Bridget McInnes > UMLS-Similarity > query-umls-similarity-webinterface.pl

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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 MSH

Note: 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/CHD

Note: 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<>cui2

SYSTEM REQUIREMENTS ^

CHEAT SHEET ^

BASIC EXAMPLE

The simplist case is:

 query-umls-similarity-webinterface.pl hand skull

which 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 skull

MODIFY 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/RN

This 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 CUI

If 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 skull

CONTACT 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.edu

AUTHOR ^

 Bridget T. McInnes, University of Minnesota

COPYRIGHT ^

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.edu

This 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.
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