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 
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_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    //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

Clone

?Clone	Evidence	#Evidence
	Remark	General_remark	?Text
		Y_remark	?Text
		PCR_remark	?Text
	Position	Map	?Map	XREF	Clone	#Map_position
		Pmap	UNIQUE	?Contig	XREF	Clone	UNIQUE	Int	UNIQUE	Int
		Clone_left_end	?Sequence
		Clone_right_end	?Sequence
		Pos_neg_data	?Pos_neg_data
	Positive	Positive_gene	?Gene	XREF	Positive_clone
		Positive_variation	?Variation	XREF	Positive_clone	?Author
		Inside_rearr	?Rearrangement	XREF	Clone_inside	?Author
		Hybridizes_to	?Clone	XREF	Positive_probe	?Grid
		Hybridizes_weak	?Clone	XREF	Pos_probe_weak	?Grid
		Positive_probe	?Clone	XREF	Hybridizes_to	?Grid
		Pos_probe_weak	?Clone	XREF	Hybridizes_weak	?Grid
	Negative	Negative_gene	?Gene	XREF	Negative_clone
		Negative_locus	?Locus	XREF	Negative_clone	?Author
		Outside_rearr	?Rearrangement	XREF	Clone_outside	?Author
		Negative_probe	?Clone	XREF	Does_not_hybridize_to	?Grid
		Does_not_hybridize_to	?Clone	XREF	Negative_probe	?Grid
	In_strain	?Strain	XREF	Clone
	Species	UNIQUE	?Species
	Sequence	?Sequence	XREF	Clone
	PCR_product	?PCR_product	XREF	Clone
	Length	Seq_length	UNIQUE	Int
		Gel_length	UNIQUE	Float
	Location	?Laboratory	#Lab_Location
	URL	Text
	Gridded	?Grid
	Grid_data	?Grid_data
	FingerPrint	Gel_Number	UNIQUE	Int
		Approximate_Match_to	UNIQUE	?Clone	XREF	Canonical_for
		Exact_Match_to	UNIQUE	?Clone	XREF	Canonical_for
		Funny_Match_to	UNIQUE	?Clone	XREF	Canonical_for
		Canonical_for	?Clone	UNIQUE	Int	UNIQUE	Int
		Bands	UNIQUE	Int	UNIQUE	Int
		Gel	?Motif	#Lane
	Contig9	Chromosome	UNIQUE	?Map
		Vaxmap	UNIQUE	Float
		In_situ	UNIQUE	Int	UNIQUE	Int
		Cosmid_grid
		Canon_for_cosmid
		Flag	UNIQUE	Int
		Autopos
	Expression_construct	Pattern	?Text
	Reference	?Paper	XREF	Clone
	cDNA_group	Contains	?Clone	XREF	Contains	Text
		Contained_in	?Clone	XREF	Contained_in
		Best_match	UNIQUE	?Text
	Expr_pattern	?Expr_pattern	XREF	Clone
	Sequence_status	Shotgun	UNIQUE	DateType
		Finished	UNIQUE	DateType
		Accession_number	UNIQUE	?Text
	DB_info	Database	?Database	?Database_field	?Accession_number	XREF	Clone
	Type	UNIQUE	Cosmid
			Fosmid
			YAC
			cDNA
			Plasmid
			Other	Text
	Transgene	?Transgene	XREF	Clone
	Derived_from	?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