protein
IRI: https://spec.industrialontologies.org/ontology/construct/Protein
Defined In: https://spec.industrialontologies.org/ontology/biopharma/MolecularEntity/
SubClass Of: organic molecular entity
Class Hierarchy
owl:Thing › bfo:entity › bfo:continuant › bfo:independent continuant › bfo:material entity › molecular entity › organic molecular entity › protein
Direct subclasses:
Definition
organic molecular entity that consists of one or more polypeptide chains of sufficient length or molecular mass to be distinguished from peptides
Explanatory Notes
1) From FDA Definition of the Term “Biological Product” : “protein” means any alpha amino acid polymer with a specific, defined sequence that is greater than 40 amino acids in size. 2) Per IUPAC, proteins are naturally occurring or synthetic polypeptides with molecular weights greater than about 10,000, while the boundary is acknowledged to be imprecise. 3) The expression “sufficient length or molecular mass” is used to capture the fact that the protein–peptide boundary is not fixed by a single universally accepted criterion. The FDA criterion provides a regulatory threshold based on amino acid count, while the IUPAC criterion reflects a broader chemical convention based on molecular weight. 4) Ribosomal synthesis is not included as a necessary condition in the definition because it describes one way in which many naturally occurring proteins are produced, rather than what the molecular entity is. Since both FDA and IUPAC definitions allow classification based on the structure and composition of the polymer, and IUPAC explicitly includes synthetic polypeptides, requiring ribosomal synthesis would make the class too narrow. Ribosomally synthesized proteins can therefore be represented as a more specific subclass where the production history is relevant.
Examples
- Albumin; Monoclonal antibody (IgG); Recombinant human growth hormone
Adapted From
- http://purl.obolibrary.org/obo/CHEBI_36080 and https://www.fda.gov/media/122985/download and Lehninger Principles of biochemistry and https://goldbook.iupac.org/terms/view/P04898
Primitive Class
This class is declared primitive and it does not have necessary and sufficient condiftions defined.
Primitive Rationale
See the primitive rationale under molecular entity
Formal Axioms
First-Order Logic Axioms
Protein(x) → OrganicMolecularEntity(x) ∧ ∃p (hasContinuantPartAtAllTimes(x, p) ∧ Polypeptide(p))
Semi-Formal Natural Language Axioms
if x is a ‘protein’ then x is an ‘organic molecular entity’ and x ‘has continuant part at all times’ some ‘polypeptide’
Description Logic
constr:Protein ⊑ constr:OrganicMolecularEntity
constr:Protein ⊑ ∃ bfo:has_continuant_part_at_all_times .constr:Polypeptide
SubClassOf: constr:OrganicMolecularEntity
SubClassOf: bfo:has_continuant_part_at_all_times some constr:Polypeptide