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Table 1 Typical data record from the joined databases Uniprot and Ensembl. The abstraction introduces the symbols of the example ontologies

From: Ontological interpretation of biomedical database content

Field Source Content Abstraction
Protein (PR) UniProt Cystathionine gamma-lyase Prot 1
Organism (NCBI Taxonomy) NCBI Taxonomy via UniProt Rattus norvegicus (Rat) Org 1
Processes (not distinguishing between ‘Biological process’ and ‘Molecular function’ in Gene Ontology (GO)) GO via UniProt hydrogen sulfide biosynthetic process; negative regulation of apoptotic signaling pathway; positive regulation of I-kappaB kinase/NF-kappaB signaling; protein homotetramerization; protein sulfhydration BProc 1, BProc 2, …, BProc k
Cell components (GO_cc) GO via UniProt cytoplasm; nucleus; extracellular vesicular exosome; CComp 1, CComp 2, …, CComp x
Small molecules (ChEBI) ChEBI Homocysteine Mol 1, Mol 2, …, Mol y
Phenotypes Ensembl Amino acid metabolism errors; cataract; Gamma-cystathionase deficiency Phen 1, Phen 2, …, Phen z