protein secondary structure

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

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

SubClass Of: physical structure

Class Hierarchy

owl:Thing › bfo:entity › bfo:continuant › bfo:specifically dependent continuant › bfo:quality › morphological quality › physical structure › protein secondary structure

Definition

physical structure of a protein that is the local three-dimensional arrangement of segments of its polypeptide backbone, commonly characterized by recurring backbone hydrogen-bonding patterns

Examples

• the alpha-helical secondary structure of a protein; the beta-sheet secondary structure of an antibody domain; the turn structure connecting two beta strands in a protein; the loop structure in an enzyme active-site region; the altered secondary structure of a protein after thermal stress

Adapted From

• https://www.fda.gov/media/182387/download

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

ProteinSecondaryStructure(x) → PhysicalStructure(x) ∧ ∃p (Protein(p) ∧ qualityOf(x, p))

Semi-Formal Natural Language Axioms

if x is a ‘protein secondary structure’ then x is a ‘physical structure’ that is the ‘quality of’ some ‘protein’

Description Logic

constr:ProteinSecondaryStructure ⊑ constr:PhysicalStructure

constr:ProteinSecondaryStructure ⊑ ∃ constr:qualityOf .constr:Protein

SubClassOf: constr:PhysicalStructure

SubClassOf: constr:qualityOf some constr:Protein