Table 4.

Representational characteristics of ‘protein aggregate’ and ‘protein complex’ in Bioportal ontologies.

	NIF Standard Ontology	Neurodegenerative Disease Data Ontology	EDAM Ontology	Semantic Science Integrated Ontology
Term	protein aggregate	protein aggregate	protein complex	protein complex
Definitions	A grouping of misfolded proteins that is often rigid and insoluble [1]	An insoluble mass of misfolded proteins [2]	3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another [22]	A protein complex is a molecular complex composed of at least two polypeptide chains.
Features of Usage Examples & Literature Definitions	Component proteins in non-native state	Insoluble Component proteins in non-native state	Constituent parts of the protein complex function together Comprised of two or more polypeptides	Comprised of two or more polypeptides
1^st Parent	Aggregate object	Material entity	Protein structure	Molecular complex
2^nd Parent	Object aggregate	Independent continuant	Structure	Chemical entity
3^rd Parent	Material entity	Continuant	Data	Material entity
4^th Parent	Independent continuant	Entity	Thing	Object
5^th Parent	Continuant			Entity
6^th Parent	Entity