Hi Helen, For the console application:
The SNOMEDCT index will take longer than the MSH index. SNOMEDCT is the largest source in the UMLS with the greatest number of PAR/CHD relations. The index traverses these relations collecting all the paths from the CUI to the root for each CUI. Once this index is created -- it should be quicker to compute the similarity between any two concepts in that source. So the second run with SNOMEDCT should be quicker because the index is already stored in the database. I hope this makes sense -- if not let me know :-) For the web interface application: Is this running locally on your machine, or the one that we have available on atlas though query-umls-similarity-webinterface ? Would you send us the command that you are using? Thanks! Bridget On Tue, May 1, 2012 at 12:59 PM, helen_geb <[email protected]> wrote: > ** > > > Hi Ted, > > > 1. Console application: > > > - When I use SNOMEDCT SAB with any of the REL's(CHD/PAR or RB/RN) and > Measure is wup it asks me to create an index and that creation goes > forever. > - When I use MSH SAB with any of the REL's it asked me for index > creation (only on the first time) and gives the result in 1-3 minutes, > which is not bad. > > > > > 2. Web Interface: > What ever I use here gives me time out with the following error. I don't > see the results in the browser. > > *Gateway Time-out > The gateway did not receive a timely response from the upstream server or > application.* > Note:The similarity_server is running successfully here it the log when I > computer similarity of cat and dog using the web interface > > *In setInterface(MSH, PAR/CHD, path)* > *FILENAME: C:\Users\ADMINI~1\AppData\Local\Temp\2\0teMudc7uG* > > *CuiFinder User Options: * > * --config option set* > > > *UMLS-Interface Configuration Information* > * Sources (SAB):* > * MSH* > * Relations (REL):* > * CHD* > * PAR* > * Database: * > * umls (MMSYS-2011AA-20110426)* > > > > *PathFinder User Options:* > * --forcerun option set* > > > *Setting measures* > > *ICFinder User Options:* > * --icpropagation > C:/WebPages/umls_similarity/icpropagation/icprop.msh.par.chd* > > > *ICFinder User Options:* > * --icpropagation > C:/WebPages/umls_similarity/icpropagation/icprop.msh.par.chd* > > > *ICFinder User Options:* > * --icpropagation > C:/WebPages/umls_similarity/icpropagation/icprop.msh.par.chd* > > *TYPE: r* > *cat dog Compute Similarity path MSH PAR/CHD* > *In setInterface(MSH, PAR/CHD, path)* > *FILENAME: C:\Users\ADMINI~1\AppData\Local\Temp\2\lYumkWJOay* > > *CuiFinder User Options: * > * --config option set* > > > *UMLS-Interface Configuration Information* > * Sources (SAB):* > * MSH* > * Relations (REL):* > * CHD* > * PAR* > * Database: * > * umls (MMSYS-2011AA-20110426)* > > > > *PathFinder User Options:* > * --forcerun option set* > > > *Setting measures* > > *ICFinder User Options:* > * --icpropagation > C:/WebPages/umls_similarity/icpropagation/icprop.msh.par.chd* > > > *ICFinder User Options:* > * --icpropagation > C:/WebPages/umls_similarity/icpropagation/icprop.msh.par.chd* > > > *ICFinder User Options:* > * --icpropagation > C:/WebPages/umls_similarity/icpropagation/icprop.msh.par.chd* > > *In getAllForms (cat)* > *Forms (cat) : C0007450* > *Returning Forms (cat) : C0007450* > *In getAllForms (dog)* > *Forms (dog) : C0012984* > *Returning Forms (dog) : C0012984* > *TYPE: p* > *In getAllForms (cat)* > *Forms (cat) : C0007450* > *Returning Forms (cat) : C0007450* > *In getAllForms (dog)* > *Forms (dog) : C0012984* > *Returning Forms (dog) : C0012984* > *HERE: C0007450 Felis catus C0012984 familiaris, Canis* > *p C0007450 (Felis catus)|C0012984 (familiaris, Canis)|C0007450 (Felis > catus) => C0524517 (Genus Felis) => C0325089 (Family Felidae) => C0007266 > (Carnivora) => C0524515 (Family canidae) => C0012984 (familiaris, Canis)* > *TYPE: g* > *HERE (Compute Similarity) g (cat)* > *In getAllForms (cat)* > *Forms (cat) : C0007450* > *Returning Forms (cat) : C0007450* > *CUIS: C0007450* > *g C0007450 MSH : The domestic cat, Felis catus, of the carnivore family > FELIDAE, comprising over 30 different breeds. The domestic cat is descended > primarily from the wild cat of Africa and extreme southwestern Asia. Though > probably present in towns in Palestine as long ago as 7000 years, actual > domestication occurred in Egypt about 4000 years ago. (From Walker's > Mammals of the World, 6th ed, p801)|NCI : The domestic cat, Felis catus.|* > *TYPE: g* > *HERE (Compute Similarity) g (dog)* > *In getAllForms (dog)* > *Forms (dog) : C0012984* > *Returning Forms (dog) : C0012984* > *CUIS: C0012984* > *g C0012984 NCI : The domestic dog, Canis familiaris.|MSH : The domestic > dog, Canis familiaris, comprising about 400 breeds, of the carnivore family > CANIDAE. They are worldwide in distribution and live in association with > people. (Walker's Mammals of the World, 5th ed, p1065)|* > > > > > > > > > > > > > --- In [email protected], Ted Pedersen <duluthted@...> > wrote: > > > > Hi Helen, > > > > What sources (SAB) and relations (REL) are you using? Also, what measure > > are you running? If you could send a few examples of what you are trying > > then we could figure out if that is expected (some combinations are > indeed > > slow) or if there might be an issue on your particular system. > > > > Thanks! > > Ted > > > > On Mon, Apr 30, 2012 at 4:42 PM, helen_geb helen_geb@... wrote: > > > > > ** > > > > > > > > > > I have installed umls similarity following the instructions. > > > > > > But it is too slow. It takes 2-3 minutes to compute similarity between > two > > > terms. > > > > > > Let me know what I need to do speed it up. > > > > > > It gets worst when I use UMLS_ALL for SAB and REF config files. > > > > > > Regards, > > > Helen. > > > > > > > > > > > > > > > > > -- > > Ted Pedersen > > http://www.d.umn.edu/~tpederse > > > > >
