SeeDev 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_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:*