Re: [umls-similarity] UMLS database in a remote machine

[Emilio Centeno Ortiz ecent...@imim.es [umls-similarity]]

Hi Ted,

We included all UMLS sources (44) in the configuration file, and the 
indexation process has been running for 3 weeks (still running). The 
umlsinterfaceindex database is currently using 117G of disk space.

We included all these sources because, once the indexing is over, we 
want to test some similarity measures between concepts of the same 
semantic type for different semantic types (which implies different 
sources)  i.e. compare diseases with diseases, compounds with compounds, 
etc. This way we do the indexing just once, and we can do any comparison 
we want without having to rebuild the umlsinterfaceindex dabatase 
everytime we switch sources

Did I wrong including too many sources? Is the package going to work 
with so many sources?

Thanks in advance,

Emilio

On 08/08/2016 04:44 AM, Ted Pedersen duluth...@gmail.com 
[umls-similarity] wrote:
The time to build an index really varies quite a bit, and depends both 
on the hardware you have available and the particular sources and 
relations you are using. If possible be patient and let the index 
build finish, since that really does speed up queries. And I hope your 
index has already been built by the time you read this!

Good luck,
Ted

On Thu, Aug 4, 2016 at 8:57 AM, Emilio Centeno Ortiz ecent...@imim.es 
<mailto:ecent...@imim.es> [umls-similarity] 
<umls-similarity@yahoogroups.com 
<mailto:umls-similarity@yahoogroups.com>> wrote:

    Hi Ted,

    Thanks for the reply. I finally could make it work.

    I didn't know that the UMLS Semantic Network was necessary in the
    initialization of the UMLS::Interface object. Since we don't have
    the Semantic Network for umls_2016AA I just switched to
    umls_2015AB. Now it is working.

    Now that I'm running a test, the package is creating an index
    database that, in the end, it will save time in future queries.
    How long this will take?

    I hope I will ask about more interesting issues shortly :)

    Thanks again,

    Emilio




    On 08/04/2016 03:30 PM, Ted Pedersen duluth...@gmail.com
    <mailto:duluth...@gmail.com> [umls-similarity] wrote:
    Hi Emilio,

    I'm afraid I haven't seen this error before. It looks like a
    fairly generic Perl DBI error, so I wonder if everything is
    working ok with that module? If possible it might be good to run
    the DBI tests again just to make sure that is installed and
    working ok. Please let us know what you find if you are able to
    do that...

    Sorry I can't be more specific, but keep us posted and we might
    be able to do more...

    Good luck,
    Ted

    On Tue, Aug 2, 2016 at 2:21 AM, Emilio Centeno Ortiz
    ecent...@imim.es <mailto:ecent...@imim.es> [umls-similarity]
    <umls-similarity@yahoogroups.com
    <mailto:umls-similarity@yahoogroups.com>> wrote:

        Hi again,

        Now that our sysadmin granted a full working access to the
        UMLS database, I'm trying to create the UMLS::Interface object:

        my $umls = UMLS::Interface->new({"driver" => "mysql",

                 "database" => "umls_2016AA",

                 "username" => "myusername",

                 "password" => "mypassword",

                 "hostname" => "localhost",

                 "port" => "3306"

             });


        But I get this output:

        UMLS-Interface Configuration Information:

        (Default Information - no config file)

           Sources (SAB):

              MSH

           Relations (REL):

              PAR

              CHD

           Sources (SABDEF):

              UMLS_ALL

           Relations (RELDEF):

              UMLS_ALL

        ERROR: UMLS::Interface::STFinder->_loadSemanticNetwork

        Database error (Error Code 1).

        Error executing database query: DBI::st=HASH(0x3b643e8)->errstr()).


        Any hint about this?

        Thanks in advance,

        Emilio

        On 07/30/2016 03:18 AM, juliana md julian...@gmail.com
        <mailto:julian...@gmail.com> [umls-similarity] wrote:

        Hi Emilio,

        Did you grant access to myusername@mylocalmachine to your
        umls_2016AA database?
        Are you able to connect to your database from mylocalmachine
        (by using workbench for example) using those credentials?

        Regards,
        Juliana

        Em 29 de jul de 2016 21:05, "Emilio Centeno Ortiz
        ecent...@imim.es <mailto:ecent...@imim.es>
        [umls-similarity]" <umls-similarity@yahoogroups.com
        <mailto:umls-similarity@yahoogroups.com>> escreveu:

            Hello,

            I have just installed the UMLS::Similarity package and
            copy-pasted the example code Since the MySQL is hosted
            in another machine (172.20.16.15) I tried to initialize
            the interface with our connection parameters:

            use UMLS::Interface;
            use UMLS::Similarity::lch;
            use UMLS::Similarity::path;
              
            $umls = UMLS::Interface->new({"driver" => "mysql",
                                          "database" => "umls_2016AA",
                                          "username" => "myusername",
                                          "password" => "mypassword",
                                          "hostname" => "myMySQLHostIP",
                                          "port" => "3306"});

            die "Unable to create UMLS::Interface object.\n" if(!$umls);
              
            my $lch = UMLS::Similarity::lch->new($umls);
            die "Unable to create measure object.\n" if(!$lch);
              
            my $path = UMLS::Similarity::path->new($umls);
            die "Unable to create measure object.\n" if(!$path);
              
            my $cui1 = "C0005767";
            my $cui2 = "C0007634";
              
            $ts1 = $umls->getTermList($cui1);
            my $term1 = pop @{$ts1};
              
            $ts2 = $umls->getTermList($cui2);
            my $term2 = pop @{$ts2};
              
            my $lvalue = $lch->getRelatedness($cui1, $cui2);
              
            my $pvalue = $path->getRelatedness($cui1, $cui2);
              
            print "The lch similarity between $cui1 ($term1) and $cui2 ($term2) is $lvalue\n";
              
            print "The path similarity between $cui1 ($term1) and $cui2 ($term2) is $pvalue\n";


            but it complains like that:

            DBI 
connect('database=umls_2016AA;mysql_socket=/var/run/mysqld/mysqld.sock;host=myMySQLHostIP','myusername',...)
 failed: Access denied for user 'myusername'@'mylocalmachinename' (using 
password: YES) at 
/soft/devel/perl-5.16.3/lib/site_perl/5.16.3/UMLS/Interface/CuiFinder.pm line 
2458.

            Can't call method "err" on an undefined value at 
/soft/devel/perl-5.16.3/lib/site_perl/5.16.3/UMLS/Interface/ErrorHandler.pm line 113.


            I have just replaced hostnames, user, etc. with "my..."
            names.
            It looks like it tries to connect to MySQL using
            sockets? Any advice about how I could overcome this issue?

            Thanks in advance,
            Emilio

            -- 
            Emilio Centeno Ortiz

            Research Programme on Biomedical Informatics (GRIB)
            Department of Experimental and Health Sciences
            Universitat Pompeu Fabra
            IMIM (Hospital del Mar Medical Research Institute)
            C/ Dr. Aiguader, 88
            Barcelona, Spain
            Tel.: +34 93 316 0536 <tel:%2B34%2093%20316%200536>
            E-mail: ecent...@imim.es <mailto:ecent...@imim.es>
            http://ibi.imim.es


        -- 
        Emilio Centeno Ortiz

        Research Programme on Biomedical Informatics (GRIB)
        Department of Experimental and Health Sciences
        Universitat Pompeu Fabra
        IMIM (Hospital del Mar Medical Research Institute)
        C/ Dr. Aiguader, 88
        Barcelona, Spain
        Tel.: +34 93 316 0536 <tel:%2B34%2093%20316%200536>
        E-mail: ecent...@imim.es <mailto:ecent...@imim.es>
        http://ibi.imim.es



    -- 
    Emilio Centeno Ortiz

    Research Programme on Biomedical Informatics (GRIB)
    Department of Experimental and Health Sciences
    Universitat Pompeu Fabra
    IMIM (Hospital del Mar Medical Research Institute)
    C/ Dr. Aiguader, 88
    Barcelona, Spain
    Tel.: +34 93 316 0536 <tel:%2B34%2093%20316%200536>
    E-mail: ecent...@imim.es <mailto:ecent...@imim.es>
    http://ibi.imim.es




--
Emilio Centeno Ortiz

Research Programme on Biomedical Informatics (GRIB)
Department of Experimental and Health Sciences
Universitat Pompeu Fabra
IMIM (Hospital del Mar Medical Research Institute)
C/ Dr. Aiguader, 88
Barcelona, Spain
Tel.: +34 93 316 0536
E-mail: ecent...@imim.es <mailto:ecent...@imim.es>
http://ibi.imim.es