NAME
query-umls-similarity-webinterface.pl - This program returns a semantic similarity score between two concepts.
SYNOPSIS
This is a utility that takes as input either two terms (DEFAULT) or two CUIs and returns the similarity between the two.
USAGE
Usage: query-umls-similarity-webinterface.pl [OPTIONS] [CUI1|TERM1] [CUI2|TERM2]
INPUT
[CUI1|TERM1] [CUI2|TERM2]
The input are two terms or two CUIs associated to concepts in the UMLS.
OPTIONS:
--url URL
The url to the server hosting the webinterface.
DEFAULT: http://atlas.ahc.umn.edu--sab SOURCES
The UMLS source(s) used to obtain the similarity or relatedness values.
Currently, for similarity the following sources are available through the web interface: MSH, OMIM, FMA or SNOMEDCT. For relatedness, the available sources are: MSH, SNOMEDCT or UMLS_ALL (which refers to the entire umls).
For example:
--sab MSHNote: In the UMLS::Similarity package, we differentiate between the sources used for relatendess and similarity measures the sabdef variable for relatedness and the sab variable for similarity but to simplify things we only use hte rel variable right now. I hope this doesn't confuse anyone.
For additional sources to be added please email me and we can see about adding them. Also note, that the UMLS::Similarity package allows for any combination of sources to be used.
--rel RELATIONS
The UMLS relations used to obtain the similarity or relatedness values. Currently, for similarity following relations are available through the web interface: PAR/CHD or RB/RN. For relatedness: CUI/PAR/CHD/RB/RN or CUI.
For example:
--rel PAR/CHDNote: The relatedness measure use definition information and therefore CUI refers to using the definition of the concept itself while PAR, for example, refers to using the definition of the concepts parent relations. In the UMLS::Similarity package, we differentiate between these using the reldef and rel variables but to simplify things we only use hte rel variable right now.
For additional relations to be added please email me and we can see about adding them. Also note, that the UMLS::Similarity package allows for any combination of sources/relations to be used.
--measure MEASURE
Use the MEASURE module to calculate the semantic similarity. The available measure are: 1. Leacock and Chodorow (1998) referred to as lch 2. Wu and Palmer (1994) referred to as wup 3. The basic path measure referred to as path 4. Rada, et. al. (1989) referred to as cdist 5. Nguyan and Al-Mubaid (2006) referred to as nam 6. Resnik (1996) referred to as res 7. Lin (1988) referred to as lin 8. Jiang and Conrath (1997) referred to as jcn 9. The vector measure referred to as vector
--infile FILE
A file containing pairs of concepts or terms in any of the following formats:
term1<>term2
cui1<>cui2
cui1<>term2
term1<>cui2SYSTEM REQUIREMENTS
Perl (version 5.8.5 or better) - http://www.perl.org
CHEAT SHEET
BASIC EXAMPLE
The simplist case is:
query-umls-similarity-webinterface.pl hand skullwhich returns the similarity between 'hand' 'skull' using the path measure where the path information is obtained from the PAR/CHD relations in MSH.
MODIFY THE DEFAULT MEASURE
There are a number of additional similarity or relatedness measures that you can use: Leacock & Chodorow (lch), Wu & Palmer (wup), Lin (lin) Resnik (res), Jiang & Conrath (jcn), Lesk (lesk and the Vector Measure (vector).
To change the measure, use the --measure option. For example:
query-umls-similarity-webinterface.pl --measure lesk hand skullMODIFY THE DEFAULT SOURCE/RELATIONS
There are also a number of additional SOURCE/RELATION options that you can use.
For the similarity measures, you can use:
Source Relations
-----------------------
SNOMEDCT PAR/CHD
SNOMEDCT RB/RN
MSH PAR/CHD
MSH RB/RN
FMA PAR/CHD
FMA RB/RN
OMIM PAR/CHD
OMIM RB/RNThis means that the path information will be obtained from the specified source following the specified relations.
For the relatedness measures, things are a little different because the relations refer to what relations the extended definition is derived from. In the interface, you can use:
Source Relations
-----------------------
SNOMEDCT CUI/PAR/CHD/RB/RN
SNOMEDCT CUI
MSH CUI/PAR/CHD/RB/RN
MSH CUI
UMLS_ALL CUI/PAR/CHD/RB/RN
UMLS_ALL CUIIf this is confusing, send me an email and I can explain in more detail.
To change the source and relations, use the --sab and --rel options. For example:
query-umls-similarity-webinterface.pl --sab SNOMEDCT --rel PAR/CHD hand skullCONTACT US
If you have any trouble installing and using UMLS-Similarity,
please contact us via the users mailing list :
umls-similarity@yahoogroups.com
You can join this group by going to:
http://tech.groups.yahoo.com/group/umls-similarity/
You may also contact us directly if you prefer :
Bridget T. McInnes: bthomson at cs.umn.edu
Ted Pedersen : tpederse at d.umn.eduAUTHOR
Bridget T. McInnes, University of MinnesotaCOPYRIGHT
Copyright (c) 2007-2011,
Bridget T. McInnes, University of Minnesota
bthomson at cs.umn.edu
Ted Pedersen, University of Minnesota Duluth
tpederse at d.umn.edu
Serguei Pakhomov, University of Minnesota Twin Cities
pakh0002 at umn.edu
Ying Liu, University of Minnesota Twin Cities
liux at umn.eduThis program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program; if not, write to:
The Free Software Foundation, Inc.,
59 Temple Place - Suite 330,
Boston, MA 02111-1307, USA.