WormBase Model:Construct

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Proposed model changes

Purpose: the technology of engineering mutations and gene replacement has been developed in C. elegans. With these new research tools, capture and display of the molecular information of these alleles needs to be updated. We propose a new class, Construct, to capture the specifics of the DNA tool used to perform the replacement or engineering, while the Variation model gets updated to record the engineering event itself and its impact on the genome. As a side benefit to the creation of the Construct model, we can use this new class to also capture the genomic arrays used create transgenes.

Example data

LP132 nmy-2(cp7[nmy-2::gfp + LoxP unc-119(+) LoxP]) I; unc-119(ed3) I

Variation

Proposed additions

?Variation
Variation_type 
Engineered_allele 
Variation_summary //to house final engineered construct
    Derived_from ?Construct XREF Variation
Identical_transgene Unique ?Transgene XREF Identical_variation
Method 
    Homologous_recombination 
    NHEJ
    MosSci
    Cas9
    Crispr
Expr_pattern ?Expr_pattern XREF Variation #Evidence

notes on variation model changes

see discussion tab

Construct (new)

Class itself is new

?Construct // any single contiguous stretch of engineered DNA sequence
Public_name  ?Text
Other_name  ?Text
Summary   ?Text //genotype like [Pmyo-2::GFP]
Sequence feature ?Feature XREF Construct
Driven_by ?Gene XREF Drives_transgene
Gene ?Gene XREF Transgene_product
Fusion_reporter ?Text //fluorescent proteins GFP, RFP, mCherry, etc.
Other_reporter ?Text //to add reporters, tags that aren’t included in model
Purification_tag ?Text //FLAG, HA, Myc, TAP, etc.  
Type_of_construct
    Chimera
    Domain_swap
    Engineered mutation
    Fusion
    Complex // complex changes (e.g. GFP fusion plus point mutations)  
    Transcriptional_fusion
    Translational_fusion 
    N-terminal_translational_fusion
    C-terminal_translational_fusion
    Internal_coding_fusion
Selection_marker     ?Text    //for elements stitched into contiguous sequence, coinjected elements will get their own construct ID, these will be joined together to create transgene 
Construction_summary  ?Text    //Backbone vector, mol bio 
     DNA_text ?text // for mapping to genome, can include entire construct sequence
Used_for
    Transgene_construction ?Transgene XREF Construct
    Variation ?Variation XREF Engineered_allele
    Topic_output_indicator ?WBProcess XREF marker_construct
    Expression_pattern ?Expr_pattern XREF Construct (redundant tag in ?Feature model?)    
Reference ?Paper XREF Construct  
Person ?Person XREF Construct
Laboratory ?Laboratory #Lab_Location 
Remark ?Text #Evidence

notes on construct model

see discussion tab

Expression_pattern

proposed addition

Variation ?Variation XREF Expression_pattern

==Gene==
proposed change
<pre>
Drives_Transgene ?Transgene XREF Driven_by_gene

changed to

Drives_construct ?Construct XREF Driven_by_gene

==Clone==
proposed addition
<pre>
Construct ?Construct XREF Clone

Transgene

Proposed changes: Many of the transgene tags have been moved to the proposed ?Construct model, the remaining tags as well as some additions are shown below in the proposed updated ?Transgene model

?Transgene      
Summary UNIQUE ?Text                               
Synonym ?Text       
Identical_variation Unique ?Variation XREF Identical_transgene //put in to unambiguously associate the allele/transgene object - see discussion
Construction //Strain_construction
     Construct       ?Construct XREF Transgene_construction
     Fragment Text ?Text  //Can this be replaced by Construct?
     Coinjection_marker ?Text
     Integration_method UNIQUE ?Text                                                    
     Laboratory ?Laboratory #Lab_Location    
     Author ?Author                   
Genetic_information                            
     Extrachromosomal                
     Integrated 
         Map ?Map  #Map_position  //needed for transgenes with no granular mapping, e.g., just mapped to a LG
Phenotype ?Phenotype XREF Transgene #Phenotype_info
Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info  
Used_for                                                     
     Expr_pattern ?Expr_pattern XREF Transgene  
     Marker_for   ?Text #Evidence 
     Gene_regulation ?Gene_regulation XREF Transgene 
     Interactor ?Interaction
     Topic_output_indicator ?WBProcess XREF marker_transgene
Associated_with                   
     Marked_rearrangement ?Rearrangement XREF By_transgene
     Clone ?Clone XREF Transgene Text 
     Strain ?Strain XREF Transgene 
Reference ?Paper XREF Transgene  
Species UNIQUE ?Species       
Remark ?Text #Evidence