Difference between revisions of "All OA tables"

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|Construction_summary||cnst_summary||BigText||Description||2||-||-||-||Transfer all trp_constructionsummary
 
|Construction_summary||cnst_summary||BigText||Description||2||-||-||-||Transfer all trp_constructionsummary
 
|-
 
|-
|N/A ||cnst_fwdprimer||BigText||FWDprimer||2&3||-||-||-||for mapping to genome, can include entire construct sequence
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|N/A ||cnst_fwdprimer||BigText||FWDprimer||3||-||-||-||for mapping to genome, can include entire construct sequence
 
|-
 
|-
|N/A ||cnst_revprimer||BigText||REVprimer||2&3||-||-||-||for mapping to genome, can include entire construct sequence
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|N/A ||cnst_revprimer||BigText||REVprimer||3||-||-||-||for mapping to genome, can include entire construct sequence
 
|-
 
|-
|DNA_text ||cnst_DNA||BigText||DNAText||2&3||-||-||-||for mapping to genome, can include entire construct sequence
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|DNA_text ||cnst_DNA||BigText||DNAText||3||-||-||-||for mapping to genome, can include entire construct sequence
 
|-
 
|-
|Sequence_feature||cnst_feature||ontology -autocomplete on ?Feature||Feature||2&3|||-||-||-||See [[Sequence_Feature | sequence feature wiki]], implementation would be like that for expression pattern and gene regulation
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|Sequence_feature||cnst_feature||ontology -autocomplete on ?Feature||Feature||3|||-||-||-||See [[Sequence_Feature | sequence feature wiki]], implementation would be like that for expression pattern and gene regulation
 
|-
 
|-
 
|Recombination_site||cnst_recombination_site||Text||||3||-||-||-||need to think about this one more
 
|Recombination_site||cnst_recombination_site||Text||||3||-||-||-||need to think about this one more
 
|-
 
|-
|Clone||cnst_clone||multiontology||Clone||2&3||||clone tables||-||
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|Clone||cnst_clone||multiontology||Clone||3||||clone tables||-||
 
|-
 
|-
 
|Laboratory||cnst_laboratory||multiontology||Laboratory||3||WB laboratory||laboratory||-||transfer all trp_laboratory
 
|Laboratory||cnst_laboratory||multiontology||Laboratory||3||WB laboratory||laboratory||-||transfer all trp_laboratory

Revision as of 09:26, 4 June 2014

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

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 Phenotype

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_anat_term 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 /kimberly/citace_upload/concise/wrapper.pl and /home/postgres/work/citace_upload/concise/dump_concise.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

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
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 Certain/Uncertain/Partial
Qualifier_text text bigtext
GO_term exp_goid multiontology GO_term all obo goid
Subcellular_localization exp_subcellloc bigtext
Life_stage exp_lifestage multi-ontology Life_stage 1 obo lifestage autocomplete on name;
term info- name, store Life_stage ID
Species exp_species Species
Type exp_type Type 2 Antibody/Reporter_gene/In_situ/RT_PCR..
Antibody_text exp_antibody Antibody_text 2
Reporter_gene_Text exp_reportergene Reporter Gene 2
In_Situ exp_insitu In Situ 2
RT_PCR exp_rtpcr RT PCR 2
Northern exp_northern Northern 2
Western exp_western Western 2
Picture_flag exp_pictureflag Picture flag 2
Antibody_Info exp_antibody Antibody_Info 2 abp_tables
Antibody_flag exp_antibodyflag Antibody flag 2
Pattern exp_pattern Pattern 2
Remark exp_remark Remark 2
Transgene exp_transgene Transgene 2 trp_tables
Transgene_flag exp_transgeneflag Transgene_flag 2
Sequence_feature exp_sequence_feature Sequence_feature 2 WBsf
No dump exp_nodump No dump 2

cnst_tables Construct

postgres tables for the Construct class
dumper on tazendra at XXXXXXX

Model tag table type OA label tab ontology_type ontology_table cross table population script comment
pgonly cnst_id not a table pgid 1 - - -
pgonly cnst_timestamp not a table none -
pgonly cnst_curator dropdown Curator 1 - - -
Reference cnst_paper multi-ontology Paper 1&2 WBPaper pap_tables - transfer all trp_paper
Person cnst_person multiontology Person 1 WBPerson person_tables - transfer all trp_person
Name cnst_name auto-generated Name 1 - - - WBCnstr: $cnstid = &pad8Zeros($newPgid)//assigned WBConstructID
Public_name cnst_publicname Text PublicName 1&2 - -
Other_name cnst_othername Text OtherName 1 - -
Summary cnst_geneticsummary Bigtext Summary 1&2 - -
Drives_transgene cnst_transgene multiontology Transgene 1 Transgene trp_tables - autocomplete on trp_name, trp_public_name, trp_synonym
transfer all values from trp_name
N/A cnst_merge text Merge 1 Construct cnst_tables
Driven_by_gene cnst_driven_by_gene multiontology DrivenByGene 2 WBGene gin_tables - transfer all values from trp_driven_by_gene
Gene cnst_gene multiontology Gene 2 WBGene gin_tables - transfer all values from trp_gene
Fusion_reporter cnst_reporter multi-dropdown Reporter 2 - - - transfer all values from trp_reporter_product
Other_reporter cnst_other_reporter Text OtherReporter 2 - - - transfer all values from trp_other_reporter
Purification_tag cnst_purification_tag multi-dropdown PurificationTag 2 - - - FLAG, HA, Myc, TAP, etc.
Type_of_construct cnst_type dropdown ConstructType 2 - - - 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
transfer all values from trp_reporter_type
Selection_marker cnst_selection_marker Text SelectionMarker 2 - - - (for elements stitched into contiguous sequence, coinjected elements will get their own construct ID, these will be joined together to create transgene)
Construction_summary cnst_summary BigText Description 2 - - - Transfer all trp_constructionsummary
N/A cnst_fwdprimer BigText FWDprimer 3 - - - for mapping to genome, can include entire construct sequence
N/A cnst_revprimer BigText REVprimer 3 - - - for mapping to genome, can include entire construct sequence
DNA_text cnst_DNA BigText DNAText 3 - - - for mapping to genome, can include entire construct sequence
Sequence_feature cnst_feature ontology -autocomplete on ?Feature Feature 3 - - - See sequence feature wiki, implementation would be like that for expression pattern and gene regulation
Recombination_site cnst_recombination_site Text 3 - - - need to think about this one more
Clone cnst_clone multiontology Clone 3 clone tables -
Laboratory cnst_laboratory multiontology Laboratory 3 WB laboratory laboratory - transfer all trp_laboratory
Remark cnst_remark BigText Remark 3 - - -
Historical_gene -

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
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 - - -

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

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
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 multi-ontology Expression_cluster 2
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

trp_tables Transgene

Model tag table type OA label tab ontology_type ontology_table cross table population script comment
Summary trp_summary bigtext Summary 1
Construction_summary trp_constructionsummary bigtext Construction Summary 1
pgonly trp_cgcremark bigtext CGC remarks 1
Reporter_type trp_reporter_type dropdown Reporter type 1
Reporter Reporter_product trp_reporter_product multidropdown Reporter Product 1
Promoter Driven_by_gene ?Gene trp_driven_by_gene multiontology Driven by Gene 1 WBGene gin_tables
Reporter ?Gene trp_gene multiontology Gene 1 WBGene gin_tables
3_UTR trp_threeutr multiontology 3 UTR 1 WBGene gin_tables
pgonly trp_id not a table pgid 1 - - -
pgonly trp_mergedinto ontology Merged Into 1 Transgene
?Transgene trp_name text Name 1 expression pattern/textpresso
Public_name trp_public_name text Public Name 1 transgene.pl parses results from
transgenes_in_ocr_papers.out and
transgenes_in_regular_papers.out

and enters them into the trp_tables
Synonym trp_synonym text Synonym 1 expression pattern see wiki
Reporter Reporter_product trp_other_reporter text Other reporter 1
Coinjection_marker trp_coinjection text Coinjection 1
Integration_method trp_integration_method dropdown Integration Method 2
Map ?Map #Map_position trp_map multidropdown Map 2
Associated_with Clone trp_clone multiontology Clone 2 obo clone
#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
Remark trp_remark bigtext Remark 3 expression pattern see wiki
pgonly trp_curator dropdown Curator 3 expression pattern/ textpresso
Reference trp_paper multiontology Paper 3 WBPaper pap_tables
Evidence trp_person multiontology Map person 3 WBPerson person_tables?
Used_for Marker_for #Evidence trp_marker_for_paper multiontology Marker for Paper 3 WBPaper pap_tables
Used_for Marker_for trp_marker_for test Marker for 3
Species trp_species text Species 3
Promoter Driven_by_construct trp_driven_by_construct text Driven by Construct 3
pgonly trp_timestamp not a table none -

PROPOSED OA tables

dbs_tables Database

postgres tables for the Database class
dumper on tazendra at /karen/database/

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)