Module: BEL::Language
- Defined in:
- lib/bel/language.rb
Defined Under Namespace
Classes: Annotation, AnnotationDefinition, Comment, DocumentProperty, E, F, Function, Newline, NullE, Signature, StatementGroup, UnsetAnnotation, UnsetStatementGroup
Constant Summary collapse
- NEW_LINE =
Newline.new
- FUNCTIONS =
{ a: { short_form: :a, long_form: :abundance, description: 'Denotes the abundance of an entity', return_type: :a, signatures: [ Signature.new(:a, E.new(:A)) ] }, bp: { short_form: :bp, long_form: :biologicalProcess, description: 'Denotes a process or population of events', return_type: :bp, signatures: [ Signature.new(:bp, E.new(:B)) ] }, cat: { short_form: :cat, long_form: :catalyticActivity, description: 'Denotes the frequency or abundance of events where a member acts as an enzymatic catalyst of biochecmial reactions', return_type: :a, signatures: [ Signature.new(:cat, F.new(:complex)), Signature.new(:cat, F.new(:p)) ] }, sec: { short_form: :sec, long_form: :cellSecretion, description: 'Denotes the frequency or abundance of events in which members of an abundance move from cells to regions outside of the cells', return_type: :a, signatures: [ Signature.new(:sec, F.new(:a)) ] }, surf: { short_form: :surf, long_form: :cellSurfaceExpression, description: 'Denotes the frequency or abundance of events in which members of an abundance move to the surface of cells', return_type: :a, signatures: [ Signature.new(:surf, F.new(:a)) ] }, chap: { short_form: :chap, long_form: :chaperoneActivity, description: 'Denotes the frequency or abundance of events in which a member binds to some substrate and acts as a chaperone for the substrate', return_type: :a, signatures: [ Signature.new(:chap, F.new(:complex)), Signature.new(:chap, F.new(:p)) ] }, complex: { short_form: :complex, long_form: :complexAbundance, description: 'Denotes the abundance of a molecular complex', return_type: :complex, signatures: [ Signature.new(:complex, E.new(:A)), Signature.new(:complex, F.new(:a, true)) ] }, composite: { short_form: :composite, long_form: :compositeAbundance, description: 'Denotes the frequency or abundance of events in which members are present', return_type: :a, signatures: [ Signature.new(:composite, F.new(:a, true)) ] }, deg: { short_form: :deg, long_form: :degradation, description: 'Denotes the frequency or abundance of events in which a member is degraded in some way such that it is no longer a member', return_type: :a, signatures: [ Signature.new(:deg, F.new(:a)) ] }, fus: { short_form: :fus, long_form: :fusion, description: 'Specifies the abundance of a protein translated from the fusion of a gene', return_type: :fus, signatures: [ Signature.new(:fus, E.new(:G)), Signature.new(:fus, E.new(:G), E.new(:*), E.new(:*)), Signature.new(:fus, E.new(:P)), Signature.new(:fus, E.new(:P), E.new(:*), E.new(:*)), Signature.new(:fus, E.new(:R)), Signature.new(:fus, E.new(:R), E.new(:*), E.new(:*)) ] }, g: { short_form: :g, long_form: :geneAbundance, description: 'Denotes the abundance of a gene', return_type: :g, signatures: [ Signature.new(:g, E.new(:G)), Signature.new(:g, E.new(:G), F.new(:fus)) ] }, gtp: { short_form: :gtp, long_form: :gtpBoundActivity, description: 'Denotes the frequency or abundance of events in which a member of a G-protein abundance is GTP-bound', return_type: :a, signatures: [ Signature.new(:gtp, F.new(:complex)), Signature.new(:gtp, F.new(:p)) ] }, kin: { short_form: :kin, long_form: :kinaseActivity, description: 'Denotes the frequency or abundance of events in which a member acts as a kinase, performing enzymatic phosphorylation of a substrate', return_type: :a, signatures: [ Signature.new(:kin, F.new(:complex)), Signature.new(:kin, F.new(:p)) ] }, list: { short_form: :list, long_form: :list, description: 'Groups a list of terms together', return_type: :list, signatures: [ Signature.new(:list, E.new(:A, true)), Signature.new(:list, F.new(:a, true)) ] }, m: { short_form: :m, long_form: :microRNAAbundance, description: 'Denotes the abundance of a processed, functional microRNA', return_type: :m, signatures: [ Signature.new(:m, E.new(:M)) ] }, act: { short_form: :act, long_form: :molecularActivity, description: 'Denotes the frequency or abundance of events in which a member acts as a causal agent at the molecular scale', return_type: :a, signatures: [ Signature.new(:act, F.new(:a)) ] }, path: { short_form: :path, long_form: :pathology, description: 'Denotes a disease or pathology process', return_type: :path, signatures: [ Signature.new(:path, E.new(:O)) ] }, pep: { short_form: :pep, long_form: :peptidaseActivity, description: 'Denotes the frequency or abundance of events in which a member acts to cleave a protein', return_type: :a, signatures: [ Signature.new(:pep, F.new(:complex)), Signature.new(:pep, F.new(:p)) ] }, phos: { short_form: :phos, long_form: :phosphataseActivity, description: 'Denotes the frequency or abundance of events in which a member acts as a phosphatase', return_type: :a, signatures: [ Signature.new(:phos, F.new(:complex)), Signature.new(:phos, F.new(:p)) ] }, products: { short_form: :products, long_form: :products, description: 'Denotes the products of a reaction', return_type: :products, signatures: [ Signature.new(:products, F.new(:a)) ] }, p: { short_form: :p, long_form: :proteinAbundance, description: 'Denotes the abundance of a protein', return_type: :p, signatures: [ Signature.new(:p, E.new(:P)), Signature.new(:p, E.new(:P), F.new(:pmod)), Signature.new(:p, E.new(:P), F.new(:sub)), Signature.new(:p, E.new(:P), F.new(:fus)), Signature.new(:p, E.new(:P), F.new(:trunc)) ] }, pmod: { short_form: :pmod, long_form: :proteinModification, description: 'Denotes a covalently modified protein abundance', return_type: :pmod, signatures: [ Signature.new(:pmod, E.new(:*)), Signature.new(:pmod, E.new(:*), E.new(:*)), Signature.new(:pmod, E.new(:*), E.new(:*), E.new(:*)) ] }, reactants: { short_form: :reactants, long_form: :reactants, description: 'Denotes the reactants of a reaction', return_type: :reactants, signatures: [ Signature.new(:reactants, F.new(:a)) ] }, rxn: { short_form: :rxn, long_form: :reaction, description: 'Denotes the frequency or abundance of events in a reaction', return_type: :a, signatures: [ Signature.new(:rxn, F.new(:reactants), F.new(:products)) ] }, ribo: { short_form: :ribo, long_form: :ribosylationActivity, description: 'Denotes the frequency or abundance of events in which a member acts to perform post-translational modification of proteins', return_type: :a, signatures: [ Signature.new(:ribo, F.new(:complex)), Signature.new(:ribo, F.new(:p)) ] }, r: { short_form: :r, long_form: :rnaAbundance, description: 'Denotes the abundance of a gene', return_type: :g, signatures: [ Signature.new(:r, E.new(:R)), Signature.new(:r, E.new(:R), F.new(:fus)) ] }, sub: { short_form: :sub, long_form: :substitution, description: 'Indicates the abundance of proteins with amino acid substitution sequence', return_type: :sub, signatures: [ Signature.new(:sub, E.new(:*), E.new(:*), E.new(:*)) ] }, tscript: { short_form: :tscript, long_form: :transcriptionalActivity, description: 'Denotes the frequency or abundance of events in which a member directly acts to control transcription of genes', return_type: :a, signatures: [ Signature.new(:tscript, F.new(:complex)), Signature.new(:tscript, F.new(:p)) ] }, tloc: { short_form: :tloc, long_form: :translocation, description: 'Denotes the frequency or abundance of events in which members move between locations', return_type: :a, signatures: [ Signature.new(:tloc, F.new(:a), E.new(:A), E.new(:A)) ] }, tport: { short_form: :tport, long_form: :transportActivity, description: 'Denotes the frequency or abundance of events in which a member directs acts to enable the directed movement of substances into, out of, within, or between cells', return_type: :a, signatures: [ Signature.new(:tport, F.new(:complex)), Signature.new(:tport, F.new(:p)) ] }, trunc: { short_form: :trunc, long_form: :truncation, description: 'Indicates an abundance of proteins with truncation sequence variants', return_type: :trunc, signatures: [ Signature.new(:trunc, E.new(:*)) ] } }
- PARAMETER_ENCODING =
{ B: [:B], O: [:O, :B], R: [:R, :A], M: [:M, :R, :A], P: [:P, :A], G: [:G, :A], A: [:A], C: [:C, :A] }
- FUNCTION_TYPES =
{ a: [:a], bp: [:bp], complex: [:complex, :a], g: [:g, :a], m: [:m, :r, :a], path: [:path, :bp], p: [:p, :a], r: [:r, :a] }
- RELATIONSHIPS =
{ :actsIn => :actsIn, :analogous => :analogous, :'--' => :association, :association => :association, :biomarkerFor => :biomarkerFor, :causesNoChange => :causesNoChange, :'-|' => :decreases, :decreases => :decreases, :'=|' => :directlyDecreases, :directlyDecreases => :directlyDecreases, :'=>' => :directlyIncreases, :directlyIncreases => :directlyIncreases, :'->' => :increases, :increases => :increases, :hasComponent => :hasComponent, :hasComponents => :hasComponents, :hasMember => :hasMember, :hasMembers => :hasMembers, :hasModification => :hasModification, :hasProduct => :hasProduct, :hasVariant => :hasVariant, :includes => :includes, :isA => :isA, :negativeCorrelation => :negativeCorrelation, :orthologous => :orthologous, :positiveCorrelation => :positiveCorrelation, :prognosticBiomarkerFor => :prognosticBiomarkerFor, :rateLimitingStepOf => :rateLimitingStepOf, :reactantIn => :reactantIn, :subProcessOf => :subProcessOf, :':>' => :transcribedTo, :transcribedTo => :transcribedTo, :'>>' => :translatedTo, :translatedTo => :translatedTo, :translocates => :translocates, }