Table 1 Classification of biological structures in 6 prototypes in the semantic network.
From: Modeling of cell signaling pathways in macrophages by semantic networks
Semantic Agent – Structure | Biological Example |
|---|---|
Cell | Human macrophage, Mycobacterium tuberculosis |
Subcellular Compartment | Plasma membrane, cytosol, phagosome, nucleus |
Macromolecule | Protein, nucleic acid, polysaccharide, fat/lipid |
Domain and Site | Catalytic domain, SH2 domain, PH domain, binding site, phosphorylation site, promoter, gene regulatory site. |
Small Molecule and Molecular Fragment | Amino acid, nucleotide, sugar, fatty acid |
Atom | Hydrogen, carbon, oxygen, nitrogen, phosphorus, sulfur |