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Class: PhysicalEssence

Description: Semantic mixin concept. Pertains to entities that have physical properties such as mass, volume, or charge.
classDiagram class PhysicalEssence PhysicalEssenceOrOccurrent <|-- PhysicalEssence PhysicalEssence <|-- PhysicalEntity PhysicalEssence <|-- ChemicalEntity PhysicalEssence <|-- NucleicAcidEntity PhysicalEssence <|-- RegulatoryRegion PhysicalEssence <|-- AccessibleDnaRegion PhysicalEssence <|-- TranscriptionFactorBindingSite PhysicalEssence <|-- AnatomicalEntity PhysicalEssence <|-- Gene PhysicalEssence <|-- Genome PhysicalEssence <|-- Genotype PhysicalEssence <|-- Haplotype PhysicalEssence <|-- SequenceVariant PhysicalEssence <|-- ReagentTargetedGene PhysicalEssence <|-- GenomicBackgroundExposure

Inheritance

Slots

Name Cardinality and Range Inheritance Examples

Mixin Usage

mixed into description
PhysicalEntity An entity that has material reality (a.k.a. physical essence).
ChemicalEntity A chemical entity is a physical entity that pertains to chemistry or biochemistry.
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
AnatomicalEntity A subcellular location, cell type or gross anatomical part
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.
Genome A genome is the sum of genetic material within a cell or virion.
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: physical essence
description: Semantic mixin concept.  Pertains to entities that have physical properties
  such as mass, volume, or charge.
from_schema: https://w3id.org/biolink/biolink-model
is_a: physical essence or occurrent
mixin: true