Add post on BEL

_posts/2020-01-15-bel.md

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+---
+layout: post
+title: "Encoding Biology in Knowledge Graphs"
+date: 2020-01-14 00:00:00 -0800
+---
+This post gives a brief introduction to Biological Expression
+Language (BEL), which is one format for this. Its purpose is to encode
+qualitative causal, correlative, and associative relations between
+biological entities across multiple scales.
+
+A BEL statement (D) is encoded as a triplet containing a subject, a
+predicate, and an object. The predicate can represents the type of
+relation while the subject and object can either represent the
+abundance of molecular entities such as genes, proteins, chemicals,
+or more abstract concepts such as biochemical reactions, biological
+processes, and pathologies. Identifiers for these concepts use
+references to external namespaces to qualify their respective names.
+In this example, [ChEBI](https://www.ebi.ac.uk/chebi/) is used to
+qualify chemicals and [MeSH](https://www.ncbi.nlm.nih.gov/mesh) for
+biological processes.
+
+<iframe 
+ src="https://widgets.figshare.com/articles/5808771/embed?show_title=1"
+ width="568"
+ height="351"
+ allowfullscreen="true"
+ frameborder="0">
+ </iframe>
+
+BEL statements are organized into BEL Scripts, which track provenance
+information like namespace references, relation provenance (e.g. citation,
+evidence), and biological context-specific relation metadata
+(e.g. anatomy, cell, disease).
+
+BEL Script, which contains three sections: A) the document metadata
+section provides provenance information such as the name, version,
+and author; B) the definitions section provides references to
+external resources that are used as identifiers and metadata in the
+relations section; and C) the relations section contains BEL
+relations and their metadata: minimally including a citation and
+evidence with the possibility to include additional information such
+as biological context (e.g. cell, anatomy, disease).
+
+Because the object of one BEL statement can be the subject of another,
+BEL can be compiled into networks that describe chains of causation.
+Often, the terms “BEL”, “BEL Script”, and “BEL Networks” are used
+interchangeably.
+
+If you’re interested in learning more, see the OpenBEL website. BEL
+can be programmatically read by [PyBEL](https://github.com/pybel/pybel)
+or used interactively with [BEL Commons](https://bel-commons.scai.fraunhofer.de)
+to search networks and run analyses.