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Specification and Tutorial
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Tutorial
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Identifiers
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Overview
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Physical Entities
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Process Entities
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<h1>Home</h1>
<p align="center">
<img src="/img/bel300.png" alt="BEL Logo"/>
</p>
<p>The Biological Expression Language (BEL) facilitates representing scientific findings in
the life sciences in a computable form. It captures causal, correlative, and associative
relationships between biological entities along with the experimental/biological context in which
they were observed as well as the provenance of the publication from which the relation was
reported.</p>
<p>The this website is a community-driven portal whose purpose
is to provide information for new users who want to learn BEL and link to the surrounding
ecosystem of software tools.</p>
<h2 id="specification-and-tutorial">Specification and Tutorial<a class="headerlink" href="#specification-and-tutorial" title="Permanent link">¶</a></h2>
<p>The current version (2.0+) specification and tutorial is available <a href="tutorial/">here</a>.
Previous versions can be found on Selventa's GitHub <a href="https://github.com/OpenBEL/language">repository</a>.</p>
<p>The <a href="https://bel.bio/">BEL.bio</a> project hosts additional programatically generated
<a href="https://language.bel.bio">language documentation</a> as well as accompanying structured
<a href="https://github.com/belbio/bel_specifications/tree/master/specifications">EBNF specifications</a> of
each version of BEL.</p>
<h2 id="language-evolution-and-history">Language Evolution and History<a class="headerlink" href="#language-evolution-and-history" title="Permanent link">¶</a></h2>
<p>Changes and improvements are submitted as BEL Enhancement Proposals (BEPs) then
reviewed by the <a href="https://github.com/belbio/bep/blob/master/CommitteeGuidelines.md">BEL Language Committee</a>.
A listing of all BEPs can be found <a href="http://bep.bel.bio/">here</a>. A tutorial on how
to submit a BEP can be found <a href="https://github.com/belbio/bep">here</a>.</p>
<ul>
<li><a href="https://medium.com/bel-news/bel-v2-2-enhancements-cfb4b27b22cb">BEL v2.2</a> was
published on September 24<sup>th</sup>, 2019.</li>
<li><a href="https://medium.com/bel-news/bel-2-1-enhancements-ac79b078ad5a">BEL v2.1</a> was
published on December 10<sup>th</sup>, 2018.</li>
<li><a href="https://github.com/OpenBEL/language/raw/master/docs/version_2.0/bel_specification_version_2.0.pdf">BEL v2.0</a>
was published in June 2014.</li>
<li><a href="https://github.com/OpenBEL/language/raw/master/docs/version_1.0/bel_specification_version_1.0.pdf">BEL v1.0</a>
was published in July 2012.</li>
</ul>
<p>BEL was created by Dexter Pratt while at Selventa, but has since become an entirely-community driven
project. A more detailed history can be found in this <a href="https://cthoyt.com/2020/04/28/history-of-bel.html">blog post</a>.</p>
<h2 id="community">Community<a class="headerlink" href="#community" title="Permanent link">¶</a></h2>
<p>The BEL community primarily uses <a href="https://groups.google.com/forum/#!forum/openbel-discuss">Google Groups</a>
for discussions, troubleshooting, and community organization. Additional
discussion may also be found in the <a href="https://forum.bel.bio">BEL.bio project forum</a>.</p>
<p>There are several openly available sources of BEL Content hosted by different organizations.
Selventa originally published two large example BEL documents that serve as a good starting point -
the <a href="https://github.com/cthoyt/selventa-knowledge/blob/master/selventa_knowledge/small_corpus.bel">Selventa Small Corpus</a>
and the <a href="https://github.com/cthoyt/selventa-knowledge/blob/master/selventa_knowledge/large_corpus.bel">Selventa Large Corpus</a>.
A summary of other publicly accessible BEL content can be found in this <a href="https://cthoyt.com/2020/04/30/public-bel-content.html">blog post</a>.</p>
<h2 id="software">Software<a class="headerlink" href="#software" title="Permanent link">¶</a></h2>
<p>The following is a mixture of web applications and software tools/ecosystems for BEL listed in
alphabetical order. If you would like your tool included in this list, please let us know via the
issue tracker. Items will be removed from this list if they are no longer maintained.</p>
<ul>
<li><a href="https://github.com/bel-commons/bel-commons">BEL Commons</a></li>
<li><a href="https://bel.bio">BEL.bio</a></li>
<li><a href="https://github.com/bio2bel/bio2bel">Bio2BEL</a></li>
<li><a href="https://biodati.com">BioDati Studio</a></li>
<li><a href="https://github.com/pybel/pybel">PyBEL</a></li>
</ul>
<h2 id="citation">Citation<a class="headerlink" href="#citation" title="Permanent link">¶</a></h2>
<p>While BEL was created by Dexter Pratt at Selventa in the early 2000's, the most recent reference
publication for the language itself is:</p>
<p><a href="https://doi.org/10.1016/j.drudis.2013.12.011"><strong>Recent advances in modeling languages for pathway maps and computable biological networks</strong></a>.
<br /> Slater, T. (2014).
<br /> <i>Drug Discovery Today</i>, <b>19</b>(2), 193–198.</p>
<p>A summary of papers using or citing BEL can be found <a href="https://cthoyt.com/2020/05/22/bel-papers.html">here</a>.</p>
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