Ontology for Chemogenomics/Systems Chemical Biology

Go to Chem2Bio2OWL website (see owl file and annotated file)
Go to Chem2Bio2RDF wiki

goto SLAP page (drug target prediction)


Current Chem2Bio2RDF already integrated a large number of public data related to Systems Chemical Biology, however, it lacks ontology to represent its data effectively, making it difficult to be understood by public. Although some attempts were performed to build ontology, no substantial progress has been made, as many data sources were involved in and the data structure is quite complicated per se, moreover, the definition of some concepts (drug target interaction) are still obscure. After a few attempts, now we are moving to the official stageJ. This document is going to track our work on creating Chemogenomics/Systems Chemical Biology ontology.

Systems Chemical Biology covers many concepts in chemical and biology domains (e.g, drug, compound, gene, protein, disease, pathway, and side effect), The ontology of many concepts have been modeled individually, here, we are not going to create for all, instead, we provide a high level of ontology to show their relations and import the well known existing ontologies for representing the entities/relations. In addition, we are focusing on the ontology of chemical gene (protein) interaction, which will be covering the BioAssay experimental data.

In addition to facilitating the integration of data, this ontology will be served as a base for the ongoing projects such as path finding, data mining (e.g., Drug Target Prediction) and reasoning.

Use cases
Version 0.0
Version 1.0
Version 1.1
Related works/sources
SPARQL cases

Bin Chen
Shanshan Chen
Kuo-Chung Peng
Ying Ding
David Wild

Please send an email to binchen@indiana.edu for participating. We welcome everyone to join us.

Cite: Bin Chen, Ying Ding, David J Wild, Improving integrative searching of systems chemical biology data using semantic annotation, Journal of Cheminformatics, 2012