Path to Root

From NCBO Wiki

Introduction

This project is used for generating a text file or populating a database with the path to root and other information for concepts from ontologies in the bioportal. This uses the REST services developed by NCBO for acessing information extracted from ontologies. For more information on the REST services please visit please visit: http://obs.bioontology.org/obs/OBS_v1_rest.html

Setting up and running the code

Steps 1,2,3 and 4 should be only be performed if you want the output to be populated into a database. If you need the output *only* to a flat file with '|' as the delimter, proceed directly to step 5.

• Create a MySQL database:
  • On the machine where the database needs to be hosted, create a new database with any name. Note the IP and name of the database. Make sure port 3306 is open(default port for MySQL).

• Create a table in the database
  • In the database created, create a table 'umls'

• Create columns in the table
  • Create the following columns in the table

 Column Name	Datatype	NotNull		Flags	Default Value
 conceptid	VARCHAR(10)	true		Binary	Null
 conceptname	TEXT					Null
 ptrs		TEXT		true			Null
 ptrsnames	TEXT					Null
 namespace	VARCHAR(45)	true		Binary	Null

The following SQL command can be used:

  CREATE TABLE `temp`.`umls` (
    `conceptid` VARCHAR(10) NOT NULL,
    `conceptname` TEXT,
    `ptrs` TEXT NOT NULL,
    `ptrsnames` TEXT,
    `namespace` VARCHAR(45) NOT NULL,
    PRIMARY KEY (`conceptid`, `ptrs`(255), `namespace`)
  )
  ENGINE = MyISAM;
  

• Note the URL of the database, the name, user and password. For eg. If you created a database 'temp' on the localhost with the user 'root' and password 'nipunb'.

   Your dbURL will be: jdbc:mysql://localhost:3306/temp
   Your dbUser will be: root
   Your dbPassword will be: nipunb
   

• Open a new command prompt.
  • Change the directory to the folder in which downloaded/copied the code.
  • run at the command line

 javac -classpath C:\lib\commons-codec-1.3.jar; C:\lib\commons-httpclient-3.1.jar; C:\lib\commons-logging-1.1.1.jar; C:\lib 
 \commons-logging-1.1.1-javadoc.jar; C:\lib\commons-logging-1.1.1-sources.jar; C:\lib\commons-logging-adapters-1.1.1.jar; C:\lib
 \commons-logging-api-1.1.1.jar; C:\lib\commons-logging-tests.jar; C:\lib\mysql-connector-java-5.0.7-bin.jar; C:\lib
 \OntologyAccess090108.jar ComputeHierarchies.java
 (make sure javac is in classpath or else use: C:\Program Files\Java\jdk1.6.02\bin\javac 	

• • Followed by

 java -classpath .;C:\lib\commons-codec-1.3.jar;C:\lib\commons-httpclient-3.1.jar;C:\lib\commons-logging-1.1.1.jar;C:\lib\commons-
 logging-1.1.1-javadoc.jar;C:\lib\commons-logging-1.1.1-sources.jar;C:\lib\commons-logging-adapters-1.1.1.jar;C:\lib\commons- 
 logging-api-1.1.1.jar;C:\lib\commons-logging-tests.jar;C:\lib\mysql-connector-java-5.0.7-bin.jar;C:\lib\OntologyAccess090108.jar 
 ComputeHierarchies -ontologies "C:\\Bioportal\\SAB\\SAbsTest.txt" -db "true" dbURL "jdbc:mysql://localhost:3306/temp" -dbUser 
 "root" -dbPassword "nipunb"
	

• • More about the arguments:
    • Arguments are

   -ontologies : The complete path of the file containing the SABs of the ontologies to be used. The file should contain one SAB 
                 on every line. Please see SABsTest.txt and SABsComplete for the correct format. The path should be of the type 
                 C:\\Bioportal\\SAB\\SABsTest.txt 

   -db : Takes in true or false as string arguments. If you are setting -db to true
         make sure that you have gone over steps 3 and 4. The default is set to false.

   -dbURL : URL of the database to be populated. Make sure the database exists and has the correct column with the correct primary 
            key. Please see 4) for more details

   -dbUser : Username for the database

   -dbPassword : Password for the user to access the database. Leave blank if the user
                 has no password.

   -outputFileName : Name of the file to which the path to root information is going to be written out to. If this file already, 
                     content is appended. The format of the file is: ConceptID |Concept Name|Path to Root|Path To Root(names)|SAB 
                     If the option is not specified, the information is not written to a file.

    Sample arguments that can be used:
    i) Output only to a file:
       -ontologies "C:\\PathToRoot\\ptrs\\SABsTest.txt " -outputFileName "C:\\PathToRoot\\ptrs\\OutputTest.txt"

    ii) Output only to a database:
        -ontologies "C:\\Bioportal\\SAB\\SAbsTest.txt" -db "true" dbURL "jdbc:mysql://localhost:3306/temp" -dbUser "root"   
        -dbPassword "nipunb"

    iii)Output to both file and DB:
        -ontologies "C:\\PathToRoot\\ptrs\\SABsTest.txt " -db "true" dbURL "jdbc:mysql://localhost:3306/temp" -dbUser "root"
        -dbPassword "nipunb" -  outputFileName "C:\\PathToRoot\\ptrs\\OutputTest.txt"