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.

Variation

?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)

?Construct 
Summary   ?Text
Sequence feature ?Feature XREF Construct
Gene ?Gene
Gene_site_targeted ?SO_term    
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 unc-119(+), lin-15(+), drug selection
Construction_summary  ?Text    //Backbone vector, mol bio 
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

Transgene

?Transgene      
Summary UNIQUE ?Text                               
Synonym ?Text                   
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
Integration_method UNIQUE ?Text                                                    
Laboratory ?Laboratory #Lab_Location    
Author ?Author                   
Genetic_information                            
     Extrachromosomal                
Integrated
Map ?Map  #Map_position  
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_marker ?Process XREF 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