diff --git a/_posts/2020-01-15-bel.md b/_posts/2020-01-15-bel.md new file mode 100644 index 0000000..6c63800 --- /dev/null +++ b/_posts/2020-01-15-bel.md @@ -0,0 +1,52 @@ +--- +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. + + + +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.