Table 1 Primary classes, their description, sample instance data sources and the number of sample annotated instances.
From: Improving integrative searching of systems chemical biology data using semantic annotation
primary classes | description | sample instance data sources | # of sample instances |
|---|---|---|---|
SmallMolecule | a small bioactive molecule | PubChem, ChEBI | 15509 |
Drug | a chemical used in the treatment, cure, prevention, or diagnosis of disease | DrugBank, PharmGKB, TTD | 6544 |
Protein | a physical entity consisting of a sequence of amino acids | Uniprot, HGNC, GOA | 12242 |
BioAssay | an experiment to measure the effects of some substance on target, cell or a living organism | PubChem BioAssay, ChEMBL, BindingDB, PDSP | 26861 |
Disease | any condition that causes pain, dysfunction, distress or social problems | OMIM, DO | 8724 |
SideEffect | undesired effect from a medicine | SIDER | 1385 |
Literature | a scientific article | Medline | 28392 |
Pathway | a set or series of a biological interactions | KEGG, Reactome | 347 |
Interaction | Â | Â | Â |
DrugDrug-Interaction | a drug affects the activity of another drug | DrugBank, DCDB | 9690 |
ProtienProtien-Interaction | two or more proteins bind together | HPRD, DIP, BioGrid | 54345 |
DrugInduced-SideEffect | a drug interaction that results in side effect | SIDER | 61102 |
DrugTreatment | the use of drug to treat disease | Diseasome | 812 |
ChemicalProtein-Interaction | genomic response to chemical compounds | ChEMBL, BindingDB, PDSP Ki, TTD, BindingMOAD, DrugBank, CTD, MATADOR, Array-Express, KEGG | 47282 |