NAME UMLS::Similarity CHANGES Changes from version 0.47 to 0.49 Note: the make test longs are not working properly on all of the systems. 1. added documentation on how to create propagation file for the the ic measure's 2. add a more complete configuration file in the samples directory 3. add --stoplist in vector method 4. modified the umls-similarity package for consistency with the new UMLS-Interface. We wanted to remove some of the redundancy in the package which meant modifying this package. The package is now not back compatible with older versions of the UMLS-Interface package. Changes from version 0.45 to 0.47 1. updated documentation 2. added to the --dictfile option the ability to have TERMS not just CUIs as input. Changes from version 0.43 to 0.45 1. Fixed some small errors that went out due to lesk 2. Updated pod documentation 3. Added README to samples/ 4. Renamed --matrixfile to --vectormatrix Renamed --indexfile to --vectorindex Renamed --propagationfile to --icpropagation 5. Added the --defraw option for lesk and vector. This will stop any cleaning that is done to the definition prior to use. 6. Created a create-propagation-file.pl program to create a file containing the information content of the CUIs in a specified set of sources to be used by umls-similarity when using the information content semantic similarity measures. 7. Created testing file vector-input.t add bigrams input file under t/tests/utils add index and matrix files under t/key/static 8. Added the --defraw option to vector.pm. If this option is set it will NOT clean the definition otherwise the words in the definition are cleaned up (ie remove punctuation, lower case, ...) 9. Created testing file create-propagation-file.t Changes from version 0.41 to 0.43 Modified documentation and cleaned up the package Updated the vector.pm that the vector method read the index file and co-occurrence matrix from the command line. Added the --dictfile options to read the definitions from a text file. Each line is a definition. def1: the first definition def2: the second definition Added the --debugfile options. It can print the definition of each concept and the vector (words) of every word covered by the co-occurrence matrix. Added the vector-input.pl. This file generates the index file and co-occurrence matrix file from the bigrams list for vector measure use. Added test cases for each of the measures in the t/ directory Added a samples/ directory which contains examples of the configuration file, matrix and index files for the vector measure, and propagation file for the information content meausres. Changes from version 0.39 to 0.41 Modified documentation and cleaned up the package Changes from version 0.37 to 0.39 Updated the way that the lcs and shortestpath was being done in UMLS-Interface. There were some complications. Added the vector.pm module and the def.pm module Added the --measure vector option to umls-similarity Changes from version 0.35 to 0.37 I messed up when modifying the way the lcs and shortestpath information was obtained in UMLS-Similarity after I had changed it in UMLS-Interface. It should all be fixed now. I also removed the vector and lesk measures. We are not quite ready for those and are in the process of getting them together for a fresh release. I changed the Jiang and Conrath measure from jnc to jcn like it is suppose to be Changes from version 0.33 to 0.35 1. Modified the way lcs and shortestpath information is returned by the UMLS-Interface. Needed to modify the UMLS-Similarity to reflect these changes Changes from version 0.31 to 0.33 1. Modified the propogation in UMLS-Interface and needed to reflect this in UMLS-Similarity Changes from version 0.29 to 0.31 1. Added the information content measures proposed by Resnik (1995), Jiang and Conrath (1997) and Lin (1998), as well as a random measure that returns a random number between one and zero as the similarity score. 2. Added a --debug option which prints out UMLS-Interface informatin for debugging purposes Changes from version 0.21 to 0.29 I used the following require command: require "UMLS::Similarity::vector" rather than require "UMLS/Similarity/vector.pm"; Not certain what I was thinking ... Changes from version 0.19 to 0.21 I fixed (for certain this time) how the modules are installed in the umls-similarity.pl program in the utils/ directory. It should not require BerkeleyDB now unless you are running the UMLS::Similarity::vector measure. For documentation puposes: 'use' loads the package at compile time where as 'require' loads the package at run time Here is some documentation on it: So when using 'use UMLS::Similarity::vector' - the program was loading vector.pm at compile time which used dbif.pm which requires BerkeleyDB to be installed. I switched to 'require "UMLS::Similarity::vector"' which now only loads vector.pm at runtime and only when use specify the vector measure. Changes from version 0.17 to 0.19 The --verbose option originally in the package is changed to a --info option. This option prints out a little more information about a concept if it doesn't exist in the sources that are being used. The reason for this change is because a new --verbose option was added to UMLS-Interface and we wanted to keep the options consistent. Since I do not think too many people were using the old --verbose option, I don't *think* it will cause too many problems. The new --verbose option will print out path information to a file rather than having this be done automatically. This will reduce the amount of storage space required to hold the path information for a given set of sources and relations. A new --forcerun option was also added. This option will just create the what we call the index - the path information - required by the program without prompting you to continue. So this will assume you know what you are doing and will not question you :) I also fixed (I hope) how the modules are installed in the umls-similarity.pl program in the utils/ directory. It should not require BerkeleyDB now unless you are running the UMLS::Similarity::vector measure. Changes from version 0.15 to 0.17 Modified the output of umls-similarity to return only the pair of CUIs that obtain the highest similarity score when terms that map to multiple concepts are being used. I added a --allsenses option if you would like the original output that displayed all possible CUIs with their similarity score for a given pair of terms. Added the vector measure. This measure is in 'beta' version so there will be some modifications to it in the future. I also removed the print statements that were displayed when the Wu and Palmer (wup) measure was being used. Sorry about the noise. Changes from version 0.13 to 0.15 Modified the output of umls-similarity so that if a concept doesn't exist you can tell which one it is. I also added a --verbose option which gives a little more information about the concept that doesn't exist. Modified the wup.pm module. The Wu and Palmer measure is twice the depth of the two concepts LCS divided by the product of the the depths of the individual concepts. I was using the minimum depths of these concepts where as I should have been using the depth of the path that contained the LCS itself. Changes from version 0.11 to 0.13 Added two new semantic similarity measure modules: i) nam.pm which is an implemantion of the semantic similarity measure described by Nguyan and Al-Mubaid, 2006 and ii) cdist.pm which is the Conceptual Distance measure described by Rada, et. al., 1989. Modified the umls-similarity.pl utility program to incorporate the nam.pm and cdist.pm similarity modules. Changes from version 0.09 to 0.11 Allow the umls-similarity.pl program to obtain the semantic similarity between a term and CUI as well as CUI-CUI and term-term pairs. Added some error checking to the umls-similarity.pl program and the measure modules. Changes from version 0.07 to 0.09 Removed the queryUMLS.pl module and put in its place umls-similarity.pl. This does exactly what the original queryUMLS.pl does but it also now accepts files and is much nicer. Changes from version 0.05 to 0.07 Added the similarity measure described by Wu and Palmer (1994) Updated the documentation Changes from version 0.03 to 0.05 Modified the Changelog directory Modified documenation - tried to get the misspelling and obvious errors removed. Removed the HTML documentation Changes from version 0.01 to 0.03 Modified documentation Modified the utils/ program