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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:*