UMLS-SIMILARITY
About
- UMLS::Similarity is a suite of Perl modules that implement a number of semantic similarity measures. The measures use the UMLS-Interface module to access the UMLS to generate similarity scores between concepts. Currently, this package includes programs that implement the similarity measures described by Leacock & Chodorow (1998), Wu & Palmer (1994), Nguyen & Al-Mubaid (2006), Rada, et. al. (1989), Jiang & Conrath (1997), Resnik (1995) and Lin (1998), and the relatedness measures proposed by Banerjee & Pedersen (2002), Patwardhan (2003).
- If you use UMLS::Similarity, please cite the following paper:
Web Services
- Try the UMLS::Similarity Web Interface here (production) or here (backup). This does not require installation on your system, so it is a good way to get started.
- Query the Web Interface using the Perl Script from the UMLS::Similarity package.
Mailing List
- Join our mailing list designed to support users of UMLS::Similarity.
- There is also extensive documentation.
Tutorials and Demos
- UMLS::Similarity: Measuring the Relatedness and Similarity of Biomedical Concepts. Bridget T. McInnes, Ted Pedersen, Ying Liu, Serguei Pakhomov, and Genevieve B. Melton. To Appear in the Proceedings of the North American Association of Computational Linguistics Demonstration Systems. June 10-12, 2013, Atlanta, Georgia.
- Measuring the Similarity and Relatedness of Concepts in the Medical Domain : IHI 2012 Tutorial Overview. Ted Pedersen, Serguei Pakhomov, Bridget T. McInnes, and Ying Liu. Appears in the Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, January 28-30, 2012, Miami, FL.
Publications
- U-path: An undirected path-based measure of semantic similarity. Bridget T. McInnes, Ted Pedersen, Ying Liu, Serguei Pakhomov, and Genevieve B. Melton. To Appear in the Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA), November 2014.
- Determining the Difficulty of Word Sense Disambiguation. Bridget T. McInnes and Mark Stevenson. Journal of Biomedical Informatics. 2014 Feb; 47:83-90.
- Evaluating Measures of Semantic Similarity and Relatedness to Disambiguate Terms in Biomedical Text. Bridget T. McInnes and Ted Pedersen. Journal of Biomedical Informatics. 2013 December; 46(6):1116-24.
- Evaluating Semantic Relatedness and Similarity Measures with Standardized MedDRA Queries. Robert W. Bill, Ying Liu, Bridget T. McInnes, Genevieve B. Melton, Ted Pedersen, and Serguei Pakhomov. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA), November 2012.
- Semantic Relatedness Study Using Second Order Co-occurrence Vectors Computed from Biomedical Corpora, UMLS and WordNet. Ying Liu, Bridget T. McInnes, Ted Pedersen, Serguei Pakhomov and Genevieve B. Melton. Appears in the Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium, January 28-30, 2012, Miami, FL.
- Evaluating Measures of Redundancy in Clinical Texts. Rui Zhang, Serguei Pakhomov, Bridget T. McInnes, and Genevieve B. Melton. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association (AMIA). Oct. 2011, Washington DC.
- Towards a Framework for Developing Semantic Relatedness Reference Standards. Serguei V. Pakhomov, Ted Pedersen, Bridget T. McInnes, Genevieve B. Melton, Alexander Ruggieri, and Christopher G. Chute. Journal of Biomedical Informatics. 2011 44(2), 251-265.
- Semantic Similarity and Relatedness between Clinical Terms: An Experimental Study. Serguei Pakhomov, Bridget T. McInnes, Terrence Adam, Ying Liu, Ted Pedersen and Genevieve B. Melton. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association. Nov 13-17, 2010, Washington, DC.
- UMLS-Interface and UMLS-Similarity : Open Source Software for Measuring Paths and Semantic Similarity. Bridget T. McInnes, Ted Pedersen and Serguei V. Pakhomov. In the Proceedings of the Annual Symposium of the American Medical Informatics Association, Nov 14-18, 2009, San Francisco, CA.
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