NAME
    UMLS::Interface README

  SYNOPSIS
        This package provides a Perl interface to the Unified Medical 
        Language System (UMLS). The UMLS is a knowledge representation 
        framework encoded designed to support broad scope biomedical 
        research queries. There exists three major sources in the UMLS. 
        The Metathesaurus which is a taxonomy of medical concepts, the 
        Semantic Network which categorizes concepts in the Metathesaurus, 
        and the SPECIALIST Lexicon which contains a list of biomedical 
        and general English terms used in the biomedical domain. The 
        UMLS-Interface package is set up to access the Metathesaurus
        and the Semantic Network present in a mysql database.

  INSTALL
        To install the module, run the following magic commands:

          perl Makefile.PL
          make
          make test
          make install

        This will install the module in the standard location. You will, most
        probably, require root privileges to install in standard system
        directories. To install in a non-standard directory, specify a prefix
        during the 'perl Makefile.PL' stage as:

          perl Makefile.PL PREFIX=/home/programs

        It is possible to modify other parameters during installation. The
        details of these can be found in the ExtUtils::MakeMaker
        documentation. However, it is highly recommended not messing around
        with other parameters, unless you know what you're doing.

  DATABASE SETUP
        The interface assumes that the UMLS is present as a mysql database. 
        The names of these databases can be passed as configuration options 
        at initialization. However, if the names of the database is not 
        provided at initialization, then default values are used -- the 
        database for the UMLS is called 'umls'.

        The UMLS database must contain six tables: 
            1. MRREL
            2. MRCONSO
            3. MRSAB
            4. MRDOC
            5. MRDEF
            6. SRDEF
            7. MRSTY

        All other tables in the databases will be ignored, and any of these
        tables missing would raise an error.

        The mysql server can be on the same machine as the module or could
        be on a remotely accessible machine. The location of the server can
        be provided during initialization of the module.

  INITIALIZING THE MODULE
        To create an instance of the interface object, using default values for
        all configuration options:

          use UMLS::Interface;
          my $interface = UMLS::Interface->new();

        Configuration options can be included in the MySQL my.cnf 
        file. This is preferable. The directions for this are in 
        the INSTALL file. It is Stage 5 Step D.  

        The following configuration options are also provided though:

        'driver'       -> Default value 'mysql'. This option specifies the 
                          Perl DBD driver that should be used to access the
                          database. This implies that the some other DBMS
                          system (such as PostgresSQL) could also be used,
                          as long as there exist Perl DBD drivers to
                          access the database.
        'umls'         -> Default value 'umls'. This option specifies the name
                          of the UMLS database.
        'hostname'     -> Default value 'localhost'. The name or the IP 
                          address of the machine on which the database 
                          server is running.
        'socket'       -> Default value '/tmp/mysql.sock'. The socket on 
                          which the database server is using.
        'port'         -> The port number on which the database server 
                          accepts connections.
        'username'     -> Username to use to connect to the database server. 
                          If not provided, the module attempts to connect as 
                          an anonymous user.
        'password'     -> Password for access to the database server. If not
                          provided, the module attempts to access the server
                          without a password.

  USING THE MODULE
        Once the object of module is successfully created after following the
        steps described in the previous section, a number of methods can be
        called upon this object:

          getError()                -- Returns the error code and error string from 
                                       the last method call on the object.
          root()                    -- Returns the concept ID of the root of the tree.
          depth()                   -- Returns the depth of the tree.
          version()                 -- Return the version of UMLS.
          exists()                  -- Determines if a CUI exists
          validCui()                -- Checks if CUI is a valid concept
          getSab()                  -- Returns the list of sources the concept
                                       exists in
          getConceptList()          -- Returns the list of all concept IDs preset in
                                       the database.
          getTermsList()            -- Returns the list of terms corresponding to a 
                                       particular concept ID.
          getParents()              -- Returns the parent of a given CUI
          getChildren()             -- Returns the children of a given CUI
          pathsToRoot()             -- Returns a list of concept IDs that denote 
                                       the path from the input concept ID to the 
                                       root 
                                       concept of the taxonomy.
          findShortestPath()        -- Returns the shortest path between two CUIs
          findLeastCommonSubsumer() -- Returns the least common subsumer between
                                       two CUIs
          getCuiDef()               -- Returns the definition(s) of a given CUI
          dropTable()               -- Drops the temporary table created by 
                                       the UMLS-Interface module of path information
                                       for a specified set of sources
          findMinimumDepth()        -- Returns the minimum depth of a given CUI
                                       in the current view of the UMLS
          findMaximumDepth()        -- Returns the maximum depth of a given CUI
                                       in the current view of the UMLS
          getSt()                   -- Returns the TUI(s) of the semantic type(s)
                                       associated with a given CUI
          getStAbr()                -- Returns the abbreviation of a semantic type 
                                       given its cooresponding TUI
          getStString()             -- Returns the name of the semantic type given 
                                       its cooresponding abbreviation      
          getStDef()                -- Returns the definition of a semantic type
                                       given its cooresponding abbreviation
          checkConceptExists()      -- Returns true or false (1 or 0) if a concept
                                       exists given the current view of the UMLS
          getRelated()              -- Returns all the CUIs related to a specified 
	                               CUI given a specified relation REL
	  getRelations()            -- Returns all the relations in the MRREL file 
	                               associated with a given CUI
	
  
        These methods essentially expose an interface as required by the
        UMLS::Similarity modules. The UMLS::Similarity modules require
        that any interface to a taxonomy provide the above methods.

  CONTACT US
      If you have any trouble installing and using UMLS-Interface, 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

  SOFTWARE COPYRIGHT AND LICENSE
        Copyright (C) 2004-2009 Bridget T McInnes, Siddharth Patwardhan, Serguei 
        Pakhomov and Ted Pedersen

        This suite of programs 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.

        Note: The text of the GNU General Public License is provided in the
        file 'GPL.txt' that you should have received with this distribution.

