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

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Files changed (153) hide show
  1. checksums.yaml +4 -4
  2. data/.gemspec +1 -1
  3. data/VERSION +1 -1
  4. data/bin/bel2_validator +7 -4
  5. data/lib/bel_parser/ast_filter.rb +2 -2
  6. data/lib/bel_parser/ast_generator.rb +11 -18
  7. data/lib/bel_parser/language/expression_validator.rb +8 -0
  8. data/lib/bel_parser/language/quoting.rb +19 -22
  9. data/lib/bel_parser/language/semantics/deeply_nested_statement.rb +65 -0
  10. data/lib/bel_parser/language/semantics/function_deprecation.rb +36 -0
  11. data/lib/bel_parser/language/semantics/list_function_subject.rb +45 -0
  12. data/lib/bel_parser/language/semantics/relationship_deprecation.rb +36 -0
  13. data/lib/bel_parser/language/semantics/signature_mapping.rb +30 -16
  14. data/lib/bel_parser/language/semantics.rb +7 -2
  15. data/lib/bel_parser/language/semantics_ast.rb +22 -12
  16. data/lib/bel_parser/language/semantics_function.rb +4 -1
  17. data/lib/bel_parser/language/semantics_result.rb +1 -0
  18. data/lib/bel_parser/language/semantics_warning.rb +2 -0
  19. data/lib/bel_parser/language/signature.rb +3 -3
  20. data/lib/bel_parser/language/syntax/invalid_function.rb +2 -2
  21. data/lib/bel_parser/language/syntax/invalid_relationship.rb +2 -2
  22. data/lib/bel_parser/language/syntax/undefined_namespace.rb +0 -1
  23. data/lib/bel_parser/language/syntax.rb +7 -2
  24. data/lib/bel_parser/language/syntax_error.rb +2 -0
  25. data/lib/bel_parser/language/syntax_function.rb +4 -1
  26. data/lib/bel_parser/language/syntax_result.rb +1 -0
  27. data/lib/bel_parser/language/syntax_warning.rb +2 -0
  28. data/lib/bel_parser/language/version1_0/functions/abundance.rb +14 -15
  29. data/lib/bel_parser/language/version1_0/functions/biological_process.rb +14 -15
  30. data/lib/bel_parser/language/version1_0/functions/catalytic_activity.rb +25 -21
  31. data/lib/bel_parser/language/version1_0/functions/cell_secretion.rb +15 -12
  32. data/lib/bel_parser/language/version1_0/functions/cell_surface_expression.rb +15 -12
  33. data/lib/bel_parser/language/version1_0/functions/chaperone_activity.rb +25 -21
  34. data/lib/bel_parser/language/version1_0/functions/complex_abundance.rb +26 -25
  35. data/lib/bel_parser/language/version1_0/functions/composite_abundance.rb +13 -12
  36. data/lib/bel_parser/language/version1_0/functions/degradation.rb +15 -12
  37. data/lib/bel_parser/language/version1_0/functions/fusion.rb +135 -129
  38. data/lib/bel_parser/language/version1_0/functions/gene_abundance.rb +34 -34
  39. data/lib/bel_parser/language/version1_0/functions/gtp_bound_activity.rb +24 -21
  40. data/lib/bel_parser/language/version1_0/functions/kinase_activity.rb +25 -21
  41. data/lib/bel_parser/language/version1_0/functions/list.rb +24 -24
  42. data/lib/bel_parser/language/version1_0/functions/micro_rna_abundance.rb +18 -17
  43. data/lib/bel_parser/language/version1_0/functions/molecular_activity.rb +14 -12
  44. data/lib/bel_parser/language/version1_0/functions/pathology.rb +14 -15
  45. data/lib/bel_parser/language/version1_0/functions/peptidase_activity.rb +23 -21
  46. data/lib/bel_parser/language/version1_0/functions/phosphatase_activity.rb +23 -21
  47. data/lib/bel_parser/language/version1_0/functions/products.rb +9 -10
  48. data/lib/bel_parser/language/version1_0/functions/protein_abundance.rb +94 -91
  49. data/lib/bel_parser/language/version1_0/functions/protein_modification.rb +60 -57
  50. data/lib/bel_parser/language/version1_0/functions/reactants.rb +9 -10
  51. data/lib/bel_parser/language/version1_0/functions/reaction.rb +18 -17
  52. data/lib/bel_parser/language/version1_0/functions/ribosylation_activity.rb +25 -21
  53. data/lib/bel_parser/language/version1_0/functions/rna_abundance.rb +34 -34
  54. data/lib/bel_parser/language/version1_0/functions/substitution.rb +29 -28
  55. data/lib/bel_parser/language/version1_0/functions/transcriptional_activity.rb +25 -21
  56. data/lib/bel_parser/language/version1_0/functions/translocation.rb +33 -32
  57. data/lib/bel_parser/language/version1_0/functions/transport_activity.rb +26 -21
  58. data/lib/bel_parser/language/version1_0/functions/truncation.rb +15 -14
  59. data/lib/bel_parser/language/version1_0/relationships/acts_in.rb +16 -2
  60. data/lib/bel_parser/language/version1_0/relationships/analogous.rb +8 -2
  61. data/lib/bel_parser/language/version1_0/relationships/association.rb +13 -2
  62. data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb +9 -2
  63. data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb +13 -2
  64. data/lib/bel_parser/language/version1_0/relationships/decreases.rb +22 -2
  65. data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb +11 -2
  66. data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb +11 -2
  67. data/lib/bel_parser/language/version1_0/relationships/has_component.rb +25 -2
  68. data/lib/bel_parser/language/version1_0/relationships/has_components.rb +20 -2
  69. data/lib/bel_parser/language/version1_0/relationships/has_member.rb +15 -2
  70. data/lib/bel_parser/language/version1_0/relationships/has_members.rb +20 -2
  71. data/lib/bel_parser/language/version1_0/relationships/has_modification.rb +13 -2
  72. data/lib/bel_parser/language/version1_0/relationships/has_product.rb +15 -2
  73. data/lib/bel_parser/language/version1_0/relationships/has_variant.rb +13 -2
  74. data/lib/bel_parser/language/version1_0/relationships/includes.rb +18 -2
  75. data/lib/bel_parser/language/version1_0/relationships/increases.rb +22 -2
  76. data/lib/bel_parser/language/version1_0/relationships/is_a.rb +15 -2
  77. data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb +13 -2
  78. data/lib/bel_parser/language/version1_0/relationships/orthologous.rb +15 -2
  79. data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb +9 -2
  80. data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb +11 -2
  81. data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb +16 -2
  82. data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb +15 -2
  83. data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb +22 -2
  84. data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb +12 -2
  85. data/lib/bel_parser/language/version1_0/relationships/translated_to.rb +13 -2
  86. data/lib/bel_parser/language/version1_0/relationships/translocates.rb +16 -2
  87. data/lib/bel_parser/language/version1_0/syntax/function.rb +0 -1
  88. data/lib/bel_parser/language/version1_0.rb +13 -2
  89. data/lib/bel_parser/language/version2_0/functions/abundance.rb +54 -53
  90. data/lib/bel_parser/language/version2_0/functions/activity.rb +8 -5
  91. data/lib/bel_parser/language/version2_0/functions/biological_process.rb +16 -16
  92. data/lib/bel_parser/language/version2_0/functions/cell_secretion.rb +15 -12
  93. data/lib/bel_parser/language/version2_0/functions/cell_surface_expression.rb +15 -12
  94. data/lib/bel_parser/language/version2_0/functions/complex_abundance.rb +61 -58
  95. data/lib/bel_parser/language/version2_0/functions/composite_abundance.rb +13 -12
  96. data/lib/bel_parser/language/version2_0/functions/degradation.rb +15 -12
  97. data/lib/bel_parser/language/version2_0/functions/fragment.rb +8 -6
  98. data/lib/bel_parser/language/version2_0/functions/from_location.rb +18 -17
  99. data/lib/bel_parser/language/version2_0/functions/fusion.rb +120 -117
  100. data/lib/bel_parser/language/version2_0/functions/gene_abundance.rb +64 -62
  101. data/lib/bel_parser/language/version2_0/functions/list.rb +24 -24
  102. data/lib/bel_parser/language/version2_0/functions/location.rb +14 -15
  103. data/lib/bel_parser/language/version2_0/functions/micro_rna_abundance.rb +58 -55
  104. data/lib/bel_parser/language/version2_0/functions/molecular_activity.rb +16 -14
  105. data/lib/bel_parser/language/version2_0/functions/pathology.rb +14 -15
  106. data/lib/bel_parser/language/version2_0/functions/products.rb +9 -10
  107. data/lib/bel_parser/language/version2_0/functions/protein_abundance.rb +96 -92
  108. data/lib/bel_parser/language/version2_0/functions/protein_modification.rb +57 -54
  109. data/lib/bel_parser/language/version2_0/functions/reactants.rb +9 -10
  110. data/lib/bel_parser/language/version2_0/functions/reaction.rb +18 -17
  111. data/lib/bel_parser/language/version2_0/functions/rna_abundance.rb +64 -62
  112. data/lib/bel_parser/language/version2_0/functions/to_location.rb +16 -16
  113. data/lib/bel_parser/language/version2_0/functions/translocation.rb +23 -22
  114. data/lib/bel_parser/language/version2_0/functions/variant.rb +13 -13
  115. data/lib/bel_parser/language/version2_0/relationships/acts_in.rb +16 -2
  116. data/lib/bel_parser/language/version2_0/relationships/analogous.rb +8 -2
  117. data/lib/bel_parser/language/version2_0/relationships/association.rb +13 -2
  118. data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb +9 -2
  119. data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb +13 -2
  120. data/lib/bel_parser/language/version2_0/relationships/decreases.rb +22 -2
  121. data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb +11 -2
  122. data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb +11 -2
  123. data/lib/bel_parser/language/version2_0/relationships/has_component.rb +25 -2
  124. data/lib/bel_parser/language/version2_0/relationships/has_components.rb +20 -2
  125. data/lib/bel_parser/language/version2_0/relationships/has_member.rb +15 -2
  126. data/lib/bel_parser/language/version2_0/relationships/has_members.rb +20 -2
  127. data/lib/bel_parser/language/version2_0/relationships/has_modification.rb +13 -2
  128. data/lib/bel_parser/language/version2_0/relationships/has_product.rb +15 -2
  129. data/lib/bel_parser/language/version2_0/relationships/has_variant.rb +13 -2
  130. data/lib/bel_parser/language/version2_0/relationships/includes.rb +18 -2
  131. data/lib/bel_parser/language/version2_0/relationships/increases.rb +22 -2
  132. data/lib/bel_parser/language/version2_0/relationships/is_a.rb +15 -2
  133. data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb +13 -2
  134. data/lib/bel_parser/language/version2_0/relationships/orthologous.rb +15 -2
  135. data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb +9 -2
  136. data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb +11 -2
  137. data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb +16 -2
  138. data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb +15 -2
  139. data/lib/bel_parser/language/version2_0/relationships/regulates.rb +14 -2
  140. data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb +22 -2
  141. data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb +12 -2
  142. data/lib/bel_parser/language/version2_0/relationships/translated_to.rb +13 -2
  143. data/lib/bel_parser/language/version2_0/relationships/translocates.rb +16 -2
  144. data/lib/bel_parser/language.rb +18 -8
  145. data/lib/bel_parser/parser.rb +1 -0
  146. data/lib/bel_parser/parsers/ast/node.rb +112 -74
  147. data/lib/bel_parser/parsers/bel_script/set.rl +1 -1
  148. data/lib/bel_parser/parsers/bel_script/set_document.rb +7087 -0
  149. data/lib/bel_parser/parsers/bel_script/set_document.rl +97 -0
  150. data/lib/bel_parser/parsers/bel_script.rb +1 -0
  151. data/lib/bel_parser/parsers/common/common.rl +1 -1
  152. data/lib/bel_parser/script/parser.rb +1 -0
  153. metadata +8 -2
@@ -5,13 +5,27 @@ module BELParser
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  module Language
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  module Version2_0
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  module Relationships
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- # 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.
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+ # ActsIn: +A actsIn f(A)+ - This relationship links
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+ # an abundance term to the activity term for the same
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+ # abundance. This relationship is direct because it is a _self_
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+ # relationship, the abundance acts in its own activity. For
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+ # protein abundance p(A) and its molecular activity kin(p(A),
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+ # +p(A) actsIn kin(p(A))+. This relationship is introduced by the
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+ # BEL Compiler and may not be used by statements in BEL documents.
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  class ActsIn
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  extend Relationship
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  SHORT = :actsIn
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  LONG = :actsIn
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- DESCRIPTION = ' +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.'.freeze
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+ DESCRIPTION = ' +A actsIn f(A)+ - This relationship links an
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+ bundance term to the activity term for the same
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+ bundance. This relationship is direct because
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+ t is a _self_ relationship, the abundance acts
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+ n its own activity. For protein abundance p(A)
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+ nd its molecular activity kin(p(A), +p(A) actsIn
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+ in(p(A))+. This relationship is introduced by the
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+ EL Compiler and may not be used by statements in
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+ EL documents.'.freeze
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  def self.short
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  SHORT
@@ -5,13 +5,19 @@ module BELParser
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  module Language
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  module Version2_0
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  module Relationships
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- # Analogous: +A analogous B+ - For terms A and B, +A analogousTo B+ indicates that A and B represent abundances or molecular activities in different species which function in a similar manner.
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+ # Analogous: +A analogous B+ - For terms A and B, +A analogousTo
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+ # B+ indicates that A and B represent abundances or molecular
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+ # activities in different species which function in a similar
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+ # manner.
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  class Analogous
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  extend Relationship
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  SHORT = :analogous
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  LONG = :analogous
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- DESCRIPTION = ' +A analogous B+ - For terms A and B, +A analogousTo B+ indicates that A and B represent abundances or molecular activities in different species which function in a similar manner.'.freeze
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+ DESCRIPTION = ' +A analogous B+ - For terms A and B, +A
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+ nalogousTo B+ indicates that A and B represent
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+ bundances or molecular activities in different
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+ pecies which function in a similar manner.'.freeze
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  def self.short
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  SHORT
@@ -5,13 +5,24 @@ module BELParser
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  module Language
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  module Version2_0
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  module Relationships
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- # Association: +A -- B+ - For terms A and B, +A association B+ or +A -- B+ indicates that A and B are associated in an unspecified manner. This relationship is used when not enough information about the association is available to describe it using more specific relationships, like increases or positiveCorrelation.
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+ # Association: +A -- B+ - For terms A and B, +A association
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+ # B+ or +A -- B+ indicates that A and B are associated in an
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+ # unspecified manner. This relationship is used when not enough
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+ # information about the association is available to describe
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+ # it using more specific relationships, like increases or
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+ # positiveCorrelation.
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  class Association
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  extend Relationship
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  SHORT = :'--'
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  LONG = :association
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- DESCRIPTION = ' +A -- B+ - For terms A and B, +A association B+ or +A -- B+ indicates that A and B are associated in an unspecified manner. This relationship is used when not enough information about the association is available to describe it using more specific relationships, like increases or positiveCorrelation.'.freeze
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+ DESCRIPTION = ' +A -- B+ - For terms A and B, +A association B+
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+ r +A -- B+ indicates that A and B are associated
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+ n an unspecified manner. This relationship
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+ s used when not enough information about the
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+ ssociation is available to describe it using
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+ ore specific relationships, like increases or
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+ ositiveCorrelation.'.freeze
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  def self.short
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  SHORT
@@ -5,13 +5,20 @@ module BELParser
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  module Language
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  module Version2_0
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  module Relationships
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- # 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.
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+ # BiomarkerFor: +A biomarkerFor P+ - For term A and process term
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+ # P, +A biomarkerFor P+ indicates that changes in or detection
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+ # of A is used in some way to be a biomarker for pathology or
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+ # biological process P.
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  class BiomarkerFor
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  extend Relationship
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  SHORT = :biomarkerFor
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  LONG = :biomarkerFor
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- DESCRIPTION = ' +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.'.freeze
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+ DESCRIPTION = ' +A biomarkerFor P+ - For term A and process
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+ erm P, +A biomarkerFor P+ indicates that changes
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+ n or detection of A is used in some way to be
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+ biomarker for pathology or biological process
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+ .'.freeze
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  def self.short
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  SHORT
@@ -5,13 +5,24 @@ module BELParser
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  module Language
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  module Version2_0
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  module Relationships
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- # 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.
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+ # CausesNoChange: +A causesNoChange B+ - For terms A and B,
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+ # +A causesNoChange B+ indicates that B was observed not to
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+ # change in response to changes in A. Statements using this
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+ # relationship correspond to cases where explicit measurement
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+ # of B demonstrates lack of significant change, not for cases
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+ # where the state of B is unknown.
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  class CausesNoChange
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  extend Relationship
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  SHORT = :causesNoChange
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  LONG = :causesNoChange
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- 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
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+ DESCRIPTION = ' +A causesNoChange B+ - For terms A and B, +A
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+ ausesNoChange B+ indicates that B was observed not
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+ o change in response to changes in A. Statements
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+ sing this relationship correspond to cases where
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+ xplicit measurement of B demonstrates lack of
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+ ignificant change, not for cases where the state
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+ f B is unknown.'.freeze
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  def self.short
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  SHORT
@@ -5,13 +5,33 @@ module BELParser
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  module Language
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  module Version2_0
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  module Relationships
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- # 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.
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+ # Decreases: +A -| B+ - For terms A and B, +A decreases B or
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+ # A -| B+ indicates that increases in A have been observed to
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+ # cause decreases in B. +A decreases B+ also represents cases
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+ # where decreases in A have been observed to cause increases in B,
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+ # for example, in recording the results of gene deletion or other
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+ # inhibition experiments. A is a BEL Term and B is either a BEL
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+ # Term or a BEL Statement. The relationship does not indicate
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+ # that the changes in A are either necessary for changes in B,
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+ # nor does it indicate that changes in A are sufficient to cause
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+ # changes in B.
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  class Decreases
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  extend Relationship
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  SHORT = :'-|'
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  LONG = :decreases
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- 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
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+ DESCRIPTION = ' +A -| B+ - For terms A and B, +A decreases B
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+ r A -| B+ indicates that increases in A have been
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+ bserved to cause decreases in B. +A decreases
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+ + also represents cases where decreases in A
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+ ave been observed to cause increases in B, for
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+ xample, in recording the results of gene deletion
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+ r other inhibition experiments. A is a BEL Term
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+ nd B is either a BEL Term or a BEL Statement. The
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+ elationship does not indicate that the changes
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+ n A are either necessary for changes in B, nor
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+ oes it indicate that changes in A are sufficient
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+ o cause changes in B.'.freeze
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  def self.short
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  SHORT
@@ -5,13 +5,22 @@ module BELParser
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  module Language
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  module Version2_0
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  module Relationships
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- # 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.
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+ # DirectlyDecreases: +A =| B+ - For terms A and B, +A
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+ # directlyDecreases B or A =| B+ indicates A decreases B and that
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+ # the mechanism of the causal relationship is based on physical
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+ # interaction of entities related to A and B. This is a direct
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+ # version of the decreases relationship.
9
13
  class DirectlyDecreases
10
14
  extend Relationship
11
15
 
12
16
  SHORT = :'=|'
13
17
  LONG = :directlyDecreases
14
- 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
18
+ DESCRIPTION = ' +A =| B+ - For terms A and B,
19
+ A directlyDecreases B or A =| B+ indicates A
20
+ ecreases B and that the mechanism of the causal
21
+ elationship is based on physical interaction
22
+ f entities related to A and B. This is a direct
23
+ ersion of the decreases relationship.'.freeze
15
24
 
16
25
  def self.short
17
26
  SHORT
@@ -5,13 +5,22 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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.
8
+ # DirectlyIncreases: +A => B+ - For terms A and B, +A
9
+ # directlyIncreases B or A => B+ indicate A increases B and that
10
+ # the mechanism of the causal relationship is based on physical
11
+ # interaction of entities related to A and B. This is a direct
12
+ # version of the increases relationship.
9
13
  class DirectlyIncreases
10
14
  extend Relationship
11
15
 
12
16
  SHORT = :'=>'
13
17
  LONG = :directlyIncreases
14
- 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
18
+ DESCRIPTION = ' +A => B+ - For terms A and B,
19
+ A directlyIncreases B or A => B+ indicate A
20
+ ncreases B and that the mechanism of the causal
21
+ elationship is based on physical interaction
22
+ f entities related to A and B. This is a direct
23
+ ersion of the increases relationship.'.freeze
15
24
 
16
25
  def self.short
17
26
  SHORT
@@ -5,13 +5,36 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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.
8
+ # HasComponent: +A hasComponent A1+ - For complexAbundance
9
+ # term A and abundance term B, +A hasComponent B+ designates
10
+ # B as a component of A, that complexes that are instances of
11
+ # A have instances of B as possible components. Note that, the
12
+ # stoichiometry of A is not described, nor is it stated that B is
13
+ # a required component. The use of hasComponent relationships is
14
+ # complementary to the use of functionally composed complexes and
15
+ # is intended to enable the assignment of components to complexes
16
+ # designated by names in external vocabularies. The assignment
17
+ # of components can potentially enable the reconciliation of
18
+ # equivalent complexes at knowledge assembly time.
9
19
  class HasComponent
10
20
  extend Relationship
11
21
 
12
22
  SHORT = :hasComponent
13
23
  LONG = :hasComponent
14
- 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
24
+ DESCRIPTION = ' +A hasComponent A1+ - For complexAbundance
25
+ erm A and abundance term B, +A hasComponent B+
26
+ esignates B as a component of A, that complexes
27
+ hat are instances of A have instances of B as
28
+ ossible components. Note that, the stoichiometry
29
+ f A is not described, nor is it stated that B
30
+ s a required component. The use of hasComponent
31
+ elationships is complementary to the use of
32
+ unctionally composed complexes and is intended to
33
+ nable the assignment of components to complexes
34
+ esignated by names in external vocabularies. The
35
+ ssignment of components can potentially enable
36
+ he reconciliation of equivalent complexes at
37
+ nowledge assembly time.'.freeze
15
38
 
16
39
  def self.short
17
40
  SHORT
@@ -5,13 +5,31 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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.
8
+ # HasComponents: +A hasComponents (B, C, D)+ - The hasComponents
9
+ # relationship is a special form which enables the assignment
10
+ # of multiple complex components in a single statement where
11
+ # the object of the statement is a set of abundance terms. A
12
+ # statement using hasComponents is exactly equivalent to multiple
13
+ # hasComponent statements. A term may not appear in both the
14
+ # subject and object of the same hasComponents statement. For
15
+ # the abundance terms A, B, C and D, +A hasComponents B, C, D+
16
+ # indicates that A has components B, C and D.
9
17
  class HasComponents
10
18
  extend Relationship
11
19
 
12
20
  SHORT = :hasComponents
13
21
  LONG = :hasComponents
14
- 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
22
+ DESCRIPTION = ' +A hasComponents (B, C, D)+ - The hasComponents
23
+ elationship is a special form which enables
24
+ he assignment of multiple complex components
25
+ n a single statement where the object of the
26
+ tatement is a set of abundance terms. A statement
27
+ sing hasComponents is exactly equivalent to
28
+ ultiple hasComponent statements. A term may not
29
+ ppear in both the subject and object of the same
30
+ asComponents statement. For the abundance terms A,
31
+ , C and D, +A hasComponents B, C, D+ indicates
32
+ hat A has components B, C and D.'.freeze
15
33
 
16
34
  def self.short
17
35
  SHORT
@@ -5,13 +5,26 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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.
8
+ # HasMember: +A hasMember A1+ - For term abundances A and B,
9
+ # +A hasMember B+ designates B as a member class of A. A member
10
+ # class is a distinguished sub-class. A is defined as a group
11
+ # by all of the members assigned to it. The member classes may
12
+ # or may not be overlapping and may or may not entirely cover
13
+ # all instances of A. A term may not appear in both the subject
14
+ # and object of the same hasMember statement.
9
15
  class HasMember
10
16
  extend Relationship
11
17
 
12
18
  SHORT = :hasMember
13
19
  LONG = :hasMember
14
- 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
20
+ DESCRIPTION = ' +A hasMember A1+ - For term abundances A and B,
21
+ A hasMember B+ designates B as a member class of
22
+ . A member class is a distinguished sub-class. A is
23
+ efined as a group by all of the members assigned to
24
+ t. The member classes may or may not be overlapping
25
+ nd may or may not entirely cover all instances
26
+ f A. A term may not appear in both the subject
27
+ nd object of the same hasMember statement.'.freeze
15
28
 
16
29
  def self.short
17
30
  SHORT
@@ -5,13 +5,31 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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.
8
+ # HasMembers: +A hasMembers (B, C, D)+ - The hasMembers
9
+ # relationship is a special form which enables the assignment of
10
+ # multiple member classes in a single statement where the object
11
+ # of the statement is a set of abundance terms. A statement
12
+ # using hasMembers is exactly equivalent to multiple hasMember
13
+ # statements. A term may not appear in both the subject and
14
+ # object of a of the same hasMembers statement. For the abundance
15
+ # terms A, B, C and D, +A hasMembers B, C, D+ indicates that A
16
+ # is defined by its member abundance classes B, C and D.
9
17
  class HasMembers
10
18
  extend Relationship
11
19
 
12
20
  SHORT = :hasMembers
13
21
  LONG = :hasMembers
14
- 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
22
+ DESCRIPTION = ' +A hasMembers (B, C, D)+ - The hasMembers
23
+ elationship is a special form which enables the
24
+ ssignment of multiple member classes in a single
25
+ tatement where the object of the statement is a set
26
+ f abundance terms. A statement using hasMembers
27
+ s exactly equivalent to multiple hasMember
28
+ tatements. A term may not appear in both the
29
+ ubject and object of a of the same hasMembers
30
+ tatement. For the abundance terms A, B, C and D,
31
+ A hasMembers B, C, D+ indicates that A is defined
32
+ y its member abundance classes B, C and D.'.freeze
15
33
 
16
34
  def self.short
17
35
  SHORT
@@ -5,13 +5,24 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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.
8
+ # HasModification: +p(A) hasModification p(A, pmod(P, S, 473))+
9
+ # - This relationship links abundance terms modified by the
10
+ # +pmod()+ function to the unmodified abundance term. This is a
11
+ # direct relationship because it is a _self_ relationship. This
12
+ # relationship is introduced by the BEL Compiler and may not be
13
+ # used by statements in BEL documents.
9
14
  class HasModification
10
15
  extend Relationship
11
16
 
12
17
  SHORT = :hasModification
13
18
  LONG = :hasModification
14
- 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
19
+ DESCRIPTION = ' +p(A) hasModification p(A, pmod(P, S, 473))+ -
20
+ his relationship links abundance terms modified by
21
+ he +pmod()+ function to the unmodified abundance
22
+ erm. This is a direct relationship because it
23
+ s a _self_ relationship. This relationship is
24
+ ntroduced by the BEL Compiler and may not be used
25
+ y statements in BEL documents.'.freeze
15
26
 
16
27
  def self.short
17
28
  SHORT
@@ -5,13 +5,26 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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.
8
+ # HasProduct: +reaction(reactants(A), products(B))
9
+ # hasProduct B+ - This relationship links abundance
10
+ # terms from the +products(<list>)+ in a reaction to the
11
+ # reaction. This is a direct relationship because it is a _self_
12
+ # relationship. Products are produced directly by a reaction. This
13
+ # relationship is introduced by the BEL Compiler and may not be
14
+ # used by statements in BEL documents.
9
15
  class HasProduct
10
16
  extend Relationship
11
17
 
12
18
  SHORT = :hasProduct
13
19
  LONG = :hasProduct
14
- 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
20
+ DESCRIPTION = ' +reaction(reactants(A), products(B)) hasProduct
21
+ + - This relationship links abundance terms
22
+ rom the +products(<list>)+ in a reaction to the
23
+ eaction. This is a direct relationship because it
24
+ s a _self_ relationship. Products are produced
25
+ irectly by a reaction. This relationship is
26
+ ntroduced by the BEL Compiler and may not be used
27
+ y statements in BEL documents.'.freeze
15
28
 
16
29
  def self.short
17
30
  SHORT
@@ -5,13 +5,24 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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.
8
+ # HasVariant: +p(A) hasVariant p(A, sub(G, 12, V))+ -
9
+ # This relationship links abundance terms modified by the
10
+ # +substitution()+, +fusion()+, or +truncation()+ functions to
11
+ # the unmodified abundance term. This relationship is introduced
12
+ # by the BEL Compiler and does not need to be used by statements
13
+ # in BEL documents.
9
14
  class HasVariant
10
15
  extend Relationship
11
16
 
12
17
  SHORT = :hasVariant
13
18
  LONG = :hasVariant
14
- 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
19
+ DESCRIPTION = ' +p(A) hasVariant p(A, sub(G, 12, V))+ - This
20
+ elationship links abundance terms modified by the
21
+ substitution()+, +fusion()+, or +truncation()+
22
+ unctions to the unmodified abundance term. This
23
+ elationship is introduced by the BEL Compiler
24
+ nd does not need to be used by statements in
25
+ EL documents.'.freeze
15
26
 
16
27
  def self.short
17
28
  SHORT
@@ -5,13 +5,29 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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.
8
+ # Includes: +compositeAbundance(A,B) includes A+ - This
9
+ # relationship links each individual abundance term in a
10
+ # +compositeAbundance(<list>)+ to the compositeAbundance. For
11
+ # example, +compositeAbundance(A, B) includes A+ and
12
+ # +compositeAbundance(A, B) includes B+. This relationship is
13
+ # direct because it is a _self_ relationship. This relationship
14
+ # is introduced by the BEL Compiler and may not be used by
15
+ # statements in BEL documents.
9
16
  class Includes
10
17
  extend Relationship
11
18
 
12
19
  SHORT = :includes
13
20
  LONG = :includes
14
- 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
21
+ DESCRIPTION = ' +compositeAbundance(A,B) includes A+ - This
22
+ elationship links each individual abundance
23
+ erm in a +compositeAbundance(<list>)+
24
+ o the compositeAbundance. For example,
25
+ compositeAbundance(A, B) includes A+ and
26
+ compositeAbundance(A, B) includes B+. This
27
+ elationship is direct because it is a _self_
28
+ elationship. This relationship is introduced by
29
+ he BEL Compiler and may not be used by statements
30
+ n BEL documents.'.freeze
15
31
 
16
32
  def self.short
17
33
  SHORT
@@ -5,13 +5,33 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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.
8
+ # Increases: +A -> B+ - For terms A and B, +A increases B or
9
+ # A -> B+ indicates that increases in A have been observed to
10
+ # cause increases in B. +A increases B+ also represents cases
11
+ # where decreases in A have been observed to cause decreases in B,
12
+ # for example, in recording the results of gene deletion or other
13
+ # inhibition experiments. A is a BEL Term and B is either a BEL
14
+ # Term or a BEL Statement. The relationship does not indicate
15
+ # that the changes in A are either necessary for changes in B,
16
+ # nor does it indicate that changes in A are sufficient to cause
17
+ # changes in B.
9
18
  class Increases
10
19
  extend Relationship
11
20
 
12
21
  SHORT = :'->'
13
22
  LONG = :increases
14
- 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
23
+ DESCRIPTION = ' +A -> B+ - For terms A and B, +A increases B
24
+ r A -> B+ indicates that increases in A have been
25
+ bserved to cause increases in B. +A increases
26
+ + also represents cases where decreases in A
27
+ ave been observed to cause decreases in B, for
28
+ xample, in recording the results of gene deletion
29
+ r other inhibition experiments. A is a BEL Term
30
+ nd B is either a BEL Term or a BEL Statement. The
31
+ elationship does not indicate that the changes
32
+ n A are either necessary for changes in B, nor
33
+ oes it indicate that changes in A are sufficient
34
+ o cause changes in B.'.freeze
15
35
 
16
36
  def self.short
17
37
  SHORT
@@ -5,13 +5,26 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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")+
8
+ # IsA: +A isA B+ - For terms A and B, +A isA B+ indicates
9
+ # that A is a subset of B. All terms in BEL represent classes,
10
+ # but given that classes implicitly have instances, one can
11
+ # also interpret +A isA B+ to mean that any instance of A must
12
+ # also be an instance of B. This relationship can be used to
13
+ # represent GO and MeSH hierarchies: +pathology(MESH:Psoriasis)
14
+ # isA pathology(MESH:"Skin Diseases")+
9
15
  class IsA
10
16
  extend Relationship
11
17
 
12
18
  SHORT = :isA
13
19
  LONG = :isA
14
- 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
20
+ DESCRIPTION = ' +A isA B+ - For terms A and B, +A isA B+
21
+ ndicates that A is a subset of B. All terms in BEL
22
+ epresent classes, but given that classes implicitly
23
+ ave instances, one can also interpret +A isA B+ to
24
+ ean that any instance of A must also be an instance
25
+ f B. This relationship can be used to represent
26
+ O and MeSH hierarchies: +pathology(MESH:Psoriasis)
27
+ sA pathology(MESH:"Skin Diseases")+'.freeze
15
28
 
16
29
  def self.short
17
30
  SHORT
@@ -5,13 +5,24 @@ module BELParser
5
5
  module Language
6
6
  module Version2_0
7
7
  module Relationships
8
- # 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.
8
+ # NegativeCorrelation: +A negativeCorrelation B+ - For terms
9
+ # A and B, +A negativeCorrelation B+ indicates that changes in A
10
+ # and B have been observed to be negatively correlated. The order
11
+ # of the subject and object does not affect the interpretation
12
+ # of the statement, thus B negativeCorrelation A is equivalent
13
+ # to A negativeCorrelation B.
9
14
  class NegativeCorrelation
10
15
  extend Relationship
11
16
 
12
17
  SHORT = :negativeCorrelation
13
18
  LONG = :negativeCorrelation
14
- 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
19
+ DESCRIPTION = ' +A negativeCorrelation B+ - For terms A and B,
20
+ A negativeCorrelation B+ indicates that changes
21
+ n A and B have been observed to be negatively
22
+ orrelated. The order of the subject and object does
23
+ ot affect the interpretation of the statement,
24
+ hus B negativeCorrelation A is equivalent to A
25
+ egativeCorrelation B.'.freeze
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26
 
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  def self.short
17
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  SHORT
@@ -5,13 +5,26 @@ module BELParser
5
5
  module Language
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  module Version2_0
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  module Relationships
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- # 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.
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+ # Orthologous: +A orthologous B+ - For geneAbundance terms A
9
+ # and B, +A orthologousTo B+ indicates that A and B represent
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+ # abundances of genes in different species which are sequence
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+ # similar and which are therefore presumed to share a common
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+ # ancestral gene. For example, +g(HGNC:AKT1) orthologousTo
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+ # g(MGI:AKT1)+ indicates that the mouse and human AKT1 genes
14
+ # are orthologous.
9
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  class Orthologous
10
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  extend Relationship
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17
 
12
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  SHORT = :orthologous
13
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  LONG = :orthologous
14
- 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
20
+ DESCRIPTION = ' +A orthologous B+ - For geneAbundance terms
21
+ and B, +A orthologousTo B+ indicates that A
22
+ nd B represent abundances of genes in different
23
+ pecies which are sequence similar and which are
24
+ herefore presumed to share a common ancestral
25
+ ene. For example, +g(HGNC:AKT1) orthologousTo
26
+ (MGI:AKT1)+ indicates that the mouse and human
27
+ KT1 genes are orthologous.'.freeze
15
28
 
16
29
  def self.short
17
30
  SHORT