Difference between revisions of "Construct"
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==Postgres script to populate cns tables=== | ==Postgres script to populate cns tables=== | ||
− | Construct tables = cns_<br> | + | Construct tables = cns_:<br> |
/home/postgres/work/pgpopulation/cns_construct/20140605_newOa<br> | /home/postgres/work/pgpopulation/cns_construct/20140605_newOa<br> | ||
− | transfer_trp_to_cst.pl<br> | + | script for data population of cns_ tables from trp_tables: transfer_trp_to_cst.pl<br> |
Summary of transfer instructions: | Summary of transfer instructions: | ||
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| align="center" style="background:#f0f0f0;"|'''OA label''' | | align="center" style="background:#f0f0f0;"|'''OA label''' | ||
| align="center" style="background:#f0f0f0;"|'''data transfer''' | | align="center" style="background:#f0f0f0;"|'''data transfer''' | ||
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|cns_curator||Curator||one-time copy from trp_curator | |cns_curator||Curator||one-time copy from trp_curator | ||
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|cns_name||Name||WBCnstr: $cnstid = &pad8Zeros($newPgid)//assigned WBConstructID | |cns_name||Name||WBCnstr: $cnstid = &pad8Zeros($newPgid)//assigned WBConstructID | ||
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− | |cns_publicname||Public Name|| | + | |cns_publicname||Public Name||/Clone: values from trp_constructionsummary |
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− | |cns_othername||Other Name|| | + | |cns_othername||Other Name||transfer Expr from trp_publicname or trp_synonym |
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− | |cns_newtransgene||New Transgene||for production- will send a daily alert to the transgene curator based on new entries. | + | |'''delete table, not necessary anymore'''cns_newtransgene||New Transgene||for production- will send a daily alert to the transgene curator based on new entries. |
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|cns_summary||Summary||one time copy from trp_summary | |cns_summary||Summary||one time copy from trp_summary | ||
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|cns_drivenbygene||Driven By Gene||transfer all values from trp_driven_by_gene<br>delete trp_driven_by_gene | |cns_drivenbygene||Driven By Gene||transfer all values from trp_driven_by_gene<br>delete trp_driven_by_gene | ||
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|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<br>transfer all values from trp_reporter_type <br>delete trp_reporter_type | |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<br>transfer all values from trp_reporter_type <br>delete trp_reporter_type | ||
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− | |cns_selectionmarker||SelectionMarker|| | + | |cns_selectionmarker||SelectionMarker|| |
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− | |cns_threeutr||3 UTR|| create cns_threeutr table | + | |cns_threeutr||3 UTR|| create cns_threeutr table, transfer from trp_threeutr <br>delete trp_threeutr |
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− | |cns_constructionsummary||ConstructionSummary||transfer values trp_driven_by_construct <br>delete trp_driven_by_construct; <br>transfer | + | |cns_constructionsummary||ConstructionSummary||transfer values in trp_driven_by_construct <br>delete trp_driven_by_construct; <br>transfer trp_constructionsummary for all trp_publicname lines that are not "Is" or are blank; transfer all associated Expr in trp_publicname or trp_synonym to cns_othername |
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− | |cns_fwdprimer||FWDprimer|| | + | |cns_fwdprimer||FWDprimer|| |
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− | |cns_revprimer||REVprimer|| | + | |cns_revprimer||REVprimer|| |
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− | |cns_dna||DNAText|| | + | |cns_dna||DNAText|| |
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− | |cns_feature||Feature|| | + | |cns_feature||Feature|| |
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− | |cns_proposedfeature||ProposedSeqFeature|| | + | |cns_proposedfeature||ProposedSeqFeature|| |
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− | |cns_genewithfeature||FeatureGene|| | + | |cns_genewithfeature||FeatureGene|| |
|- | |- | ||
|cns_clone||Clone|| | |cns_clone||Clone|| |
Revision as of 19:35, 1 July 2014
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
script for data population of cns_ tables from trp_tables: transfer_trp_to_cst.pl
Summary of transfer instructions:
table | OA label | data transfer |
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 | /Clone: values from trp_constructionsummary |
cns_othername | Other Name | transfer Expr from trp_publicname or trp_synonym |
delete table, not necessary anymorecns_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_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 | |
cns_threeutr | 3 UTR | create cns_threeutr table, transfer from trp_threeutr delete trp_threeutr |
cns_constructionsummary | ConstructionSummary | transfer values in trp_driven_by_construct delete trp_driven_by_construct; transfer trp_constructionsummary for all trp_publicname lines that are not "Is" or are blank; transfer all associated Expr in trp_publicname or trp_synonym to cns_othername |
cns_fwdprimer | FWDprimer | |
cns_revprimer | REVprimer | |
cns_dna | DNAText | |
cns_feature | Feature | |
cns_proposedfeature | ProposedSeqFeature | |
cns_genewithfeature | FeatureGene | |
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 |