biomolecule primary structure

IRI: https://spec.industrialontologies.org/ontology/construct/BiomoleculePrimaryStructure

Defined In: https://spec.industrialontologies.org/ontology/biopharma/BiopharmaParameter/

SubClass Of: bfo:quality

Class Hierarchy

owl:Thing › bfo:entity › bfo:continuant › bfo:specifically dependent continuant › bfo:quality › biomolecule primary structure

Definition

quality of a DNA, RNA, peptide, or protein molecule that is determined by the linear order of its nucleotide or amino acid residues

Explanatory Notes

Biomolecule primary structure may be described together with covalent modifications of particular residues, such as methylation or phosphorylation; these modifications do not change the linear residue order.

Examples

• the primary structure of a monoclonal antibody heavy chain; the primary structure of a phosphorylated peptide; the primary structure of a methylated DNA molecule; the primary structure of an mRNA molecule; the primary structure of a protein variant with a single amino acid substitution

Adapted From

• http://www.bioassayontology.org/bao#BAO_0000013

Primitive Class

This class is declared primitive and it does not have necessary and sufficient condiftions defined.

Primitive Rationale

There are insufficient constructs for creating a set of necessary and sufficient conditions

Formal Axioms

First-Order Logic Axioms

BiomoleculePrimaryStructure(x) → Quality(x) ∧ ∃m∃s((DeoxyribonucleicAcid(m) ∨ RibonucleicAcid(m) ∨ Peptide(m) ∨ Protein(m)) ∧ qualityOf(x,m) ∧ BiologicalSequence(s) ∧ concretizesAtAllTimes(x,s) ∧ genericallyDependsOnAtSomeTime(s,m))

Semi-Formal Natural Language Axioms

if x is a ‘biomolecule primary structure’ then x is a ‘quality’ that is the ‘quality of’ some ‘deoxyribonucleic acid’, ‘ribonucleic acid’, ‘peptide’, or ‘protein’ m and x ‘concretizes at all times’ some ‘biological sequence’ that ‘generically depends on at some time’ that same m

Description Logic

constr:BiomoleculePrimaryStructure ⊑ bfo:quality

constr:BiomoleculePrimaryStructure ⊑ ∃ bfo:concretizes_at_all_times .constr:BiologicalSequence

constr:BiomoleculePrimaryStructure ⊑ ∃ constr:qualityOf .(constr:DeoxyribonucleicAcid ⊔ constr:Peptide ⊔ constr:Protein ⊔ constr:RibonucleicAcid)

SubClassOf: bfo:quality

SubClassOf: bfo:concretizes_at_all_times some constr:BiologicalSequence

SubClassOf: constr:qualityOf some (constr:DeoxyribonucleicAcid or constr:Peptide or constr:Protein or constr:RibonucleicAcid)