Thank you Ted, this is very helpful.
Le Jeudi 6 février 2014 18h21, Ted Pedersen <duluth...@gmail.com> a écrit : It looks like those two concepts do not have paths to the root of Mesh, so the path based and information content measures won't return a result. ted@maraca:~$ findPathToRoot.pl C1311834 UMLS-Interface Configuration Information: (Default Information - no config file) Sources (SAB): MSH Relations (REL): PAR CHD Sources (SABDEF): UMLS_ALL Relations (RELDEF): UMLS_ALL There are no paths between 2-methyl-3(2-pyridyl-methyl)-3h-pyrido-(2,3-d)-pyrimidin-4-on dihydrochloride (C1311834) and the root. ted@maraca:~$ findPathToRoot.pl C0633633 UMLS-Interface Configuration Information: (Default Information - no config file) Sources (SAB): MSH Relations (REL): PAR CHD Sources (SABDEF): UMLS_ALL Relations (RELDEF): UMLS_ALL There are no paths between substance p (5-11), cyclo(11-5(epsilon))lysine(5)- (C0633633) and the root. It seems like these concepts do not have any parent (PAR) relations associated with them, which is why you don't find a path to the root... ted@maraca:~$ getParents.pl C0633633 UMLS-Interface Configuration Information: (Default Information - no config file) Sources (SAB): MSH Relations (REL): PAR CHD Sources (SABDEF): UMLS_ALL Relations (RELDEF): UMLS_ALL The term substance P (5-11), cyclo(11-5(epsilon))Lys(5)- (C0633633) does not have any parents ted@maraca:~$ getParents.pl C1311834 UMLS-Interface Configuration Information: (Default Information - no config file) Sources (SAB): MSH Relations (REL): PAR CHD Sources (SABDEF): UMLS_ALL Relations (RELDEF): UMLS_ALL The term 2-methyl-3(2-pyridyl-methyl)-3H-pyrido-(2,3-D)-pyrimidin-4-on dihydrochloride (C1311834) does not have any parents For concepts that are not a part of a tree structure, you might consider using vector or lesk - these measures are based on comparing the definitions of the concepts and do not require paths between concepts. ted@maraca:~$ umls-similarity.pl --measure vector C0633633 C1311834 Default Settings: --precision 4 User Settings: --measure vector UMLS-Interface Configuration Information: (Default Information - no config file) Sources (SAB): MSH Relations (REL): PAR CHD Sources (SABDEF): UMLS_ALL Relations (RELDEF): UMLS_ALL 0.1870<>C0633633(substance P (5-11), cyclo(11-5(epsilon))Lys(5)-)<>C1311834(2-methyl-3(2-pyridyl-methyl)-3H-pyrido-(2,3-D)-pyrimidin-4-on dihydrochloride) ted@maraca:~$ umls-similarity.pl --measure lesk C0633633 C1311834 Default Settings: --precision 4 User Settings: --measure lesk UMLS-Interface Configuration Information: (Default Information - no config file) Sources (SAB): MSH Relations (REL): PAR CHD Sources (SABDEF): UMLS_ALL Relations (RELDEF): UMLS_ALL 64.0000<>C0633633(substance P (5-11), cyclo(11-5(epsilon))Lys(5)-)<>C1311834(2-methyl-3(2-pyridyl-methyl)-3H-pyrido-(2,3-D)-pyrimidin-4-on dihydrochloride) I hope this makes sense. I'm not familiar with these concepts so I don't know if the results above are intuitive or not. Please let us know as additional questions arise. Cordially, Ted On Thu, Feb 6, 2014 at 9:04 AM, Drame Khadim <khadimdrame...@yahoo.fr> wrote: > >Thank you Ted, it works fine on windows. > >But why does Lin similarity between two concepts in MeSH, C0633633 and >C1311834, is -1? > >Best regards > > > > > > > >Le Mardi 4 février 2014 15h20, Ted Pedersen <duluth...@gmail.com> a écrit : > > >It looks like you got somewhat closer to running successfully. The error >message you got is actually fairly descriptive - apparently at some point >earlier a command may have been run that started to create an index, but that >didn't finish for some reason. That has left behind an incomplete index that >you could remove via the removeConfigData.pl program. Then, when you run this >command again it should build an index and return a result. The intial >building of the index can take a few minutes, but once you have done that one >time you don't have to do it again. > > >And of course running on Ubuntu is another option, although if you are >submitting this command to the same server you may still have this index >problem. So, you may need to resolve this even if running on Ubuntu. > > >Good luck! >Ted > > > >On Tue, Feb 4, 2014 at 7:07 AM, Drame Khadim <khadimdrame...@yahoo.fr> wrote: > > >> >>Hi Ted, >> >>In the first case, I set the parameters in the my.ini file in Windows, but it >>doesn't work . The program doesn't take account the configuration. >>When I use --socket option with empty value, It throws another error: >> >>C:\>umls-similarity.pl --socket='' --hostname=172.16.5.107:22774 >>--username=Khad >>im --password=************ --database=UMLS2012AA --measure lch hand skull >>Default Settings: >> --precision 4 >> >> >>User Settings: >> --username Khadim >> --password XXXXXXX >> --database UMLS2012AA >> --hostname 172.16.5.107:22774 >> --socket '' >> --measure lch >> >> >> >>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::PathFinder->_checkIndex >>Index Error (Error Code 9). >>Index did not complete. Remove using the removeConfigData.pl program and >>re-run. >> >>I will try to use it on ubuntu. >> >>Thank you, >> >> >> >> >>Le Lundi 3 février 2014 18h32, Drame Khadim <khadimdrame...@yahoo.fr> a écrit >>: >> >> >> >>Thanks Ted. >> >>I will follow your instructions and let you know later. >> >>Regards, >> >> >>Khadm >> >> >> >> >>Le Lundi 3 février 2014 18h03, Ted Pedersen <duluth...@gmail.com> a écrit : >> >> >>There was a recent post to this group that gave a few steps in installing on >>Windows. Perhaps that would be helpful. >> >> >>https://www.mail-archive.com/umls-similarity@yahoogroups.com/msg00303.html >> >> >> >>Also, the following thread is from a Windows user who had exactly the same >>error. >> >> >>https://www.mail-archive.com/umls-similarity@yahoogroups.com/msg00122.html >> >> >> >>In the first case the user set these parameters in the my.ini file in >>Windows, and in the second case it involved the installation of the DBI >>module. >> >> >>But, you might need to provide a different value for --socket - the default >>is based on Linux and won't work on Windows. I'm not sure if that is the >>cause of your problem, but it would be something to look at. I would also >>check and make sure the DBI module was installed correctly, it seems like >>problems with that not installing can cause this particular error. >> >> >>Let us know how things go. >> >> >>Good luck, >>Ted >> >> >> >>On Mon, Feb 3, 2014 at 10:34 AM, <khadimdrame...@yahoo.fr> wrote: >> >> >>> >>>This is my error : >>> >>>C:\UMLS-Similarity>umls-similarity.pl --hostname=172.16.5.107:22774 >>>--username=K >>>hadim --password=******** --database=UMLS2012AA hand skull >>>Default Settings: >>> --precision 4 >>> --socket /tmp/mysql.sock >>> >>> --measure path >>> >>>User Settings: >>> --username Khadim >>> --password XXXXXXX >>> --database UMLS2012AA >>> --hostname 172.16.5.107:22774 >>> >>>DBI connect('database=UMLS2012AA;mysql_socket=/tmp/mysql.sock >>>;host=172.16.5.107:22774','Khadim',...) failed: AccÞs refusÚ pour >>>l'utilisateur: >>> 'Khadim'@'@localhost' (mot de passe: NON) at >>>C:/perl/site/lib/UMLS/Interface/Cu >>>iFinder.pm line 2425 >>>Can't call method "err" on an undefined value at >>>C:/perl/site/lib/UMLS/Interface >>>/ErrorHandler.pm line 113. >> >> >> >>-- >>Ted Pedersen >>http://www.d.umn.edu/~tpederse >> >> >> >> > > > >-- >Ted Pedersen >http://www.d.umn.edu/~tpederse > > -- Ted Pedersen http://www.d.umn.edu/~tpederse
