Class: GenomicEntity
classDiagram
class GenomicEntity
GenomicEntity <|-- NucleicAcidEntity
GenomicEntity <|-- RegulatoryRegion
GenomicEntity <|-- AccessibleDnaRegion
GenomicEntity <|-- TranscriptionFactorBindingSite
GenomicEntity <|-- Gene
GenomicEntity <|-- NucleosomeModification
GenomicEntity <|-- Genome
GenomicEntity <|-- CodingSequence
GenomicEntity <|-- Genotype
GenomicEntity <|-- Haplotype
GenomicEntity <|-- SequenceVariant
GenomicEntity <|-- ReagentTargetedGene
GenomicEntity <|-- GenomicBackgroundExposure
GenomicEntity : has_biological_sequence
Slots
| Name | Cardinality and Range | Inheritance | Examples |
|---|---|---|---|
| has_biological_sequence: connects a genomic feature to its sequence |
0..1 BiologicalSequence |
direct |
Mixin Usage
| mixed into | description |
|---|---|
| NucleicAcidEntity | A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included. |
| RegulatoryRegion | A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene |
| AccessibleDnaRegion | A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose |
| TranscriptionFactorBindingSite | A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription |
| Gene | A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions. |
| NucleosomeModification | A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A. |
| Genome | A genome is the sum of genetic material within a cell or virion. |
| CodingSequence | None |
| Genotype | An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background |
| Haplotype | A set of zero or more Alleles on a single instance of a Sequence[VMC] |
| SequenceVariant | A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. |
| ReagentTargetedGene | A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi. |
| GenomicBackgroundExposure | A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome. |
LinkML Source
name: genomic entity
in_subset:
- translator_minimal
from_schema: https://w3id.org/biolink/biolink-model
narrow_mappings:
- STY:T028
- GENO:0000897
mixin: true
slots:
- has biological sequence