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An open platform for capturing, integrating, storing, and sharing biological knowledge in and across organizations.

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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.

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 openbel-discuss+subscribe@googlegroups.com 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 openbel-announce+subscribe@googlegroups.com 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 BEL Editor.
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 downloads 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

Copyright 2013 OpenBEL Consortium

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Further Reference

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