README.pod

- SYNOPSIS
- INSTALL
- DATABASE SETUP
- INITIALIZING THE MODULE
- USING THE MODULE
- SOFTWARE COPYRIGHT AND LICENSE

UMLS::Interface

## SYNOPSIS

        This package provides a Perl interface to UMLS, a taxonomy of
        medical concepts. The package is set up to access UMLS present in
        a mysql database. The package was essentially created for use with
        the Semantic::Similarity package for measuring the semantic
        relatedness of concepts.

## 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/sid

        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.

        Next set the UMLSINTERFACE environment variable

## 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 four tables:
            1. MRREL
            2. MRCONSO
            3. MRSAB
            4. MRDOC

        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 specifes 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
          getStDef                  -- Returns the definition of a given ST
          dropTable                 -- Drops the temporary table created by
                                       the UMLS-Interface module of path information
                                       for a specified set of sources

        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.

## 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.