VCU Natural Language Processing Lab news . research . people . publications . teaching . software . data . lab . contact software [see also the research page for related information] This page contains the various software modules developed in our lab. They are made available under the terms of GNU General Public License. Both data and software are distributed without any warranty. For any questions regarding the content of this page, please contact Bridget McInnes, btmcinnes at vcu.edu Software Algorith-LDA CuiTools MetaMap-DataStructures SemMed-Interface UMLS-Association UMLS-Interface UMLS-SenseRelate UMLS-Similarity UMLS-Assocation UMLS-Association is a suite of Perl Modules that can quantify the association between biomedical and clinical terms using co-occurrence information from the Medline Baseline. [download]. UMLS-Interface UMLS-Interface provides a Perl interface to the Unified Medical Language System (UMLS), a knowledge representation framework encoded designed to support broad scope biomedical research queries. The package is set up to access the Metathesaurus and the Semantic Network present in a mysql database [download]. UMLS-Interface and UMLS-Similarity : Open Source Software for Measuring Paths and Semantic Similarity. Bridget T. McInnes, Ted Pedersen, and Serguei V. Pakhomov. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, Nov 14-18, 2009, San Francisco, CA. UMLS-SenseRelate UMLS-SenseRelate is a suite of Perl modules that implement the sense relate word sense disambiguation algorithm using the semantic similarity and relatedness measures from the UMLS-Similarity package [download]. 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. UMLS-Similarity UMLS-Similarity is a suite of Perl Modules that implement a number of semantic similarity and relatedness measures. The package was designed to quantify the similarity or relatedness between biomedical and clinical terms using information from the UMLS [download] [web interface]. UMLS-Interface and UMLS-Similarity : Open Source Software for Measuring Paths and Semantic Similarity. Bridget T. McInnes, Ted Pedersen, and Serguei V. Pakhomov. Appears in the Proceedings of the Annual Symposium of the American Medical Informatics Association, Nov 14-18, 2009, San Francisco, CA. SemMed-Interface SemMed-Interface is a suite of perl modules that interfaces with SemMedDB. [download]. Algorithm-LDA Algorithm-LDA is a perl module that implements Latent Dirichlet Allocation for Topic Modeling. [download]. MetaMap-Datastrutcures MetaMap-Datastrutures is a perl module that provides a container for the information extracted from machine readable MetaMap mapped text. [download]. CuiTools CuiTools is a freely available package of Perl programs for unsupervised and supervised word sense disambiguation (WSD) experiments. [download]. 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.