Semantic MEDLINE Database

The Semantic MEDLINE Database (SemMedDB) [1] is a repository of semantic predications (subject-predicate-object triples) extracted by SemRep, a semantic interpreter of biomedical text [2]. SemMedDB currently contains information about approximately 94.0 million predications from all of PubMed citations (about 27.9 million citations, as of December 31 2017) and forms the backbone of the Semantic MEDLINE application [3, 4].

For details about the SemMedDB schema, click here.

To download the SemMedDB, a UTS account is required. Users that already have one need to click here and provide their UTS account information. To get a UTS account, click here.

For more information about SemMedDB, contact


  1. Kilicoglu, H, Shin D, Fiszman M, Rosemblat G, Rindflesch TC. (2012) SemMedDB: A PubMed-scale repository of biomedical semantic predications. Bioinformatics, 28(23), 3158-60.
  2. Rindflesch, T.C. and Fiszman, M. (2003). The interaction of domain knowledge and linguistic structure in natural language processing: Interpreting hypernymic propositions in biomedical text. Journal of Biomedical Informatics, 36(6), 462-477.
  3. Kilicoglu, H. et al. (2008). Semantic MEDLINE: A Web Application to Manage the Results of PubMed Searches. In Proceedings of the Third International Symposium on Semantic Mining in Biomedicine (SMBM 2008), 69-76.
  4. Rindflesch, T.C. et al. (2011) Semantic MEDLINE: An advanced information management application for biomedicine. Information Services & Use, 31, 15-21.