bears no epigenetic modifications from the ones included in the Regulatory Build." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000340 .
glossary:ENSGLOSSARY_0000247 a rdfs:Class ;
rdfs:label "GWAS catalog" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000243 .
glossary:ENSGLOSSARY_0000372 a rdfs:Class ;
rdfs:label "UniProt Match" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000212 .
glossary:ENSGLOSSARY_0000074 a rdfs:Class ;
rdfs:label "Constitutive exon" ;
rdfs:comment "Exons that are not spliced out, therefore present in all transcripts of a given gene." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000071 .
glossary:ENSGLOSSARY_0000116 a rdfs:Class ;
rdfs:label "Global MAF" ;
rdfs:comment "The frequency of the second most common allele in the global population, defined in human by the 1000 Genomes Project phase 3." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000114 .
glossary:ENSGLOSSARY_0000124 a rdfs:Class ;
rdfs:label "Interchromosomal translocation" ;
rdfs:comment "A translocation where the regions involved are from different chromosomes." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000105 .
glossary:ENSGLOSSARY_0000381 a rdfs:Class ;
rdfs:label "AlphaMissense" ;
rdfs:comment "A deep learning model developed by Google DeepMind that predicts the pathogenicity of single nucleotide missense variants." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000194 a rdfs:Class ;
rdfs:label "Cytogenetic band" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000361 a rdfs:Class ;
rdfs:label "REVEL" ;
rdfs:comment "A tool for predicting the pathogenicity of single nucleotide variants using an ensemble method." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000350 a rdfs:Class ;
rdfs:label "Histone modification" ;
rdfs:comment "Covalent modifications to the histone proteins that make up the nucleosome, which are known to regulate gene expression." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000346 .
glossary:ENSGLOSSARY_0000105 a rdfs:Class ;
rdfs:label "Translocation" ;
rdfs:comment "A region of nucleotide sequence that has translocated to a new position" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000082 a rdfs:Class ;
rdfs:label "Orthologues" ;
rdfs:comment "Orthologues are genes derived from a common ancestor through vertical descent (or speciation) and can be thought of as the direct evolutionary counterpart." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000080 .
glossary:ENSGLOSSARY_0000167 a rdfs:Class ;
rdfs:label "TFBS amplification" ;
rdfs:comment "A feature amplification of a region containing a transcription factor binding site" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000102 a rdfs:Class ;
rdfs:label "Substitution" ;
rdfs:comment "A sequence alteration where the length of the deleted sequence is the same as the length of the inserted sequence." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000096 .
glossary:ENSGLOSSARY_0000308 a rdfs:Class ;
rdfs:label "Low complexity regions" ;
rdfs:comment "Poly-purine or poly-pyrimidine stretches, or regions of extremely high AT or GC content." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000221 a rdfs:Class ;
rdfs:label "HGNC" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000127 a rdfs:Class ;
rdfs:label "Loss of heterozygosity" ;
rdfs:comment "A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000280 a rdfs:Class ;
rdfs:label "Ensembl default (VEP)" ;
rdfs:comment "Ensembl default is an input format for the VEP, used to describe the position and alleles of a variant." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000337 a rdfs:Class ;
rdfs:label "CTCF binding sites " ;
rdfs:comment "Regions that bind CTCF, the insulator protein that demarcates open and closed chromatin." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000333 .
glossary:ENSGLOSSARY_0000183 a rdfs:Class ;
rdfs:label "Genome" ;
rdfs:comment "The complete set of DNA found in each cell." .
glossary:ENSGLOSSARY_0000001 a rdfs:Class ;
rdfs:label "Genome annotation" ;
rdfs:comment "A genomic locus that has been annotated." .
glossary:ENSGLOSSARY_0000010 a rdfs:Class ;
rdfs:label "TSL 5" ;
rdfs:comment "A transcript where no single transcript supports the model structure." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000005 .
glossary:ENSGLOSSARY_0000172 a rdfs:Class ;
rdfs:label "Regulatory region variant" ;
rdfs:comment "A sequence variant located within a regulatory region" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000309 a rdfs:Class ;
rdfs:label "RNA repeats" ;
rdfs:comment "Non-functional copies of RNA genes which have been reintegrated into the genome with the assistance of a reverse transcriptase." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000056 a rdfs:Class ;
rdfs:label "TR gene" ;
rdfs:comment "T cell receptor gene that undergoes somatic recombination, annotated in collaboration with IMGT http://www.imgt.org/." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000025 .
glossary:ENSGLOSSARY_0000190 a rdfs:Class ;
rdfs:label "Novel patch" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000188 .
glossary:ENSGLOSSARY_0000327 a rdfs:Class ;
rdfs:label "Pecan" ;
rdfs:comment "Pecan is a global multiple sequence alignment program that makes practical the probabilistic consistency methodology for significant numbers of sequences of practically arbitrary length." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000321 .
glossary:ENSGLOSSARY_0000031 a rdfs:Class ;
rdfs:label "Antisense" ;
rdfs:comment "Transcripts that overlap the genomic span (i.e. exon or introns) of a protein-coding locus on the opposite strand." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000028 .
glossary:ENSGLOSSARY_0000322 a rdfs:Class ;
rdfs:label "Synteny" ;
rdfs:comment "In a genomic context we refer to syntenic regions if the sequence is globally conserved between two species." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000319 .
glossary:ENSGLOSSARY_0000316 a rdfs:Class ;
rdfs:label "Type II Transposons" ;
rdfs:comment "Elements that have been transposed and duplicated around the genome by excision and ligation." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000295 a rdfs:Class ;
rdfs:label "VEP cache" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000175 a rdfs:Class ;
rdfs:label "Ambiguity code" ;
rdfs:comment "A single letter code that represents two or more possible nucleotides at a single base locus." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000355 a rdfs:Class ;
rdfs:label "Transcription factor binding motif" ;
rdfs:comment "Short genomic sequence that is known to bind to a particular transcription factor." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000333 .
glossary:ENSGLOSSARY_0000269 a rdfs:Class ;
rdfs:label "PolyPhen" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000243 a rdfs:Class ;
rdfs:label "Phenotype source database" ;
rdfs:comment "Database from which Ensembl imports phenotype associations with genes and/or variants." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000208 .
glossary:ENSGLOSSARY_0000060 a rdfs:Class ;
rdfs:label "IG D gene" ;
rdfs:comment "Diversity chain immunoglobulin gene that undergoes somatic recombination before transcription" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000055 .
glossary:ENSGLOSSARY_0000146 a rdfs:Class ;
rdfs:label "Start lost" ;
rdfs:comment "A codon variant that changes at least one base of the canonical start codo" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000055 a rdfs:Class ;
rdfs:label "IG gene" ;
rdfs:comment "Immunoglobulin gene that undergoes somatic recombination, annotated in collaboration with IMGT http://www.imgt.org/." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000025 .
glossary:ENSGLOSSARY_0000284 a rdfs:Class ;
rdfs:label "PSL" ;
rdfs:comment "PSL represents alignments and can be viewed in Ensembl." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000157 a rdfs:Class ;
rdfs:label "Mature miRNA variant" ;
rdfs:comment "A transcript variant located with the sequence of the mature miRNA" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000333 a rdfs:Class ;
rdfs:label "Regulatory features" ;
rdfs:comment "Regions that are predicted to regulate the expression of genes, based on the Ensembl regulatory build." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000001 .
glossary:ENSGLOSSARY_0000045 a rdfs:Class ;
rdfs:label "vaultRNA" ;
rdfs:comment "Short non coding RNA genes that form part of the vault ribonucleoprotein complex." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000037 .
glossary:ENSGLOSSARY_0000092 a rdfs:Class ;
rdfs:label "Variant" ;
rdfs:comment "Locus where the sequence differs between individuals of the same species" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000001 .
glossary:ENSGLOSSARY_0000225 a rdfs:Class ;
rdfs:label "zFIN" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000304 a rdfs:Class ;
rdfs:label "Soft masked" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000302 .
glossary:ENSGLOSSARY_0000259 a rdfs:Class ;
rdfs:label "InterProScan" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000311 a rdfs:Class ;
rdfs:label "Simple repeats" ;
rdfs:comment "Duplications of simple sets of DNA bases (typically 1-5bp) such as A, CA, CGG etc." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000359 a rdfs:Class ;
rdfs:label "External reference" ;
rdfs:comment "Mapping between Ensembl genes, transcripts and proteins to the same features in other databases." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000001 .
glossary:ENSGLOSSARY_0000132 a rdfs:Class ;
rdfs:label "Tandem duplication" ;
rdfs:comment "A duplication consisting of 2 identical adjacent regions." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000023 a rdfs:Class ;
rdfs:label "Ensembl canonical" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000371 a rdfs:Class ;
rdfs:label "RefSeq Match" ;
rdfs:comment "RefSeq transcripts that match 100% across the sequence, exon/intron structure and UTRs as part of the MANE project" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000365 .
glossary:ENSGLOSSARY_0000262 a rdfs:Class ;
rdfs:label "DUST" ;
rdfs:comment "A standalone application that looks for low complexity sequences." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000066 a rdfs:Class ;
rdfs:label "TR C gene" ;
rdfs:comment "Constant chain T cell receptor gene that undergoes somatic recombination before transcription" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000056 .
glossary:ENSGLOSSARY_0000161 a rdfs:Class ;
rdfs:label "Intron variant" ;
rdfs:comment "A transcript variant occurring within an intron" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000326 a rdfs:Class ;
rdfs:label "Similarity" ;
rdfs:comment "How well one sequence matches another determined by calculation by an alignment program of identical and conserved residues/nucleotides." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000318 .
glossary:ENSGLOSSARY_0000139 a rdfs:Class ;
rdfs:label "Modifier impact variant consequence" ;
rdfs:comment "Usually non-coding variants or variants affecting non-coding genes, where predictions are difficult or there is no evidence of impact." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000135 .
glossary:ENSGLOSSARY_0000291 a rdfs:Class ;
rdfs:label "GenBank (file format)" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000034 a rdfs:Class ;
rdfs:label "Sense intronic" ;
rdfs:comment "A long non-coding transcript in introns of a coding gene that does not overlap any exons." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000028 .
glossary:ENSGLOSSARY_0000164 a rdfs:Class ;
rdfs:label "Upstream gene variant" ;
rdfs:comment "A sequence variant located 5' of a gene" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000287 a rdfs:Class ;
rdfs:label "Pairwise interactions (WashU)" ;
rdfs:comment "Pairwise interactions, such as those derived from Hi-C, can be stored in the WashU format and viewed in Ensembl." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000013 a rdfs:Class ;
rdfs:label "APPRIS P1" ;
rdfs:comment "Transcript(s) expected to code for the main functional isoform based solely on the core modules in the APPRIS." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000012 .
glossary:ENSGLOSSARY_0000208 a rdfs:Class ;
rdfs:label "Ensembl sources" ;
rdfs:comment "Publicly available database that Ensembl imports data from." .
glossary:ENSGLOSSARY_0000113 a rdfs:Class ;
rdfs:label "Ancestral allele" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000106 .
glossary:ENSGLOSSARY_0000273 a rdfs:Class ;
rdfs:label "File formats" .
glossary:ENSGLOSSARY_0000142 a rdfs:Class ;
rdfs:label "Splice donor variant" ;
rdfs:comment "A splice variant that changes the 2 base region at the 5' end of an intron" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000229 a rdfs:Class ;
rdfs:label "ENCODE" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000228 .
glossary:ENSGLOSSARY_0000189 a rdfs:Class ;
rdfs:label "Haplotype (genome)" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000187 .
glossary:ENSGLOSSARY_0000210 a rdfs:Class ;
rdfs:label "GENCODE" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000009 a rdfs:Class ;
rdfs:label "TSL 4" ;
rdfs:comment "A transcript where the best supporting EST is flagged as suspect" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000005 .
glossary:ENSGLOSSARY_0000279 a rdfs:Class ;
rdfs:label "BigBed" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000349 a rdfs:Class ;
rdfs:label "Transcription factor" ;
rdfs:comment "A protein that binds to DNA and controls the rate of transcription." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000346 .
glossary:ENSGLOSSARY_0000236 a rdfs:Class ;
rdfs:label "DGVa" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000041 a rdfs:Class ;
rdfs:label "siRNA" ;
rdfs:comment "A small RNA (20-25bp) that silences the expression of target mRNA through the RNAi pathway." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000037 .
glossary:ENSGLOSSARY_0000088 a rdfs:Class ;
rdfs:label "Gene split" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000086 .
glossary:ENSGLOSSARY_0000300 a rdfs:Class ;
rdfs:label "AGP" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000218 a rdfs:Class ;
rdfs:label "GenBank (database)" ;
rdfs:comment "The US branch of INSDC. https://www.ncbi.nlm.nih.gov/genbank/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000216 .
glossary:ENSGLOSSARY_0000255 a rdfs:Class ;
rdfs:label "Ensembl Genebuild" ;
rdfs:comment "The automatic process by which Ensembl plot known RNA and protein sequence onto the genome, using sequence similarity." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000030 a rdfs:Class ;
rdfs:label "3' overlapping ncRNA" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000028 .
glossary:ENSGLOSSARY_0000375 a rdfs:Class ;
rdfs:label "MANE Plus Clinical" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000364 .
glossary:ENSGLOSSARY_0000168 a rdfs:Class ;
rdfs:label "TF binding site variant" ;
rdfs:comment "A sequence variant located within a transcription factor binding site" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000136 a rdfs:Class ;
rdfs:label "High impact variant consequence" ;
rdfs:comment "The variant is assumed to have high (disruptive) impact in the protein, probably causing protein truncation, loss of function or triggering nonsense mediated decay." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000135 .
glossary:ENSGLOSSARY_0000150 a rdfs:Class ;
rdfs:label "Missense variant" ;
rdfs:comment "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000348 a rdfs:Class ;
rdfs:label "DNase sensitivity" ;
rdfs:comment "A method to determine regions of open and closed chromatin." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000346 .
glossary:ENSGLOSSARY_0000071 a rdfs:Class ;
rdfs:label "Exon" ;
rdfs:comment "Transcribed genomic region that remains in the RNA after splicing, includes both the CDS and the UTRs." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000315 a rdfs:Class ;
rdfs:label "Type I Transposons/SINE" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000077 a rdfs:Class ;
rdfs:label "Untranslated region" ;
rdfs:comment "The region of a coding cDNA which is not translated." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000016 a rdfs:Class ;
rdfs:label "APPRIS P4" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000012 .
glossary:ENSGLOSSARY_0000203 a rdfs:Class ;
rdfs:label "PAR" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000117 a rdfs:Class ;
rdfs:label "Genotype" ;
rdfs:comment "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)." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000106 .
glossary:ENSGLOSSARY_0000083 a rdfs:Class ;
rdfs:label "1-to-1 orthologues" ;
rdfs:comment "A type of orthologue assigned for a pair of species where only one copy is found in each species." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000082 .
glossary:ENSGLOSSARY_0000318 a rdfs:Class ;
rdfs:label "Alignments" ;
rdfs:comment "A comparison between two or more sequences by matching identical and/or similar residues/nucleotides and assigning a score to the match." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000001 .
glossary:ENSGLOSSARY_0000382 a rdfs:Class ;
rdfs:label "ESM1b" ;
rdfs:comment "A tool that predicts pathogenic effects of coding variants using a 650-million-parameter protein language model." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000095 a rdfs:Class ;
rdfs:label "Evidence status" ;
rdfs:comment "Codes that reflect the amount and type of evidence that supports the existence of a variant." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000021 a rdfs:Class ;
rdfs:label "5' incomplete" ;
rdfs:comment "A protein-coding transcript which is missing the start codon due to incomplete evidence." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000373 a rdfs:Class ;
rdfs:label "Nonsense Mediated Decay" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000025 .
glossary:ENSGLOSSARY_0000114 a rdfs:Class ;
rdfs:label "Minor allele frequency" ;
rdfs:comment "The frequency of the second most common allele in the specified population." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000111 .
glossary:ENSGLOSSARY_0000005 a rdfs:Class ;
rdfs:label "Transcript support level" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000264 a rdfs:Class ;
rdfs:label "GeneWise" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000173 a rdfs:Class ;
rdfs:label "Feature truncation" ;
rdfs:comment "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000130 a rdfs:Class ;
rdfs:label "Novel sequence insertion" ;
rdfs:comment "An insertion the sequence of which cannot be mapped to the reference genome." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000353 a rdfs:Class ;
rdfs:label "Signal" ;
rdfs:comment "A count of the number of NGS reads from an epigenome experiment aligned to a locus, shown as a BigWig across the genome." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000346 .
glossary:ENSGLOSSARY_0000275 a rdfs:Class ;
rdfs:label "VCF" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000002 a rdfs:Class ;
rdfs:label "Gene" ;
rdfs:comment "Genomic locus where transcription occurs. A gene may have one or more transcripts, which may or may not encode proteins." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000001 .
glossary:ENSGLOSSARY_0000121 a rdfs:Class ;
rdfs:label "Complex structural alteration" ;
rdfs:comment "A structural sequence alteration or rearrangement encompassing one or more genome fragments, with four or more breakpoints." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000180 a rdfs:Class ;
rdfs:label "D'" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000178 .
glossary:ENSGLOSSARY_0000301 a rdfs:Class ;
rdfs:label "Repeat" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000001 .
glossary:ENSGLOSSARY_0000364 a rdfs:Class ;
rdfs:label "MANE" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000222 a rdfs:Class ;
rdfs:label "Rfam" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000244 a rdfs:Class ;
rdfs:label "OMIM" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000243 .
glossary:ENSGLOSSARY_0000026 a rdfs:Class ;
rdfs:label "Protein coding" ;
rdfs:comment "Gene/transcipt that contains an open reading frame (ORF)." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000025 .
glossary:ENSGLOSSARY_0000075 a rdfs:Class ;
rdfs:label "Phase" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000071 .
glossary:ENSGLOSSARY_0000230 a rdfs:Class ;
rdfs:label "Blueprint Epigenomes" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000228 .
glossary:ENSGLOSSARY_0000278 a rdfs:Class ;
rdfs:label "BAM/CRAM" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000178 a rdfs:Class ;
rdfs:label "Linkage disequilibrium" ;
rdfs:comment "A measure of how often two variants or specific sequences are inherited together." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000195 a rdfs:Class ;
rdfs:label "Clone" ;
rdfs:comment "A segment of DNA that has been inserted into a vector molecule, such as a plasmid, and then replicated to form many identical copies." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000331 a rdfs:Class ;
rdfs:label "BlastZ" ;
rdfs:comment "BlastZ is a program for aligning DNA sequences in a pairwise manner. It has been replaced by LASTZ." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000320 .
glossary:ENSGLOSSARY_0000334 a rdfs:Class ;
rdfs:label "Promoters " ;
rdfs:comment "Regions at the 5' end of genes where transcription factors and RNA polymerase bind to initiate transcription." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000333 .
glossary:ENSGLOSSARY_0000268 a rdfs:Class ;
rdfs:label "SIFT" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000149 a rdfs:Class ;
rdfs:label "Inframe deletion" ;
rdfs:comment "An inframe non synonymous variant that deletes bases from the coding sequenc" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000053 a rdfs:Class ;
rdfs:label "Unitary pseudogene" ;
rdfs:comment "A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000047 .
glossary:ENSGLOSSARY_0000103 a rdfs:Class ;
rdfs:label "CNV" ;
rdfs:comment "Copy Number Variation: increases or decreases the copy number of a given locus. Subcategorised into Loss and Gain compared to the reference." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000064 a rdfs:Class ;
rdfs:label "TR D gene" ;
rdfs:comment "Diversity chain T cell receptor gene that undergoes somatic recombination before transcription" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000056 .
glossary:ENSGLOSSARY_0000048 a rdfs:Class ;
rdfs:label "Processed pseudogene" ;
rdfs:comment "Pseudogene that lack introns and is thought to arise from reverse transcription of mRNA followed by reinsertion of DNA into the genome." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000047 .
glossary:ENSGLOSSARY_0000281 a rdfs:Class ;
rdfs:label "BedGraph" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000019 a rdfs:Class ;
rdfs:label "APPRIS ALT2" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000012 .
glossary:ENSGLOSSARY_0000296 a rdfs:Class ;
rdfs:label "GVF" ;
rdfs:comment "Genome Variation Format (GVF) is used to store variation data. It can be found on the Ensembl FTP site." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000166 a rdfs:Class ;
rdfs:label "TFBS ablation" ;
rdfs:comment "A feature ablation whereby the deleted region includes a transcription factor binding site" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000191 a rdfs:Class ;
rdfs:label "Fix patch" ;
rdfs:comment "Fix patches are where the primary assembly was found to be incorrect, and the patch reflects the corrected sequence." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000188 .
glossary:ENSGLOSSARY_0000233 a rdfs:Class ;
rdfs:label "dbSNP" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000250 a rdfs:Class ;
rdfs:label "HGMD" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000032 a rdfs:Class ;
rdfs:label "lincRNA (long intergenic ncRNA)" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000028 .
glossary:ENSGLOSSARY_0000215 a rdfs:Class ;
rdfs:label "TrEMBL" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000212 .
glossary:ENSGLOSSARY_0000206 a rdfs:Class ;
rdfs:label "Placed scaffold" ;
rdfs:comment "A scaffold that can be positioned on a chromosome based on genetic mapping information." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000193 .
glossary:ENSGLOSSARY_0000086 a rdfs:Class ;
rdfs:label "Paralogues" ;
rdfs:comment "Genes (homologues) that have evolved by duplication." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000080 .
glossary:ENSGLOSSARY_0000184 a rdfs:Class ;
rdfs:label "Genome assembly" ;
rdfs:comment "A computational representation of the sequence of a haploid genome, representative of a species or strain." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000183 .
glossary:ENSGLOSSARY_0000110 a rdfs:Class ;
rdfs:label "Major allele" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000106 .
glossary:ENSGLOSSARY_0000286 a rdfs:Class ;
rdfs:label "BigWig" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000360 a rdfs:Class ;
rdfs:label "CADD" ;
rdfs:comment "A tool that integrates multiple annotations into one metric for scoring the deleteriousness of single nucleotide variants." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000128 a rdfs:Class ;
rdfs:label "Mobile element deletion" ;
rdfs:comment "A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element)." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000200 a rdfs:Class ;
rdfs:label "Golden path (genome size)" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000043 a rdfs:Class ;
rdfs:label "snoRNA" ;
rdfs:comment "Small RNA molecules that are found in the cell nucleolus and are involved in the post-transcriptional modification of other RNAs." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000037 .
glossary:ENSGLOSSARY_0000307 a rdfs:Class ;
rdfs:label "Centromere" ;
rdfs:comment "The region of the chromosome at which the two sister chromatids are joined during mitosis and meiosis, mostly composed of satellite DNA." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000037 a rdfs:Class ;
rdfs:label "ncRNA" ;
rdfs:comment "A non-coding gene." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000027 .
glossary:ENSGLOSSARY_0000106 a rdfs:Class ;
rdfs:label "Allele (variant)" ;
rdfs:comment "One of a number of alternative forms of the same genetic locus/variant." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000248 a rdfs:Class ;
rdfs:label "IMPC" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000243 .
glossary:ENSGLOSSARY_0000029 a rdfs:Class ;
rdfs:label "Non coding" ;
rdfs:comment "Transcripts which are known from the literature to not be protein coding." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000028 .
glossary:ENSGLOSSARY_0000061 a rdfs:Class ;
rdfs:label "IG J gene" ;
rdfs:comment "Joining chain immunoglobulin gene that undergoes somatic recombination before transcription" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000055 .
glossary:ENSGLOSSARY_0000237 a rdfs:Class ;
rdfs:label "1000 Genomes project" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000356 a rdfs:Class ;
rdfs:label "Epigenome" ;
rdfs:comment "A cell type, such as a primary tissue or lab cell line, for which we have epigenome evidence and can predict regulatory features." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000340 .
glossary:ENSGLOSSARY_0000297 a rdfs:Class ;
rdfs:label "PhyloXML" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000044 a rdfs:Class ;
rdfs:label "tRNA" ;
rdfs:comment "A transfer RNA, which acts as an adaptor molecule for translation of mRNA." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000037 .
glossary:ENSGLOSSARY_0000254 a rdfs:Class ;
rdfs:label "Algorithm" ;
rdfs:comment "A sequence of computational tasks or actions that carry out a specific function." .
glossary:ENSGLOSSARY_0000162 a rdfs:Class ;
rdfs:label "NMD transcript variant" ;
rdfs:comment "A variant in a transcript that is the target of NMD" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000138 a rdfs:Class ;
rdfs:label "Low impact variant consequence" ;
rdfs:comment "A variant that is assumed to be mostly harmless or unlikely to change protein behaviour." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000135 .
glossary:ENSGLOSSARY_0000033 a rdfs:Class ;
rdfs:label "Retained intron" ;
rdfs:comment "An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000028 .
glossary:ENSGLOSSARY_0000292 a rdfs:Class ;
rdfs:label "EMF Alignment format" ;
rdfs:comment "Ensembl Multi Format (EMF) stores genomic alignments in Ensembl." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000323 a rdfs:Class ;
rdfs:label "CIGAR" ;
rdfs:comment "The cigar line defines the sequence of matches/mismatches and deletions (or gaps) in an alignment" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000318 .
glossary:ENSGLOSSARY_0000285 a rdfs:Class ;
rdfs:label "Wiggle" ;
rdfs:comment "Wiggle format expresses scores across genomic loci, requiring fixed size bins for the scores. It can be uploaded to view in Ensembl." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000050 a rdfs:Class ;
rdfs:label "Transcribed pseudogene" ;
rdfs:comment "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'." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000047 .
glossary:ENSGLOSSARY_0000140 a rdfs:Class ;
rdfs:label "Transcript ablation" ;
rdfs:comment "A feature ablation whereby the deleted region includes a transcript feature" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000042 a rdfs:Class ;
rdfs:label "snRNA" ;
rdfs:comment "Small RNA molecules that are found in the cell nucleus and are involved in the processing of pre messenger RNAs" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000037 .
glossary:ENSGLOSSARY_0000059 a rdfs:Class ;
rdfs:label "IG V gene" ;
rdfs:comment "Variable chain immunoglobulin gene that undergoes somatic recombination before transcription" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000055 .
glossary:ENSGLOSSARY_0000312 a rdfs:Class ;
rdfs:label "Tandem repeats" ;
rdfs:comment "Typically found at the centromeres and telomeres of chromosomes these are duplications of more complex 100-200 base sequences." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000204 a rdfs:Class ;
rdfs:label "Slice" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000145 a rdfs:Class ;
rdfs:label "Stop lost" ;
rdfs:comment "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000188 a rdfs:Class ;
rdfs:label "Patch" ;
rdfs:comment "New sequences that have been added to the genome assembly since its release. There are two types: fix and nove patches." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000187 .
glossary:ENSGLOSSARY_0000177 a rdfs:Class ;
rdfs:label "Clinical significance" ;
rdfs:comment "A classification of a variant's impact on disease, taken from ClinVar." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000211 a rdfs:Class ;
rdfs:label "RefSeq" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000098 a rdfs:Class ;
rdfs:label "SNP" ;
rdfs:comment "Single Nucleotide Polymorphism, substitution of a single nucleotide for another nucleotide" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000096 .
glossary:ENSGLOSSARY_0000270 a rdfs:Class ;
rdfs:label "RepeatMasker" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000012 a rdfs:Class ;
rdfs:label "APPRIS" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000341 a rdfs:Class ;
rdfs:label "Active" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000340 .
glossary:ENSGLOSSARY_0000207 a rdfs:Class ;
rdfs:label "Unplaced scaffold" ;
rdfs:comment "A scaffold that cannot be positioned on a chromosome." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000193 .
glossary:ENSGLOSSARY_0000008 a rdfs:Class ;
rdfs:label "TSL 3" ;
rdfs:comment "A transcript where the only support is from a single EST" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000005 .
glossary:ENSGLOSSARY_0000352 a rdfs:Class ;
rdfs:label "Bisulfite sequencing" ;
rdfs:comment "A method to determine the methylation of genomic cytosines." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000346 .
glossary:ENSGLOSSARY_0000091 a rdfs:Class ;
rdfs:label "Homoeologues" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000080 .
glossary:ENSGLOSSARY_0000072 a rdfs:Class ;
rdfs:label "Intron" ;
rdfs:comment "Transcribed genomic regions that is removed from the RNA by splicing." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000258 a rdfs:Class ;
rdfs:label "Ensembl gene tree pipeline" ;
rdfs:comment "The process by which Ensembl compare gene sequences in order to construct gene trees and predict homologues." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000217 a rdfs:Class ;
rdfs:label "ENA" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000216 .
glossary:ENSGLOSSARY_0000377 a rdfs:Class ;
rdfs:label "Protein coding CDS not defined" ;
rdfs:comment "Alternatively spliced transcript of a protein coding gene for which we cannot define a CDS." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000025 .
glossary:ENSGLOSSARY_0000228 a rdfs:Class ;
rdfs:label "Epigenome source database" ;
rdfs:comment "Database from which Ensembl imports ChIP-seq, DNase-seq and other related datasets, which are used in the Ensembl regulatory build." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000208 .
glossary:ENSGLOSSARY_0000374 a rdfs:Class ;
rdfs:label "Non-ATG start" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000156 a rdfs:Class ;
rdfs:label "Coding sequence variant" ;
rdfs:comment "A sequence variant that changes the coding sequence" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000199 a rdfs:Class ;
rdfs:label "Base pairs (genome size)" ;
rdfs:comment "The actual number of bases of sequence we have for a full genome assembly, including alternative sequences and PARs, excluding gaps." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000320 a rdfs:Class ;
rdfs:label "Pairwise whole genome alignment" ;
rdfs:comment "An alignment between two whole genomes." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000319 .
glossary:ENSGLOSSARY_0000367 a rdfs:Class ;
rdfs:label "TAGENE" ;
rdfs:comment "Long-read sequence data is computationally processed into non-redundant transcript models which are manually appraised by the Ensembl-Havana annotation team." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000319 a rdfs:Class ;
rdfs:label "Whole genome alignment" ;
rdfs:comment "An alignment carried out using the whole genome sequence." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000318 .
glossary:ENSGLOSSARY_0000239 a rdfs:Class ;
rdfs:label "TOPMed" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000125 a rdfs:Class ;
rdfs:label "Intrachromosomal breakpoint" ;
rdfs:comment "A rearrangement breakpoint within the same chromosome." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000105 .
glossary:ENSGLOSSARY_0000263 a rdfs:Class ;
rdfs:label "Eponine" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000135 a rdfs:Class ;
rdfs:label "Variant impact" ;
rdfs:comment "A subjective classification of the severity of the variant consequence, based on agreement with SNPEff." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000226 a rdfs:Class ;
rdfs:label "SGD" ;
rdfs:comment "Canonical database for the molecular biology and genetics of Saccharomyces cerevisiae, source of the annotation seen in Ensembl. https://www.yeastgenome.org/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000345 a rdfs:Class ;
rdfs:label "NA" ;
rdfs:comment "When there is no available data in the cell type for this regulatory feature." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000340 .
glossary:ENSGLOSSARY_0000274 a rdfs:Class ;
rdfs:label "HGVS nomenclature" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000151 a rdfs:Class ;
rdfs:label "Protein altering variant" ;
rdfs:comment "A sequence_variant which is predicted to change the protein encoded in the coding sequence" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000022 a rdfs:Class ;
rdfs:label "3' incomplete" ;
rdfs:comment "A protein-coding transcript which is missing the stop codon due to incomplete evidence." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000015 a rdfs:Class ;
rdfs:label "APPRIS P3" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000012 .
glossary:ENSGLOSSARY_0000073 a rdfs:Class ;
rdfs:label "Codon" ;
rdfs:comment "Three base pairs in either DNA or RNA that code for an amino acid (or stop translation)." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000068 .
glossary:ENSGLOSSARY_0000257 a rdfs:Class ;
rdfs:label "Ensembl Regulatory Build" ;
rdfs:comment "The process by which Ensembl predict the location of regions that regulate gene expression using epigenomic evidence." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000245 a rdfs:Class ;
rdfs:label "OMIA" ;
rdfs:comment "An online database that describes the function and phenotypes associated with animal genes. Ensembl display phenotypes from OMIA. https://www.omia.org/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000243 .
glossary:ENSGLOSSARY_0000076 a rdfs:Class ;
rdfs:label "Flanking sequence" ;
rdfs:comment "Sequence 5' or 3' to a DNA or RNA sequence of interest (for example gene, transcript, SNP or repeat)." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000001 .
glossary:ENSGLOSSARY_0000084 a rdfs:Class ;
rdfs:label "1-to-many orthologues" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000082 .
glossary:ENSGLOSSARY_0000122 a rdfs:Class ;
rdfs:label "Complex substitution" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000006 a rdfs:Class ;
rdfs:label "TSL 1" ;
rdfs:comment "A transcript where all splice junctions are supported by at least one non-suspect mRNA." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000005 .
glossary:ENSGLOSSARY_0000109 a rdfs:Class ;
rdfs:label "Alternative allele" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000106 .
glossary:ENSGLOSSARY_0000277 a rdfs:Class ;
rdfs:label "FASTA" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000192 a rdfs:Class ;
rdfs:label "Contig" ;
rdfs:comment "A contig is a contiguous stretch of DNA sequence without gaps that has been assembled solely based on direct sequencing information." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000100 a rdfs:Class ;
rdfs:label "Deletion" ;
rdfs:comment "Deletion of one or more nucleotides" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000096 .
glossary:ENSGLOSSARY_0000115 a rdfs:Class ;
rdfs:label "Highest population MAF" ;
rdfs:comment "The highest minor allele frequency observed in any population typed for this variant. For human this includes the 1000 Genomes Project, gnomAD and UK10K." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000114 .
glossary:ENSGLOSSARY_0000148 a rdfs:Class ;
rdfs:label "Inframe insertion" ;
rdfs:comment "An inframe non synonymous variant that inserts bases into in the coding sequenc" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000069 a rdfs:Class ;
rdfs:label "Peptide" ;
rdfs:comment "A sequence of amino acids, translated from a CDS." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000185 a rdfs:Class ;
rdfs:label "Coverage" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000058 a rdfs:Class ;
rdfs:label "Readthrough" ;
rdfs:comment "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)." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000025 .
glossary:ENSGLOSSARY_0000227 a rdfs:Class ;
rdfs:label "UCSC Genome Browser" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000251 a rdfs:Class ;
rdfs:label "COSMIC" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000051 a rdfs:Class ;
rdfs:label "Translated pseudogene" ;
rdfs:comment "Pseudogenes that have mass spec data suggesting that they are also translated. These can be classified into 'Processed', 'Unprocessed'" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000047 .
glossary:ENSGLOSSARY_0000087 a rdfs:Class ;
rdfs:label "Between species paralogues" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000086 .
glossary:ENSGLOSSARY_0000131 a rdfs:Class ;
rdfs:label "Short tandem repeat variant" ;
rdfs:comment "A variation that expands or contracts a tandem repeat with regard to a reference." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000196 a rdfs:Class ;
rdfs:label "BAC" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000195 .
glossary:ENSGLOSSARY_0000181 a rdfs:Class ;
rdfs:label "Haplotype (variation)" ;
rdfs:comment "A set of variant alleles in a contiguous genomic region. A haplotype block describes a set of alleles which tend to be inherited together." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000178 .
glossary:ENSGLOSSARY_0000065 a rdfs:Class ;
rdfs:label "TR J gene" ;
rdfs:comment "Joining chain T cell receptor gene that undergoes somatic recombination before transcription" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000056 .
glossary:ENSGLOSSARY_0000201 a rdfs:Class ;
rdfs:label "Coordinate system" ;
rdfs:comment "Which level of the assembly we are working on." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000159 a rdfs:Class ;
rdfs:label "3 prime UTR variant" ;
rdfs:comment "A UTR variant of the 3' UTR" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000249 a rdfs:Class ;
rdfs:label "Animal QTLdb" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000243 .
glossary:ENSGLOSSARY_0000165 a rdfs:Class ;
rdfs:label "Downstream gene variant" ;
rdfs:comment "A sequence variant located 3' of a gene" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000104 a rdfs:Class ;
rdfs:label "Inversion" ;
rdfs:comment "A continuous nucleotide sequence is inverted in the same position" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000097 .
glossary:ENSGLOSSARY_0000293 a rdfs:Class ;
rdfs:label "MAF" ;
rdfs:comment "Multiple alignment format (MAF) stores genomic alignments." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000080 a rdfs:Class ;
rdfs:label "Homologues" ;
rdfs:comment "Specific genes that are descended from the same common sequence in an ancestor." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000002 .
glossary:ENSGLOSSARY_0000223 a rdfs:Class ;
rdfs:label "miRbase" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000054 a rdfs:Class ;
rdfs:label "IG pseudogene" ;
rdfs:comment "Inactivated immunoglobulin gene." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000047 .
glossary:ENSGLOSSARY_0000266 a rdfs:Class ;
rdfs:label "Projection build" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000255 .
glossary:ENSGLOSSARY_0000216 a rdfs:Class ;
rdfs:label "INSDC" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000335 a rdfs:Class ;
rdfs:label "Promoter flanking regions " ;
rdfs:comment "Transcription factor binding regions that flank promoters." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000333 .
glossary:ENSGLOSSARY_0000174 a rdfs:Class ;
rdfs:label "Intergenic variant" ;
rdfs:comment "A sequence variant located in the intergenic region, between genes" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000062 a rdfs:Class ;
rdfs:label "IG C gene" ;
rdfs:comment "Constant chain immunoglobulin gene that undergoes somatic recombination before transcription" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000055 .
glossary:ENSGLOSSARY_0000111 a rdfs:Class ;
rdfs:label "Minor allele" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000106 .
glossary:ENSGLOSSARY_0000234 a rdfs:Class ;
rdfs:label "EVA" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000152 a rdfs:Class ;
rdfs:label "Splice region variant" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000342 a rdfs:Class ;
rdfs:label "Poised" ;
rdfs:comment "When a regulatory feature displays a epigenetic signature with the potential to be activated. It is analogous to a sprinter in the blocks." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000340 .
glossary:ENSGLOSSARY_0000079 a rdfs:Class ;
rdfs:label "3' UTR" ;
rdfs:comment "The region of a coding cDNA downstream of the stop codon which is not translated." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000313 a rdfs:Class ;
rdfs:label "LTRs" ;
rdfs:comment "Long tandem repeats." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
glossary:ENSGLOSSARY_0000028 a rdfs:Class ;
rdfs:label "Long non-coding RNA (lncRNA)" ;
rdfs:comment "A non-coding gene/transcript >200bp in length" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000027 .
glossary:ENSGLOSSARY_0000205 a rdfs:Class ;
rdfs:label "Toplevel" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000108 a rdfs:Class ;
rdfs:label "Reference allele" ;
rdfs:comment "The allele of a variant found in the reference genome currently being studied. The reference allele is not necessarily the major or ancestral allele." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000106 .
glossary:ENSGLOSSARY_0000163 a rdfs:Class ;
rdfs:label "Non coding transcript variant" ;
rdfs:comment "A transcript variant of a non coding RNA gene" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000324 a rdfs:Class ;
rdfs:label "Identity" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000318 .
glossary:ENSGLOSSARY_0000176 a rdfs:Class ;
rdfs:label "Flagged variant" ;
rdfs:comment "Variants that failed our quality control analyses, therefore they are flagged as suspicious." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000036 a rdfs:Class ;
rdfs:label "Macro lncRNA" ;
rdfs:comment "Unspliced lncRNAs that are several kb in size." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000028 .
glossary:ENSGLOSSARY_0000271 a rdfs:Class ;
rdfs:label "BLOSUM 62" ;
rdfs:comment "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)." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000011 a rdfs:Class ;
rdfs:label "TSL NA" ;
rdfs:comment "A transcript that was not analysed for TSL." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000005 .
glossary:ENSGLOSSARY_0000282 a rdfs:Class ;
rdfs:label "GTF" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000267 a rdfs:Class ;
rdfs:label "GENSCAN" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000097 a rdfs:Class ;
rdfs:label "Structural variant" ;
rdfs:comment "Variant that affects a large locus" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000212 a rdfs:Class ;
rdfs:label "UniProt" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000209 .
glossary:ENSGLOSSARY_0000047 a rdfs:Class ;
rdfs:label "Pseudogene" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000025 .
glossary:ENSGLOSSARY_0000238 a rdfs:Class ;
rdfs:label "gnomAD" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000155 a rdfs:Class ;
rdfs:label "Synonymous variant" ;
rdfs:comment "A sequence variant where there is no resulting change to the encoded amino acid" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000170 a rdfs:Class ;
rdfs:label "Regulatory region amplification" ;
rdfs:comment "A feature amplification of a region containing a regulatory region" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000329 a rdfs:Class ;
rdfs:label "Progressive cactus" ;
rdfs:comment "Progressive-Cactus is a next-generation aligner that stores whole-genome alignments in a graph structure." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000321 .
a rdfs:Class ;
rdfs:comment "An unconstrained type or object" .
glossary:ENSGLOSSARY_0000346 a rdfs:Class ;
rdfs:label "Epigenome evidence" ;
rdfs:comment "Experimental data that is used to construct and determine activity of regulatory features." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000333 .
glossary:ENSGLOSSARY_0000134 a rdfs:Class ;
rdfs:label "Variant consequence" ;
rdfs:comment "The effect that the variant has on each feature that it overlaps. A variant will have a consequence for each feature that it overlaps." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000253 a rdfs:Class ;
rdfs:label "PDB" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000252 .
glossary:ENSGLOSSARY_0000025 a rdfs:Class ;
rdfs:label "Biotype" ;
rdfs:comment "A gene or transcript classification." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000002 .
glossary:ENSGLOSSARY_0000368 a rdfs:Class ;
rdfs:label "Stop codon readthrough" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000025 .
glossary:ENSGLOSSARY_0000040 a rdfs:Class ;
rdfs:label "rRNA" ;
rdfs:comment "The RNA component of a ribosome." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000037 .
glossary:ENSGLOSSARY_0000119 a rdfs:Class ;
rdfs:label "Tandem repeat" ;
rdfs:comment "Two or more adjacent copies of a region (of length greater than 1)." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000092 .
glossary:ENSGLOSSARY_0000126 a rdfs:Class ;
rdfs:label "Intrachromosomal translocation" ;
rdfs:comment "A translocation where the regions involved are from the same chromosome." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000105 .
glossary:ENSGLOSSARY_0000289 a rdfs:Class ;
rdfs:label "Newick" ;
rdfs:comment "Newick is a tree format. Ensembl gene trees can be downloaded in Newick and it is used to store Ensembl species trees." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000357 a rdfs:Class ;
rdfs:label "Marker" ;
rdfs:comment "A short sequence whose placement on the genome is known." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000001 .
glossary:ENSGLOSSARY_0000260 a rdfs:Class ;
rdfs:label "BLAST" ;
rdfs:comment "A sequence comparison algorithm optimised for speed which is used to search sequence databases for optimal local alignments to a query." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000254 .
glossary:ENSGLOSSARY_0000241 a rdfs:Class ;
rdfs:label "HapMap" ;
rdfs:comment "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/" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000232 .
glossary:ENSGLOSSARY_0000018 a rdfs:Class ;
rdfs:label "APPRIS ALT1" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000012 .
glossary:ENSGLOSSARY_0000299 a rdfs:Class ;
rdfs:label "RDF" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000273 .
glossary:ENSGLOSSARY_0000198 a rdfs:Class ;
rdfs:label "Cosmid" ;
rdfs:comment "DNA from a bacterial virus spliced with a small fragment of a genome (up to 50 kb) to be amplified and sequenced." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000195 .
glossary:ENSGLOSSARY_0000376 a rdfs:Class ;
rdfs:label "GENCODE Comprehensive" ;
rdfs:comment "The full GENCODE transcript set, containing both complete transcripts and 5' and 3' incomplete transcripts." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000003 .
glossary:ENSGLOSSARY_0000144 a rdfs:Class ;
rdfs:label "Frameshift variant" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000187 a rdfs:Class ;
rdfs:label "Alternative sequence" ;
rdfs:comment "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." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000184 .
glossary:ENSGLOSSARY_0000003 a rdfs:Class ;
rdfs:label "Transcript" ;
rdfs:comment "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" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000002 .
glossary:ENSGLOSSARY_0000094 a rdfs:Class ;
rdfs:label "eQTL" ;
rdfs:comment "Genetic loci where allelic variation is associated with expression levels of other genes." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000093 .
glossary:ENSGLOSSARY_0000039 a rdfs:Class ;
rdfs:label "piRNA" ;
rdfs:comment "An RNA that interacts with piwi proteins involved in genetic silencing." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000037 .
glossary:ENSGLOSSARY_0000141 a rdfs:Class ;
rdfs:label "Splice acceptor variant" ;
rdfs:comment "A splice variant that changes the 2 base region at the 3' end of an intron" ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000134 .
glossary:ENSGLOSSARY_0000302 a rdfs:Class ;
rdfs:label "Repeat masking" ;
rdfs:comment "The method by which repeated sequences and low-complexity regions are hidden, usually used in searches by alignment and homology-searching programs." ;
rdfs:subClassOf glossary:ENSGLOSSARY_0000301 .
a rdf:Property ;
rdfs:label "definition" ;
rdfs:range xsd:string .