PubChem is an open repository for chemical substance description, biological activities and biomedical annotations. PubChem databases have been cross-referenced with other National Center for Biotechnology Information (NCBI) resources, such as PubMed, Gene, Biosystems, and so on. Semantic Web standards offer a well-defined syntax for the formal representation of the PubChem knowledgebase, and Semantic Web technologies facilitate the query and reasoning of PubChem data. PubChemRDF project focused on the semantic annotations of PubChem databases, which were accomplished by using standardized ontologies that promise the high compatibility and consistency with currently existing cheminformatics and bioinformatics resources. Semantic annotations may help PubChem data to be shared, reused, and analyzed across chemical, biological, and life science domains. PubChemRDF provides a new ability for researchers to utilize schema-less database with rule-based reasoner to search and analyze data. We will demonstrate how to combine SPARQL queries and Description Logic (DL) queries for question answering using PubChemRDF data.

PubChemRDF: Semantic annotation and search

251st National Meeting (2016)

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