Entity types
Gene
Gene_Family
Box
Promoter
RNA
Protein
Protein_Family
Protein_Complex
Protein_Domain
Hormone
Regulatory_Network
Pathway
Genotype
Tissue
Development_Phase
Environmental_Factor
Entity groups
Entity groups are not used as entity types, but to make more concise the description of the event signature below.
DNA_Product = RNA|Protein|Protein_Family|Protein_Complex|Protein_Domain
DNA = Gene|Gene_Family|Box,Promoter
Functional_Molecule = DNA_Product|Hormone
Molecule = DNA|Functional_Molecule
Dynamic_Process = Regulatory_Network|Pathway
Biological_context = Tissue|Development_Phase|Genotype
Context = Biological_context|Environmental_Factor
Events
Their description follows the syntax:
event label
list of required arguments (role, list of entity types separated by | )
Binding
Functional_Molecule:Functional_Molecule
Molecule:Molecule
Primary_Structure_Composition
DNA_Part:Box|Promoter
DNA:DNA
Protein_Complex_Composition
Amino_Acid_Sequence:Protein|Protein_Family|Protein_Complex|Protein_Domain
Protein_Complex:Protein_Complex
Presence_At_Stage
Functional_Molecule:Functional_Molecule
Development:Development_Phase
Presence_In_Genotype
Molecule: Molecule
Element: Biological context
Genotype: Genotype
(Molecule et Element are mutually exclusive)
Sequence_Identity
Element1:*
Element2:*
Interaction
Agent: Molecule
Target: Molecule
Functional_Equivalence
Element1: *
Element2: *
Involvement_In_Process
Participant:Molecule
Process:Dynamic_Process
Localization
Functional_Molecule: Functional_Molecule
Process:Dynamic_Process
Target_Tissue:Tissue
(Functional_Molecule et Process are mutuelly exclusive)
Family_Membership
Element:Gene|Gene_Family|Protein|Protein_Domain|Protein_Family|RNA
Family:Gene_Family|Protein_Family|RNA
Protein_Domain_Composition
Domain:Protein_Domain
Product:DNA_Product
Occurrence_During
Process:Dynamic_Process
Development:Development_Phase
Occurrence_In_Genotype
Process:Dynamic_Process
Genotype:Genotype
Regulation_Of_Accumulation
Agent:*
Functional_Molecule:Functional_Molecule
Regulation_Of_Development_Phase
Agent:*
Development:Development_Phase
Regulation_Of_Expression
Agent:*
DNA:DNA
Regulation_Of_Molecule_Activity
Agent:*
Molecule:Molecule
Regulation_Of_Process
Agent:*
Process:Dynamic_Process
Regulation_Of_Tissue_Development
Agent:*
Target_Tissue:Tissue
Transcription_Or_Translation
Source:DNA|RNA
Product:DNA_Product
All event types, except Exists_In_Genotype may have the following optional arguments
Tissue:Tissue
Developmental_Stage:Development_Phase
Organism_Genotype:Genotype
Environmental_Factor:Environmental_Factor
Hormone:Hormone
Binary relations
Their description follows the syntax:
relation label
list of required arguments (role, list of entity types separated by | )
Binds_To
Functional_Molecule:Functional_Molecule
Molecule:Molecule
Composes_Primary_Structure
DNA_Part:Box|Promoter
DNA:DNA
Composes_Protein_Complex
Amino_Acid_Sequence:Protein|Protein_Family|Protein_Complex|Protein_Domain
Protein_Complex:Protein_Complex
Exists_At_Stage
Functional_Molecule:Functional_Molecule
Development:Development_Phase
Exists_In_Genotype
Molecule: Molecule
Element: Biological context
Genotype: Genotype
(Molecule et Element are mutually exclusive)
Has_Sequence_Identical_To
Element1:*
Element2:*
Interacts_With
Agent: Molecule
Target: Molecule
Is_Functionally_Equivalent_To
Element1: *
Element2: *
Is_Involved_In_Process
Participant:Molecule
Process:Dynamic_Process
Is_Localized_In
Functional_Molecule: Functional_Molecule
Process:Dynamic_Process
Target_Tissue:Tissue
(Functional_Molecule et Process are mutuelly exclusive)
Is_Member_Of_Family
Element:Gene|Gene_Family|Protein|Protein_Domain|Protein_Family|RNA
Family:Gene_Family|Protein_Family|RNA
Is_Protein_Domain_Of
Domain:Protein_Domain
Product:DNA_Product
Occurs_During
Process:Dynamic_Process
Development:Development_Phase
Occurs_In_Genotype
Process:Dynamic_Process
Genotype:Genotype
Regulates_Accumulation
Agent:*
Functional_Molecule:Functional_Molecule
Regulates_Development_Phase
Agent:*
Development:Development_Phase
Regulates_Expression
Agent:*
DNA:DNA
Regulates_Molecule_Activity
Agent:*
Molecule:Molecule
Regulates_Process
Agent:*
Process:Dynamic_Process
Regulates_Tissue_Development
Agent:*
Target_Tissue:Tissue
Transcribes_Or_Translates_To
Source:DNA|RNA
Product:DNA_Product
Is_Linked_To
Agent:*
Target:*