bel_parser 1.0.0.alpha.1 → 1.0.0.alpha.2
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- checksums.yaml +4 -4
- data/.gemspec +1 -1
- data/VERSION +1 -1
- data/bin/bel2_termcheck +2 -2
- data/lib/bel_parser/expression/term_semantics.rb +2 -2
- data/lib/bel_parser/language/expression_validator.rb +42 -0
- data/lib/bel_parser/language/function.rb +8 -0
- data/lib/bel_parser/language/relationship.rb +57 -0
- data/lib/bel_parser/language/{semantic_ast.rb → semantics/semantic_ast.rb} +5 -27
- data/lib/bel_parser/language/semantics/semantic_match.rb +28 -0
- data/lib/bel_parser/language/semantics.rb +2 -0
- data/lib/bel_parser/language/specification.rb +34 -10
- data/lib/bel_parser/language/syntax.rb +0 -0
- data/lib/bel_parser/language/{version1 → version1_0}/functions/abundance.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/biological_process.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/catalytic_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/cell_secretion.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/cell_surface_expression.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/chaperone_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/complex_abundance.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/composite_abundance.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/degradation.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/fusion.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/gene_abundance.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/gtp_bound_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/kinase_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/list.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/micro_rna_abundance.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/molecular_activity.rb +5 -5
- data/lib/bel_parser/language/{version2 → version1_0}/functions/pathology.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/peptidase_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/phosphatase_activity.rb +6 -6
- data/lib/bel_parser/language/{version2 → version1_0}/functions/products.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/protein_abundance.rb +8 -8
- data/lib/bel_parser/language/{version1 → version1_0}/functions/protein_modification.rb +4 -4
- data/lib/bel_parser/language/{version2 → version1_0}/functions/reactants.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/reaction.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/ribosylation_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/rna_abundance.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/substitution.rb +4 -4
- data/lib/bel_parser/language/{version1 → version1_0}/functions/transcriptional_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/translocation.rb +5 -5
- data/lib/bel_parser/language/{version1 → version1_0}/functions/transport_activity.rb +6 -6
- data/lib/bel_parser/language/{version1 → version1_0}/functions/truncation.rb +4 -4
- data/lib/bel_parser/language/version1_0/relationships/acts_in.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/analogous.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/association.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/biomarker_for.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/causes_no_change.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/decreases.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/directly_decreases.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/directly_increases.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_component.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_components.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_member.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_members.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_modification.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_product.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/has_variant.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/includes.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/increases.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/is_a.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/negative_correlation.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/orthologous.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/positive_correlation.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/prognostic_biomarker_for.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/rate_limiting_step_of.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/reactant_in.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/sub_process_of.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/transcribed_to.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/translated_to.rb +31 -0
- data/lib/bel_parser/language/version1_0/relationships/translocates.rb +31 -0
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/any.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/biological_process.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/catalytic_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/chaperone_activity.rb +1 -1
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/complex_abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/fusion.rb +1 -1
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/gene_abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/gtp_bound_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/kinase_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/list.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/micro_rna_abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/molecular_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/pathology.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/peptidase_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/phosphatase_activity.rb +1 -1
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/products.rb +1 -1
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/protein_abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/protein_modification.rb +1 -1
- data/lib/bel_parser/language/{version2 → version1_0}/return_types/reactants.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/ribosylation_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/rna_abundance.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/substitution.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/transcriptional_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/transport_activity.rb +1 -1
- data/lib/bel_parser/language/{version1 → version1_0}/return_types/truncation.rb +1 -1
- data/lib/bel_parser/language/version1_0/syntax/function.rb +29 -0
- data/lib/bel_parser/language/version1_0.rb +89 -0
- data/lib/bel_parser/language/{version2 → version2_0}/functions/abundance.rb +6 -6
- data/lib/bel_parser/language/{version2 → version2_0}/functions/activity.rb +7 -7
- data/lib/bel_parser/language/{version2 → version2_0}/functions/biological_process.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/cell_secretion.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/cell_surface_expression.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/complex_abundance.rb +8 -8
- data/lib/bel_parser/language/{version2 → version2_0}/functions/composite_abundance.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/degradation.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/fragment.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/from_location.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/fusion.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/gene_abundance.rb +7 -7
- data/lib/bel_parser/language/{version2 → version2_0}/functions/list.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/location.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/micro_rna_abundance.rb +6 -6
- data/lib/bel_parser/language/{version2 → version2_0}/functions/molecular_activity.rb +4 -4
- data/lib/bel_parser/language/{version1 → version2_0}/functions/pathology.rb +4 -4
- data/lib/bel_parser/language/{version1 → version2_0}/functions/products.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/protein_abundance.rb +9 -9
- data/lib/bel_parser/language/{version2 → version2_0}/functions/protein_modification.rb +7 -7
- data/lib/bel_parser/language/{version1 → version2_0}/functions/reactants.rb +5 -5
- data/lib/bel_parser/language/{version2 → version2_0}/functions/reaction.rb +6 -6
- data/lib/bel_parser/language/{version2 → version2_0}/functions/rna_abundance.rb +11 -11
- data/lib/bel_parser/language/{version2 → version2_0}/functions/to_location.rb +4 -4
- data/lib/bel_parser/language/{version2 → version2_0}/functions/translocation.rb +8 -8
- data/lib/bel_parser/language/{version2 → version2_0}/functions/variant.rb +4 -4
- data/lib/bel_parser/language/version2_0/relationships/acts_in.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/analogous.rb +35 -0
- data/lib/bel_parser/language/version2_0/relationships/association.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/biomarker_for.rb +35 -0
- data/lib/bel_parser/language/version2_0/relationships/causes_no_change.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/decreases.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/directly_decreases.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/directly_increases.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_component.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_components.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_member.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_members.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_modification.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_product.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/has_variant.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/includes.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/increases.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/is_a.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/negative_correlation.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/orthologous.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/positive_correlation.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/prognostic_biomarker_for.rb +35 -0
- data/lib/bel_parser/language/version2_0/relationships/rate_limiting_step_of.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/reactant_in.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/regulates.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/sub_process_of.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/transcribed_to.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/translated_to.rb +31 -0
- data/lib/bel_parser/language/version2_0/relationships/translocates.rb +31 -0
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/activity.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/any.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/biological_process.rb +1 -1
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/complex_abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/fragment.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/from_location.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/fusion.rb +1 -1
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/gene_abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/list.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/location.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/micro_rna_abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/molecular_activity.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/pathology.rb +1 -1
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/products.rb +1 -1
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/protein_abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/protein_modification.rb +1 -1
- data/lib/bel_parser/language/{version1 → version2_0}/return_types/reactants.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/rna_abundance.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/to_location.rb +1 -1
- data/lib/bel_parser/language/{version2 → version2_0}/return_types/variant.rb +1 -1
- data/lib/bel_parser/language/version2_0.rb +73 -0
- data/lib/bel_parser/language.rb +90 -2
- data/lib/bel_parser/parsers/ast/node.rb +11 -1
- metadata +172 -111
- data/lib/bel_parser/language/syntax/expression/incomplete_node.rb +0 -14
- data/lib/bel_parser/language/syntax/expression/invalid_term_function.rb +0 -22
- data/lib/bel_parser/language/version1.rb +0 -50
- data/lib/bel_parser/language/version2.rb +0 -50
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require_relative '../../
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module BELParser
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module Language
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module Version1_0
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module Functions
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# GeneAbundance: Denotes the abundance of a gene
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class GeneAbundance
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SHORT = :g
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RETURN_TYPE = BELParser::Language::
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RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::GeneAbundance
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DESCRIPTION = 'Denotes the abundance of a gene'.freeze
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def self.short
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term(
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end
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private_constant :AST
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module BELParser
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# GTPBoundActivity: Denotes the frequency or abundance of events in which a member of a G-protein abundance is GTP-bound
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DESCRIPTION = 'Denotes the frequency or abundance of events in which a member of a G-protein abundance is GTP-bound'.freeze
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def self.short
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term(
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term(
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end
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module BELParser
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# KinaseActivity: Denotes the frequency or abundance of events in which a member acts as a kinase, performing enzymatic phosphorylation of a substrate
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class KinaseActivity
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SHORT = :kin
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RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::KinaseActivity
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DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a kinase, performing enzymatic phosphorylation of a substrate'.freeze
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term(
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return_type_of(BELParser::Language::
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end
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term(
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end
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private_constant :AST
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require_relative '../../signature'
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-
require_relative '../../
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+
require_relative '../../semantics'
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module BELParser
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module Language
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-
module
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+
module Version1_0
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module Functions
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# List: Groups a list of terms together
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class List
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@@ -13,7 +13,7 @@ module BELParser
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SHORT = :list
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LONG = :list
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RETURN_TYPE = BELParser::Language::
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+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::List
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DESCRIPTION = 'Groups a list of terms together'.freeze
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def self.short
|
@@ -87,7 +87,7 @@ module BELParser
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term(
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function(
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identifier(
|
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-
return_type_of(BELParser::Language::
|
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+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
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end
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private_constant :AST
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@@ -1,11 +1,11 @@
|
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-
require_relative '../../
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1
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+
require_relative '../../version1_0'
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require_relative '../../function'
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require_relative '../../signature'
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-
require_relative '../../
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require_relative '../../semantics'
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module BELParser
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module Language
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module
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module Version1_0
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module Functions
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# MicroRNAAbundance: Denotes the abundance of a processed, functional microRNA
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class MicroRNAAbundance
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@@ -13,7 +13,7 @@ module BELParser
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SHORT = :m
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LONG = :microRNAAbundance
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RETURN_TYPE = BELParser::Language::
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+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::MicroRNAAbundance
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DESCRIPTION = 'Denotes the abundance of a processed, functional microRNA'.freeze
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def self.short
|
@@ -1,11 +1,11 @@
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-
require_relative '../../
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1
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+
require_relative '../../version1_0'
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require_relative '../../function'
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require_relative '../../signature'
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-
require_relative '../../
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+
require_relative '../../semantics'
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module BELParser
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module Language
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-
module
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+
module Version1_0
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module Functions
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# MolecularActivity: Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale
|
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class MolecularActivity
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@@ -13,7 +13,7 @@ module BELParser
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SHORT = :act
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LONG = :molecularActivity
|
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-
RETURN_TYPE = BELParser::Language::
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+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::MolecularActivity
|
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DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale'.freeze
|
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def self.short
|
@@ -52,7 +52,7 @@ module BELParser
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term(
|
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function(
|
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identifier(
|
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-
return_type_of(BELParser::Language::
|
55
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+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
|
56
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|
end
|
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private_constant :AST
|
58
58
|
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
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+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# Pathology: Denotes a disease or pathology process
|
11
11
|
class Pathology
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
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|
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|
SHORT = :path
|
15
15
|
LONG = :pathology
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Pathology
|
17
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|
DESCRIPTION = 'Denotes a disease or pathology process'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
|
+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# PeptidaseActivity: Denotes the frequency or abundance of events in which a member acts to cleave a protein
|
11
11
|
class PeptidaseActivity
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
|
|
14
14
|
SHORT = :pep
|
15
15
|
LONG = :peptidaseActivity
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::PeptidaseActivity
|
17
17
|
DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts to cleave a protein'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -52,7 +52,7 @@ module BELParser
|
|
52
52
|
term(
|
53
53
|
function(
|
54
54
|
identifier(
|
55
|
-
return_type_of(BELParser::Language::
|
55
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
|
56
56
|
end
|
57
57
|
private_constant :AST
|
58
58
|
|
@@ -82,7 +82,7 @@ module BELParser
|
|
82
82
|
term(
|
83
83
|
function(
|
84
84
|
identifier(
|
85
|
-
return_type_of(BELParser::Language::
|
85
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
|
86
86
|
end
|
87
87
|
private_constant :AST
|
88
88
|
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
|
+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# PhosphataseActivity: Denotes the frequency or abundance of events in which a member acts as a phosphatase
|
11
11
|
class PhosphataseActivity
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
|
|
14
14
|
SHORT = :phos
|
15
15
|
LONG = :phosphataseActivity
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::PhosphataseActivity
|
17
17
|
DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts as a phosphatase'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -52,7 +52,7 @@ module BELParser
|
|
52
52
|
term(
|
53
53
|
function(
|
54
54
|
identifier(
|
55
|
-
return_type_of(BELParser::Language::
|
55
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
|
56
56
|
end
|
57
57
|
private_constant :AST
|
58
58
|
|
@@ -82,7 +82,7 @@ module BELParser
|
|
82
82
|
term(
|
83
83
|
function(
|
84
84
|
identifier(
|
85
|
-
return_type_of(BELParser::Language::
|
85
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
|
86
86
|
end
|
87
87
|
private_constant :AST
|
88
88
|
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
|
+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# Products: Denotes the products of a reaction
|
11
11
|
class Products
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
|
|
14
14
|
SHORT = :products
|
15
15
|
LONG = :products
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Products
|
17
17
|
DESCRIPTION = 'Denotes the products of a reaction'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -52,7 +52,7 @@ module BELParser
|
|
52
52
|
term(
|
53
53
|
function(
|
54
54
|
identifier(
|
55
|
-
return_type_of(BELParser::Language::
|
55
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
|
56
56
|
end
|
57
57
|
private_constant :AST
|
58
58
|
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
|
+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# ProteinAbundance: Denotes the abundance of a protein
|
11
11
|
class ProteinAbundance
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
|
|
14
14
|
SHORT = :p
|
15
15
|
LONG = :proteinAbundance
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance
|
17
17
|
DESCRIPTION = 'Denotes the abundance of a protein'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -62,7 +62,7 @@ module BELParser
|
|
62
62
|
term(
|
63
63
|
function(
|
64
64
|
identifier(
|
65
|
-
return_type_of(BELParser::Language::
|
65
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
|
66
66
|
end
|
67
67
|
private_constant :AST
|
68
68
|
|
@@ -102,7 +102,7 @@ module BELParser
|
|
102
102
|
term(
|
103
103
|
function(
|
104
104
|
identifier(
|
105
|
-
return_type_of(BELParser::Language::
|
105
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinModification))))))
|
106
106
|
end
|
107
107
|
private_constant :AST
|
108
108
|
|
@@ -142,7 +142,7 @@ module BELParser
|
|
142
142
|
term(
|
143
143
|
function(
|
144
144
|
identifier(
|
145
|
-
return_type_of(BELParser::Language::
|
145
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::Substitution))))))
|
146
146
|
end
|
147
147
|
private_constant :AST
|
148
148
|
|
@@ -182,7 +182,7 @@ module BELParser
|
|
182
182
|
term(
|
183
183
|
function(
|
184
184
|
identifier(
|
185
|
-
return_type_of(BELParser::Language::
|
185
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::Truncation))))))
|
186
186
|
end
|
187
187
|
private_constant :AST
|
188
188
|
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
|
+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# ProteinModification: Denotes a covalently modified protein abundance
|
11
11
|
class ProteinModification
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
|
|
14
14
|
SHORT = :pmod
|
15
15
|
LONG = :proteinModification
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::ProteinModification
|
17
17
|
DESCRIPTION = 'Denotes a covalently modified protein abundance'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
|
+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# Reactants: Denotes the reactants of a reaction
|
11
11
|
class Reactants
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
|
|
14
14
|
SHORT = :reactants
|
15
15
|
LONG = :reactants
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Reactants
|
17
17
|
DESCRIPTION = 'Denotes the reactants of a reaction'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -52,7 +52,7 @@ module BELParser
|
|
52
52
|
term(
|
53
53
|
function(
|
54
54
|
identifier(
|
55
|
-
return_type_of(BELParser::Language::
|
55
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::Abundance))))))
|
56
56
|
end
|
57
57
|
private_constant :AST
|
58
58
|
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
|
+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# Reaction: Denotes the frequency or abundance of events in a reaction
|
11
11
|
class Reaction
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
|
|
14
14
|
SHORT = :rxn
|
15
15
|
LONG = :reaction
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Abundance
|
17
17
|
DESCRIPTION = 'Denotes the frequency or abundance of events in a reaction'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -52,12 +52,12 @@ module BELParser
|
|
52
52
|
term(
|
53
53
|
function(
|
54
54
|
identifier(
|
55
|
-
return_type_of(BELParser::Language::
|
55
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::Reactants))))),
|
56
56
|
argument(
|
57
57
|
term(
|
58
58
|
function(
|
59
59
|
identifier(
|
60
|
-
return_type_of(BELParser::Language::
|
60
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::Products))))))
|
61
61
|
end
|
62
62
|
private_constant :AST
|
63
63
|
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
|
+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# RibosylationActivity: Denotes the frequency or abundance of events in which a member acts to perform post-translational modification of proteins
|
11
11
|
class RibosylationActivity
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
|
|
14
14
|
SHORT = :ribo
|
15
15
|
LONG = :ribosylationActivity
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::RibosylationActivity
|
17
17
|
DESCRIPTION = 'Denotes the frequency or abundance of events in which a member acts to perform post-translational modification of proteins'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -52,7 +52,7 @@ module BELParser
|
|
52
52
|
term(
|
53
53
|
function(
|
54
54
|
identifier(
|
55
|
-
return_type_of(BELParser::Language::
|
55
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
|
56
56
|
end
|
57
57
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private_constant :AST
|
58
58
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|
@@ -82,7 +82,7 @@ module BELParser
|
|
82
82
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term(
|
83
83
|
function(
|
84
84
|
identifier(
|
85
|
-
return_type_of(BELParser::Language::
|
85
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
|
86
86
|
end
|
87
87
|
private_constant :AST
|
88
88
|
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
|
+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# RNAAbundance: Denotes the abundance of a gene
|
11
11
|
class RNAAbundance
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
|
|
14
14
|
SHORT = :r
|
15
15
|
LONG = :rnaAbundance
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::GeneAbundance
|
17
17
|
DESCRIPTION = 'Denotes the abundance of a gene'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -62,7 +62,7 @@ module BELParser
|
|
62
62
|
term(
|
63
63
|
function(
|
64
64
|
identifier(
|
65
|
-
return_type_of(BELParser::Language::
|
65
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::Fusion))))))
|
66
66
|
end
|
67
67
|
private_constant :AST
|
68
68
|
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
|
+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# Substitution: Indicates the abundance of proteins with amino acid substitution sequence
|
11
11
|
class Substitution
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
|
|
14
14
|
SHORT = :sub
|
15
15
|
LONG = :substitution
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::Substitution
|
17
17
|
DESCRIPTION = 'Indicates the abundance of proteins with amino acid substitution sequence'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -1,11 +1,11 @@
|
|
1
|
-
require_relative '../../
|
1
|
+
require_relative '../../version1_0'
|
2
2
|
require_relative '../../function'
|
3
3
|
require_relative '../../signature'
|
4
|
-
require_relative '../../
|
4
|
+
require_relative '../../semantics'
|
5
5
|
|
6
6
|
module BELParser
|
7
7
|
module Language
|
8
|
-
module
|
8
|
+
module Version1_0
|
9
9
|
module Functions
|
10
10
|
# TranscriptionalActivity: Denotes the frequency or abundance of events in which a member directly acts to control transcription of genes
|
11
11
|
class TranscriptionalActivity
|
@@ -13,7 +13,7 @@ module BELParser
|
|
13
13
|
|
14
14
|
SHORT = :tscript
|
15
15
|
LONG = :transcriptionalActivity
|
16
|
-
RETURN_TYPE = BELParser::Language::
|
16
|
+
RETURN_TYPE = BELParser::Language::Version1_0::ReturnTypes::TranscriptionalActivity
|
17
17
|
DESCRIPTION = 'Denotes the frequency or abundance of events in which a member directly acts to control transcription of genes'.freeze
|
18
18
|
|
19
19
|
def self.short
|
@@ -52,7 +52,7 @@ module BELParser
|
|
52
52
|
term(
|
53
53
|
function(
|
54
54
|
identifier(
|
55
|
-
return_type_of(BELParser::Language::
|
55
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::ComplexAbundance))))))
|
56
56
|
end
|
57
57
|
private_constant :AST
|
58
58
|
|
@@ -82,7 +82,7 @@ module BELParser
|
|
82
82
|
term(
|
83
83
|
function(
|
84
84
|
identifier(
|
85
|
-
return_type_of(BELParser::Language::
|
85
|
+
return_type_of(BELParser::Language::Version1_0::ReturnTypes::ProteinAbundance))))))
|
86
86
|
end
|
87
87
|
private_constant :AST
|
88
88
|
|