biological sequence variant classifier

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

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

SubClass Of: classifier

Class Hierarchy

owl:Thing › bfo:entity › bfo:continuant › bfo:generically dependent continuant › information content entity › denoter › classifier › biological sequence variant classifier

Definition

classifier that classifies a DNA molecule, RNA molecule, peptide, or protein which has a biological sequence that differs from a specified reference biological sequence by one or more substitutions, insertions, deletions, truncations, or extensions

Explanatory Notes

A biological sequence variant classifier is grounded in comparison with a specified reference biological sequence. Classification by such a classifier indicates that the classified molecular entity is treated as a sequence variant relative to that reference sequence. It does not imply that the molecular entity is intrinsically a variant independently of the selected reference. Different classifiers may classify the same molecular entity differently when they are grounded in different reference sequences or comparison criteria

Examples

• a classifier grounded in a specified BRCA1 reference sequence that classifies a BRCA1 DNA molecule containing the c.68_69delAG deletion as a biological sequence variant; a classifier grounded in a specified monoclonal-antibody heavy-chain reference sequence that classifies a heavy-chain molecule containing an amino-acid substitution as a biological sequence variant; a classifier grounded in the intended full-length protein sequence that classifies a truncated heavy-chain molecule as a biological sequence variant; a classifier grounded in a specified RNA reference sequence that classifies an RNA molecule containing an insertion as a biological sequence variant; a classifier grounded in a specified peptide reference sequence that classifies a clipped peptide as a biological sequence variant

Adapted From

• http://purl.obolibrary.org/obo/SO_0001060 and https://www.cancer.gov/publications/dictionaries/genetics-dictionary/def/variant and https://www.rapidnovor.com/sequence-variant-analysis-monoclonal-antibodies/#:~:text=Variant%20Analysis%20Service-,Introduction,variants%20and%20their%20associated%20risks.

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 necessary and sufficient conditions.

Formal Axioms

First-Order Logic Axioms

BiologicalSequenceVariantClassifier(x) → Classifier(x) ∧ ∃s(BiologicalSequence(s) ∧ isAbout(x, s)) ∧ ∃m((DeoxyribonucleicAcid(m) ∨ RibonucleicAcid(m) ∨ Peptide(m) ∨ Protein(m)) ∧ classifies(x, m))

Semi-Formal Natural Language Axioms

if x is a ‘biological sequence variant classifier’, then x is a ‘classifier’ that ‘is about’ some ‘biological sequence’ and ‘classifies’ some ‘deoxyribonucleic acid’, ‘ribonucleic acid’, ‘peptide’, or ‘protein’

Description Logic

constr:BiologicalSequenceVariantClassifier ⊑ constr:Classifier

constr:BiologicalSequenceVariantClassifier ⊑ ∃ constr:classifies .(constr:DeoxyribonucleicAcid ⊔ constr:Peptide ⊔ constr:Protein ⊔ constr:RibonucleicAcid)

constr:BiologicalSequenceVariantClassifier ⊑ ∃ constr:isAbout .constr:BiologicalSequence

SubClassOf: constr:Classifier

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

SubClassOf: constr:isAbout some constr:BiologicalSequence