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
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 //WBConstructID
Public_name ?Text //Expr#_  or Transgene public name
Other_name ?Text
Summary   ?Text  //genotype ex. [Ppha-4::GFP]
Sequence_feature ?Feature XREF Construct //WBsf object, created by Hinxton when needed, with precise ends for mapping to genome. 
Driven_by_gene ?Gene XREF Drives_construct
Gene ?Gene  
Fusion_reporter ?Text //fluorescent proteins GFP, RFP, mCherry, etc.
Other_reporter ?Text //to add reporters, e.g., reporters not in Fusion_reporter list or genes from other species
Purification_tag ?Text //FLAG, HA, Myc, TAP, etc.  
Type_of_construct 
      Chimera
      Domain_swap
      Engineered mutation
      Fusion
         Complex_fusion // 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 unc-119(+), lin-15(+), drug selection
Construction_summary  ?Text    //
Clone ?Clone XREF Construct 
Used_for
    Transgene_construction ?Transgene XREF Construct
    Variation ?Variation XREF Engineered_allele    
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

?Transgene                                                
Construction //Strain_construction
Construct       ?Construct XREF Transgene_construction
Fragment Text ?Text  //Can this be replaced by Construct?
Coinjection_marker ?Text //remove?, replaced by selection_marker in ?Construct
Used_for                                                     
  Topic_marker ?Process XREF Transgene