Available biomedical ontologies and knowledge bases currently lack formal and standards-based interconnections between disease, disease vector, and drug treatment vocabularies. The PNNL Medical Linked Dataset (PNNL-MLD) addresses this gap. This paper describes the PNNL-MLD, which provides a unified vocabulary and dataset of drug, disease, side effect, and vector transmission background information. Currently, the PNNL-MLD combines and curates data from the following research projects: DrugBank, DailyMed, Diseasome, DisGeNet, Wikipedia Infobox, Sider, and PharmGKB. The main outcomes of this effort are a dataset aligned to Schema.org, including a parsing framework, and extensible hooks ready for integration with selected medical ontologies. The PNNL-MLD enables researchers more quickly and easily to query distinct datasets. Future extensions to the PNNL-MLD will include Traditional Chinese Medicine, broader interlinks across genetic structures, a larger thesaurus of synonyms and hypernyms, explicit coding of diseases and drugs across research systems, and incorporating vector-borne transmission vocabularies.
Revised: December 22, 2015 |
Published: April 21, 2015
Citation
Smith W.P., A.R. Chappell, and C.D. Corley. 2015.Medical and Transmission Vector Vocabulary Alignment with Schema.org. In Proceedings of the International Conference on Biomedical Ontology (ICBO 2015), July 27-30, 2015, Lisbon, Portugal, edited by FM Couto and J Hastings. Aachen:CEUR Workshop Proceedings.PNNL-SA-108585.