Skip to main content

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
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
  1. Data sources were described in [32]