bel_parser 1.0.8-java → 1.1.1-java

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

@@ -19,17 +19,18 @@ module BELParser
 
           SHORT       = :hasComponents
           LONG        = :hasComponents
-          DESCRIPTION = ' +A hasComponents (B, C, D)+ -  The hasComponents
-          elationship is a special form which enables
-          he assignment of multiple complex components
-          n a single statement where the object of the
-          tatement is a set of abundance terms. A statement
-          sing hasComponents is exactly equivalent to
-          ultiple hasComponent statements. A term may not
-          ppear in both the subject and object of the same
-          asComponents statement. For the abundance terms A,
-          , C and D, +A hasComponents B, C, D+ indicates
-          hat A has components B, C and D.'.freeze
+
+          DESCRIPTION = <<-DOC
+HasComponents:  +A hasComponents (B, C, D)+ -  The hasComponents
+relationship is a special form which enables the assignment
+of multiple complex components in a single statement where
+the object of the statement is a set of abundance terms. A
+statement using hasComponents is exactly equivalent to multiple
+hasComponent statements. A term may not appear in both the
+subject and object of the same hasComponents statement. For
+the abundance terms A, B, C and D, +A hasComponents B, C, D+
+indicates that A has components B, C and D.
+          DOC
 
           def self.short
             SHORT

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

@@ -17,14 +17,15 @@ module BELParser
 
           SHORT       = :hasMember
           LONG        = :hasMember
-          DESCRIPTION = ' +A hasMember A1+ -  For term abundances A and B,
-          A hasMember B+ designates B as a member class of
-          . A member class is a distinguished sub-class. A is
-          efined as a group by all of the members assigned to
-          t. The member classes may or may not be overlapping
-          nd may or may not entirely cover all instances
-          f A. A term may not appear in both the subject
-          nd object of the same hasMember statement.'.freeze
+          DESCRIPTION = <<-DOC
+HasMember:  +A hasMember A1+ -  For term abundances A and B,
++A hasMember B+ designates B as a member class of A. A member
+class is a distinguished sub-class. A is defined as a group
+by all of the members assigned to it. The member classes may
+or may not be overlapping and may or may not entirely cover
+all instances of A. A term may not appear in both the subject
+and object of the same hasMember statement.
+          DOC
 
           def self.short
             SHORT

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

@@ -19,17 +19,18 @@ module BELParser
 
           SHORT       = :hasMembers
           LONG        = :hasMembers
-          DESCRIPTION = ' +A hasMembers (B, C, D)+ -  The hasMembers
-          elationship is a special form which enables the
-          ssignment of multiple member classes in a single
-          tatement where the object of the statement is a set
-          f abundance terms. A statement using hasMembers
-          s exactly equivalent to multiple hasMember
-          tatements. A term may not appear in both the
-          ubject and object of a of the same hasMembers
-          tatement. For the abundance terms A, B, C and D,
-          A hasMembers B, C, D+ indicates that A is defined
-          y its member abundance classes B, C and D.'.freeze
+
+          DESCRIPTION = <<-DOC
+HasMembers:  +A hasMembers (B, C, D)+ -  The hasMembers
+relationship is a special form which enables the assignment of
+multiple member classes in a single statement where the object
+of the statement is a set of abundance terms. A statement
+using hasMembers is exactly equivalent to multiple hasMember
+statements. A term may not appear in both the subject and
+object of a of the same hasMembers statement. For the abundance
+terms A, B, C and D, +A hasMembers B, C, D+ indicates that A
+is defined by its member abundance classes B, C and D.
+          DOC
 
           def self.short
             SHORT

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

@@ -16,13 +16,15 @@ module BELParser
 
           SHORT       = :hasModification
           LONG        = :hasModification
-          DESCRIPTION = ' +p(A) hasModification p(A, pmod(P, S, 473))+ -
-          his relationship links abundance terms modified by
-          he +pmod()+ function to the unmodified abundance
-          erm. This is a direct relationship because it
-          s a _self_ relationship. This relationship is
-          ntroduced by the BEL Compiler and may not be used
-          y statements in BEL documents.'.freeze
+
+          DESCRIPTION = <<-DOC
+HasModification:  +p(A) hasModification p(A, pmod(P, S, 473))+
+-  This relationship links abundance terms modified by the
++pmod()+ function to the unmodified abundance term. This is a
+direct relationship because it is a _self_ relationship. This
+relationship is introduced by the BEL Compiler and may not be
+used by statements in BEL documents.
+          DOC
 
           def self.short
             SHORT

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

@@ -17,14 +17,16 @@ module BELParser
 
           SHORT       = :hasProduct
           LONG        = :hasProduct
-          DESCRIPTION = ' +reaction(reactants(A), products(B)) hasProduct
-          + -  This relationship links abundance terms
-          rom the +products(<list>)+ in a reaction to the
-          eaction. This is a direct relationship because it
-          s a _self_ relationship. Products are produced
-          irectly by a reaction. This relationship is
-          ntroduced by the BEL Compiler and may not be used
-          y statements in BEL documents.'.freeze
+
+          DESCRIPTION = <<-DOC
+HasProduct:  +reaction(reactants(A), products(B))
+hasProduct B+ -  This relationship links abundance
+terms from the +products(<list>)+ in a reaction to the
+reaction. This is a direct relationship because it is a _self_
+relationship. Products are produced directly by a reaction. This
+relationship is introduced by the BEL Compiler and may not be
+used by statements in BEL documents.
+          DOC
 
           def self.short
             SHORT

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

@@ -16,13 +16,15 @@ module BELParser
 
           SHORT       = :hasVariant
           LONG        = :hasVariant
-          DESCRIPTION = ' +p(A) hasVariant p(A, sub(G, 12, V))+ -  This
-          elationship links abundance terms modified by the
-          substitution()+, +fusion()+, or +truncation()+
-          unctions to the unmodified abundance term. This
-          elationship is introduced by the BEL Compiler
-          nd does not need to be used by statements in
-          EL documents.'.freeze
+
+          DESCRIPTION = <<-DOC
+HasVariant:  +p(A) hasVariant p(A, sub(G, 12, V))+ -
+This relationship links abundance terms modified by the
++substitution()+, +fusion()+, or +truncation()+ functions to
+the unmodified abundance term. This relationship is introduced
+by the BEL Compiler and does not need to be used by statements
+in BEL documents.
+          DOC
 
           def self.short
             SHORT

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

@@ -18,16 +18,17 @@ module BELParser
 
           SHORT       = :includes
           LONG        = :includes
-          DESCRIPTION = ' +compositeAbundance(A,B) includes A+ -  This
-          elationship links each individual abundance
-          erm in a +compositeAbundance(<list>)+
-          o the compositeAbundance. For example,
-          compositeAbundance(A, B) includes A+ and
-          compositeAbundance(A, B) includes B+. This
-          elationship is direct because it is a _self_
-          elationship. This relationship is introduced by
-          he BEL Compiler and may not be used by statements
-          n BEL documents.'.freeze
+
+          DESCRIPTION = <<-DOC
+Includes:  +compositeAbundance(A,B) includes A+ -  This
+relationship links each individual abundance term in a
++compositeAbundance(<list>)+ to the compositeAbundance. For
+example, +compositeAbundance(A, B) includes A+ and
++compositeAbundance(A, B) includes B+. This relationship is
+direct because it is a _self_ relationship. This relationship
+is introduced by the BEL Compiler and may not be used by
+statements in BEL documents.
+          DOC
 
           def self.short
             SHORT

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

@@ -20,18 +20,19 @@ module BELParser
 
           SHORT       = :'->'
           LONG        = :increases
-          DESCRIPTION = ' +A -> B+ -  For terms A and B, +A increases B
-          r A -> B+ indicates that increases in A have been
-          bserved to cause increases in B. +A increases
-          + also represents cases where decreases in A
-          ave been observed to cause decreases in B, for
-          xample, in recording the results of gene deletion
-          r other inhibition experiments. A is a BEL Term
-          nd B is either a BEL Term or a BEL Statement. The
-          elationship does not indicate that the changes
-          n A are either necessary for changes in B, nor
-          oes it indicate that changes in A are sufficient
-          o cause changes in B.'.freeze
+
+          DESCRIPTION = <<-DOC
+Increases:  +A -> B+ -  For terms A and B, +A increases B or
+A -> B+ indicates that increases in A have been observed to
+cause increases in B. +A increases B+ also represents cases
+where decreases in A have been observed to cause decreases in B,
+for example, in recording the results of gene deletion or other
+inhibition experiments. A is a BEL Term and B is either a BEL
+Term or a BEL Statement. The relationship does not indicate
+that the changes in A are either necessary for changes in B,
+nor does it indicate that changes in A are sufficient to cause
+changes in B.
+          DOC
 
           def self.short
             SHORT

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

@@ -17,14 +17,16 @@ module BELParser
 
           SHORT       = :isA
           LONG        = :isA
-          DESCRIPTION = ' +A isA B+ -  For terms A and B, +A isA B+
-          ndicates that A is a subset of B. All terms in BEL
-          epresent classes, but given that classes implicitly
-          ave instances, one can also interpret +A isA B+ to
-          ean that any instance of A must also be an instance
-          f B. This relationship can be used to represent
-          O and MeSH hierarchies: +pathology(MESH:Psoriasis)
-          sA pathology(MESH:"Skin Diseases")+'.freeze
+
+          DESCRIPTION = <<-DOC
+IsA:  +A isA B+ -  For terms A and B, +A isA B+ indicates
+that A is a subset of B. All terms in BEL represent classes,
+but given that classes implicitly have instances, one can
+also interpret +A isA B+ to mean that any instance of A must
+also be an instance of B. This relationship can be used to
+represent GO and MeSH hierarchies: +pathology(MESH:Psoriasis)
+isA pathology(MESH:"Skin Diseases")+
+          DOC
 
           def self.short
             SHORT

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

@@ -16,13 +16,15 @@ module BELParser
 
           SHORT       = :negativeCorrelation
           LONG        = :negativeCorrelation
-          DESCRIPTION = ' +A negativeCorrelation B+ -  For terms A and B,
-          A negativeCorrelation B+ indicates that changes
-          n A and B have been observed to be negatively
-          orrelated. The order of the subject and object does
-          ot affect the interpretation of the statement,
-          hus B negativeCorrelation A is equivalent to A
-          egativeCorrelation B.'.freeze
+
+          DESCRIPTION = <<-DOC
+NegativeCorrelation:  +A negativeCorrelation B+ -  For terms
+A and B, +A negativeCorrelation B+ indicates that changes in A
+and B have been observed to be negatively correlated. The order
+of the subject and object does not affect the interpretation
+of the statement, thus B negativeCorrelation A is equivalent
+to A negativeCorrelation B.
+          DOC
 
           def self.short
             SHORT

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

@@ -17,14 +17,16 @@ module BELParser
 
           SHORT       = :orthologous
           LONG        = :orthologous
-          DESCRIPTION = ' +A orthologous B+ -  For geneAbundance terms
-           and B, +A orthologousTo B+ indicates that A
-          nd B represent abundances of genes in different
-          pecies which are sequence similar and which are
-          herefore presumed to share a common ancestral
-          ene. For example, +g(HGNC:AKT1) orthologousTo
-          (MGI:AKT1)+ indicates that the mouse and human
-          KT1 genes are orthologous.'.freeze
+
+          DESCRIPTION = <<-DOC
+Orthologous:  +A orthologous B+ -  For geneAbundance terms A
+and B, +A orthologousTo B+ indicates that A and B represent
+abundances of genes in different species which are sequence
+similar and which are therefore presumed to share a common
+ancestral gene. For example, +g(HGNC:AKT1) orthologousTo
+g(MGI:AKT1)+ indicates that the mouse and human AKT1 genes
+are orthologous.
+          DOC
 
           def self.short
             SHORT

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

@@ -14,11 +14,13 @@ module BELParser
 
           SHORT       = :positiveCorrelation
           LONG        = :positiveCorrelation
-          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
+
+          DESCRIPTION = <<-DOC
+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.
+          DOC
 
           def self.short
             SHORT

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

@@ -15,12 +15,14 @@ module BELParser
 
           SHORT       = :prognosticBiomarkerFor
           LONG        = :prognosticBiomarkerFor
-          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
+
+          DESCRIPTION = <<-DOC
+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.
+          DOC
 
           def self.short
             SHORT

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

@@ -17,15 +17,16 @@ module BELParser
 
           SHORT       = :rateLimitingStepOf
           LONG        = :rateLimitingStepOf
-          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
+
+          DESCRIPTION = <<-DOC
+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>
+          DOC
 
           def self.short
             SHORT

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

@@ -17,14 +17,16 @@ module BELParser
 
           SHORT       = :reactantIn
           LONG        = :reactantIn
-          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
+
+          DESCRIPTION = <<-DOC
+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.
+          DOC
 
           def self.short
             SHORT

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

@@ -16,14 +16,15 @@ module BELParser
 
           SHORT       = :reg
           LONG        = :regulates
-          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
+
+          DESCRIPTION = <<-DOC
+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.
+          DOC
 
           def self.short
             SHORT

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

@@ -20,18 +20,19 @@ module BELParser
 
           SHORT       = :subProcessOf
           LONG        = :subProcessOf
-          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
+
+          DESCRIPTION = <<-DOC
+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>
+          DOC
 
           def self.short
             SHORT

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

@@ -15,13 +15,14 @@ module BELParser
 
           SHORT       = :':>'
           LONG        = :transcribedTo
-          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
+
+          DESCRIPTION = <<-DOC
+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.
+          DOC
 
           def self.short
             SHORT

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

@@ -16,13 +16,15 @@ module BELParser
 
           SHORT       = :>>
           LONG        = :translatedTo
-          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
+
+          DESCRIPTION = <<-DOC
+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.
+          DOC
 
           def self.short
             SHORT

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

@@ -17,15 +17,16 @@ module BELParser
 
           SHORT       = :translocates
           LONG        = :translocates
-          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
+
+          DESCRIPTION = <<-DOC
+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.
+          DOC
 
           def self.short
             SHORT

data/lib/bel_parser/mixin/levenshtein.rb

@@ -0,0 +1,20 @@
+module BELParser
+  # Adds a levenshtein implementation based on which ruby engine is used.
+  module Levenshtein
+
+    unless self.methods.include?(:distance)
+
+      if RUBY_ENGINE =~ /^jruby/i
+        require 'levenshtein'
+        define_singleton_method(:distance) do |string1, string2|
+          ::Levenshtein.distance(string1, string2)
+        end
+      else
+        require "damerau-levenshtein"
+        define_singleton_method(:distance) do |string1, string2|
+          ::DamerauLevenshtein.distance(string1, string2)
+        end
+      end
+    end
+  end
+end