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

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

@@ -5,13 +5,24 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class CausesNoChange
           extend Relationship
 
           SHORT       = :causesNoChange
           LONG        = :causesNoChange
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,33 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class Decreases
           extend Relationship
 
           SHORT       = :'-|'
           LONG        = :decreases
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,22 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class DirectlyDecreases
           extend Relationship
 
           SHORT       = :'=|'
           LONG        = :directlyDecreases
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,22 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class DirectlyIncreases
           extend Relationship
 
           SHORT       = :'=>'
           LONG        = :directlyIncreases
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,36 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class HasComponent
           extend Relationship
 
           SHORT       = :hasComponent
           LONG        = :hasComponent
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,31 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class HasComponents
           extend Relationship
 
           SHORT       = :hasComponents
           LONG        = :hasComponents
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,26 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class HasMember
           extend Relationship
 
           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. 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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,31 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class HasMembers
           extend Relationship
 
           SHORT       = :hasMembers
           LONG        = :hasMembers
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,24 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class HasModification
           extend Relationship
 
           SHORT       = :hasModification
           LONG        = :hasModification
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,26 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class HasProduct
           extend Relationship
 
           SHORT       = :hasProduct
           LONG        = :hasProduct
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,24 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class HasVariant
           extend Relationship
 
           SHORT       = :hasVariant
           LONG        = :hasVariant
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,29 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class Includes
           extend Relationship
 
           SHORT       = :includes
           LONG        = :includes
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,33 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class Increases
           extend Relationship
 
           SHORT       = :'->'
           LONG        = :increases
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,26 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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")+
+        # 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")+
         class IsA
           extend Relationship
 
           SHORT       = :isA
           LONG        = :isA
-          DESCRIPTION = ' +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")+'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,24 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class NegativeCorrelation
           extend Relationship
 
           SHORT       = :negativeCorrelation
           LONG        = :negativeCorrelation
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,26 @@ module BELParser
   module Language
     module Version1_0
       module Relationships
-        # 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.
+        # 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.
         class Orthologous
           extend Relationship
 
           SHORT       = :orthologous
           LONG        = :orthologous
-          DESCRIPTION = ' +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.'.freeze
+          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
 
           def self.short
             SHORT

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

@@ -5,13 +5,20 @@ module BELParser
   module Language
     module Version1_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/version1_0/relationships/prognostic_biomarker_for.rb

@@ -5,13 +5,22 @@ module BELParser
   module Language
     module Version1_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/version1_0/relationships/rate_limiting_step_of.rb

@@ -5,13 +5,27 @@ module BELParser
   module Language
     module Version1_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/version1_0/relationships/reactant_in.rb

@@ -5,13 +5,26 @@ module BELParser
   module Language
     module Version1_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