protein low molecular weight variant classifier

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

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

SubClass Of: protein size variant classifier

Class Hierarchy

owl:Thing › bfo:entity › bfo:continuant › bfo:generically dependent continuant › information content entity › denoter › classifier › size variant classifier › protein size variant classifier › protein low molecular weight variant classifier

Definition

protein size variant classifier that classifies a molecular entity population composed of proteins or protein fragments as having lower molecular size or molecular weight than a reference protein form

Explanatory Notes

A protein low molecular weight variant classifier classifies protein-related molecular populations whose molecular size or molecular weight is lower than the reference protein form under the relevant analytical method. The classified population may include fragments, clipped forms, truncated forms, partially degraded chains, light-chain or heavy-chain fragments, half-antibody species, or other low-molecular-weight product-related material.

Examples

• a classifier that classifies the population corresponding to a low-molecular-weight species peak in a monoclonal antibody size exclusion chromatography-high performance liquid chromatography (SEC-HPLC) assay; a classifier that classifies clipped antibody fragment populations detected by Capillary Electrophoresis-Sodium Dodecyl Sulfate (CE-SDS); a classifier that classifies protein fragments formed during stability testing as low-molecular-weight species; a classifier that classifies a half-antibody population as lower molecular weight than the reference antibody form;

Adapted From

• https://www.agilent.com/cs/library/applications/application-intact-protein-analysis-1290-bio-5994-3021en-agilent.pdf?srsltid=AfmBOord0gYpA_izWG5ho6VxaMiEr6N9eFGWe1h-RuEb88akGHX2gVrA and https://www.biopharminternational.com/view/protein-impurities-pose-challenges and https://www.sciencedirect.com/science/article/pii/S0022354922003392

Primitive Class

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

Primitive Rationale

There are insufficient constructs to create a set of necessary and sufficient conditions.

Formal Axioms

First-Order Logic Axioms

ProteinLowMolecularWeightVariantClassifier(x) → ProteinSizeVariantClassifier(x) ∧ ∃p (MolecularEntityPopulation(p) ∧ classifies(x, p) ∧ ∃m ((Protein(m) ∨ ProteinFragment(m)) ∧ hasMemberPartAtSomeTime(p, m)) ∧ ∀m (hasMemberPartAtSomeTime(p, m) → (Protein(m) ∨ ProteinFragment(m))))

Semi-Formal Natural Language Axioms

if x is a ‘protein low molecular weight variant classifier’ then x is a ‘protein size variant classifier’ that classifies some ‘molecular entity population’ whose members are proteins or protein fragments

Description Logic

constr:ProteinLowMolecularWeightVariantClassifier ⊑ constr:ProteinSizeVariantClassifier

constr:ProteinLowMolecularWeightVariantClassifier ⊑ ∃ constr:classifies .(constr:MolecularEntityPopulation ⊓ ∀ bfo:has_member_part_at_some_time .(constr:Protein ⊔ constr:ProteinFragment))

constr:ProteinLowMolecularWeightVariantClassifier ⊓ constr:ProteinHighMolecularWeightVariantClassifier ⊑ ⊥

SubClassOf: constr:ProteinSizeVariantClassifier

SubClassOf: constr:classifies some (constr:MolecularEntityPopulation and bfo:has_member_part_at_some_time only (constr:Protein or constr:ProteinFragment))

constr:ProteinLowMolecularWeightVariantClassifier DisjointWith: constr:ProteinHighMolecularWeightVariantClassifier