bel_parser 1.0.0.alpha.7 → 1.0.0.alpha.8

data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb

@@ -5,13 +5,20 @@ module BELParser
   module Language
     module Version2_0
       module Relationships
-        # PositiveCorrelation:  +A positiveCorrelation B+ -  For terms A and B, +A positiveCorrelation B+ indicates that changes in A and B have been observed to be positively correlated, thus B positiveCorrelation A is equivalent to A positiveCorrelation B.
+        # PositiveCorrelation:  +A positiveCorrelation B+ -  For terms
+        # A and B, +A positiveCorrelation B+ indicates that changes in
+        # A and B have been observed to be positively correlated, thus B
+        # positiveCorrelation A is equivalent to A positiveCorrelation B.
         class PositiveCorrelation
           extend Relationship
 
           SHORT       = :positiveCorrelation
           LONG        = :positiveCorrelation
-          DESCRIPTION = ' +A positiveCorrelation B+ -  For terms A and B, +A positiveCorrelation B+ indicates that changes in A and B have been observed to be positively correlated, thus B positiveCorrelation A is equivalent to A positiveCorrelation B.'.freeze
+          DESCRIPTION = ' +A positiveCorrelation B+ -  For terms A and B,
+          A positiveCorrelation B+ indicates that changes
+          n A and B have been observed to be positively
+          orrelated, thus B positiveCorrelation A is
+          quivalent to A positiveCorrelation B.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb

@@ -5,13 +5,22 @@ module BELParser
   module Language
     module Version2_0
       module Relationships
-        # PrognosticBiomarkerFor:  +A prognosticBiomarkerFor P+ -  For term A and process term P, +A prognosticBiomarkerFor P+ indicates that changes in or detection of A is used in some way to be a prognostic biomarker for the subsequent development of pathology or biological process P.
+        # PrognosticBiomarkerFor:  +A prognosticBiomarkerFor P+ -
+        # For term A and process term P, +A prognosticBiomarkerFor P+
+        # indicates that changes in or detection of A is used in some
+        # way to be a prognostic biomarker for the subsequent development
+        # of pathology or biological process P.
         class PrognosticBiomarkerFor
           extend Relationship
 
           SHORT       = :prognosticBiomarkerFor
           LONG        = :prognosticBiomarkerFor
-          DESCRIPTION = ' +A prognosticBiomarkerFor P+ -  For term A and process term P, +A prognosticBiomarkerFor P+ indicates that changes in or detection of A is used in some way to be a prognostic biomarker for the subsequent development of pathology or biological process P.'.freeze
+          DESCRIPTION = ' +A prognosticBiomarkerFor P+ -  For term A
+          nd process term P, +A prognosticBiomarkerFor P+
+          ndicates that changes in or detection of A is used
+          n some way to be a prognostic biomarker for the
+          ubsequent development of pathology or biological
+          rocess P.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb

@@ -5,13 +5,27 @@ module BELParser
   module Language
     module Version2_0
       module Relationships
-        # RateLimitingStepOf:  +A rateLimitingStepOf B+ -  For process, activity, or transformation term A and process term B, +A rateLimitingStepOf B+ indicates +A subProcessOf B+ and +A -> B+. For example, the catalytic activity of HMG CoA reductase is a rate-limiting step for cholesterol biosynthesis: <pre> <code> cat(p(HGNC:HMGCR)) rateLimitingStepOf\ bp(GO:"cholesterol biosynthetic process") </code> </pre>
+        # RateLimitingStepOf:  +A rateLimitingStepOf B+ -  For process,
+        # activity, or transformation term A and process term B, +A
+        # rateLimitingStepOf B+ indicates +A subProcessOf B+ and +A ->
+        # B+. For example, the catalytic activity of HMG CoA reductase
+        # is a rate-limiting step for cholesterol biosynthesis: <pre>
+        # <code> cat(p(HGNC:HMGCR)) rateLimitingStepOf\ bp(GO:"cholesterol
+        # biosynthetic process") </code> </pre>
         class RateLimitingStepOf
           extend Relationship
 
           SHORT       = :rateLimitingStepOf
           LONG        = :rateLimitingStepOf
-          DESCRIPTION = ' +A rateLimitingStepOf B+ -  For process, activity, or transformation term A and process term B, +A rateLimitingStepOf B+ indicates +A subProcessOf B+ and +A -> B+. For example, the catalytic activity of HMG CoA reductase is a rate-limiting step for cholesterol biosynthesis: <pre> <code> cat(p(HGNC:HMGCR)) rateLimitingStepOf\ bp(GO:"cholesterol biosynthetic process") </code> </pre>'.freeze
+          DESCRIPTION = ' +A rateLimitingStepOf B+ -  For process,
+          ctivity, or transformation term A and process
+          erm B, +A rateLimitingStepOf B+ indicates
+          A subProcessOf B+ and +A -> B+. For example,
+          he catalytic activity of HMG CoA reductase is a
+          ate-limiting step for cholesterol biosynthesis:
+          pre> <code> cat(p(HGNC:HMGCR)) rateLimitingStepOf\
+          p(GO:"cholesterol biosynthetic process") </code>
+          /pre>'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb

@@ -5,13 +5,26 @@ module BELParser
   module Language
     module Version2_0
       module Relationships
-        # ReactantIn:  +A reactantIn reaction(reactants(A), products(B))+ -  This relationship links abundance terms from the +reactants(<list>)+ in a reaction to the reaction. This is a direct relationship because it is a _self_ relationship. Reactants are consumed directly by a reaction. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.
+        # ReactantIn:  +A reactantIn reaction(reactants(A),
+        # products(B))+ -  This relationship links abundance
+        # terms from the +reactants(<list>)+ in a reaction to the
+        # reaction. This is a direct relationship because it is a
+        # _self_ relationship. Reactants are consumed directly by a
+        # reaction. This relationship is introduced by the BEL Compiler
+        # and may not be used by statements in BEL documents.
         class ReactantIn
           extend Relationship
 
           SHORT       = :reactantIn
           LONG        = :reactantIn
-          DESCRIPTION = ' +A reactantIn reaction(reactants(A), products(B))+ -  This relationship links abundance terms from the +reactants(<list>)+ in a reaction to the reaction. This is a direct relationship because it is a _self_ relationship. Reactants are consumed directly by a reaction. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.'.freeze
+          DESCRIPTION = ' +A reactantIn reaction(reactants(A),
+          roducts(B))+ -  This relationship links abundance
+          erms from the +reactants(<list>)+ in a reaction
+          o the reaction. This is a direct relationship
+          ecause it is a _self_ relationship. Reactants are
+          onsumed directly by a reaction. This relationship
+          s introduced by the BEL Compiler and may not be
+          sed by statements in BEL documents.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/relationships/regulates.rb

@@ -5,13 +5,25 @@ module BELParser
   module Language
     module Version2_0
       module Relationships
-        # Regulates:  +A regulates B+ - For terms A and B, A regulates B or A reg B indicate that A is reported to have an effect on B, but information is missing about whether A increases B or A decreases B. This relationship provides more information than association, because the upstream entity (source term) and downstream entity (target term) can be assigned.
+        # Regulates:  +A regulates B+ - For terms A and B, A regulates
+        # B or A reg B indicate that A is reported to have an effect on
+        # B, but information is missing about whether A increases B or
+        # A decreases B. This relationship provides more information
+        # than association, because the upstream entity (source term)
+        # and downstream entity (target term) can be assigned.
         class Regulates
           extend Relationship
 
           SHORT       = :reg
           LONG        = :regulates
-          DESCRIPTION = '+A regulates B+ - For terms A and B, A regulates B or A reg B indicate that A is reported to have an effect on B, but information is missing about whether A increases B or A decreases B. This relationship provides more information than association, because the upstream entity (source term) and downstream entity (target term) can be assigned.'.freeze
+          DESCRIPTION = '+A regulates B+ - For terms A and B, A regulates
+           or A reg B indicate that A is reported to
+          ave an effect on B, but information is missing
+          bout whether A increases B or A decreases
+          . This relationship provides more information
+          han association, because the upstream entity
+          source term) and downstream entity (target term)
+          an be assigned.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb

@@ -5,13 +5,33 @@ module BELParser
   module Language
     module Version2_0
       module Relationships
-        # SubProcessOf:  +A subProcessOf B+ -  For process, activity, or transformation term A and process term B, +A subProcessOf B+ indicates that instances of process B, by default, include one or more instances of A in their composition. For example, the reduction of HMG-CoA to mevalonate is a subprocess of cholesterol biosynthesis: <pre> <code> rxn(reactants(a(CHEBI:"(S)-3-hydroxy-3-methylglutaryl-CoA"),\ a(CHEBI:NADPH), a(CHEBI:hydron)), products(a(CHEBI:Mevalonate),\ a(CHEBI:"CoA-SH"), a(CHEBI:"NADP+"))) subProcessOf bp(GO:"cholesterol\ biosynthetic process") </code> </pre>
+        # SubProcessOf:  +A subProcessOf B+ -  For process, activity, or
+        # transformation term A and process term B, +A subProcessOf B+
+        # indicates that instances of process B, by default, include
+        # one or more instances of A in their composition. For
+        # example, the reduction of HMG-CoA to mevalonate is
+        # a subprocess of cholesterol biosynthesis: <pre> <code>
+        # rxn(reactants(a(CHEBI:"(S)-3-hydroxy-3-methylglutaryl-CoA"),\
+        # a(CHEBI:NADPH), a(CHEBI:hydron)), products(a(CHEBI:Mevalonate),\
+        # a(CHEBI:"CoA-SH"), a(CHEBI:"NADP+"))) subProcessOf
+        # bp(GO:"cholesterol\ biosynthetic process") </code> </pre>
         class SubProcessOf
           extend Relationship
 
           SHORT       = :subProcessOf
           LONG        = :subProcessOf
-          DESCRIPTION = ' +A subProcessOf B+ -  For process, activity, or transformation term A and process term B, +A subProcessOf B+ indicates that instances of process B, by default, include one or more instances of A in their composition. For example, the reduction of HMG-CoA to mevalonate is a subprocess of cholesterol biosynthesis: <pre> <code> rxn(reactants(a(CHEBI:"(S)-3-hydroxy-3-methylglutaryl-CoA"),\ a(CHEBI:NADPH), a(CHEBI:hydron)), products(a(CHEBI:Mevalonate),\ a(CHEBI:"CoA-SH"), a(CHEBI:"NADP+"))) subProcessOf bp(GO:"cholesterol\ biosynthetic process") </code> </pre>'.freeze
+          DESCRIPTION = ' +A subProcessOf B+ -  For process, activity,
+          r transformation term A and process term B,
+          A subProcessOf B+ indicates that instances
+          f process B, by default, include one or more
+          nstances of A in their composition. For example,
+          he reduction of HMG-CoA to mevalonate is a
+          ubprocess of cholesterol biosynthesis: <pre> <code>
+          xn(reactants(a(CHEBI:"(S)-3-hydroxy-3-methylglutaryl-CoA"),\
+          (CHEBI:NADPH), a(CHEBI:hydron)),
+          roducts(a(CHEBI:Mevalonate),\ a(CHEBI:"CoA-SH"),
+          (CHEBI:"NADP+"))) subProcessOf bp(GO:"cholesterol\
+          iosynthetic process") </code> </pre>'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb

@@ -5,13 +5,23 @@ module BELParser
   module Language
     module Version2_0
       module Relationships
-        # TranscribedTo:  +G :> R+ -  For rnaAbundance term R and geneAbundance term G, +G transcribedTo R+ or +G :> R+ indicates that members of R are produced by the transcription of members of G. For example: +g(HGNC:AKT1) :> r(HGNC:AKT1)+ indicates that the human AKT1 RNA is transcribed from the human AKT1 gene.
+        # TranscribedTo:  +G :> R+ -  For rnaAbundance term R and
+        # geneAbundance term G, +G transcribedTo R+ or +G :> R+ indicates
+        # that members of R are produced by the transcription of members
+        # of G. For example: +g(HGNC:AKT1) :> r(HGNC:AKT1)+ indicates
+        # that the human AKT1 RNA is transcribed from the human AKT1 gene.
         class TranscribedTo
           extend Relationship
 
           SHORT       = :':>'
           LONG        = :transcribedTo
-          DESCRIPTION = ' +G :> R+ -  For rnaAbundance term R and geneAbundance term G, +G transcribedTo R+ or +G :> R+ indicates that members of R are produced by the transcription of members of G. For example: +g(HGNC:AKT1) :> r(HGNC:AKT1)+ indicates that the human AKT1 RNA is transcribed from the human AKT1 gene.'.freeze
+          DESCRIPTION = ' +G :> R+ -  For rnaAbundance term R and
+          eneAbundance term G, +G transcribedTo R+ or +G :>
+          + indicates that members of R are produced by
+          he transcription of members of G. For example:
+          g(HGNC:AKT1) :> r(HGNC:AKT1)+ indicates that
+          he human AKT1 RNA is transcribed from the human
+          KT1 gene.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/relationships/translated_to.rb

@@ -5,13 +5,24 @@ module BELParser
   module Language
     module Version2_0
       module Relationships
-        # TranslatedTo:  +R >> P+ -  For rnaAbundance term R and proteinAbundance term P, +R translatedTo P+ or +R >> P+ indicates that members of P are produced by the translation of members of R. For example: +r(HGNC:AKT1) >> p(HGNC:AKT1)+ indicates that AKT1 protein is produced by translation of AKT1 RNA.
+        # TranslatedTo:  +R >> P+ -  For rnaAbundance term R and
+        # proteinAbundance term P, +R translatedTo P+ or +R >> P+
+        # indicates that members of P are produced by the translation
+        # of members of R. For example: +r(HGNC:AKT1) >> p(HGNC:AKT1)+
+        # indicates that AKT1 protein is produced by translation of
+        # AKT1 RNA.
         class TranslatedTo
           extend Relationship
 
           SHORT       = :>>
           LONG        = :translatedTo
-          DESCRIPTION = ' +R >> P+ -  For rnaAbundance term R and proteinAbundance term P, +R translatedTo P+ or +R >> P+ indicates that members of P are produced by the translation of members of R. For example: +r(HGNC:AKT1) >> p(HGNC:AKT1)+ indicates that AKT1 protein is produced by translation of AKT1 RNA.'.freeze
+          DESCRIPTION = ' +R >> P+ -  For rnaAbundance term R and
+          roteinAbundance term P, +R translatedTo P+ or
+          R >> P+ indicates that members of P are produced
+          y the translation of members of R. For example:
+          r(HGNC:AKT1) >> p(HGNC:AKT1)+ indicates that
+          KT1 protein is produced by translation of AKT1
+          NA.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/relationships/translocates.rb

@@ -5,13 +5,27 @@ module BELParser
   module Language
     module Version2_0
       module Relationships
-        # Translocates:  +translocation(A, ns1:v1, ns2:v2) translocates A+ -  This relationship links the abundance term in a +translocation()+ to the translocation. This relationship is direct because it is a _self_ relationship. The translocated abundance is directly acted on by the translocation process. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.
+        # Translocates:  +translocation(A, ns1:v1, ns2:v2) translocates
+        # A+ -  This relationship links the abundance term in a
+        # +translocation()+ to the translocation. This relationship is
+        # direct because it is a _self_ relationship. The translocated
+        # abundance is directly acted on by the translocation
+        # process. This relationship is introduced by the BEL Compiler
+        # and may not be used by statements in BEL documents.
         class Translocates
           extend Relationship
 
           SHORT       = :translocates
           LONG        = :translocates
-          DESCRIPTION = ' +translocation(A, ns1:v1, ns2:v2) translocates A+ -  This relationship links the abundance term in a +translocation()+ to the translocation. This relationship is direct because it is a _self_ relationship. The translocated abundance is directly acted on by the translocation process. This relationship is introduced by the BEL Compiler and may not be used by statements in BEL documents.'.freeze
+          DESCRIPTION = ' +translocation(A, ns1:v1, ns2:v2) translocates
+          + -  This relationship links the abundance term
+          n a +translocation()+ to the translocation. This
+          elationship is direct because it is a _self_
+          elationship. The translocated abundance
+          s directly acted on by the translocation
+          rocess. This relationship is introduced by the
+          EL Compiler and may not be used by statements in
+          EL documents.'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language.rb

@@ -7,8 +7,20 @@ require_relative 'language/specification'
 require_relative 'language/expression_validator'
 
 module BELParser
+  # Language defines the concepts needed to define, represent, and
+  # validate a BEL specification. This includes:
+  #
+  # - {BELParser::Language::Specification BEL specifications}
+  #   - Functions
+  #   - ReturnTypes
+  #   - Signatures
+  #   - Relationships
+  #   - Encodings
+  #   - Syntax validations
+  #   - Semantic validations
+  # - Generic Syntax validations
+  # - Generic signature validation
   module Language
-
     # Mutex to synchronize creation of BEL specifications.
     LOCK = Mutex.new
     private_constant :LOCK
@@ -18,12 +30,10 @@ module BELParser
     # @param  [#to_s] version the BEL version string (e.g. +"2.0"+)
     # @return [Boolean] +true+ if +version+ is defined; +false+ if not
     def self.defines_version?(version)
-      begin
-        specification(version)
-        true
-      rescue ArgumentError, LoadError
-        false
-      end
+      specification(version)
+      true
+    rescue ArgumentError, LoadError
+      false
     end
 
     # Returns all version strings that are defined and supported by this
@@ -60,7 +70,7 @@ module BELParser
     def self.specification(version)
       version_string = version.to_s
       unless version_string =~ /^[0-9]+\.[0-9]+/
-        raise ArgumentError, "Version format incorrect; expecting MAJOR.MINOR"
+        raise ArgumentError, 'Version format incorrect; expecting MAJOR.MINOR'
       end
 
       LOCK.synchronize do

data/lib/bel_parser/parser.rb

@@ -27,6 +27,7 @@ module BELParser
       :annotation_definition,
       :namespace_definition,
       :set,
+      :document_property,
       :unset
     )