Hi Steve, The icpropagation files need to go into the: /var/www/umls_similarity/icpropagation/
Example ones are located in the UMLS-Similarity package in the directory web/docs/icpropagation. These were created using information from the UMLSonMedline and a different version of the UMLS though. If you can give me a couple days, I can get you new icpropagation files for 2014AA. For creating your own, you need to do as follows: Step 1: create an icfrequency file using the create-icfrequency.pl program. The program command is: create-icfrequency.pl ICFREQUENCY_FILE INPUTFILE INPUTFILE = raw text ICFREQUENCY_FILE = output file generated by the program There are four main options for create-icfrequency.pl: --config: this tells the program which taxonomy you are using in the UMLS --compoundify: this tells the program that the input text contains compounds depicted by an underscore --term: calculates the frequency counts using the words in the input file (matching them to the terms associated with the concept in the UMLS); this is the default --metamap TWO_DIGIT_YEAR: this uses metamap to assign CUIs to the text (I haven't used this option in awhile and need to double check it). Step 2: create an icpropgation file using the create-icpropagation.pl program create-icpropagation.pl ICPROPAGATION_FILE ICFREQUENCY_FILE ICFREQUENCY_FILE = output file generated by create-icfrequency.pl ICPROPAGATION_FILE = output file generated by the program I hope above makes sense. Let me know if you have any additional questions and/or would like the icpropagation files for 2014AA. Thanks! Bridget On Tue, Jul 29, 2014 at 6:25 PM, Steven Bethard beth...@cis.uab.edu [umls-similarity] <umls-similarity@yahoogroups.com> wrote: > Thanks for the recent update to UMLS::Similarity - I was able to cleanly > install it with no errors this time. > > I’d like to start up the similarity server on a machine here so that we can > make queries to it. I tried running /usr/local/bin/umls_similarity_server.pl > but it immediately and silently exits. I re-ran it as > /usr/local/bin/umls_similarity_server.pl --logfile umls.log, and umls.log > gives me: > > ------------------------------------------------------------ > In setInterface(MSH, PAR/CHD, path) > FILENAME: /tmp/Ded6K86IZu > > CuiFinder User Options: > --config option set > > > UMLS-Interface Configuration Information > Sources (SAB): > MSH > Relations (REL): > CHD > PAR > Database: > umls (MMSYS-2014AA-20140401) > > > > PathFinder User Options: > --forcerun option set > > > Setting measures > > ICFinder User Options: > --icpropagation /var/www/umls_similarity/icpropagation/icprop.msh.par.chd > > Could not open file /var/www/umls_similarity/icpropagation/icprop.msh.par.chd > —————————————————————————————— > > Seems like I need to create some icpropagation files. How do I do that? I > looked at: > > http://search.cpan.org/dist/UMLS-Similarity/utils/create-icpropagation.pl > > But I don’t know what I should be providing as the OUTPUTFILE and > ICFREQUENCY_FILE arguments. > > While I’m at it, are there other prerequisites to running > umls_similarity_server.pl that I should know about before I try to start it > again? > > Thanks, > > Steve >