Thanks for the detailed instructions. What did you use as the raw text? If it’s something easily available, there’s probably no need for you to generate the icpropagation files for me.
Steve On Jul 30, 2014, at 10:55 AM, Bridget McInnes btmcin...@gmail.com [umls-similarity] <umls-similarity@yahoogroups.com> wrote: > 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 > > > >
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