Difference between revisions of "All OA tables"
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| DB_info||mop_chemi||text||CasRN||all||-||-||-|| | | DB_info||mop_chemi||text||CasRN||all||-||-||-|| | ||
|- | |- | ||
− | | DB_info||mop_chebi||ontology||ChEBI_id||all||obo||chebi||||populated from ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo | + | | 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||-||-||-|| | | DB_info||mop_kegg||text||Kegg compound (Acc#)||all||-||-||-|| |
Revision as of 22:36, 9 June 2014
Contents
- 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 Allele phenotype
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_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 |
cns_tables Construct
postgres tables for the Construct class
dumper on tazendra at XXXXXXX
paper term info will show cns_name, cns_publicname, cns_constructionsummary, cns_newtransgene.
Model tag | table | type | OA label | tab | ontology_type | ontology_table | cross table population script | comment |
pgonly | cns_id | not a table | pgid | 1 | - | - | - | |
pgonly | cns_timestamp | not a table | none | - | ||||
pgonly | cns_curator | dropdown | Curator | 1 | - | - | - | one-time copy from trp_curator |
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 |
Name | cns_name | Auto-generated | Name | 1 | - | - | - | WBCnstr: $cnstid = &pad8Zeros($newPgid)//assigned WBConstructID |
Public_name | cns_publicname | Text | Public Name | all | - | - | ||
Other_name | cns_othername | Text | Other Name | 1 | - | - | ||
N/A | cns_newtransgene | Text | New Transgene | 1 | - | - | for production- will send a daily alert to the transgene curator based on new entries. | |
Summary | cns_summary | Bigtext | Summary | all | - | - | one time copy from trp_summary | |
pgonly | cns_merge | Text | Merge | 1 | Construct | cns_tables | ||
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 | 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 | OtherReporter | 2 | - | - | - | transfer all values from trp_other_reporter delete trp_other_reporter |
Purification_tag | cns_purificationtag | multidropdown | PurificationTag | 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 | 2 | - | - | - | LoxP, FRT |
Type_of_construct | cns_constructtype | dropdown | ConstructType | 2 | - | - | - | 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 |
Selection_marker | cns_selectionmarker | 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 within the Transgene OA) |
Construction_summary | cns_constructionsummary | BigText | ConstructionSummary | 2 | - | - | - | transfer values trp_driven_by_construct delete trp_driven_by_construct (note: original instructions were to transfer values from trp_constructionsummary, this is no longer requested) |
N/A | cns_fwdprimer | BigText | FWDprimer | 3 | - | - | - | for mapping to genome, can include entire construct sequence |
N/A | cns_revprimer | BigText | REVprimer | 3 | - | - | - | for mapping to genome, can include entire construct sequence |
DNA_text | cns_dna | BigText | DNAText | 3 | - | - | - | for mapping to genome, can include entire construct sequence |
Sequence_feature | cns_feature | ontology -autocomplete on ?Feature | Feature | 3 | - | - | - | See sequence feature wiki, implementation would be like that for expression pattern and gene regulation |
N/A | cns_proposedfeature | text | ProposedSeqFeature | 3 | - | - | - | where trp_threeutr had a value, populate with "3'UTR" |
N/A | cns_genewithfeature | ontology | FeatureGene | 3 | - | - | - | transfer from trp_threeutr |
Clone | cns_clone | multiontology | Clone | 3 | clone tables | - | ||
Laboratory | cns_laboratory | multiontology | Laboratory | 3 | WB laboratory | laboratory | - | populate (copy) from trp_laboratory |
Remark | cns_remark | BigText | Remark | 3 | - | - | - | |
Historical_gene | - |
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 | 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 | |||
pgonly | exp_transgeneflag | toggle | Transgene_flag | 2 | ||||
Associated_feature | exp_sequence_feature | multiontology | Sequence_feature | 2 | WBsf | |||
No dump | exp_nodump | No dump | 2 |
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 Process (Topic) curation
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"
| |||
Remark | pro_remark | bigtext | Remark | all |
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_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 | 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 | |||
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 delete after move | |
Reporter Reporter_product | trp_reporter_product | multidropdown | Reporter Product | 1 | move all values to cns_reporter delete after move | |||
Reporter Reporter_product | trp_other_reporter | text | Other reporter | 1 | move all values to cns_otherreporter delete after move | |||
Reporter ?Gene | trp_gene | multiontology | Gene | 1 | WBGene | gin_tables | move all values to cns_gene delete after move | |
3_UTR | trp_threeutr | multiontology | 3 UTR | 1 | WBGene | gin_tables | need to fit into sequence feature, create cns table then move data delete after move | |
Coinjection | trp_coinjectionconstruct | multiontology | CoinjectionConstruct | 1 | construct | cns_tables | ||
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 delete after move | |||
Construction_summary | trp_constructionsummary | bigtext | Construction Summary | 1 | did not move to cns_constructionsummary | |||
pgonly | trp_mergedinto | ontology | Merged Into | 1 | Transgene | |||
Associated_with Clone | trp_clone | multiontology | Clone | 2 | obo | clone | move all values to cns_clone delete after move | |
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 | FAIL | 3 | ||||||
Remark | trp_remark | bigtext | Remark | 3 | expression pattern see wiki | |||
pgonly | trp_cgcremark | bigtext | CGC remarks | 3 |
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 | |||
dbs_email | text | Contact e-mail | 1 | |||||
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 |
- for example in git file output, the URL http://www.signalink.org/protein/%s
should be written as
protein = 'http://www.signalink.org/protein/%s' --kjy 20:57, 11 October 2013 (UTC)