protein charge variant classifier

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

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

SubClass Of: charge variant classifier

Class Hierarchy

owl:Thing › bfo:entity › bfo:continuant › bfo:generically dependent continuant › information content entity › denoter › classifier › charge variant classifier › protein charge variant classifier

Direct subclasses:

• protein acidic charge variant classifier
• protein basic charge variant classifier
• protein main charge variant classifier

Definition

charge variant classifier that classifies a molecular entity population composed of proteins or protein fragments according to charge-related analytical behavior relative to a reference protein form

Explanatory Notes

A protein charge variant classifier classifies populations of protein or protein-fragment molecules by charge-related analytical behavior, such as net electric charge, isoelectric point, ion-exchange retention behavior, capillary isoelectric focusing behavior, or electrophoretic mobility. The classified population may contain multiple molecular forms grouped together by the analytical method, rather than one structurally uniform molecular species. The reference protein form is specified by the relevant design specification.

Examples

• a classifier that classifies the acidic peak population of a monoclonal antibody in cation-exchange chromatography as a protein charge variant; a classifier that classifies a basic peak population of a recombinant protein by imaged capillary isoelectric focusing; a classifier that classifies deamidated antibody-related molecular populations as acidic charge variants under a product-specific charge variant method

Adapted From

• https://pmc.ncbi.nlm.nih.gov/articles/PMC5392216/ and https://www.chromatographyonline.com/view/charge-variant-profiling-biopharmaceuticals and https://www.agilent.com/cs/library/applications/compendium-chargevariant-advancebio-5994-0034EN-us-agilent.pdf?srsltid=AfmBOorRMu0dQH4wotghCeKwXSMCdNuuNsAEkA06EkLXupvMO6SBKJaN

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

ProteinChargeVariantClassifier(x) → ChargeVariantClassifier(x) ∧ ∃s(DesignSpecification(s) ∧ isAbout(x,s) ∧ ∃r(Protein(r) ∧ prescribes(s,r))) ∧ ∃p(MolecularEntityPopulation(p) ∧ classifies(x,p) ∧ ∃m((Protein(m) ∨ ProteinFragment(m)) ∧ hasMemberPartAtSomeTime(p,m)) ∧ ∀n(hasMemberPartAtSomeTime(p,n) → (Protein(n) ∨ ProteinFragment(n))))

Semi-Formal Natural Language Axioms

if x is a ‘protein charge variant classifier’ then x is a ‘charge variant classifier’ that classifies some ‘molecular entity population’ whose members are proteins or protein fragments, and x is about some ‘design specification’ that prescribes some protein

Description Logic

constr:ProteinChargeVariantClassifier ⊑ constr:ChargeVariantClassifier

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

constr:ProteinChargeVariantClassifier ⊑ ∃ constr:isAbout .(constr:DesignSpecification ⊓ ∃ constr:prescribes .constr:Protein)

SubClassOf: constr:ChargeVariantClassifier

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

SubClassOf: constr:isAbout some (constr:DesignSpecification and constr:prescribes some constr:Protein)