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 |