Construct
This page documents the creation of the construct class and all tools needed for its curation.
Overview
A construct is defined as any single contiguous stretch of engineered DNA sequence. Constructs will be curated as objects used in the generation of transgenes, engineered alleles, and expression markers used in analysis of expression patterns, gene regulation, and biological topics.
Model
The official model page is here along with compensatory changes to related models and test data. Constructs will be curation for the benefit of a number of other data classes: Variation, Transgene, Gene Regulation, Topic, and Expression Pattern.
Construct OA
- create construct tables see tables on OA tables page
- assign all transgene objects a unique WBConstruct ID.
- move/rename/rededicate(?) many of the trp tables to be construct tables
- reorganize the transgene OA to include construct curation - don't know if this is possible as both constructs and transgenes need to be assigned unique ids also any given transgene could have multiple constructs and any given construct could be used by multiple transgenes
- add functionality to exprpat, genereg, and topic OAs to enter construct requests
Postgres script to populate cns tables=
Construct tables = cns_
/home/postgres/work/pgpopulation/cns_construct/20140605_newOa
transfer_trp_to_cst.pl
Summary of transfer instructions:
table | OA label | data transfer |
cns_id | pgid | |
cns_timestamp | not a table | |
cns_curator | Curator | one-time copy from trp_curator |
cns_paper | Paper | one-time copy from trp_paper |
cns_person | Person | one-time copy from trp_person |
cns_name | Name | WBCnstr: $cnstid = &pad8Zeros($newPgid)//assigned WBConstructID |
cns_publicname | Public Name | extract Clone = /Clone: values from trp_constructionsummary and use to populated this field |
cns_othername | Other Name | |
cns_newtransgene | New Transgene | for production- will send a daily alert to the transgene curator based on new entries. |
cns_summary | Summary | one time copy from trp_summary |
cns_merge | Merge | |
cns_drivenbygene | Driven By Gene | transfer all values from trp_driven_by_gene delete trp_driven_by_gene |
cns_gene | Gene | transfer all values from trp_gene delete trp_gene |
cns_reporter | Reporter | transfer all values from trp_reporter_product except when the value is equal to a purification_tag value reporter values are: GFP, GFP(S65C), EGFP, pGFP(photoactivated GFP), YFP, EYFP, BFP, CFP, Cerulian, RFP, mRFP, tagRFP, mCherry, wCherry, tdTomato, mStrawberry, DsRed, DsRed2, Venus, YC2.1 (yellow cameleon), YC12.12 (yellow cameleon),YC3.60 (yellow cameleon), Yellow cameleon, Dendra, Dendra2, tdimer2(12)/dimer2, GCaMP, mkate2, Luciferase, LacI, LacO, LacZ delete trp_reporter |
cns_otherreporter | OtherReporter | transfer all values from trp_other_reporter delete trp_other_reporter |
cns_purificationtag | PurificationTag | Transfer all values from trp_reporter_product that equals any of the following values: His-tag, FLAG, HA-tag, MYC/c-myc, Stag, Histone H2B |
cns_recombinationsite | RecombinationSite | LoxP, FRT |
cns_constructtype | ConstructType | transfer all values from reporter_type: Chimera, Domain_swap,Engineered mutation, Fusion, Complex (e.g., GFP fusion plus point mutations), Transcriptional_fusion, Translational_fusion, N-terminal_translational_fusion, C-terminal_translational_fusion, Internal_coding_fusion transfer all values from trp_reporter_type delete trp_reporter_type |
cns_selectionmarker | SelectionMarker | (for elements stitched into contiguous sequence, coinjected elements will get their own construct ID, these will be joined together to create transgene within the Transgene OA) |
cns_threeutr | 3 UTR | create cns_threeutr table then move data from trp_threeutr delete after move |
cns_constructionsummary | ConstructionSummary | transfer values trp_driven_by_construct delete trp_driven_by_construct; transfer trp_rconstructionsummary for all trp_publicname lines that are not "Is" or are blank |
cns_fwdprimer | FWDprimer | for mapping to genome, can include entire construct sequence |
cns_revprimer | REVprimer | for mapping to genome, can include entire construct sequence |
cns_dna | DNAText | for mapping to genome, can include entire construct sequence |
cns_feature | Feature | See sequence feature wiki, implementation would be like that for expression pattern and gene regulation |
cns_proposedfeature | ProposedSeqFeature | where trp_threeutr had a value, populate with "3'UTR" |
cns_genewithfeature | FeatureGene | transfer from trp_threeutr |
cns_clone | Clone | |
cns_laboratory | Laboratory | copy from trp_laboratory |
cns_remark | Remark | transfer trp_remark for all trp_publicname lines that are not "Is" or are blank |