Difference between revisions of "All OA tables"

From WormBaseWiki
Jump to navigationJump to search
 
(26 intermediate revisions by 3 users not shown)
Line 4: Line 4:
 
*all fields have a corresponding postgres history table  
 
*all fields have a corresponding postgres history table  
 
*ontology type "obo" refers to all three obo_name_<>, obo_syn_<>, and obo_term_<> tables
 
*ontology type "obo" refers to all three obo_name_<>, obo_syn_<>, and obo_term_<> tables
 +
 +
===access all table names===
 +
This postgres query will return all table names for a given OA without the _hst tables:
 +
SELECT table_schema, table_name FROM information_schema.tables WHERE table_schema = 'public' AND table_name ~ '^app' AND table_name ! ~ 'hst$';
  
 
===abp_tables  Antibody===
 
===abp_tables  Antibody===
Line 66: Line 70:
  
 
===app_tables Allele phenotype===
 
===app_tables Allele phenotype===
 +
-----> '''[[OA-phenotype#Phenotype_OA_postgres_tables | up to date tables]]'''<br>
 
'''postgres tables for the Variation/Strain/Transgene/Rearrangement Phenotype Curation<br> dumper on tazendra at /home/acedb/work/allele_phenotype/use_package.pl ''' <br> note: this dumper makes both allele_phenotype.ace and mol_phene.ace files
 
'''postgres tables for the Variation/Strain/Transgene/Rearrangement Phenotype Curation<br> dumper on tazendra at /home/acedb/work/allele_phenotype/use_package.pl ''' <br> note: this dumper makes both allele_phenotype.ace and mol_phene.ace files
 
{| border="1" cellpadding="2" cellspacing="2" {{table}}
 
{| border="1" cellpadding="2" cellspacing="2" {{table}}
Line 116: Line 121:
 
| Phenotype_info Affected_by ||app_molecule||multiontology||Molecule||2||Molecule||mop_tables||||
 
| Phenotype_info Affected_by ||app_molecule||multiontology||Molecule||2||Molecule||mop_tables||||
 
|-
 
|-
−
| Phenotype_info Anatomy_term||app_anat_term||multiontology||Anatomy||2||obo||anatomy||||
+
| Phenotype_info Anatomy_term||app_anatomy||multiontology||Anatomy||2||obo||anatomy||||
 
|-
 
|-
 
| Phenotype_info Phenotype_assay Life_stage||app_lifestage||multiontology||Life Stage||2||obo||lifestage||||
 
| Phenotype_info Phenotype_assay Life_stage||app_lifestage||multiontology||Life Stage||2||obo||lifestage||||
Line 226: Line 231:
  
 
===cns_tables  Construct===
 
===cns_tables  Construct===
 +
[[WormBase_Model:Construct | construct model page]]<br>
 +
[[Construct | construct wiki page]]<br>
 
'''postgres tables for the Construct class'''<br> '''dumper on tazendra at /home/postgres/work/citace_upload/cns_construct/use_package.pl''' <br> dumper errors will record dead papers from pap_status and dead genes from gin_dead<br> paper term info will show cns_name, cns_publicname, cns_constructionsummary, cns_newtransgene.
 
'''postgres tables for the Construct class'''<br> '''dumper on tazendra at /home/postgres/work/citace_upload/cns_construct/use_package.pl''' <br> dumper errors will record dead papers from pap_status and dead genes from gin_dead<br> paper term info will show cns_name, cns_publicname, cns_constructionsummary, cns_newtransgene.
 
{| border="1" cellpadding="2" cellspacing="2" {{table}}  
 
{| border="1" cellpadding="2" cellspacing="2" {{table}}  
Line 245: Line 252:
 
|-
 
|-
 
| style="color: grey;"| pgonly||cns_curator||dropdown||Curator||||1||-||-||-||one-time copy from trp_curator||<strike>dump as Curator_confirmed</strike><br>no dump
 
| style="color: grey;"| pgonly||cns_curator||dropdown||Curator||||1||-||-||-||one-time copy from trp_curator||<strike>dump as Curator_confirmed</strike><br>no dump
 +
|-
 +
|N/A ||cns_assoctransgene||text||Used for transgene||||3-between Laboratory and Remark||-||-||-||-||no dump
 +
|-
 +
|N/A ||cns_coinjectedwith||text||Coinjected with||||3 below Used for transgene||-||-||-||-||no dump
 +
|-
 +
|N/A ||cns_integrationmethod||single ontology||Integrated by||||3 below Coijencted with ||trp_integration_method||-||-||-||no dump
 +
|-
 +
|N/A ||cns_strain||text||Strain||||3 below Integrated by||-||-||-||-||no dump
 
|-
 
|-
 
|Reference||cns_paper||Multiontology||Paper||||all||WBPaper||pap_tables||-||one-time copy from trp_paper||
 
|Reference||cns_paper||Multiontology||Paper||||all||WBPaper||pap_tables||-||one-time copy from trp_paper||
Line 250: Line 265:
 
|Person||cns_person||Multiontology||Person||||1||WBPerson||person_tables||-||one-time copy from trp_person||
 
|Person||cns_person||Multiontology||Person||||1||WBPerson||person_tables||-||one-time copy from trp_person||
 
|-
 
|-
−
|||cns_name||Auto-generated||Name||autofilled||1||-||-||-||WBCnstr: $cnstid = &pad8Zeros($newPgid)//assigned WBConstructID||dump as Construct (Object header)
+
|||cns_name||Auto-generated||Name||autofilled||1||-||-||-||WBCnstr: $cnstid = &pad8Zeros($newPgid)//assigned WBConstructID||dump as Construct (Object header)<br> can term info for construct show associated transgenes?
 
|-
 
|-
 
|Public_name||cns_publicname||Text||Public Name||use clone name if any||all||-|-||-||||/Clone: values from trp_constructionsummary and use to populated this field.||
 
|Public_name||cns_publicname||Text||Public Name||use clone name if any||all||-|-||-||||/Clone: values from trp_constructionsummary and use to populated this field.||
Line 258: Line 273:
 
|N/A||cns_newtransgene||Text||New Transgene||hidden||1||-|-||-||||sends daily alert to the transgene curator based on new entries. not in use||no dump
 
|N/A||cns_newtransgene||Text||New Transgene||hidden||1||-|-||-||||sends daily alert to the transgene curator based on new entries. not in use||no dump
 
|-
 
|-
−
|Summary||cns_summary||Bigtext||Summary||genetic expression||all||-|-||-||||one time copy from trp_summary||
+
|Summary||cns_summary||Bigtext||Summary||genetic expression, stuff between brackets||all||-|-||-||||one time copy from trp_summary||
 
|-
 
|-
 
| style="color: grey;"| pgonly||cns_merge||Ontology||Merge||for duplicates||1||Construct||cns_tables||||||no dump
 
| style="color: grey;"| pgonly||cns_merge||Ontology||Merge||for duplicates||1||Construct||cns_tables||||||no dump
Line 268: Line 283:
 
|Fusion_reporter||cns_reporter||Multi-dropdown||Reporter||for fluorescent tag||2||-||-||-||transfer all values from trp_reporter_product except when the value is equal to a purification_tag value<br> 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<br>delete trp_reporter||
 
|Fusion_reporter||cns_reporter||Multi-dropdown||Reporter||for fluorescent tag||2||-||-||-||transfer all values from trp_reporter_product except when the value is equal to a purification_tag value<br> 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<br>delete trp_reporter||
 
|-
 
|-
−
|Other_reporter||cns_otherreporter||Text||OtherReporter||for anything not in other reporter dropdowns<br> for non-nematode genetic elements<br> pipe separate multiple objects||2||-||-||-||transfer all values from trp_other_reporter<br>delete trp_other_reporter||dump multiple objects (pipe separated)
+
|Other_reporter||cns_otherreporter||Text||Other Reporter||for anything not in other reporter dropdowns<br> for non-nematode genetic elements<br> pipe separate multiple objects||2||-||-||-||transfer all values from trp_other_reporter<br>delete trp_other_reporter||dump multiple objects (pipe separated)
 
|-
 
|-
−
|Purification_tag||cns_purificationtag||multidropdown||PurificationTag||for tags used for protein purification||2||-||-||-||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||
+
|Purification_tag||cns_purificationtag||multidropdown||Purification Tag||for tags used for protein purification||2||-||-||-||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||
 
|-
 
|-
−
|Recombination_site||cns_recombinationsite||multidropdown||RecombinationSite||for sites used in constructs made for engineering insertions||2||-||-||-||LoxP, FRT||
+
|Recombination_site||cns_recombinationsite||multidropdown||Recombination Site||for sites used in constructs made for engineering insertions||2||-||-||-||LoxP, FRT||
 
|-
 
|-
−
|Type_of_construct||cns_constructtype||dropdown||ConstructType||expanded to include descriptions for engineered variations||2||-||-||-||Dropdown values: Chimera, Domain_swap, Engineered_mutation, Fusion, Complex (e.g., GFP fusion plus point mutations), Transcriptional_fusion, Translational_fusion, Nterminal_translational_fusion, Cterminal_translational_fusion, Internal_coding_fusion<br>transfer all values from trp_reporter_type <br>delete trp_reporter_type||
+
|Type_of_construct||cns_constructtype||dropdown||Construct Type||expanded to include descriptions for engineered variations||2||-||-||-||Dropdown values: Chimera, Domain_swap, Engineered_mutation, Fusion, Complex (e.g., GFP fusion plus point mutations), Transcriptional_fusion, Translational_fusion, Nterminal_translational_fusion, Cterminal_translational_fusion, Internal_coding_fusion<br>transfer all values from trp_reporter_type <br>delete trp_reporter_type||
 
|-
 
|-
−
|Selection_marker||cns_selectionmarker||Text||SelectionMarker||for elements stitched into the contiguous sequence, coinjected elements will get their own construct ID, pipe separate multiple objects||2||-||-||-||||dump multiple objects (pipe separated)
+
|Selection_marker||cns_selectionmarker||Text||Selection Marker||for elements stitched into the contiguous sequence, coinjected elements will get their own construct ID, pipe separate multiple objects||2||-||-||-||||dump multiple objects (pipe separated)
 
|-
 
|-
 
|3_UTR||cns_threeutr||multiontology||3 UTR||||2||WBGene||gin_tables||||create cns_threeutr table, transfer from trp_threeutr <br>delete trp_threeutr table after move||
 
|3_UTR||cns_threeutr||multiontology||3 UTR||||2||WBGene||gin_tables||||create cns_threeutr table, transfer from trp_threeutr <br>delete trp_threeutr table after move||
 
|-
 
|-
−
|Construction_summary||cns_constructionsummary||BigText||ConstructionSummary||||2||-||-||-||transfer values trp_driven_by_construct <br>delete trp_driven_by_construct<br> all trp_constructionsummary Expr elements (in trp_publicname or trp_synonym) have been transfered, will be deleted from trp tables ||
+
|Construction_summary||cns_constructionsummary||BigText||Construction Details||For details about the construction of the construct||2||-||-||-||transfer values trp_driven_by_construct <br>delete trp_driven_by_construct<br> all trp_constructionsummary Expr elements (in trp_publicname or trp_synonym) have been transfered, will be deleted from trp tables ||
 
|-
 
|-
 
|N/A ||cns_fwdprimer||BigText||FWDprimer||not dumped||3||-||-||-||for mapping to genome, can include entire construct sequence||
 
|N/A ||cns_fwdprimer||BigText||FWDprimer||not dumped||3||-||-||-||for mapping to genome, can include entire construct sequence||
Line 286: Line 301:
 
|N/A ||cns_revprimer||BigText||REVprimer||not dumped||3||-||-||-||for mapping to genome, can include entire construct sequence||
 
|N/A ||cns_revprimer||BigText||REVprimer||not dumped||3||-||-||-||for mapping to genome, can include entire construct sequence||
 
|-
 
|-
−
|DNA_text ||cns_dna||BigText||DNAText||not dumped||3||-||-||-||for mapping to genome, can include entire construct sequence||
+
|DNA_text ||cns_dna||BigText||DNAText||dumped||3||-||-||-||for mapping to genome, can include entire construct sequence||
 
|-
 
|-
 
|Sequence_feature||cns_feature||ontology -autocomplete on ?Feature||Feature||value requested from Hinxton||2 and 3|||-||-||-||See [[Sequence_Feature | sequence feature wiki]], implementation would be like that for expression pattern and gene regulation||
 
|Sequence_feature||cns_feature||ontology -autocomplete on ?Feature||Feature||value requested from Hinxton||2 and 3|||-||-||-||See [[Sequence_Feature | sequence feature wiki]], implementation would be like that for expression pattern and gene regulation||
 
|-
 
|-
−
|N/A ||cns_proposedfeature||text||ProposedSeqFeature||for possible use for communication with hinxton||3||-||-||-||||
+
|N/A ||cns_proposedfeature||text||Proposed Seq Feature||for possible use for communication with hinxton||3||-||-||-||||
 
|-
 
|-
−
|N/A ||cns_genewithfeature||ontology||FeatureGene||for possible use for communication with hinxton|||3||-||-||-||||
+
|N/A ||cns_genewithfeature||ontology||Feature Gene||for possible use for communication with hinxton|||3||-||-||-||||
 
|-
 
|-
 
|Clone||cns_clone||multiontology||Clone||for vector, cosmid, fosmid, etc., used in the generation of the construct||3||||clone tables||-||||
 
|Clone||cns_clone||multiontology||Clone||for vector, cosmid, fosmid, etc., used in the generation of the construct||3||||clone tables||-||||
Line 299: Line 314:
 
|-
 
|-
 
|Remark||cns_remark||BigText||Remark||curation comments||3||-||-||-||||
 
|Remark||cns_remark||BigText||Remark||curation comments||3||-||-||-||||
 +
|-
 +
|N/A||N/A||entered from uP form||Used for Transgene||||3||-||-||-||||
 +
|-
 +
|N/A||N/A||entered from uP form||Coinjected with||||3||-||-||-||||
 +
|-
 +
|N/A||N/A||entered from uP form||Integration Method||||3||-||-||-||||
 +
|-
 +
|N/A||N/A||entered from uP form||Strain||||3||-||-||-||||
 
|-
 
|-
 
|Historical_gene||||||||||||||||-||||
 
|Historical_gene||||||||||||||||-||||
 
|-
 
|-
 +
|construct_for_disease||cnshumandiod||multiontology||Disease||||4||-||DO||-||||
 +
|-
 +
|N/A||cns_diseasepaper||multiontology, paper||Disease paper||reference for paper that uses construct for studying disease model||4||-||pap_tables||-|||||-
 +
|-
 +
| DB_info||cns_transgenome||text||Transgenome(Acc#)||||4||-||-||-||
 +
|-
 +
| DB_info||cns_addgene||text||Addgene ID||||4||-||-||-||
 +
|-
 +
| align="center" style="background:#f0f0f0;"|Model tag||align="center" style="background:#f0f0f0;"|pg table|| align="center" style="background:#f0f0f0;"|type|| align="center" style="background:#f0f0f0;"|OA label|| align="center" style="background:#f0f0f0;"|curator instructions|| align="center" style="background:#f0f0f0;"|OA tab|| align="center" style="background:#f0f0f0;"|ontology type|| align="center" style="background:#f0f0f0;"|ontology table|| align="center" style="background:#f0f0f0;"|cross table popuation script||align="center" style="background:#f0f0f0;"|pgcomment|| align="center" style="background:#f0f0f0;"|dumper comments
 
|}
 
|}
  
Line 328: Line 360:
 
|-
 
|-
 
| Gene||exp_gene||multiontology||Gene||1||WBGene||gin_tables||||
 
| Gene||exp_gene||multiontology||Gene||1||WBGene||gin_tables||||
 +
|-
 +
| Endogenous||exp_endogenous||toggle||Endogenous||1||||||||
 
|-
 
|-
 
| Anatomy_term||exp_anatomy||multi-ontology||Anatomy_term||1||obo||anatomy||||autocomplete on name;<br> term info- name, WBbt ID, store ID  
 
| Anatomy_term||exp_anatomy||multi-ontology||Anatomy_term||1||obo||anatomy||||autocomplete on name;<br> term info- name, WBbt ID, store ID  
Line 437: Line 471:
 
|}
 
|}
  
−
===pro_tables Process (Topic) curation===
+
===pro_tables Topic===
 
'''postgres tables for the topic term class<br> dumper on tazendra at /home/postgres/work/citace_upload/process/use_process_curation_package.pl* '''
 
'''postgres tables for the topic term class<br> dumper on tazendra at /home/postgres/work/citace_upload/process/use_process_curation_package.pl* '''
 
{| border="1" cellpadding="2" cellspacing="2" {{table}}  
 
{| border="1" cellpadding="2" cellspacing="2" {{table}}  
Line 457: Line 491:
 
|-
 
|-
 
| Paper_evidence||pro_paper||multi-ontology||WBPaper||1||WBPaper||pap_tables||||
 
| Paper_evidence||pro_paper||multi-ontology||WBPaper||1||WBPaper||pap_tables||||
 +
|-
 +
| not in model || pro_paperprimarystatus|| disabled OA field (not editable, read-only)||Paper Primary Status||1||||pap_tables|||| displays whether paper is 'primary', 'non-primary' (research article vs. review, for example); updated nightly on cronjob
 
|-
 
|-
 
| Topic Paper Status||pro_topicpaperstatus||dropdown||Topic Paper Status||1||||||||unchecked, relevant, irrelevant
 
| Topic Paper Status||pro_topicpaperstatus||dropdown||Topic Paper Status||1||||||||unchecked, relevant, irrelevant
Line 555: Line 591:
 
| ?Transgene||trp_name ||text||Name||1||||||||WBTransgeneID padded to 8, autogenerated for each new line
 
| ?Transgene||trp_name ||text||Name||1||||||||WBTransgeneID padded to 8, autogenerated for each new line
 
|-
 
|-
−
| Public_name||trp_public_name ||text||Public Name||1||||||/postgres/work/pgpopulation/textpresso/transgene/update_textpreso_transgene.pl| transgene.pl parses results from <br>[http://textpresso-dev.caltech.edu/transgene/Transgene transgenes_in_ocr_papers.out and<br>transgenes_in_regular_papers.out]<br>and enters them into the trp_tables||
+
| Public_name||trp_publicname ||text||Public Name||1||||||textpresso script for finding transgenes: update_textpreso_transgene.pl <br> transgene.pl parses results from <br>[http://textpresso-dev.caltech.edu/transgene/Transgene transgenes_in_ocr_papers.out and<br>transgenes_in_regular_papers.out]<br>and enters them into the trp_tables|| needs to be modified to create a construct as well.
 
|-
 
|-
 
| Synonym||trp_synonym ||text||Synonym||1||||||Expr_ [[Expression_Pattern#Exporting_Reporter_Gene_description_from_Expr_pattern_OA_to_Transgene_OA|wiki]]||
 
| Synonym||trp_synonym ||text||Synonym||1||||||Expr_ [[Expression_Pattern#Exporting_Reporter_Gene_description_from_Expr_pattern_OA_to_Transgene_OA|wiki]]||
Line 564: Line 600:
 
|-
 
|-
 
| Summary||trp_summary||bigtext||Summary||1||||||||copy to cns_geneticsummary
 
| Summary||trp_summary||bigtext||Summary||1||||||||copy to cns_geneticsummary
−
|-
 
−
| ''Promoter  Driven_by_gene ?Gene''||''trp_driven_by_gene'' ||multiontology||Driven by Gene||1||WBGene||gin_tables|||| move all values to cns_driven_by_gene<br>delete after move
 
−
|-
 
−
| ''Reporter  Reporter_product''||''trp_reporter_product'' ||multidropdown||Reporter Product||1||||||||move all values to cns_reporter<br>delete after move
 
−
|-
 
−
| ''Reporter  Reporter_product''||''trp_other_reporter'' ||text||Other reporter||1||||||||move all values to cns_otherreporter<br>delete after move
 
−
|-
 
−
| ''Reporter  ?Gene''||''trp_gene''||multiontology||Gene||1||WBGene||gin_tables||||move all values to cns_gene<br>delete after move
 
−
|-
 
−
| ''3_UTR''||''trp_threeutr''||multiontology||3 UTR||1||WBGene||gin_tables|||| create cns_threeutr table then move data <br>delete after move
 
 
|-
 
|-
 
|'''Coinjection'''||trp_coinjectionconstruct||multiontology||CoinjectionConstruct||1||construct||cns_tables||||autocomplete on cns_name, cns_publicname, cns_othername
 
|'''Coinjection'''||trp_coinjectionconstruct||multiontology||CoinjectionConstruct||1||construct||cns_tables||||autocomplete on cns_name, cns_publicname, cns_othername
 
|-
 
|-
 
| Coinjection_other||trp_coinjection||text||Coinjection||1||||||||Model name changed from Coinjection_marker - change dumper
 
| Coinjection_other||trp_coinjection||text||Coinjection||1||||||||Model name changed from Coinjection_marker - change dumper
−
|-
 
−
| ''Reporter_type''||trp_reporter_type ||dropdown||Reporter type||1||||||||move all values to cns_type<br>delete after move
 
 
|-
 
|-
 
| Construction_summary||trp_constructionsummary ||bigtext||Construction Summary||1||||||||did not move to cns_constructionsummary
 
| Construction_summary||trp_constructionsummary ||bigtext||Construction Summary||1||||||||did not move to cns_constructionsummary
 
|-
 
|-
 
| style="color: grey;"| pgonly||trp_mergedinto||ontology||Merged Into||1||Transgene||||||
 
| style="color: grey;"| pgonly||trp_mergedinto||ontology||Merged Into||1||Transgene||||||
−
|-
 
−
| ''Associated_with Clone''||trp_clone||multiontology||Clone||2||obo||clone||||move all values to cns_clone<br>delete after move
 
 
|-
 
|-
 
|'''Integrated_from'''||trp_integratedfrom||ontology||Integrated from||2||transgene||trp_ tables||||
 
|'''Integrated_from'''||trp_integratedfrom||ontology||Integrated from||2||transgene||trp_ tables||||
Line 611: Line 633:
 
| style="color: grey;"| pgonly||||||Search new||3|||||||
 
| style="color: grey;"| pgonly||||||Search new||3|||||||
 
|-
 
|-
−
| style="color: grey;"| pgonly||||||FAIL||3|||||||
+
| style="color: grey;"| pgonly||trp_objpap_falsepos||toggle||FAIL||3|||||||
 
|-
 
|-
 
| Remark||trp_remark||bigtext||Remark||3||||||expression pattern see [[Expression_Pattern#Exporting_Reporter_Gene_description_from_Expr_pattern_OA_to_Transgene_OA|wiki]]||
 
| Remark||trp_remark||bigtext||Remark||3||||||expression pattern see [[Expression_Pattern#Exporting_Reporter_Gene_description_from_Expr_pattern_OA_to_Transgene_OA|wiki]]||
 
|-
 
|-
 
| style="color: grey;"| pgonly||trp_cgcremark||bigtext||CGC remarks||3||||||||
 
| style="color: grey;"| pgonly||trp_cgcremark||bigtext||CGC remarks||3||||||||
 +
|-
 +
|Transgene_for_disease||trp_humandoid||multiontology||Disease||3||-||DO||-||added for WS251
 +
|-
 +
|N/A||trp_diseasepaper||multiontology, paper||Disease paper||3||-||pap_tables||-||added for WS251
 +
|-
 +
|||trp_variation||single ontology||Corresponding variation||2||-||obo_variation||-||added for crispr/engineered alleles
 +
|-
 +
| align="center" style="background:#f0f0f0;"|Model tag||align="center" style="background:#f0f0f0;"|pg table|| align="center" style="background:#f0f0f0;"|type|| align="center" style="background:#f0f0f0;"|OA label|| align="center" style="background:#f0f0f0;"|OA tab|| align="center" style="background:#f0f0f0;"|ontology type|| align="center" style="background:#f0f0f0;"|ontology table|| align="center" style="background:#f0f0f0;"|cross table popuation script||align="center" style="background:#f0f0f0;"|comment
 +
|}
  
−
|-
+
Tables removed 07/16/14
 +
trp_driven_by_gene<br>
 +
trp_reporter_product<br>
 +
trp_other_reporter<br>
 +
trp_gene<br>
 +
trp_threeutr<br>
 +
trp_clone<br>
 +
trp_reporter_type<br>
  
−
|}
+
Uncurated Expr constructs removed from trp tables. These objects have trp_synonym=Expr AND trp_publicname=blank; also all trp_publicname=Expr objects were deleted.
  
 
==PROPOSED OA tables==
 
==PROPOSED OA tables==

Latest revision as of 19:07, 27 June 2019

To OA form summaries

  • all in Tab column means the field exists in all tabs, or that there is only one tab in the OA.
  • all fields have a corresponding postgres history table
  • ontology type "obo" refers to all three obo_name_<>, obo_syn_<>, and obo_term_<> tables

access all table names

This postgres query will return all table names for a given OA without the _hst tables: 

SELECT table_schema, table_name FROM information_schema.tables WHERE table_schema = 'public' AND table_name ~ '^app' AND table_name ! ~ 'hst$';

abp_tables Antibody

postgres tables for the Antibody class
dumper on tazendra at /xiaodong/antibody/use_package.pl

Model tag table type OA label tab ontology_type ontology_table cross table population script comment
pgonly abp_id not a table pgid all* - - -
pgonly abp_timestamp not a table none -
pgonly abp_curator dropdown Curator all - - -
Antibody abp_name text Name all
Summary abp_summary bigtext Summary all
Other_name abp_other_name bigtext Other Name all
Gene abp_gene multiontology Gene all WBGene gin_tables
Original_publication abp_original_publication ontology Original Publication all WBPaper pap_tables
Person (not used??)
Laboratory abp_laboratory multiontology Laboratory all obo laboratory
Clonality abp_clonality dropdown Clonality all
Antigen abp_antigen dropdown Antigen all
Peptide abp_peptide bigtext Peptide all
Protein abp_protein bigtext Protein all
Source abp_source dropdown Source all
Animal abp_animal dropdown Animal all
Other_animal abp_other_animal bigtext Other Animal all
Other_antigen abp_other_antigen bigtext Other Antigen all
Possible_pseudonym abp_possible_pseudonym bigtext Possible Pseudonym all
Expr_pattern exp_antibody multiontology Antibody_info EXPRPAT tab2 Antibody abp_tables
Gene_regulation grg_antibody multiontology Antibody_info GENEREG tab2 Antibody abp_tables
Reference abp_paper multiontology Reference all WBPaper pap_tables
Remark abp_remark bigtext Remark all

app_tables Allele phenotype

> up to date tables

postgres tables for the Variation/Strain/Transgene/Rearrangement Phenotype Curation
dumper on tazendra at /home/acedb/work/allele_phenotype/use_package.pl
note: this dumper makes both allele_phenotype.ace and mol_phene.ace files

Model tag table type OA label tab ontology_type ontology_table cross table population script comment
pgonly app_legacy_info bigtext Legacy Info 1 NO DUMP field
pgonly app_curator dropdown Curator 1 - - -
pgonly app_allele_status dropdown Allele Status 1 used to trigger population a form for Mary Ann necessary?
pgonly app_curation_status dropdown Curation Status 1 NO DUMP field
Phenotype_info- Person_evidence app_person multiontology Person 1 WBPerson ?
pgonly app_id not a table pgid 1 - - -
Rearrangement app_rearrangement ontolog Rearrangement 1 obo rearrangement
Phenotype_info- Paper_evidence app_paper ontology Pub 1 WBPaper pap_tables
Variation app_variation ontology Variation 1 obo variation
Transgene app_transgene ontology Transgene 1 Transgene trp_tables
Phenotype_info- Caused_by ?Gene app_caused_by ontology Caused by 1 WBGene gin_tables
Strain app_strain text Strain 1
pgonly app_obj_remark text Object Remark 1 for Mary Ann- information displayed on ~postgres/cgi-bin/new_objects.cgi for a queried allele
Phenotype_info- Caused_by app_caused_by_other text Caused by Other 1
Phenotype_info Remark app_phen_remark bigtext Phenotype_remark 2 columnWidth=600
Phenotype_info Ease_of_scoring app_easescore dropdown ES 2
Variation Mating_efficiency app_mmateff dropdown ME 2
Variation Mating_efficiency app_hmateff dropdown HME 2
Phenotype_info Affected_by app_molecule multiontology Molecule 2 Molecule mop_tables
Phenotype_info Anatomy_term app_anatomy multiontology Anatomy 2 obo anatomy
Phenotype_info Phenotype_assay Life_stage app_lifestage multiontology Life Stage 2 obo lifestage
Rescued_by_transgene app_rescuedby multiontology Rescued By 2 Transgene trp_tables
?Variation Phentoype app_term ontology Phenotype 2 obo phenotype
Phenotype_info- Not_in tags app_not toggle NOT 2
Phenotype_info Phenotype_assay Temperature app_treatment bigtext Treatment 3
Phenotype_info Penetrance text app_percent bigtext Penetrance Remark 3
Phenotype_info by value app_nature dropdown Allele Nature 3
Phenotype_info Loss_of_function/Gain_of_function app_func dropdown Functional Change 3
Phenotype_info Penetrance app_penetrance dropdown Penetrance 3
Phenotype_info Maternal app_mat_effect dropdown Maternal Effect 3
Phenotype_info Phenotype_assay Temperature app_temperature text Temperature 3
Phenotype_info Phenotype_assay ? app_control_isolate text Control Isolate 3 needs to be added to model, used for parasitic nematodes
Phenotype_info Cold_sensitive app_cold_degree text Cold Sensitive Degree 3
Phenotype_info Heat_sensitive app_heat_degree text Heat Sensitive Degree 3
Phenotype_info Paternal app_pat_effect toggle Paternal Effect 3
Phenotype_info Haplo_insufficient app_haplo toggle Haploinsufficient 3
Phenotype_info Cold_sensitive app_cold_sens toggle_text Cold Sensitive 3
Phenotype_info Heat_sensitive app_heat_sens toggle_text Heat Sensitive 3
pgonly app_suggested_definition bigtext Suggested Definition 4 Cross posts on http://tazendra.caltech.edu/~postgres/cgi-bin/new_objects.cgi
pgonly app_child_of multiontology Child of 4 obo phenotype Cross posts on http://tazendra.caltech.edu/~postgres/cgi-bin/new_objects.cgi
pgonly app_suggested text Suggested 4 Cross posts on http://tazendra.caltech.edu/~postgres/cgi-bin/new_objects.cgi
Phenotype_assay Genotype app_genotype bigtext Genotype 5
pgonly app_intx_desc bigtext Genetic Intx Desc 5
pgonly app_nbp bigtext NBP 5
Phenotype #Evidence app_laboratory multiontology Laboratory Evidence 5 obo laboratory
pgonly app_entity ontology Entity 5 obo Entity PATO
pgonly app_quality ontology Quality 5 obo quality PATO
pgonly app_filereaddate text NBP / File Date 5
pgonly app_timestamp not a table none -

con_tables Concise description

postgres tables for Concise descriptions
dumper on tazendra at /home/postgres/work/citace_upload/concise/dump_concise.pl
sym link in /kimberly/citace_upload/concise/wrapper.pl

Model tag table type OA label tab ontology_type ontology_table cross table population script comment
pgonly con_id not a table pgid all* - - -
pgonly con_timestamp not a table none -
pgonly con_curator dropdown Curator all - - -
Gene con_wbgene ontology WBGene all WBGene gin_tables
con_curhistory ontology Curator History all Concurhst
Structured_description con_desctype dropdown Description Type all
con_desctext textarea Description Text all cols_size =90, rows_size=12
con_paper multiontology Reference all WBPaper pap_tables
con_accession text Accession Evidence all
con_lastupdate text Last Updated all
con_comment bigtext Comment all
con_nodump toggle NO DUMP all
con_person multiontology Person all WBPerson ?
con_exprtext text Expression Pattern all
con_rnai text RNAi all
con_microarray text Microarray all

cns_tables Construct

construct model page
construct wiki page
postgres tables for the Construct class
dumper on tazendra at /home/postgres/work/citace_upload/cns_construct/use_package.pl
dumper errors will record dead papers from pap_status and dead genes from gin_dead
paper term info will show cns_name, cns_publicname, cns_constructionsummary, cns_newtransgene.

Model tag table type OA label curator instructions tab ontology_type ontology_table cross table population script postgres comment dumper comments
pgonly cns_id not a table pgid autofilled 1 - - - no dump
pgonly cns_timestamp not a table none - no dump
pgonly cns_curator dropdown Curator 1 - - - one-time copy from trp_curator dump as Curator_confirmed
no dump
N/A cns_assoctransgene text Used for transgene 3-between Laboratory and Remark - - - - no dump
N/A cns_coinjectedwith text Coinjected with 3 below Used for transgene - - - - no dump
N/A cns_integrationmethod single ontology Integrated by 3 below Coijencted with trp_integration_method - - - no dump
N/A cns_strain text Strain 3 below Integrated by - - - - no dump
Reference cns_paper Multiontology Paper all WBPaper pap_tables - one-time copy from trp_paper
Person cns_person Multiontology Person 1 WBPerson person_tables - one-time copy from trp_person
cns_name Auto-generated Name autofilled 1 - - - WBCnstr: $cnstid = &pad8Zeros($newPgid)//assigned WBConstructID dump as Construct (Object header)
can term info for construct show associated transgenes?
Public_name cns_publicname Text Public Name use clone name if any all - - /Clone: values from trp_constructionsummary and use to populated this field.
Other_name cns_othername Text Other Name ex. Expr##Ex pipe separate multiple objects 1 - - dump multiple objects (pipe separated)
N/A cns_newtransgene Text New Transgene hidden 1 - - sends daily alert to the transgene curator based on new entries. not in use no dump
Summary cns_summary Bigtext Summary genetic expression, stuff between brackets all - - one time copy from trp_summary
pgonly cns_merge Ontology Merge for duplicates 1 Construct cns_tables no dump
Driven_by_gene cns_drivenbygene Multiontology Driven By Gene 2 WBGene gin_tables - transfer all values from trp_driven_by_gene
delete trp_driven_by_gene
Gene cns_gene Multiontology Gene 2 WBGene gin_tables - transfer all values from trp_gene
delete trp_gene
Fusion_reporter cns_reporter Multi-dropdown Reporter for fluorescent tag 2 - - - 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
Other_reporter cns_otherreporter Text Other Reporter for anything not in other reporter dropdowns
for non-nematode genetic elements
pipe separate multiple objects		 2 - - - transfer all values from trp_other_reporter
delete trp_other_reporter		 dump multiple objects (pipe separated)
Purification_tag cns_purificationtag multidropdown Purification Tag for tags used for protein purification 2 - - - 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
Recombination_site cns_recombinationsite multidropdown Recombination Site for sites used in constructs made for engineering insertions 2 - - - LoxP, FRT
Type_of_construct cns_constructtype dropdown Construct Type expanded to include descriptions for engineered variations 2 - - - Dropdown values: Chimera, Domain_swap, Engineered_mutation, Fusion, Complex (e.g., GFP fusion plus point mutations), Transcriptional_fusion, Translational_fusion, Nterminal_translational_fusion, Cterminal_translational_fusion, Internal_coding_fusion
transfer all values from trp_reporter_type
delete trp_reporter_type
Selection_marker cns_selectionmarker Text Selection Marker for elements stitched into the contiguous sequence, coinjected elements will get their own construct ID, pipe separate multiple objects 2 - - - dump multiple objects (pipe separated)
3_UTR cns_threeutr multiontology 3 UTR 2 WBGene gin_tables create cns_threeutr table, transfer from trp_threeutr
delete trp_threeutr table after move
Construction_summary cns_constructionsummary BigText Construction Details For details about the construction of the construct 2 - - - transfer values trp_driven_by_construct
delete trp_driven_by_construct
all trp_constructionsummary Expr elements (in trp_publicname or trp_synonym) have been transfered, will be deleted from trp tables
N/A cns_fwdprimer BigText FWDprimer not dumped 3 - - - for mapping to genome, can include entire construct sequence
N/A cns_revprimer BigText REVprimer not dumped 3 - - - for mapping to genome, can include entire construct sequence
DNA_text cns_dna BigText DNAText dumped 3 - - - for mapping to genome, can include entire construct sequence
Sequence_feature cns_feature ontology -autocomplete on ?Feature Feature value requested from Hinxton 2 and 3 - - - See sequence feature wiki, implementation would be like that for expression pattern and gene regulation
N/A cns_proposedfeature text Proposed Seq Feature for possible use for communication with hinxton 3 - - -
N/A cns_genewithfeature ontology Feature Gene for possible use for communication with hinxton 3 - - -
Clone cns_clone multiontology Clone for vector, cosmid, fosmid, etc., used in the generation of the construct 3 clone tables -
Laboratory cns_laboratory multiontology Laboratory 3 WB laboratory laboratory - populate (copy) from trp_laboratory
Remark cns_remark BigText Remark curation comments 3 - - -
N/A N/A entered from uP form Used for Transgene 3 - - -
N/A N/A entered from uP form Coinjected with 3 - - -
N/A N/A entered from uP form Integration Method 3 - - -
N/A N/A entered from uP form Strain 3 - - -
Historical_gene -
construct_for_disease cnshumandiod multiontology Disease 4 - DO -
N/A cns_diseasepaper multiontology, paper Disease paper reference for paper that uses construct for studying disease model 4 - pap_tables - -
DB_info cns_transgenome text Transgenome(Acc#) 4 - - -
DB_info cns_addgene text Addgene ID 4 - - -
Model tag pg table type OA label curator instructions OA tab ontology type ontology table cross table popuation script pgcomment dumper comments

exp_tables Expression Pattern

postgres tables for the Expression Pattern class
dumper on tazendra at /home/acedb/draciti/oa_expr_ace_dumper/use_package.pl

Model tag table type OA label tab ontology_type ontology_table cross table population script comment
pgonly exp_id not a table pgid all* - - -
pgonly exp_timestamp not a table none -
pgonly exp_curator dropdown Curator 2 - - -
Expr_pattern exp_name text Expr Pattern 1
Reference exp_paper ontology Reference 1 WBPaper pap_tables
Gene exp_gene multiontology Gene 1 WBGene gin_tables
Endogenous exp_endogenous toggle Endogenous 1
Anatomy_term exp_anatomy multi-ontology Anatomy_term 1 obo anatomy autocomplete on name;
term info- name, WBbt ID, store ID
Qualifier exp_qualifier dropdown Qualifier 1 Certain/Uncertain/Partial
Qualifier_text text bigtext Qualifier_text 1
GO_term exp_goid multiontology GO_term 1 obo goid
Subcellular_localization exp_subcellloc bigtext Subcellular Localization 1
Life_stage exp_lifestage multi-ontology Life_stage 1 obo lifestage autocomplete on name;
term info- name, store Life_stage ID
Species exp_species dropdown Species 1
Type exp_type multidropdown Type 2 Antibody/Reporter_gene/In_situ/RT_PCR..
Antibody exp_antibody bigtext Antibody_text 2
Reporter_gene exp_reportergene bigtext Reporter Gene 2
In_situ exp_insitu bigtext In Situ 2
RT_PCR exp_rtpcr bigtext RT PCR 2
Northern exp_northern bigtext Northern 2
Western exp_western bigtext Western 2
pgonly exp_pictureflag toggle Picture flag 2
Antibody_Info exp_antibody multidropdown Antibody_Info 2 abp_tables
pgonly exp_antibodyflag toggle Antibody flag 2
Pattern exp_pattern bigtext Pattern 2
Remark exp_remark bigtext Remark 2
Transgene exp_transgene multiontology Transgene 2 trp_tables
Construct exp_construct multiontology Construct 2 cns_tables
pgonly exp_transgeneflag toggle Transgene_flag 2
Associated_feature exp_sequence_feature multiontology Sequence_feature 2 WBsf
No dump exp_nodump No dump 2
Variation exp_variation multiontology Variation 2 variations obo

mop_tables Molecule

postgres tables for the Molecule class
dumper on tazendra at karen/Molecule/dump_molecule_ace.pl

Model tag table type OA label tab ontology_type ontology_table cross table population script comment
pgonly mop_id not a table pgid all* - - - WBMol: $molId = &pad8Zeros($newPgid)
pgonly mop_timestamp not a table none - - - -
pgonly mop_curator dropdown Curator all - - - same values in all OA curation tables
Name mop_name text Name all - - - WBMolID -added after tables were built
Public_name mop_publicname bigtext Public_name all - - -
Synonym mop_synonym bigtext Synonyms all - - -
DB_info mop_molecule text MeSH / CTD or default all - - - use MeSh ID here
originally used as Name
DB_info mop_chemi text CasRN all - - -
DB_info mop_chebi ontology ChEBI_id all obo chebi populated monthly from ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo (file on the chebi ftp site is updated monthly on the first Monday)
DB_info mop_kegg text Kegg compound (Acc#) all - - -
Remark mop_remark bigtext Remark all - - -
Reference mop_paper multiontology WBPaper all WBPaper pap_tables -
Molecule_use mop_moleculeuse bigtext Molecule use all - - -
Not in model mop_gotarget multiontology GO target all obo goid -
Not in model mop_genetarget multiontology Gene target all WBGene gin_tables -
DB_info mop_smmid text SMID-DB all - - -
Gene_regulation grg_moleculeregulator multiontology Molecule Regulator GENEREG tab3 Molecule mop_tables -
WBProcess pro_molecule multiontology Molecule PROCESS tab1 Molecule mop_tables -
Phenotype app_molecule multiontology Molecule PHENOTYPE tab2 Molecule mop_tables -
RNAi rna_molecule multiontology Molecule RNAi tab2 Molecule mop_ tables -
Interaction int_otheronetype
int_othertwotype		 dropdown Effected other type
Affected other type		 INTERACTION tab4 - - -

pro_tables Topic

postgres tables for the topic term class
dumper on tazendra at /home/postgres/work/citace_upload/process/use_process_curation_package.pl*

Model tag table type OA label tab ontology_type ontology_table cross table population script comment
pgonly pro_id not a table pgid all* - - -
pgonly pro_timestamp not a table none -
pgonly pro_curator dropdown Curator 1 - - -
Paper_evidence pro_paper multi-ontology WBPaper 1 WBPaper pap_tables
not in model pro_paperprimarystatus disabled OA field (not editable, read-only) Paper Primary Status 1 pap_tables displays whether paper is 'primary', 'non-primary' (research article vs. review, for example); updated nightly on cronjob
Topic Paper Status pro_topicpaperstatus dropdown Topic Paper Status 1 unchecked, relevant, irrelevant
WBProcess pro_process single ontology Process 1 autocomplete (term and syn)
store WBProcessID
term info: WBProcess ID, WBProcess,
Summary, other_name, WBPaper
Gene pro_wbgene multi-ontology Gene 1 obo gin_ tables autocomplete (public_name);
term info-name, WBGeneID, WBProcess, WBPaper
Phenotype pro_phenotype multi-ontology Phenotype 1 obo phenotype autocomplete (name and syn);
term info -description
Molecule pro_molecule multi-ontology Molecule 1 obo mop_ tables autocomplete (name and syn);
term info-molecule ID, name, syn
Anatomy_term pro_anatomy multi-ontology Anatomy_term 2 obo anatomy autocomplete on name;
term info- name, WBbt ID, store ID
Life_stage pro_lifestage multi-ontology Life_stage 2 obo lifestage autocomplete on name;
term info- name, store Life_stage ID
NCBITaxonomyID pro_taxon multi-ontology Taxon 2 obo obo_taxon autocomplete on species name
Expression_cluster pro_exprcluster multiontology Expression_cluster 2
Marker_construct pro_construct multiontology Marker_construct 2 (under expression cluster
Not in model yet pro_humdisease multiontology Human_disease 3 human disease table?
Picture pro_picture multiontology Picture 3 picture tables
Movie pro_movie Movie 3
Pathway pro_pathwaydb bigtext Pathway 3 "Database" "Database Field" "Accession Number"


pipe separate if there is more than one

Remark pro_remark bigtext Remark all
N/A pro_curationstatusomit toggle Curation Status Omit 3 A toggle on alerts Kimberly to papers that might the wrong or no primary/not primary paper status, and will prevent papers from showing up on the curation status form when filtering by topic.

prt_tables Process term

postgres tables for the topic term class
dumper on tazendra at /home/postgres/work/citace_upload/process/use_process_package.pl*

Model tag table type OA label tab ontology_type ontology_table cross table population script comment
pgonly prt_id not a table pgid all* - - -
pgonly prt_timestamp not a table none -
pgonly prt_curator dropdown Curator all - - -
WBProcess prt_processid auto-incremental based on new record WBbioprID all dump as WBProcess:"WBbiopr:00000000" 8 digits
Public_name prt_processname text Process Name all
Summary prt_summary bigtext Summary all
Other_name prt_othername bigtext Other_name all
GO_term prt_goid multiontology GO_term all obo goid
Specialisation_of prt_specialisationof multiontology Specialisation_of all
Generalisation_of prt_generalisationof multiontology Generalisation_of all
Reference prt_paper multiontology Reference all WBPaper pap_tables
Remark prt_remark bigtext Remark all

trp_tables Transgene

Paper TermInfo include trp_name, trp_publicname, trp_synonym, trp_summary, trp_construct(s)

Model tag table type OA label tab ontology_type ontology_table cross table population script comment
pgonly trp_timestamp not a table none -
pgonly trp_id not a table pgid 1 - - -
pgonly trp_curator dropdown Curator 1 copy to cns_curator
Reference trp_paper multiontology Paper 1 WBPaper pap_tables copy to cns_paper
Evidence trp_person multiontology Map person 1 WBPerson person_tables? copy to cns_person
?Transgene trp_name text Name 1 WBTransgeneID padded to 8, autogenerated for each new line
Public_name trp_publicname text Public Name 1 textpresso script for finding transgenes: update_textpreso_transgene.pl
transgene.pl parses results from
transgenes_in_ocr_papers.out and
transgenes_in_regular_papers.out
and enters them into the trp_tables		 needs to be modified to create a construct as well.
Synonym trp_synonym text Synonym 1 Expr_ wiki
Corresponding_variation trp_variation ontology CorrespodingVariation 1 Variation variation obo
Construct trp_construct multiontology Construct 1 construct cns_tables initially populate with corresponding WBConstruct IDs
Summary trp_summary bigtext Summary 1 copy to cns_geneticsummary
Coinjection trp_coinjectionconstruct multiontology CoinjectionConstruct 1 construct cns_tables autocomplete on cns_name, cns_publicname, cns_othername
Coinjection_other trp_coinjection text Coinjection 1 Model name changed from Coinjection_marker - change dumper
Construction_summary trp_constructionsummary bigtext Construction Summary 1 did not move to cns_constructionsummary
pgonly trp_mergedinto ontology Merged Into 1 Transgene
Integrated_from trp_integratedfrom ontology Integrated from 2 transgene trp_ tables
Integration_method trp_integration_method dropdown Integration Method 2
Map ?Map #Map_position trp_map multidropdown Map 2
#Map #Evidence trp_map_person multiontology Map person 2 WBPerson person tables
#Map #Evidence trp_map_paper multiontology Map Paper 2 WBPaper pap_ tables
Laboratory trp_laboratory multiontology Laboratory 2 obo laboratory
Associated_with_strain trp_strain text Strain 2
Used_for Marker_for trp_marker_for text Marker for 3
Used_for Marker_for #Evidence trp_marker_for_paper multiontology Marker for Paper 3 WBPaper pap_tables
Species trp_species text Species 3
Promoter Driven_by_construct trp_driven_by_construct text Driven by Construct 3 move to cns_constructionsummary
delete after move
pgonly Search new 3
pgonly trp_objpap_falsepos toggle FAIL 3
Remark trp_remark bigtext Remark 3 expression pattern see wiki
pgonly trp_cgcremark bigtext CGC remarks 3
Transgene_for_disease trp_humandoid multiontology Disease 3 - DO - added for WS251
N/A trp_diseasepaper multiontology, paper Disease paper 3 - pap_tables - added for WS251
trp_variation single ontology Corresponding variation 2 - obo_variation - added for crispr/engineered alleles
Model tag pg table type OA label OA tab ontology type ontology table cross table popuation script comment

Tables removed 07/16/14 trp_driven_by_gene
trp_reporter_product
trp_other_reporter
trp_gene
trp_threeutr
trp_clone
trp_reporter_type

Uncurated Expr constructs removed from trp tables. These objects have trp_synonym=Expr AND trp_publicname=blank; also all trp_publicname=Expr objects were deleted.

PROPOSED OA tables

dbs_tables Database

postgres tables for the Database class

Model tag table type OA label tab ontology_type ontology_table cross table population script comment
pgonly dbs_id not a table pgid 1 - - -
pgonly dbs_timestamp not a table none -
pgonly dbs_curator dropdown Curator 1 - - -
Database dbs_database text Database 1 (main label)
Database dbs_name text Public name 1 description
github only dbs_person text Database maintainer 1 maintainer
Email dbs_email text Contact e-mail 1 email
Description dbs_description bigtext Description 1
URL dbs_url text Database URL 1 base cols_size=90
URL_constructor dbs_urlconstructor bigtext URL constructor 1 search
pgonly dbs_remark bigtext Remark 1
github only dbs_otherurl text Database page URL 2 for git file output use name from URL page name*
github only dbs_otherurl text Database page URL 2 for git file output use name from URL page name
github only dbs_otherurl text Database page URL 2 for git file output use name from URL page name
github only dbs_otherurl text Database page URL 2 for git file output use name from URL page name
github only dbs_otherurl text Database page URL 2 for git file output use name from URL page name
github only dbs_otherurl text Database page URL 2 for git file output use name from URL page name
github only dbs_otherurl text Database page URL 2 for git file output use name from URL page name

protein = 'http://www.signalink.org/protein/%s' --kjy 20:57, 11 October 2013 (UTC)

Retrieved from "https://wiki.wormbase.org/index.php?title=All_OA_tables&oldid=34234"