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 82.2 million predications from all of PubMed citations (more than 25 million citations, as of June 30th, 2015) and forms the backbone of Semantic MEDLINE application [2, 3].

For details about the SemMedDB schema, click "Database Details" tab.

To download the current version of SemMedDB (as of June 30th, 2012), 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

  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.