OpenBEL Framework

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
• Distribution
• Building
  • Nightly Builds
• 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.

Distribution

The OpenBEL Framework is distributed as an archive that can be extracted and used on many platforms. See releases for the latest release archive.

Building

The OpenBEL Framework is built using Apache Maven.

mvn -Pdistribution clean package assembly:assembly install

Alternatively, you can use package.sh which does the same thing.

Nightly Builds

Builds of the master and experimental branches are made available each day after rigorous testing.

master

The master branch is the latest stable version of the framework that has yet to be released.

experimental

The experimental branch is the latest unstable version of the framework containing experimental features, improvements, and API changes.

API Documentation

Pushes to the master branch instruct our build server to update the API documentation. It will always be up-to-date for the current master. The documentation is published under the gh-pages branch of the official repository.

License

This program is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

The OpenBEL Framework 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 Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with the OpenBEL Framework. If not, see <http://www.gnu.org/licenses/>.

Additional Terms under LGPL v3:

This license does not authorize you and you are prohibited from using the name, trademarks, service marks, logos or similar indicia of Selventa, Inc., or, in the discretion of other licensors or authors of the program, the name, trademarks, service marks, logos or similar indicia of such authors or licensors, in any marketing or advertising materials relating to your distribution of the program or any covered product. This restriction does not waive or limit your obligation to keep intact all copyright notices set forth in the program as delivered to you.

If you distribute the program in whole or in part, or any modified version of the program, and you assume contractual liability to the recipient with respect to the program or modified version, then you will indemnify the authors and licensors of the program for any liabilities that these contractual assumptions directly impose on those licensors and authors.

Further Reference

• BEL Portal: http://openbel.org
• OpenBEL Wiki: http://wiki.openbel.org
• Mailing list: https://groups.google.com/forum/#!forum/openbel-discuss
• Selventa: http://www.selventa.com/
• API documentation: http://openbel.github.com/openbel-framework
• User documentation: http://openbel-framework.readthedocs.org/en/master/
• Ohloh: https://www.ohloh.net/p/openbel-framework
• Freecode: http://freecode.com/projects/openbel-framework
• OpenBEL build server: http://build.openbel.org
• GitHub: https://github.com/OpenBEL
• Freecode: http://freecode.com/projects/openbel-framework

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