Difference between revisions of "All OA tables"
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| ||con_microarray||text||Microarray||all|||||||| | | ||con_microarray||text||Microarray||all|||||||| | ||
|} | |} | ||
− | + | ===cnstr_tables Construct=== | |
+ | '''postgres tables for the Construct class<br> dumper on tazendra at XXXXXXX ''' | ||
+ | {| border="1" cellpadding="2" cellspacing="2" {{table}} | ||
+ | | align="center" style="background:#f0f0f0;"|'''Model tag''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''table''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''type''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''OA label''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''tab''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''ontology_type''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''ontology_table''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''cross table population script''' | ||
+ | | align="center" style="background:#f0f0f0;"|'''comment''' | ||
+ | |- | ||
+ | | style="color: grey;"| pgonly||cnstr_id||not a table||pgid||all*||-||-||-|| | ||
+ | |- | ||
+ | | style="color: grey;"| pgonly||cnstr_timestamp||not a table||none||||-|||||| | ||
+ | |- | ||
+ | | style="color: grey;"| pgonly||cnstr_curator||dropdown||Curator||all||-||-||-|| | ||
+ | |- | ||
+ | |Name ||cnstr_name|| ||Name||all*||-||-||-||WBMol: $molId = &pad8Zeros($newPgid)//assigned WBConstructID mop_id | ||
+ | |- | ||
+ | |Public_name ?Text | ||
+ | |- | ||
+ | |Other_name ?Text | ||
+ | |- | ||
+ | |Summary ?Text //genotype like [Pmyo-2::GFP] | ||
+ | |- | ||
+ | |Sequence_feature ?Feature XREF Construct | ||
+ | |- | ||
+ | |Driven_by_gene ?Gene XREF Drives_transgene | ||
+ | |- | ||
+ | |Gene ?Gene XREF Transgene_product | ||
+ | |- | ||
+ | |Fusion_reporter ?Text //fluorescent proteins GFP, RFP, mCherry, etc. | ||
+ | |- | ||
+ | |Other_reporter ?Text //to add reporters, tags that aren’t included in model | ||
+ | |- | ||
+ | |Purification_tag ?Text //FLAG, HA, Myc, TAP, etc. | ||
+ | |- | ||
+ | |Recombination_site ?Text //LoxP, FRT | ||
+ | |- | ||
+ | |Type_of_construct|| | ||
+ | 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 | ||
+ | |Selection_marker ?Text //for elements stitched into contiguous sequence, coinjected elements will get their own construct ID, these will be joined together to create transgene | ||
+ | |Construction_summary ?Text //Backbone vector, mol bio | ||
+ | DNA_text ?text // for mapping to genome, can include entire construct sequence | ||
+ | Clone ?Clone XREF Clone | ||
+ | |Used_for | ||
+ | Transgene_construct ?Transgene XREF Construct | ||
+ | Transgene_coinjection ?Transgene XREF Coinjection | ||
+ | Engineered_variation ?Variation XREF Derived_from | ||
+ | Topic_output_indicator ?WBProcess XREF marker_construct | ||
+ | Expression_pattern ?Expr_pattern XREF Construct | ||
+ | |Reference ?Paper XREF Construct | ||
+ | |Person ?Person XREF Construct | ||
+ | |Laboratory ?Laboratory #Lab_Location | ||
+ | |Historical_gene ?Gene #Evidence | ||
+ | |Remark ?Text #Evidence | ||
+ | |} | ||
===mop_tables Molecule=== | ===mop_tables Molecule=== | ||
'''postgres tables for the Molecule class<br> dumper on tazendra at karen/Molecule/dump_molecule_ace.pl''' | '''postgres tables for the Molecule class<br> dumper on tazendra at karen/Molecule/dump_molecule_ace.pl''' |
Revision as of 20:15, 12 May 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 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 |
cnstr_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 | cnstr_id | not a table | pgid | all* | - | - | - | ||
pgonly | cnstr_timestamp | not a table | none | - | |||||
pgonly | cnstr_curator | dropdown | Curator | all | - | - | - | ||
Name | cnstr_name | Name | all* | - | - | - | WBMol: $molId = &pad8Zeros($newPgid)//assigned WBConstructID mop_id | ||
Public_name ?Text | |||||||||
Other_name ?Text | |||||||||
Summary ?Text //genotype like [Pmyo-2::GFP] | |||||||||
Sequence_feature ?Feature XREF Construct | |||||||||
Driven_by_gene ?Gene XREF Drives_transgene | |||||||||
Gene ?Gene XREF Transgene_product | |||||||||
Fusion_reporter ?Text //fluorescent proteins GFP, RFP, mCherry, etc. | |||||||||
Other_reporter ?Text //to add reporters, tags that aren’t included in model | |||||||||
Purification_tag ?Text //FLAG, HA, Myc, TAP, etc. | |||||||||
Recombination_site ?Text //LoxP, FRT | |||||||||
Type_of_construct |
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 |
Selection_marker ?Text //for elements stitched into contiguous sequence, coinjected elements will get their own construct ID, these will be joined together to create transgene | Construction_summary ?Text //Backbone vector, mol bio
DNA_text ?text // for mapping to genome, can include entire construct sequence Clone ?Clone XREF Clone |
Used_for
Transgene_construct ?Transgene XREF Construct Transgene_coinjection ?Transgene XREF Coinjection Engineered_variation ?Variation XREF Derived_from Topic_output_indicator ?WBProcess XREF marker_construct Expression_pattern ?Expr_pattern XREF Construct |
Reference ?Paper XREF Construct | Person ?Person XREF Construct | Laboratory ?Laboratory #Lab_Location | Historical_gene ?Gene #Evidence | Remark ?Text #Evidence |
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 | - | - | - |
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 | |||
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)