Identifiers

BEL uses compact uniform resource locators, or CURIEs, to reference entries in ontologies and other external vocabularies. A CURIE has two parts, a prefix and an identifier that are delimited by a colon :. They can be used to reference entities in ontologies like the Gene Ontology, vocabularies like the HGNC, and hierarchies like MeSH. You've probably seen entities written this way before like in:

// CURIE for apopototic process in the Gene Ontology
go:0006915

// CURIE for MAPT in HGNC
hgnc:6893

// CURIE for Parkinson's disease in the NCIT
ncit:C26845

// CURIE for homo sapiens in the NCBI Taxonomy
taxonomy:9606

CURIEs are great because they can be resolved to their own resources using services like https://identifiers.org. They're also easier to deal with than PURLs becuase you don't have to understand all of the assumptions made by the PURL community in modeling. However, CURIEs are hard to read, so BEL adopts an OBO-like syntax for allowing CURIEs to be written with an optional label like in:

go:0006915 ! "apopototic process"

hgnc:6893 ! MAPT

ncit:C26845 ! "Parkinson's disease"

taxonomy:9606 ! "Homo sapiens"

Therefore, anywhere in this tutorial that identifier is referenced, it can take the following form:

prefix:identifier [! name]

BEL is also designed to be extensible to custom vocabularies and does not necessarily rely on the existence of CURIEs. More information can be found in the BEL Script section of this tutorial.

More information about how BEL uses CURIEs can be found in BEP-0008.