bel_parser 1.0.8-java → 1.1.1-java

data/lib/bel_parser/language/version1_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/version1_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/version1_0/relationships/increases.rb

@@ -20,19 +20,18 @@ 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
           end

data/lib/bel_parser/language/version1_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/version1_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/version1_0/relationships/orthologous.rb

@@ -17,15 +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
           end

data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb

@@ -14,11 +14,14 @@ 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/version1_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/version1_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/version1_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/version1_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/version1_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/version1_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/version1_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/language/version2_0/functions/protein_modification.rb

@@ -17,8 +17,7 @@ module BELParser
           LONG        = :proteinModification
           RETURN_TYPE = Version2_0::ReturnTypes::ProteinModification
           E_ENC       = Version2_0::ValueEncodings::ProteinModification
-          DESCRIPTION = 'Denotes a covalently modified protein
-          abundance'.freeze
+          DESCRIPTION = 'Denotes a covalently modified protein abundance'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/translocation.rb

@@ -15,8 +15,7 @@ module BELParser
           SHORT       = :tloc
           LONG        = :translocation
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Abundance
-          DESCRIPTION = 'Denotes the frequency or abundance of events
-          in which members move between locations'.freeze
+          DESCRIPTION = 'Denotes the frequency or abundance of events in which members move between locations'.freeze
 
           def self.short
             SHORT

data/lib/bel_parser/language/version2_0/functions/variant.rb

@@ -14,8 +14,7 @@ module BELParser
           SHORT       = :var
           LONG        = :variant
           RETURN_TYPE = BELParser::Language::Version2_0::ReturnTypes::Variant
-          DESCRIPTION = 'Denotes a sequence variant of the specified
-          abundance.'.freeze
+          DESCRIPTION = 'Denotes a sequence variant of the specified abundance.'.freeze
 
           def self.short
             SHORT

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

@@ -17,15 +17,16 @@ module BELParser
 
           SHORT       = :actsIn
           LONG        = :actsIn
-          DESCRIPTION = ' +A actsIn f(A)+ -  This relationship links an
-          bundance term to the activity term for the same
-          bundance. This relationship is direct because
-          t is a _self_ relationship, the abundance acts
-          n its own activity. For protein abundance p(A)
-          nd its molecular activity kin(p(A), +p(A) actsIn
-          in(p(A))+. This relationship is introduced by the
-          EL Compiler and may not be used by statements in
-          EL documents.'.freeze
+
+          DESCRIPTION = <<-DOC
+ActsIn:  +A actsIn f(A)+ -  This relationship links
+an abundance term to the activity term for the same
+abundance. This relationship is direct because it is a _self_
+relationship, the abundance acts in its own activity. For
+protein abundance p(A) and its molecular activity kin(p(A),
++p(A) actsIn kin(p(A))+. 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/biomarker_for.rb

@@ -14,11 +14,13 @@ module BELParser
 
           SHORT       = :biomarkerFor
           LONG        = :biomarkerFor
-          DESCRIPTION = ' +A biomarkerFor P+ -  For term A and process
-          erm P, +A biomarkerFor P+ indicates that changes
-          n or detection of A is used in some way to be
-           biomarker for pathology or biological process
-          .'.freeze
+
+          DESCRIPTION = <<-DOC
+BiomarkerFor:  +A biomarkerFor P+ -  For term A and process term
+P, +A biomarkerFor P+ indicates that changes in or detection
+of A is used in some way to be a biomarker for pathology or
+biological process P.
+          DOC
 
           def self.short
             SHORT

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

@@ -16,13 +16,15 @@ module BELParser
 
           SHORT       = :causesNoChange
           LONG        = :causesNoChange
-          DESCRIPTION = ' +A causesNoChange B+ -  For terms A and B, +A
-          ausesNoChange B+ indicates that B was observed not
-          o change in response to changes in A. Statements
-          sing this relationship correspond to cases where
-          xplicit measurement of B demonstrates lack of
-          ignificant change, not for cases where the state
-          f B is unknown.'.freeze
+
+          DESCRIPTION = <<-DOC
+CausesNoChange:  +A causesNoChange B+ -  For terms A and B,
++A causesNoChange B+ indicates that B was observed not to
+change in response to changes in A. Statements using this
+relationship correspond to cases where explicit measurement
+of B demonstrates lack of significant change, not for cases
+where the state of B is unknown.
+          DOC
 
           def self.short
             SHORT

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

@@ -20,18 +20,19 @@ module BELParser
 
           SHORT       = :'-|'
           LONG        = :decreases
-          DESCRIPTION = ' +A -| B+ -  For terms A and B, +A decreases B
-          r A -| B+ indicates that increases in A have been
-          bserved to cause decreases in B. +A decreases
-          + also represents cases where decreases in A
-          ave been observed to cause increases 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
+Decreases:  +A -| B+ -  For terms A and B, +A decreases B or
+A -| B+ indicates that increases in A have been observed to
+cause decreases in B. +A decreases B+ also represents cases
+where decreases in A have been observed to cause increases 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/directly_decreases.rb

@@ -15,12 +15,14 @@ module BELParser
 
           SHORT       = :'=|'
           LONG        = :directlyDecreases
-          DESCRIPTION = ' +A =| B+ -  For terms A and B,
-          A directlyDecreases B or A =| B+ indicates A
-          ecreases B and that the mechanism of the causal
-          elationship is based on physical interaction
-          f entities related to A and B. This is a direct
-          ersion of the decreases relationship.'.freeze
+
+          DESCRIPTION = <<-DOC
+DirectlyDecreases:  +A =| B+ -  For terms A and B, +A
+directlyDecreases B or A =| B+ indicates A decreases B and that
+the mechanism of the causal relationship is based on physical
+interaction of entities related to A and B. This is a direct
+version of the decreases relationship.
+          DOC
 
           def self.short
             SHORT

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

@@ -15,12 +15,14 @@ module BELParser
 
           SHORT       = :'=>'
           LONG        = :directlyIncreases
-          DESCRIPTION = ' +A => B+ -  For terms A and B,
-          A directlyIncreases B or A => B+ indicate A
-          ncreases B and that the mechanism of the causal
-          elationship is based on physical interaction
-          f entities related to A and B. This is a direct
-          ersion of the increases relationship.'.freeze
+
+          DESCRIPTION = <<-DOC
+DirectlyIncreases:  +A => B+ -  For terms A and B, +A
+directlyIncreases B or A => B+ indicate A increases B and that
+the mechanism of the causal relationship is based on physical
+interaction of entities related to A and B. This is a direct
+version of the increases relationship.
+          DOC
 
           def self.short
             SHORT

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

@@ -21,20 +21,21 @@ module BELParser
 
           SHORT       = :hasComponent
           LONG        = :hasComponent
-          DESCRIPTION = ' +A hasComponent A1+ -  For complexAbundance
-          erm A and abundance term B, +A hasComponent B+
-          esignates B as a component of A, that complexes
-          hat are instances of A have instances of B as
-          ossible components. Note that, the stoichiometry
-          f A is not described, nor is it stated that B
-          s a required component. The use of hasComponent
-          elationships is complementary to the use of
-          unctionally composed complexes and is intended to
-          nable the assignment of components to complexes
-          esignated by names in external vocabularies. The
-          ssignment of components can potentially enable
-          he reconciliation of equivalent complexes at
-          nowledge assembly time.'.freeze
+
+          DESCRIPTION = <<-DOC
+HasComponent:  +A hasComponent A1+ -  For complexAbundance
+term A and abundance term B, +A hasComponent B+ designates
+B as a component of A, that complexes that are instances of
+A have instances of B as possible components. Note that, the
+stoichiometry of A is not described, nor is it stated that B is
+a required component. The use of hasComponent relationships is
+complementary to the use of functionally composed complexes and
+is intended to enable the assignment of components to complexes
+designated by names in external vocabularies. The assignment
+of components can potentially enable the reconciliation of
+equivalent complexes at knowledge assembly time.
+          DOC
+          
 
           def self.short
             SHORT