Thanks for pointing this out Ali, That's a kind of problem I would have faced soon.
Regards, Helen --- In [email protected], ali hasnain <ali.hasnain@...> wrote: > > Hello Ted, > > Agreed with the value of -1 for the unknown concepts. > Finger crossed to see the new code with all these fixes. > > Best Regards, > Ali Hasnain > > > > > > > > On Tue, Apr 17, 2012 at 4:19 PM, ted_pedersen <duluthted@...> wrote: > > > ** > > > > > > Hi Ali, > > > > We have a fix in the works that will be released later today, stay tuned! > > > > However, we will return -1 in the case where one or both of the terms/CUIs > > is unknown. This is to be consistent with umls-similarity.pl (the command > > line interface that runs on installed systems) and also to avoid an > > ambiguity in the value of 0. > > > > 0 means that the two terms / CUIs are known to UMLS, but that there is no > > similarity between them. > > > > -1 means that one or both of the terms / CUIs are unknown to the UMLS, and > > so the measurment isn't really valid. > > > > So, we'd like to keep a distinction between these two cases because they > > are quite distinct. I hope this makes sense. > > > > More soon, > > Ted > > > > > > --- In [email protected], "ShopingPrincess99785" > > <ali.hasnain@> wrote: > > > > > > Hello Ted, > > > > > > Thank you very much for your timely response. > > > I really appreciate. > > > > > > It would be good if the similarity/ relatedness score would be > > calculated as "0" when one or both the concepts are unknown to UMLS. > > > This can be a simple way of saying that there is no similarity- > > irrespective of the fact weather the term is unknown or known to UMLS. > > > > > > Anyway looking forward for your timely response with the new code that > > resolves this problem. > > > > > > Best Regards, > > > Ali Hasnain > > > > > > > > > > > > --- In [email protected], "ted_pedersen" <duluthted@> > > wrote: > > > > > > > > Hi Ali, > > > > > > > > Thanks for reporting this, and I can confirm your observation, the > > program does indeed hang when one of the input terms is unknown to UMLS. We > > will take a look at this and report back via the mailing list. > > > > > > > > Cordially, > > > > Ted > > > > > > > > --- In [email protected], "ShopingPrincess99785" > > <ali.hasnain@> wrote: > > > > > > > > > > Hello, > > > > > > > > > > I am using the UMLS Perl implementation from the command line to > > find the relatedness of two concepts. > > > > > So it is noticed that it gives some score when I try to find the > > relatedness for two concepts that are defined in UMLS example is as follow: > > > > > > > > > > When I give the command > > > > > "query-umls-similarity-webinterface.pl--measure vector drug molecule" > > > > > it gives the score value: 0.4835 . > > > > > Similarly it computes the values of all other concepts available in > > UMLS but the problem arrives when one of the two concept is asked that is > > not defined in UMLS, rather it should give value of 0 meaning there is no > > relatedness the command line become hanged and stops and waited for > > unlimited time giving no value or even no error. > > > > > > > > > > Example is When I give the command " > > query-umls-similarity-webinterface.pl --measure vector drug ABCD", so the > > concept ABCD is nothing defined in UMLS, it should give me some error or > > some numeric value e.g "0" showing no relatedness. > > > > > > > > > > Actually I am much relying on the numeric value that comes as an > > output for the relatedness and what I want is that it should give some > > value irrespective of what word has been asked. If that word is not > > available in the UMLS it should give me "0" or at least it should stop and > > give some message that this word is not available and computes the values > > for next pair when I give the words in a LOOP. > > > > > > > > > > > > > > > As I am new to PERL, can you please guide me where should I make > > changes in the PERL code file of ""query-umls-similarity-webinterface.pl"" > > (that comes with the package) so it gives the value of "0" rather than the > > program hangs and go further. > > > > > > > > > > > > > > > I consider this as a limitation or an error so please send me as an > > attachment the edited version of the code file of "" > > query-umls-similarity-webinterface.pl"" or any other that I can replaced > > with the existing files so I can continue computing relatedness > > irrespective of the fact weather any of the concept available in the UMLS > > or not. > > > > > > > > > > Looking forward for your timely response. > > > > > > > > > > Best Regards, > > > > > Ali Hasnain > > > > > > > > > > > > > > > > > > >
