biological sequence

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

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

SubClass Of: bfo:generically dependent continuant

Class Hierarchy

owl:Thing › bfo:entity › bfo:continuant › bfo:generically dependent continuant › biological sequence

Direct subclasses:

• amino acid sequence
• nucleotide sequence

Definition

generically dependent continuant that is the ordered pattern of residues that constitute a particular continuous DNA, RNA, peptide, or protein molecule

Examples

• The nucleotide sequence of a plasmid DNA molecule; The nucleotide sequence of an mRNA transcript; The amino acid sequence of a monoclonal antibody heavy chain; The amino acid sequence of a synthetic peptide; The RNA sequence of a viral genome segment; The DNA sequence of a gene coding region.

Adapted From

• https://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/BIOSEQ.HTML#:~:text=A%20biological%20sequence%20is%20a,DNA%2C%20RNA%2C%20or%20protein. and http://purl.obolibrary.org/obo/SO_0000001

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

BiologicalSequence(x) → GenericallyDependentContinuant(x) ∧ ∀y (genericallyDependsOnAtSomeTime(x, y) → (DeoxyribonucleicAcid(y) ∨ Peptide(y) ∨ Protein(y) ∨ RibonucleicAcid(y)))

Semi-Formal Natural Language Axioms

if x is a ‘biological sequence’ then x is a ‘generically dependent continuant’ and x ‘generically depends on at some time’ only on some ‘deoxyribonucleic acid’, ‘peptide’, ‘protein’, or ‘ribonucleic acid’

Description Logic

constr:BiologicalSequence ⊑ bfo:generically_dependent_continuant

constr:BiologicalSequence ⊑ ∀ bfo:generically_depends_on_at_some_time .(constr:DeoxyribonucleicAcid ⊔ constr:Peptide ⊔ constr:Protein ⊔ constr:RibonucleicAcid)

SubClassOf: bfo:generically_dependent_continuant

SubClassOf: bfo:generically_depends_on_at_some_time only (constr:DeoxyribonucleicAcid or constr:Peptide or constr:Protein or constr:RibonucleicAcid)