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<http://atlas.ahc.umn.edu/cgi-bin/umls_similarity.cgi?word1=C0633633&word2=C1311834&sab=MSH&rel=PAR%2FCHD&similarity=lin&button=Compute+Similarity&sabdef=UMLS_ALL&reldef=CUI%2FPAR%2FCHD%2FRB%2FRN&relatedness=vector#>and
> C1311834<http://atlas.ahc.umn.edu/cgi-bin/umls_similarity.cgi?word1=C0633633&word2=C1311834&sab=MSH&rel=PAR%2FCHD&similarity=lin&button=Compute+Similarity&sabdef=UMLS_ALL&reldef=CUI%2FPAR%2FCHD%2FRB%2FRN&relatedness=vector#>,
> 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
