caBIO Quick Start
caBIO provides its users with three different Application Programming Interfaces (APIs):

• Java Interface via the caBIO.jar file
• Web Services Interface via SOAP
• HTTP/XML Interface via a servlet

1. Download the caBIO_ver2-1.zip file

2. Unzip the file at the root of your drive (i.e., c:\ or /usr/local/mydrive/)

3. Read the included readme file for detailed installation instructions.

4. Java classpath setup:
   The following jars must be on your classpath to run or compile the code:
   

   caBIO.jar	http://ncicb.nci.nih.gov/core/caBIO
   xercesImpl.jar	http://xml.apache.org/xerces-j/
   xml-apis.jar	http://xml.apache.org/xalan-j/
   jaxb-rt-1.0-ea.jar	http://java.sun.com/xml/jaxb/

   
   Example classpath to run GeneDemo:
   
   Windows:
   java -classpath .\JavaDemos;.\jars\caBIO.jar;.\jars\xercesImpl.jar;.\jars\xml-apis.jar;.\jars\jaxb-rt-1.0-ea.jar; -Djava.security.policy=java.policy GeneDemo

   Unix:
   java -classpath ./JavaDemos:./jars/caBIO.jar:./jars/xercesImpl.jar:./jars/xml-apis.jar:./jars/jaxb-rt-1.0-ea.jar: -Djava.security.policy=java.policy GeneDemo

   These jar files are included in the distribution and are located in the jars directory. The caBIO.jar is configured to point at the public caBIO server.
   

5. RMI Configuration:
   The caBIO.jar communicates to the caBIO server located at NCICB via Java's Remote Invocation Method (RMI) protocol. The jar file is already configured to connect to the caBIO server using a fixed port RMI custom socket factory.
   

   Server Address	Ports
   cabio-server.nci.nih.gov	8080 (RMI registration port)
   	8443 (RMI Data Port)

   
   You can learn more about Java RMI at RMI and Object Serialization FAQ

6. Java Security Policy File:
   A Java security policy is also required to make calls against the caBIO server because of the RMI protocol used by the caBIO.jar. A default java.policy file is included in the distribution. The policies defined in this java.policy file are for the protection of your system and NOT the caBIO server. Therefore, you are free (and encouraged) to edit the included java.policy file as appropriate for your system. For more information, see: http://java.sun.com/security/

7. Example Demo files:
   To verify proper installation and communication to the caBIO server, you can run one of the following Java example files included in the distribution:
   
        GeneDemo.java
        EVSDemo.java
        OntologyDemo.java
        CaseReportFormDemo.java
        CancerModelDemo.java
   
   The Java examples source code as well as compiled byte code have been included as part of the distribution along with batch/shell scripts that will correctly set up the classpath.
   

8. Executing the Examples:
   To run an example, type the following at the command prompt:
   
        run_caBIO.bat [name] (Windows)
   
   or
   
        sh run_caBIO.sh [name] (Unix)
   
   For example, to run the GeneDemo on Windows, type the following at the command prompt:
   
        run_caBIO.bat GeneDemo
   
   To run the GeneDemo on Unix, type the following at the command prompt:
   
        sh run_caBIO.sh GeneDemo
   

9. Recompile the examples
   If you would like to recompile an example, you can use the compile_caBIO scripts or Ant.
   
   compile_caBIO
   To use the compile_caBIO script, type the following at the command prompt:
   
        compile_caBIO.bat JavaDemos/[name].java
   
   For example, if you would like to recompile GeneDemo.java on Windows, type the following at the command prompt:
   
        compile_caBIO.bat JavaDemos/GeneDemo.java
   
   On Unix, type the following at the command prompt:
   
        sh compile_caBIO.sh JavaDemos/GeneDemo.java
   
   Ant
   Ant is an open source compile tool available at: http://ant.apache.org/. Refer to the installation directions included with the Ant distribution. After you have installed Ant, change to the build directory and type:
   
        ant
   

The caBIO project provides a SOAP interface for non-Java applications. In this model the client issues XML-encoded requests specifying the desired data services to the appropriate caBIO host address and port and, in exchange, receives XML-encoded responses.

1. Install a SOAP client package:
   SOAP client package handles the implementation of the envelope and the resolution of the SOAP types. A number of SOAP packages catering to different programming languages are available at http://www.w3.org/TR/SOAP/ and at Soapware. The PERL examples included in the distribution utilize SOAP::LITE for Perl, which can be freely downloaded from the http://www.soaplite.com/ or ActiveState web site .
   

2. Accessing the caBIO SOAP Services:
   The following link points to the list of caBIO SOAP services provided by the NCICB server:
   http://cabio.nci.nih.gov/soap/services/index.html
   

3. caBIO SOAP Configuration:
   

   server:	cabio.nci.nih.gov
   Listening Port:	80
   URI	such as 'urn:nci-gene-service', See caBIO SOAP Services
   Method	such as 'getGenes', See caBIO SOAP Services

4. Executing the Examples:
   To run the geneClient.pl example, type the following at the command prompt from the /PerlSOAP folder:
   
        geneClient.pl cabio.nci.nih.gov 80 getGenes -symbol brca1
   
   

For example, to query for Genes where the Gene name is "BRCA1"

     http://cabio.nci.nih.gov/servlet/GetXML?query=Gene&crit_name=BRCA1

To query for Chromosome information where Gene name is "BRCA1"

     http://cabio.nci.nih.gov/servlet/GetXML?query=Chromosome&crit_genes_name=BRCA1

In this case the association role from Chromosome to Gene is called "genes"

To further refine the query for only human chromosomes where Gene name is "BRCA1"

     http://cabio.nci.nih.gov/servlet/GetXML?query=Chromosome&crit_genes_name=BRCA1&crit_taxon_commonName=Human

In this case the association role from Chromosome and Gene is called "genes" and the association role from Chromosome and Taxon is called "taxon".
And "name" is an attribute of both "genes" and "taxon".

In another example, we can simply formulate the query to return Gene information for Targets which have an association to Agents named "ADENO-P53" or just "ADENO*".

     http://cabio.nci.nih.gov/servlet/GetXML?query=Gene&crit_targets_agents_name=ADENO*