Difference between revisions of "WormBase Model:Construct"
From WormBaseWiki
Jump to navigationJump to search| Line 4: | Line 4: | ||
=Proposed model changes= | =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. | 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== | ||
Revision as of 21:00, 4 March 2014
back to WormBase_Models
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.
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 // any single contiguous stretch of engineered DNA sequence
Public_name ?Text
Other_name ?Text
Summary ?Text //genotype like [Pmyo-2::GFP]
Sequence feature ?Feature XREF Construct
Driven_by ?Gene XREF Drives_transgene
Gene ?Gene XREF Transgene_product
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 elements stitched into contiguous sequence, coinjected elements will get their own construct ID, these will be joined together to create transgene
Construction_summary ?Text //Backbone vector, mol bio
DNA_text ?text // for mapping to genome, can include entire construct sequence
Used_for
Transgene_construction ?Transgene XREF Construct
Variation ?Variation XREF Engineered_allele
Topic_output_indicator ?WBProcess XREF marker_construct
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: Many of the transgene tags have been moved to the proposed ?Construct model, the remaining tags as well as some additions are shown below in the proposed updated ?Transgene model
?Transgene
Summary UNIQUE ?Text
Synonym ?Text
Identical_variation Unique ?Variation XREF Identical_transgene //put in to unambiguously associate the allele/transgene object - see discussion
Construction //Strain_construction
Construct ?Construct XREF Transgene_construction
Coinjection_marker ?Construct XREF Transgene_construction
Integration_method UNIQUE ?Text
Laboratory ?Laboratory #Lab_Location
Author ?Author
Genetic_information
Extrachromosomal
Integrated
Map ?Map #Map_position //needed for transgenes with no granular mapping, e.g., just mapped to a LG
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_output_indicator ?WBProcess XREF marker_transgene
Associated_with
Marked_rearrangement ?Rearrangement XREF By_transgene
Strain ?Strain XREF Transgene
Reference ?Paper XREF Transgene
Species UNIQUE ?Species
Remark ?Text #Evidence
