This volume contains the papers presented at SWAT4HCLS 2019: Semantic Web Applications and Tools in Healthcare and Life Sciences 2019 held on December 9-12, 2019 in Edinburgh. Each submission was reviewed by on the average 2.5, program committee members. The committee decided to accept 35 papers, of which 14 were selected for oral presentation. In addition to these, the following keynotes were presented: { Denny Vrandecic^a Wikidata and beyond { Knowledge for everyone by everyone { Birgitta Konig-Ries Semantics for FAIR research data management { Dov Greenbaum Data Ownership and protection within the FAIR Framework { Helen Parkinson A FAIR Vocabulary Odyssey SWAT4HCLS is the 12th edition of the conference series, and was held in Edinburgh for the 3rd time. We like to thank Godan, Global Open Data for Agriculture and Nutrition, for their generous sponsorship. These proceedings were generated using EasyChair, and published in the CEUR-WS series.