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
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)
?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