Difference between revisions of "WormBase Model:Construct"
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===notes on construct model=== | ===notes on construct model=== | ||
''see discussion tab'' | ''see discussion tab'' | ||
+ | ==Expression_pattern== | ||
+ | proposed addition | ||
+ | <pre> | ||
+ | Variation ?Variation XREF Expression_pattern | ||
==Clone== | ==Clone== | ||
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Construct ?Construct XREF Clone | Construct ?Construct XREF Clone | ||
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Revision as of 21:09, 22 January 2014
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Contents
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 XREF Drives_reporter 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 ==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