amino acid residue
IRI: https://spec.industrialontologies.org/ontology/construct/AminoAcidResidue
Defined In: https://spec.industrialontologies.org/ontology/biopharma/MolecularEntity/
SubClass Of: chemical moiety
Class Hierarchy
owl:Thing › bfo:entity › bfo:continuant › bfo:independent continuant › bfo:material entity › chemical moiety › amino acid residue
Direct subclasses:
Definition
chemical moiety that is a proper part of a peptide or protein and that is the remaining portion of an amino acid resulting from peptide-bond formation
Explanatory Notes
During peptide-bond formation, each amino acid loses the atoms corresponding to one molecule of water. The remaining portion constitutes the amino-acid residue within the polypeptide chain.
Examples
- Alanine residue in a peptide; Glycine residue in a synthetic peptide; Lysine residue in a monoclonal antibody heavy chain; Cysteine residue participating in a disulfide bond in a protein; Serine residue in a phosphorylated protein.
Adapted From
- http://purl.obolibrary.org/obo/CHEBI_33708
Primitive Class
This class is declared primitive and it does not have necessary and sufficient condiftions defined.
Primitive Rationale
This term is expected to remain primitive as the detailed treatment of chemical bonds, structure and formation is outside of the current scope of IOF. Other biological and chemical ontologies should be used for these purposes
Formal Axioms
First-Order Logic Axioms
AminoAcidResidue(x) → ChemicalMoiety(x) ∧ ∃y (properContinuantPartOfAtAllTimes(x, y) ∧ (Peptide(y) ∨ Protein(y)))
Semi-Formal Natural Language Axioms
if x is an ‘amino acid residue’ then x is a ‘chemical moiety’ and x is a ‘proper continuant part of at all times’ some ‘peptide’ or ‘protein’
Description Logic
constr:AminoAcidResidue ⊑ constr:ChemicalMoiety
constr:AminoAcidResidue ⊑ ∃ bfo:proper_continuant_part_of_at_all_times .(constr:Peptide ⊔ constr:Protein)
SubClassOf: constr:ChemicalMoiety
SubClassOf: bfo:proper_continuant_part_of_at_all_times some (constr:Peptide or constr:Protein)