Data representation
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_Pro
Events
Their description follows the syntax:
- event label
- list of required arguments (role, list of entity types separated by | )
Full version
- 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:*