Table 1.
Commonly used interoperable ontologies and their usages in omics-related projects
| Domain | Ontology | Omics-related applications |
|---|---|---|
| Taxonomy | NCBITaxon [86] | LINCS [55] |
| Anatomy | UBERON [87] | ENCODE [39], KPMP [16, 17], LINCS |
| In vivo cells, cell line cells | CL [88] | ENCODE, KPMP |
| CLO [89] | ENCODE, LINCS | |
| Molecular entities | ChEBI [33] | ENCODE |
| OGG [90] | KPMP | |
| PR [91] | KPMP | |
| Biological processes, cellular components and molecular functions of gene products | GO [37] | GEO [92], KPMP, STRING [82] |
| Diseases and phenotypes | DO [93] | CGI [94] |
| MONDO [95] | KPMP | |
| HPO [42] | KPMP | |
| Adverse event | OAE [96] | KMMP |
| Vaccine | VO [44] | ImmPort [97]; KPMP |
| Experimental assays | OBI [25, 26] | ENCODE, KPMP |
Abbreviations: CGI: Cancer Genome Interpreter; CL: Cell Ontology; CLO: Cell Line Ontology; ChEBI: Chemical Entities of Biological Interest; DO: Disease Ontology; ENCODE: Encyclopedia of DNA Elements; GEO: Gene Expression Omnibus; GO: Gene Ontology; HPO: Human Phenotype Ontology; ImmPort: The Immunology Database and Analysis Portal; KPMP: Kidney Precision Medicine Project; LINCS: The Library of Integrated Network-Based Cellular Signatures; MONDO: Mondo Disease Ontology; NCBITaxon: NCBI Taxonomy Ontology; OAE: Ontology of Adverse Events; OBI: Ontology for Biomedical Investigations; OGG: Ontology of Genes and Genomes; PR: Protein Ontology; UBERON: Uber Anatomy Ontology; VO: Vaccine Ontology.