Construct

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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
  • add functionality to exprpat, genereg, int and topic OAs to enter construct requests

Adding new Reporter types

the cns_reporter obo_ tables don't seem to get often updated (looking at timestamp values). When there is a new reporter just add it directly like this (example for mNeonGreen):

  • INSERT INTO obo_name_cnsreporter VALUES ('mNeonGreen', 'mNeonGreen');
  • INSERT INTO obo_data_cnsreporter VALUES ('mNeonGreen', 'id: mNeonGreen');

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
In cases all cases where "Expr" is in trp_publicname, delete object from trp tables.
in cases where Expr is in trp_synonym and trp_publicname is blank, delete object from trp_tables.
hide table cns_newtransgene New Transgene for production
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 Construction Details 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_clone Clone copy from trp_clone NOTE: might have been deemed empty and deleted already, if not, delete trp_clone table
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

Going live to do list

Make new tables and run scripts :

  • create exp_construct + exp_variation tables for expression pattern :

/home/postgres/work/pgpopulation/exp_exprpattern/20140606_exp_construct_variation/create_datatype_tables.pl

  • create grg_construct table for gene regulation :

/home/postgres/work/pgpopulation/grg_generegulation/20140606_grg_construct/create_datatype_tables.pl

  • create int_construct table for interaction :

/home/postgres/work/pgpopulation/interaction/20140710_int_construct/create_datatype_tables.pl

  • create pro_construct table for process :

/home/postgres/work/pgpopulation/pro_process/20140708_pro_construct/create_datatype_tables.pl

  • create trp_variation trp_construct trp_coinjectionconstruct trp_integratedfrom tables for transgene :

/home/postgres/work/pgpopulation/transgene/20140605_construct_tables/create_transgene_construct_tables.pl

  • create all cns_ tables for construct objects :

/home/postgres/work/pgpopulation/cns_construct/20140605_newOa/create_construct_tables.pl


  • transfer construct data from transgene trp_ to construct cns_ :

/home/postgres/work/pgpopulation/cns_construct/20140605_newOa/transfer_trp_to_cns.pl

  • populate construct field of exp_ grg_ and int_ tables based on transgene to construct mappings :

/home/postgres/work/pgpopulation/cns_construct/20140710_transfer_construct_exp_grg_int/transfer_construct.pl


Sync dumpers at /home/postgres/work/citace_upload/

  • process/get_process_curation_ace.pm
  • transgene/get_transgene_ace.pm
  • expr_pattern/get_expr_pattern_ace.pm
  • interaction/get_interaction_ace.pm
  • gene_regulation/get_gene_regulation_ace.pm
  • whole new directory cns_construct/

Sync OA