Semantic MEDLINE Database

Semantic MEDLINE Database (SemMedDB) is a repository of semantic predications (subject-predicate-object triples) extracted by SemRep, a semantic interpreter of biomedical text [1]. SemMedDB currently contains information about approximately 85.8 million predications from all of PubMed citations ( about 26 million citations, as of April 30th, 2016) and forms the backbone of Semantic MEDLINE application [2, 3].

For details about the SemMedDB schema, click here.

To download the SemMedDB, a UTS account is required. If you have one, click here and provide the UTS account information. To get a UTS account, click here.

For more information about SemMedDB, contact semmed@nlm.nih.gov.

  1. 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.
  2. 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), pp. 69-76.
  3. Rindflesch, T.C. et al. (2011) Semantic MEDLINE: An advanced information management application for biomedicine. Information Services & Use, 31, 15-21.
  4. 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.