Thalia: semantic search engine for biomedical abstracts

SUMMARY: Although the publication rate of the biomedical literature has been growing steadily during the last decades, the accessibility of pertinent research publications for biologist and medical practitioners remains a challenge. This article describes Thalia, which is a semantic search engine that can recognize eight different types of concepts occurring in biomedical abstracts. Thalia is available via a web-based interface or a RESTful API. A key aspect of our search engine is that it is updated from PubMed on a daily basis. We describe here the main building blocks of our tool as well as an evaluation of the retrieval capabilities of Thalia in the context of a precision medicine dataset. AVAILABILITY AND IMPLEMENTATION: Thalia is available at http://nactem.ac.uk/Thalia_BI/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.