The purpose of this BEP is to introduce syntax for defining namespaces with regular expressions to mirror the syntax used for defining annotations with regular expressions. This will allow definitions from https://identifiers.org to be more quickly incorporated in to BEL, without the overhead of defining a BELNS file, but also with the caveat of a weaker semantic check.
BEP-Id: BEP-0005
Status: Published
Version: 1
BEL-Version: 2.0.0+
Authors: Charles Tapley Hoyt ([email protected])
Created-Date: 2018-07-17
Type: Standards Track
Most biological resources have both standardized identifiers and human-readable labels. While BEL curators and users will likely continue to use these labels, automatically generated resources would benefit greatly from the flexibility provided by defining entities with their standardized identifiers.
These are listed on https://identifiers.org. For example, the PFAM page
contains the regular expression for its standardized identifiers (^PF\d{5}$)
A BEL document can be written using a mix of namespace definitions from several sources
DEFINE NAMESPACE PFAM AS PATTERN "^PF\d{5}$"
DEFINE NAMESPACE HGNC AS URL "http://bel.scai.fraunhofer.de/namespace/hgnc/hgnc-20180215.belns"
...
# Disambiguation: PF02171 is the "Piwi domain"
p(HGNC:PIWIL1) isA p(PFAM:PF02171)
...
Additionally, namespaces that are restrictively large to use as BEL namespaces (such as dbSNP) can be much more easily incorporated into BEL documents.
Namespaces will be defined with the following syntax:
DEFINE NAMESPACE X AS PATTERN "Y"
where X refers to the keyword that will be used for the document and Y is a valid
regular expression string representing the pattern of the identifiers.
It is reccomended to use a capitalized version of the namespace name from https://identifiers.org and also to acquire the regular expression from https://identifiers.org.
Example:
DEFINE NAMESPACE PFAM AS PATTERN "^PF\d{5}$"
This proposed feature is for 2.0.0+ and will be added to the language so does not require any efforts to migrate older BEL knowledge.