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 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.