Table 1 Main biomedical ontologies used for RNA-KG construction (* modified to include only human and viral proteins).

Human Phenotype Ontology⁴⁴

HPO

Terms representing medically relevant phenotypes and disease-phenotype annotations.

Gene Ontology⁴⁰

GO

Terms representing attributes of gene products in all organisms. Cellular component, molecular function, and biological process domains are covered.

Monarch Merged Disease Ontology⁹⁸

Mondo

Terms representing human diseases.

Vaccine Ontology⁹⁹

VO

Terms in the domain of vaccine and vaccination.

Chemical Entities of Biological Interest¹⁰⁰

ChEBI

Structured classification of molecular entities of biological interest focusing on “small” chemical compounds.

Uber-anatomy Ontology¹⁰¹

Uberon

Terms representing body parts, organs and tissues in a variety of animal species, with a focus on vertebrates.

Cell Line Ontology¹⁰²

CLO

Terms representing publicly available cell lines.

PRotein Ontology¹⁰³*

PRO

Terms representing protein-related entities (including specific modified forms, orthologous isoforms, and protein complexes).

Sequence Ontology¹⁰⁴

SO

Terms representing features and properties of nucleic acid used in biological sequence annotation.

Pathway Ontology¹⁰⁵

PW

Terms for annotating gene products to pathways.

Relation Ontology²⁸

RO

Terms and properties representing relationships used across a wide variety of biological ontologies.