VCU NLP Lab: Software

CONTENT

ALGORITHM-LDA
CUITOOLS
METAMAP-DATASTRUCTURES
SEMMED-INTERFACE
UMLS-ASSOCIATION
UMLS-INTERFACE
UMLS-SENSERELATE
UMLS-SIMILARITY

SOFTWARE

Please see our GitHub site for more recent tools, or visit our research page.

This page contains the various software modules developed in our lab. For any questions regarding the content of this page, please contact Bridget McInnes. [see also the research page for related information].

Algorithm-LDA

Algorithm-LDA is a perl module that implements Latent Dirichlet Allocation for Topic Modeling [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.

MetaMap-DataStructures

MetaMap-Datastrutures is a perl module that provides a container for the information extracted from machine readable MetaMap mapped text [download].

SemMed-Interface

SemMed-Interface is a suite of perl modules that interfaces with SemMedDB [download].

UMLS-Association

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.

NATURAL LANGUAGE PROCESSING LAB

SOFTWARE

CONTENT

SOFTWARE

Algorithm-LDA

CuiTools

MetaMap-DataStructures

SemMed-Interface

UMLS-Association

UMLS-Interface

UMLS-SenseRelate

UMLS-Similarity