++ed by:
EMAZEP

1 PAUSE user

Bridget McInnes

Documentation

  • create-icfrequency.pl - This program sums the frequency counts of the CUIs from a specified set of sources in plain text.
  • create-icpropagation.pl - This program determines the probability of the CUIs in a specified set of sources and relations.
  • query-umls-similarity-webinterface.pl - This program returns a semantic similarity score between two concepts.
  • sim2r.pl - This program converts a series of umls-similarity output to R format in order to run the SignificanceTesting.r program.
  • spearmans.pl - This program calculates Spearman's Rank Correlation between two datasets.
  • umls-similarity.pl - This program returns a semantic similarity score between two concepts.
  • umls_similarity_server.pl - [Web] The backend UMLS::Similarity server for the Web Interface
  • vector-input.pl - This program builds the term index file and co-occrrence matrix for umls-similarity.pl to calculate the vector relatedness.

Modules

  • UMLS::Similarity - A suite of Perl modules that implement a number of semantic similarity measures in order to calculate the similarity between two concepts in the UMLS. The measures use the UMLS-Interface module to access the UMLS present in a mysql database.
  • UMLS::Similarity::ErrorHandler - Provides the error handling of the configuration files for the measures in the UMLS-Similarity package.
  • UMLS::Similarity::batet - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Batet, et al. (2011)
  • UMLS::Similarity::cdist - Perl module for computing semantic relatedness of concepts in the UMLS by simple edge counting proposed by Rada, et. al. (1989).
  • UMLS::Similarity::cmatch - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Maedche and Staab (2001).
  • UMLS::Similarity::faith - Perl module for computing the semantic relatednessof concepts in the Unified Medical Language System (UMLS) using the method described by Pirro and Euzenat (2010).
  • UMLS::Similarity::jcn - Perl module for computing the semantic relatednessof concepts in the Unified Medical Language System (UMLS) using the method described by Jiang and Conrath (1997).
  • UMLS::Similarity::lch - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Leacock and Chodorow (1998).
  • UMLS::Similarity::lesk - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Banerjee and Pedersen (2002).
  • UMLS::Similarity::lin - Perl module for computing the semantic relatednessof concepts in the Unified Medical Language System (UMLS) using the method described by Lin (1997).
  • UMLS::Similarity::nam - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Nguyen and Al-Mubaid (2006)
  • UMLS::Similarity::path - Perl module for computing semantic similarity of concepts in the UMLS by simple edge counting.
  • UMLS::Similarity::pks - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Pekar and Staab (2002)
  • UMLS::Similarity::random - Perl module for computing a random baseline by assigning a random number between zero and one as the similarity score.
  • UMLS::Similarity::res - Perl module for computing the semantic relatednessof concepts in the Unified Medical Language System (UMLS) using the method described by Resnik (1995).
  • UMLS::Similarity::sanchez - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Sanchez, et al. (2012).
  • UMLS::Similarity::upath - Perl module for computing semantic similarity of concepts in the UMLS by simple edge counting regardless of the direction
  • UMLS::Similarity::vector - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Patwardhan and Pedersen (2006).
  • UMLS::Similarity::wup - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Wu and Palmer (1994).
  • UMLS::Similarity::zhong - Perl module for computing semantic relatedness of concepts in the Unified Medical Language System (UMLS) using the method described by Zhong, et al 2002.