BEL Specifications

Overview

BEL specifications are defined within the bel_parser gem. The components of the specifications were designed to be separate from its application (e.g. semantic analysis, autocomplete, etc) to maximize reuse.

Currently BEL 1.0 and 2.0 are implemented separately within the gem.

Components

BEL specifications comprise:

• Functions
  • Indicates the types one ore more biological entities. A Function plus its Arguments comprise a Term.
  • Example: proteinAbundance, biologicalProcess, ...
  • See BEL Terms as Functional Expressions
  • BEL 2.0 functions: bel_parser/language/version2_0/functions/
• Return Types
  • Functions return a Return Type to allow composition. Return types are hierarchical.
  • Example: tloc(p(HGNC:CDKN1A), fromLoc(MESHCS:"Cell Nucleus"), toLoc(MESHCS:Cytoplasm)); translocation accepts an Abundance in the first position and p(HGNC:CDKN1A) returns a ProteinAbundance which is a sub-type of Abundance.
  • BEL 2.0 return types: bel_parser/language/version2_0/return_types/
• Value Encodings
  • A biological identifier is given one or more types to specify what it codes for. Value encodings are hierarchical.
  • Example: AKT1 as defined by HGNC can code for a Gene, Protein, or RNA, which we specify as value encodings.
  • BEL 2.0 value encodings: bel_parser/language/version2_0/value_encodings/
• Relationships
  • The observed interaction between a subject and object in a BEL expression. The most used relationship classes are either causal or correlative.
  • Example: directlyIncreases represents a direct, physical interaction where increase in the amount of a subject causes an increase in the amount of an object
  • BEL 2.0 relationships: bel_parser/language/version2_0/relationships/
• Upgrades
  • Mechanisms for upgrading BEL expressions from one specification version to another.
  • Example: Converting BEL 1.0 kin(HGNC:AKT1) to BEL 2.0 act(p(HGNC:AKT1), ma(DEFAULT:kin))
  • BEL 1.0 upgrades: bel_parser/language/version1_0/upgrades/

These components are loaded automatically by BaseSpecification. You just have describe the specification and which path to load the components from.

# Loads components within version2_0/. 
# Describe the version (major.minor) and URI.

module BELParser
  module Language
    module Version2_0
      # Version2_0 specification defines the BEL 2.0 specification.
      class Specification < BaseSpecification
        BaseSpecification.load_version_path('version2_0')

        def initialize
          @version = '2.0'.freeze
          @uri     = 'http://www.openbel.org/2.0'
          load_language_constants(Version2_0)
          freeze
        end
      end 
    end 
  end 
end

BEL specifications can be loaded in one simple call.

BELParser::Language.specification('2.0')

# [7] pry(main)> ls -m BELParser::Language.specification('2.0')
# BELParser::Language::Specification#methods: 
#   causal_relationships       deprecated_relationships  freeze_categories  genomic_relationships     inspect                 relationships  self_relationships  value_encoding
#   correlative_relationships  direct_relationships      function           increasing_relationships  listable_relationships  return_type    upgrades            version       
#   decreasing_relationships   directed_relationships    functions          indirect_relationships    relationship            return_types   uri