Hello Steve, I am responding to this portion of your email:
> A further question about using the UMLS::Similarity server. What is the format that it > expects if I interact directly with the socket? The documentation[1] suggests that 'g > car#n#1\015\012\015\012’ should work, but this causes errors on the server side (and > nothing is printed to the client): I apologize, the examples in the documentation are not correct. The server is expecting the following format: g|$button|$word1|\015\012 where : $button = <Compute Similarity|Compute Relatedness> $word = <CUI|word> For example: g|Computer Similarity|C0026769|\015\012 The servers response for this example would be: g C0026769 MSH : An autoimmune disorder mainly affecting you ---- I will modify the documentation but here are the interactions that are set up: # returns version information v\015\012\015\012 # returns the preferred term for <CUI> t|<CUI>|\015\012 # return the similarity information r|<word1>|<word2>|<Compute Similarity|Compute Relatedness>|<measure>|<source>|<relations>|\015\012 # returns the path information p|<word1>|<word2>|\015\012 # returns the definition or extended definition g|<Compute Similarity|Compute Relatedness>|<word>|\015\012 I am using <word> here to refer to either a CUI (e.g. C0026769) or a term (e.g. university hospital). I hope above makes sense and is helpful. Please let me know if something is not clear. I will go through and modify the documentation. I am very sorry for the confusion with it. Thank you for looking at this and letting us know. I do not think we have had anyone look so closely at the documentation for the web server before -- this has been very helpful for us although frustrating for you! Thank you. Best regards, Bridget From: Steven Bethard beth...@cis.uab.edu [umls-similarity] < > umls-similarity@yahoogroups.com> > Date: Sat, Aug 16, 2014 at 4:04 PM > Subject: Re: [umls-similarity] running UMLS::Similarity server > To: umls-similarity@yahoogroups.com > > > On Jul 29, 2014, at 6:25 PM, Steven Bethard <beth...@cis.uab.edu> wrote: > > 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: > [snip] > > Could not open file > /var/www/umls_similarity/icpropagation/icprop.msh.par.chd > > > On Jul 30, 2014, at 9:55 AM, Bridget McInnes btmcin...@gmail.com > [umls-similarity] <umls-similarity@yahoogroups.com> wrote: > > The icpropagation files need to go into the: > > /var/www/umls_similarity/icpropagation/ > [snip] > > create-icfrequency.pl ICFREQUENCY_FILE INPUTFILE > [snip] > > create-icpropagation.pl ICPROPAGATION_FILE ICFREQUENCY_FILE > > Thanks, this solved the problem. Some notes for anyone else who has to do > this: > > * The create-icfrequency.pl script took about 20 minutes on a text file > of about 160M words. > * The create-icpropagation.pl script took about 10 minutes > * The icpropagation file has to be named > /var/www/umls_similarity/icpropagation/icprop.msh.par.chd for the sever to > run > > A further question about using the UMLS::Similarity server. What is the > format that it expects if I interact directly with the socket? The > documentation[1] suggests that 'g car#n#1\015\012\015\012’ should work, but > this causes errors on the server side (and nothing is printed to the > client): > > TYPE: g > Use of uninitialized value $button in concatenation (.) or string at > /usr/local/bin/umls_similarity_server.pl line 340, <GEN51> line 2. > Use of uninitialized value $word in concatenation (.) or string at > /usr/local/bin/umls_similarity_server.pl line 340, <GEN51> line 2. > HERE () g () > Use of uninitialized value $word in pattern match (m//) at /usr/local/bin/ > umls_similarity_server.pl line 342, <GEN51> line 2. > Use of uninitialized value $button in string eq at /usr/local/bin/ > umls_similarity_server.pl line 346, <GEN51> line 2. > Use of uninitialized value $word in concatenation (.) or string at > /usr/local/bin/umls_similarity_server.pl line 553, <GEN51> line 2. > In getDefAllForms () > Use of uninitialized value $word in pattern match (m//) at /usr/local/bin/ > umls_similarity_server.pl line 558, <GEN51> line 2. > ERROR: UMLS::Interface::CuiFinder->_getDefConceptList > Undefined input value (Error Code 4). > Error with input variable $term. > > If I instead read the source code[2], it appears that I should instead be > using something like ‘g||car|\015\012\015\012’ which does indeed work: > > $ printf 'g||fracture|\015\012\015\012' | nc localhost 31135 > g C0016658 NCI : A finding of traumatic injury to the bone in which the > continuity of the bone is broken... > > Should I keep reading the source code, or is there something better I > should be looking at? > > Steve > > [1] > https://metacpan.org/pod/distribution/UMLS-Similarity/utils/umls_similarity_server.pl > [2] > https://metacpan.org/source/BTMCINNES/UMLS-Similarity-1.41/utils/umls_similarity_server.pl > > > > > > >
