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The BEL Framework tools are designed to work "out of the box". Once you have downloaded and unpacked the installation it should be ready to work. However, there are a few things you need to do first. This section will lead you through the steps necessary to get you started working with the BEL Framework tools.

Download Knowledge

First you need to find some knowledge in the form of BEL Documents to work against. Some publicly available knowledge is provided to get you started: http://resource.belframework.org/belframework/1.0/knowledge/.

  1. Download the small BEL Document named 'small_corpus.bel'. This contains a small set of BEL Statements drawn from 57 PubMeds.
  2. Create a folder on your computer and place the BEL document in it. For this tutorial, create a folder called BELDocuments on your computer and add the small_corpus.bel document to it.

Start the BEL Framework Server

The BEL Framework server hosts the BEL Framework Web API applications. You must first start the server in order to access these applications.

Starting the Server

To start the BEL Framework Server:

  1. Open a command window in the BEL Framework installation directory.
  2. Run the StartServer script.

For Linux:         ./StartServer.sh

For Windows:   StartServer.cmd

This will launch the Tomcat server that is provided with the distribution.
BEL Server successfully started at http://localhost:8080/
WebAPI is available at http://localhost:8080/openbel-ws/belframework.wsdl

Stopping the Server

Because the server has a live access to the KAM Store database, it is important that the server be correctly shutdown to avoid any possible corruption of KAM Store database.
To stop the server:

  1. Open a command window in the BEL Framework installation directory.
  2. Run the StopServer script.

For Linux:         ./StopServer.sh

For Windows:   StopServer.cmd


This will terminate Tomcat server if it is running and gracefully shut down and database operations that are open.
Server is successfully stopped.

Create a KAM

Knowledge Assembly Models (KAMs) are graphs representing biological networks that are compiled from one or more BEL Documents. KAMs are created by running the BEL Framework Compiler/Assembler utility.
To compile a BEL Document:

  1. Ensure that one or more BEL Documents are available. This example will compile the small_corpus.bel document that has already been downloaded.
  2. Open a command window in the BEL Framework installation directory.
  3. If you are using the default Derby configuration, ensure that the BEL Framework Server is not running. Derby only allows one JVM (Java Virtual Machine) to access the KAMStore database at a time.
  4. Run the belc.sh script passing in the parameters to specify which BEL Documents to compile and the name of the KAM to create. This will start the multi-phase compiler/assembler and will create a KAM named test. We will use defaults for most of the operations but you can look at the BEL Framework Compiler/Assembler User Guide for a detailed description of all the command line options available.


$./belc.sh -f ~/Desktop/BELDocuments/small_corpus.bel -k test -d "Test KAM"
The compiler/assembler will start to run and provide a log of the phases and any warnings that are generated as the compiler works.
BEL Framework V2.0: Compiler/Assembler

=== Phase I: Compiling proto-networks ===
Compiling 1 BEL Documents
[WARNING]: SYMBOL WARNINGS in NLP Corpus Document (NLP Corpus Document)
reason: 98 invalid symbols
symbol FGB, location http://download.belscripts.org/belframework/ns/mgi-marker-symbols.belns
(rows skipped)
[WARNING]: SEMANTIC FAILURE in NLP Corpus Document
reason: 128 semantic warnings for document
SEMANTIC WARNING in Parameter [namespace=Namespace [prefix=MGI, resourceLocation=http://download.belscripts.org/belframework/ns/mgi-marker-symbols.belns\], value=CRP]
reason: CRP does not exist in MGI: http://download.belscripts.org/belframework/ns/mgi-marker-symbols.belns
SEMANTIC WARNINGS
reason: term failed semantic checks
signature: complexAbundance(F:biologicalProcess,F:proteinAbundance)moleculeAbundance
function signatures: 2
the function argument is not valid for signature complexAbundance(E:moleculeAbundance)moleculeAbundance
the function argument is not valid for signature complexAbundance(F:abundance...)moleculeAbundance
(rows skipped)
=== Phase Complete ===
=== Phase II: Merging proto-networks ===
=== Phase Complete ===
=== Phase III: Expansion and augmentation of composite network ===
=== Phase Complete ===
=== Phase IV: Exporting final network to the KAM Store ===
=== Phase Complete ===
Once the compiler has completed, the KAM will have been generated and available for use in the KAM Store.

Validate the KAM

The KAMs are designed for use only by the BEL Framework APIs. However there are several tools that can be used to check the KAM. One of the more useful ways to do this is to use the KamManager to export the compiled KAM to XGMML. This way the KAM can be imported and viewed in Cytoscape. This has been made even easier with the release of the KAM Navigator, which is a Cytoscape plug-in from OpenBEL.

Exporting the KAM to XGMML

All actions relating to KAM's, including exporting to XGMML, is handled through the KamManager.


For Linux :        $ ./tools/KamManager.sh --export <KAM name> -t XGMML -o out_file.XGMML

For Windows:   KamManager.cmd --export <KAM name> -t XGMML -o out_file.XGMML

This will export the names KAM to a file called out_file in XGMML format. This file can then be imported into Cytoscape to be viewed and further analyzed.

 

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