Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Dec 1;28(23):3158-60.
doi: 10.1093/bioinformatics/bts591. Epub 2012 Oct 8.

SemMedDB: a PubMed-scale repository of biomedical semantic predications

Halil Kilicoglu  1 , Dongwook Shin, Marcelo Fiszman, Graciela Rosemblat, Thomas C Rindflesch
Affiliations

SemMedDB: a PubMed-scale repository of biomedical semantic predications

Halil Kilicoglu et al. Bioinformatics. .

Abstract

Summary: Effective access to the vast biomedical knowledge present in the scientific literature is challenging. Semantic relations are increasingly used in knowledge management applications supporting biomedical research to help address this challenge. We describe SemMedDB, a repository of semantic predications (subject-predicate-object triples) extracted from the entire set of PubMed citations. We propose the repository as a knowledge resource that can assist in hypothesis generation and literature-based discovery in biomedicine as well as in clinical decision-making support.

Availability and implementation: The SemMedDB repository is available as a MySQL database for non-commercial use at http://skr3.nlm.nih.gov/SemMedDB. An UMLS Metathesaurus license is required.

Contact: kilicogluh@mail.nih.gov.

PubMed Disclaimer

References

    1. Ahlers CB, et al. Pacific Symposium on Biocomputing. Maui, HI, USA: World Scientific; 2007. Extracting semantic predications from Medline citations for pharmacogenomics; pp. 209–220. - PubMed
    1. Björne J, et al. Proceedings of the Workshop on Biomedical Natural Language Processing (BioNLP’10) Uppsala, Sweden: Association of Computational Linguistics; 2010. Scaling up biomedical event extraction to the entire PubMed; pp. 28–36.
    1. Björne J, et al. Proceedings of the Workshop on Biomedical Natural Language Processing (BioNLP’12) Montreal, Canada: Association of Computational Linguistics; 2012. PubMed-scale event extraction for post-translational modifications, epigenetics and protein structural relations; pp. 82–90.
    1. Bodenreider O. The unified medical language system (UMLS): integrating biomedical terminology. Nucleic Acids Res. 2004;32:D267–D270. - PMC - PubMed
    1. Cohen T, et al. EpiphaNet: an interactive tool to support biomedical discoveries. J. Biomed. Discov. Collab. 2010;5:21–49. - PMC - PubMed

Publication types