Difference between revisions of "WormBase Model:Construct"
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Class itself is new | Class itself is new | ||
<pre> | <pre> | ||
− | ?Construct | + | ?Construct |
− | Public_name ?Text | + | Public_name ?Text |
− | Other_name ?Text | + | Other_name ?Text |
− | Summary ?Text | + | Summary ?Text //genotype like [Pmyo-2::GFP] |
− | + | Sequence feature ?Feature XREF Construct (Do we need this cross reference? Also who will be curating this feature?) | |
− | + | Gene ?Gene | |
− | Gene ?Gene | ||
Fusion_reporter ?Text //fluorescent proteins GFP, RFP, mCherry, etc. | Fusion_reporter ?Text //fluorescent proteins GFP, RFP, mCherry, etc. | ||
− | Other_reporter ?Text //to add reporters, | + | Other_reporter ?Text //to add reporters, tags that aren’t included in model |
Purification_tag ?Text //FLAG, HA, Myc, TAP, etc. | Purification_tag ?Text //FLAG, HA, Myc, TAP, etc. | ||
− | Type_of_construct | + | 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 | Selection_marker ?Text //for unc-119(+), lin-15(+), drug selection | ||
− | Construction_summary ?Text // | + | Construction_summary ?Text //Backbone vector, mol bio |
− | Clone ?Clone XREF Construct | + | Clone ?Clone XREF Construct |
Used_for | Used_for | ||
Transgene_construction ?Transgene XREF Construct | Transgene_construction ?Transgene XREF Construct | ||
− | Variation ?Variation XREF Engineered_allele | + | Variation ?Variation XREF Engineered_allele |
+ | Expression_pattern ?Expr_pattern XREF Construct (redundant tag in ?Feature model?) | ||
Reference ?Paper XREF Construct | Reference ?Paper XREF Construct | ||
Person ?Person XREF Construct | Person ?Person XREF Construct |
Revision as of 21:08, 25 February 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 Identical_transgene Unique ?Transgene XREF Identical_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 Public_name ?Text Other_name ?Text Summary ?Text //genotype like [Pmyo-2::GFP] Sequence feature ?Feature XREF Construct (Do we need this cross reference? Also who will be curating this feature?) Gene ?Gene 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 Clone ?Clone XREF Construct Used_for Transgene_construction ?Transgene XREF Construct Variation ?Variation XREF Engineered_allele Expression_pattern ?Expr_pattern XREF Construct (redundant tag in ?Feature model?) 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