Ok…I’m sorry, I’ll try to be more clear…I ran metamorphosis to create a new
umls subset. At a certain point it is possible to apply filters to obtain a
subset of the umls (it’s what metamorphosis is meant for), so I selected the
language filter to exclude non english sources and the semantic type filter to
have only T024 and T023 semantic types. Then I simply executed their script to
save the data into mysql tables. I wanted to include all the sources in T024
and T023 semantic types so I used UMLS_ALL in my configuration file. The
removeConfigData doesn’t work. As a solution I simply drop the the index
database. None of the issues is solved, even when selecting only SNOMEDCT_US as
source and PAR/CHD as relationships in the config file.
Eugenia Galeota, PhD
Center for Genomic Science of IIT@SEMM
Computational Epigenomics
Email: eugenia.gale...@iit.it
Tel: +39 02 9437 5046
Via Adamello 16, 20139 Milan, Italy
On 08 Oct 2014, at 22:30, Bridget McInnes btmcin...@gmail.com [umls-similarity]
<umls-similarity@yahoogroups.com> wrote:
>
> Hello Eugenia,
>
> I am not completely certain what you mean by a UMLS subset with only two
> semantic types, but I know that there are many subset configuration that I am
> not aware of or use. Are you able to build the index over smaller sets of
> sources/relation (e.g. MSH with the PAR/CHD relations) in the UMLS now? Does
> the removeConfigData.pl program work? Or are those not resolved?
>
> Thank you!
>
> Bridget
>
> On Wed, Oct 8, 2014 at 10:19 AM, Eugenia Galeota eugenia.gale...@iit.it
> [umls-similarity] <umls-similarity@yahoogroups.com> wrote:
>
> Hi,
>
> yes the problem is that at the end of the code the index is not builded
> completely and the removeConfigData.pl is not working (see the error in
> previous message). I had this problem while I was using an UMLS subset with
> only two semantic types obtained using Metamorphosis.
> After noticing the first error I tried to build an index over the entire UMLS
> and this time the program seems to never end. I was also keeping track of the
> queries and in my general log table there where more than 5 million queries
> on umls and umlsindex databases.
> After your message I stopped the execution to add the realtime option as you
> suggested. As before I’m logging the queries. Actually after more than one
> hour I can count about 1800000 selects on cuis and the program is still
> running. My configuration file is simply
> SAB :: include UMLS_ALL
> REL :: include PAR, CHD
>
> while the other parameters (database, password, socket…, and now realtime)
> are specified in the code as you can see in the previous message.
> Thanks for your help,
>
> Eugenia
>
>
>
> Eugenia Galeota, PhD
> Center for Genomic Science of IIT@SEMM
> Computational Epigenomics
> Email: eugenia.gale...@iit.it
> Tel: +39 02 9437 5046
> Via Adamello 16, 20139 Milan, Italy
>
> On 08 Oct 2014, at 14:33, Bridget McInnes btmcin...@gmail.com
> [umls-similarity] <umls-similarity@yahoogroups.com> wrote:
>
>>
>> Hi Eugenia,
>>
>> I apologize that things are not running smoothly. I would like to verify a
>> few things with you:
>>
>> 1. the problem is that the index will not build; and removing the index
>> using the removeConfigData.pl is not working? What configuration file where
>> you using for this?
>>
>>
>> 2. you are running the index over the entire UMLS? If so, we recommend that
>> you use the --realtime option if you would like to take the similarity
>> scores between concepts using the path information from the entire UMLS. The
>> UMLS is so large, that there is typically not enough space to store all the
>> path-to-root information for all the CUIs. The --realtime option allows the
>> path information to be collected on the fly. It takes a little longer
>> though; so we created the index for smaller sources/relation configurations
>> and the --realtime option for the larger configurations. I hope that makes
>> sense. Please let me know if it does not.
>>
>> Thank you!
>>
>> Best regards,
>>
>> Bridget
>>
>>
>> On Wed, Oct 8, 2014 at 7:09 AM, Eugenia Galeota eugenia.gale...@iit.it
>> [umls-similarity] <umls-similarity@yahoogroups.com> wrote:
>>
>>
>> Dear developers,
>> I’ve been trying in many ways to let UMLS::Similarity work, but it seems
>> that there are some problems I’m not able to solve. Initially I had issues
>> with my.cnf and mysql.socket. I had different versions of the same files,
>> then the mysql.socket disappeared from the /tmp folder. Actually they seems
>> to be solved, since I completely removed any previous mysql server
>> installation and reinstalled the latest version using brew on my mac. I was
>> using UMLS similarity on a small subset with only two semantic types created
>> using Metamorphosys. I tested some of the Interface methods and they seems
>> to be working, anyway when trying to create an index to use with umps
>> similarity I always get the following error
>>
>> ERROR: UMLS::Interface::PathFinder->_checkIndex
>> Index Error (Error Code 9).
>> Index did not complete. Remove using the removeConfigData.pl program and
>> re-run.
>>
>> and when I try to use the removeConfigData.pl to rebuild it from scratch the
>> program never ends (it is still running since last friday).
>> I thought that another possibility is that in some way the Pathfinder module
>> cannot build the paths to the root of the UMLS because tables in mysql
>> don't contain the UMLS root concept C0000000 and its relationships. By
>> looking at the code I still wasn’t able to understand how the path from
>> concepts without a parent to the UMLS root is created. I found a call at a
>> certain point to some function getCuiChildren where the passed cui string
>> seems to be an empty string empty. I also modified the my.cnf file as you
>> specify in the documentation of the perl module.
>> Finally I’m trying to do the same operations on the entire UMLS database. My
>> code is the following
>>
>> use lib '/Library/Perl/5.16/';
>> use UMLS::Interface;
>> use UMLS::Similarity::lin;
>> %params = ();
>> $params{"intrinsic"} = "sanchez";
>> $params{"username"} = "egaleota";
>> $params{"password"} = “password";
>> $params{"socket"} = "/tmp/mysql.sock";
>> $params{"config"} =
>> "/Users/egaleota/umls/UMLS-Interface-1.41/myconfig.conf";
>> #$cuifinder = UMLS::Interface::CuiFinder->new(\%params);
>> my $umls = UMLS::Interface->new(\%params);
>> die "Unable to create UMLS::Interface object.\n" if(!$umls);
>> $paramtri{"intrinsic"}="sanchez";
>> my $lin = UMLS::Similarity::lin->new($umls, \%paramtri);
>> #die "Unable to create measure object.\n" if(!$lin);
>> my $cui1 = "C0459385";
>> my $cui2 = "C0440746";
>> $ts1 = $umls->getTermList($cui1);
>> my $term1 = pop @{$ts1};
>> $ts2 = $umls->getTermList($cui2);
>> my $term2 = pop @{$ts2};
>> my $value = $lin->getRelatedness($cui1, $cui2);
>> print "The similarity between $cui1 ($term1) and $cui2 ($term2) is $value\n";
>>
>>
>>
>> Actually I’m running the code above. The index seems to be in creation
>> phase. When I check for the current queries in the db I obtain results like
>> the following which let me believe that the problems are not related to how
>> perl communicates with mysql
>>
>> +----+----------+-----------+--------------------+---------+------+------------+------------------------------------------------------------------------------------------------------+
>> | Id | User | Host | db | Command | Time | State
>> | Info
>> |
>> +----+----------+-----------+--------------------+---------+------+------------+------------------------------------------------------------------------------------------------------+
>> | 51 | egaleota | localhost | umls | Query | 0 |
>> statistics | select distinct CUI2 from MRREL where CUI1='C3135343' and
>> ((REL='CHD') ) and CUI2!='C3135343' and SU |
>> | 52 | egaleota | localhost | umlsinterfaceindex | Sleep | 0 |
>> | NULL
>> |
>> | 54 | egaleota | localhost | NULL | Query | 0 | init
>> | show processlist
>> |
>> +----+----------+-----------+--------------------+---------+------+------------+------------------
>>
>>
>> Since all this tasks are really time consuming I was kindly wondering if you
>> could help me to solve this issues. Thanks,
>>
>> Eugenia Galeota, PhD
>> Center for Genomic Science of IIT@SEMM
>> Computational Epigenomics
>> Email: eugenia.gale...@iit.it
>> Tel: +39 02 9437 5046
>> Via Adamello 16, 20139 Milan, Italy
>>
>>
>>
>>
>
>
>
>
>
