BEL Framework REST API

For a more complete guide to using the BEL Framework, we encourage you to check out the OpenBEL Wiki.

The OpenBEL Framework is an open-platform technology for managing, publishing, and using biological knowledge represented using the Biological Expression Language (BEL). BEL is an easy to understand, computable format for representing biological knowledge. The OpenBEL Framework is specifically designed to overcome many of the challenges associated with capturing, integrating, and storing biological knowledge within an organization, and sharing the knowledge across the organization and between business partners. The framework provides mechanisms for:

1. Capture and management of biological knowledge
2. Integration of knowledge from multiple sources
3. Knowledge representation in a standard and open format
4. Creation of custom, computable biological networks from captured knowledge
5. Enabling applications to query knowledge networks using web and Java APIs

Central to the design of the framework is the ability to integrate knowledge across different representational vocabularies and ontologies. This allows organizations to combine knowledge from disparate sources into centralized knowledge repositories. The combined knowledge can be made available to a variety of decision support and analytical applications through a standardized set of computable networks and APIs.

Contents

• The OpenBEL Ecosystem
• Requirements
• Use
• API Documentation
• License
• Further Reference

The OpenBEL Ecosystem

Various smaller projects are connected with the framework. Each project is intended on serving a particular purpose.

OpenBEL Discussion Group

This group is used to discuss OpenBEL technologies, the BEL language, and anything relevant to the OpenBEL ecosystem as a whole.

You can subscribe to these announcements by visiting the link, or by sending an email to [email protected] with the subject subscribe.

OpenBEL Announcement Group

This group is used to issue announcements related to OpenBEL.

You can subscribe to these announcements by visting the link, or by sending an email to [email protected] with the subject subscribe.

freenode IRC network

We maintain the #openbel channel on the freenode network.

To connect to freenode, you can use chat.freenode.net as an IRC server. On Linux and Windows, you can use XChat as an IRC client. On Mac OS X, there is Xirc.

openbel-framework-resources

The framework's resources provide a set of files derived from biological and chemical ontologies. These resources are used to better describe biological statements and their context.

openbel-framework-examples

This repository is for helping developers get started with different uses of the framework. It contains a number of examples in various programming languages.

Cytoscape Plugins

The Cytoscape plugins enable Cytoscape to access and manipulate the OpenBEL Framework knowledge assembly models using the framework's web service API.

OpenBEL Eclipse Repository

The OpenBEL Eclipse p2 repository. It currently holds the stable and unstable repositories of the OpenBEL Workbench.

BEL Editor

The BEL Editor enables the BEL language and the framework to be used in Eclipse - from the syntax and semantics of the BEL language to the compilation of BEL knowledge into knowledge assembly models.

REST API

Provides a RESTful API for the BEL language and framework.

Requirements

• Java 7: http://java.com/en/download/index.jsp
• Clojure 1.5: http://clojure.org/download
• Python 3.3: http://www.python.org/download/
• Apache Buildr: http://buildr.apache.org/download.html
• MongoDB 2.4.3: http://www.mongodb.org/downloads
• Leiningen: https://github.com/technomancy/leiningen
• Linux or OS X

Use

Prior to use, the BEL REST API must be built and have BEL data loaded into it. Follow these steps:

1. scripts/build.sh
2. scripts/mongo-check.sh
3. scripts/load.sh

Once these three steps have completed, use scripts/run.sh to run.

Alternatively, use go.sh as a frontend to the scripts.

API Documentation

Nothing here yet.

License

Apache License, Version 2.0.

Further Reference

• BEL Portal: http://openbel.org
• OpenBEL Wiki: http://wiki.openbel.org
• Mailing list: https://groups.google.com/forum/#!forum/openbel-discuss
• OpenBEL build server: http://build.openbel.org
• GitHub: https://github.com/OpenBEL
• Freecode: http://freecode.com/projects/openbel-framework