Refined JST thesaurus extended with data from other open life science data sources

Abstract

We are developing a refined Japan Science and Technology (JST) thesaurus with thirty-five relations to enable description of rigorous relationships among concepts. In this study, we prepared an environment for performing SPARQL queries and evaluated the JST thesaurus in the life sciences by comparing query results with the originals. Based on the results of the investigation, we constructed a fibrinolysis network from the thesaurus as a collection of concepts connected with fibrinolysis within three steps, and we discovered that fibrinolysis was associated with fifty-four concepts, including sixteen diseases and twelve physiological phenomena. Subsequently, using the sub-classified relations, we divided the sixteen diseases into two diseases that developed after fibrinolysis progressed, seven diseases that shared common molecules in the development mechanism with fibrinolysis, and other associated conditions. Furthermore, we mapped concepts between the JST thesaurus, ChEBI, and Gene Ontology by matching the labels and synonyms. As a result, we could integrate the fibrinolysis network with thirty-seven chemicals, including four antifibrinolytic agents and twenty-seven human gene products that can regulate fibrinolysis. Thus, we were able to handle the information relating to a series of molecules, molecular-level biological phenomena, and diseases by integrating the refined JST thesaurus with information regarding chemicals and gene products from other resources.