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 > > > > > >
