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 [email protected]
[umls-similarity] <[email protected]> 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
>
