OA forms, tables, scripts, etc
From WormBaseWiki
Contents
OA form summaries
OA form wiki page model (all models) |
Curation focus | Postgres Tables ( oa tables) |
Dumper Script | Ontologies used | Other dependencies | Curator | Other remarks |
antibody model |
C. elegans antibodies | abp_ | /home/postgres/work/citace_upload/antibody/use_package.pl sym link: /home/acedb/xiaodong/antibody/use_package.pl |
Paper Gene Laboratory |
Xiaodong Wang | ||
concise gene model |
Concise Description | con_ | /home/postgres/work/citace_upload/concise/use_package.pl sym link: /home/acedb/kimberly/citace_upload/concise/wrapper.pl and /home/postgres/work/citace_upload/concise/dump_concise.pl |
n/a | n/a | Ranjana Kishore, Kimberly Van Auken | |
construct construct wiki model |
Constructs used in various classes | cns_ cns_tables |
/home/postgres/work/citace_upload/cns_construct/use_package.pl |
Karen Yook, Daniela Raciti, Xiaodong Wang | |||
disease disease wiki |
Worm models of human disease | dis_ | Ranjana Kishore | ||||
exprpat model |
Expression pattern of genes | exp_ | /home/postgres/work/citace_upload/expr_pattern/use_package.pl sym link: /home/acedb/draciti/oa_expr_ace_dumper/use_package.pl |
Paper Gene Anatomy GO Lifestage Type Transgene Antibody Clone Strain Laboratory |
Daniela Raciti | ||
gene class model |
Concise description of gene classes | Gene Paper |
Karen Yook | ||||
go go code model go term model |
Gene ontology annotation | Kimberly Van Auken, Ranjana Kishore | GO pipeline is currently in flux as we migrate to using Protein2GO | ||||
gene regulation genereg wiki model |
Gene regulation | grg_ grg_tables |
/home/postgres/work/citace_upload/gene_regulation/use_package.pl | Paper Interaction RNAi Antibody Transgene Variation Rearrangement Expr_pattern Sentence Gene Molecule Sequence Anatomy Lifestage |
/home/postgres/work/citace_upload/gene_regulation/get_gene_regulation_ace.pm (Required Perl module) |
Xiaodong Wang | |
gene interaction interaction wiki model |
Genetic and physical interactions | int_ int_tables |
/home/postgres/work/citace_upload/interaction/use_package.pl | Paper Gene Variation Phenotype Person Laboratory Antibody Rearrangement Transgene RNAi |
/home/acedb/xiaodong/assigning_interaction_ids/assign_interaction_ids.pl Nightly cronjob script to assign Interaction IDs to PGIDs that do not already have one |
Chris Grove, Gary Schindelman, Kimberly Van Auken, Karen Yook | Only one PGID per Interaction object. Some physical interactions are currently in BioGrid and will need to be migrated to postgres. |
molecule molecule wiki model |
Drug/Chemical/Small molecule objects | mop_ mop_tables |
acedb/karen/Molecule/dump_molecule_ace.pl acedb/karen/Molecule/database.ace |
Paper Chebi |
Karen Yook | ||
movie model |
Movies | mov_ | /home/acedb/draciti/oa_movie_ace_dumper use_movie_package.pl | Paper Expr_pattern Variation |
Daniela Raciti | ||
phenotype model |
Annotation of phenotypes to variations, strains, rearrangements, transgenes | app_ app_tables |
acedb/work/allele_phenotype/use_package.pl acedb/karen/phenote/paper_object/get_paper_object.pl |
Paper Person Variation Rearrangements Transgene Gene Phenotype Molecule Anatomy Lifestage Laboratory |
Karen Yook | 20131024 changed dumper to include signify dead gene status and invalid papers in err.out file | |
picture model |
Paper figure | pic_ | /home/acedb/draciti/oa_picture_ace_dumper/dump_picture_ace.pl | Paper Person Expr_pattern Anatomy GO Lifestage Cropped_from |
Daniela Raciti | ||
biological_topic WS225 model |
Topic curation | pro_ pro_tables |
/home/acedb/karen/process/use_process_curation_package.pl | Paper Person Phenotype Gene Molecule Anatomy Lifestage Expression cluster Taxon Picture |
Karen Yook | ||
process_term WS225 model |
Process term creation | prt_ prt_tables |
/home/acedb/karen/process/use_process_package.pl | Paper GO |
Karen Yook | ||
RNAi RNAi wiki model |
RNAi phenotype curation | rna_ rna_tables |
/home/postgres/work/citace_upload/rnai/use_package.pl | Paper Lifestage Phenotype Molecule Person Strain Laboratory PCR Product |
/home/postgres/work/citace_upload/rnai/get_rnai_ace.pm (Required Perl module) |
Chris Grove, Gary Schindelman, Wen Chen | Possible to have multiple PGIDs per WBRNAi object |
transgene transgene wiki model |
Transgene object curation | trp_ trp_tables |
/home/postgres/work/citace_upload/transgene/use_package.pl sym link: acedb/karen/WS_upload/transgene/use_package.pl |
Gene Paper Laboratory Person |
transgene.pl parses results from transgenes_in_ocr_papers.out and transgenes_in_regular_papers.out and enters them into the trp_tables transgenes_summary.pl finds Is/In/Ex transgenes and genomic expressions (not put in any pipeline yet /home/citpub/Karen/TgSummary/getNewTg.pl finds Ex transgenes and # of occurrences for prioritization |
Karen Yook |
OA form ontology/autocomplete dependencies and update scripts
Any field within an OA that works by autocomplete is in a postgres table. Many of them are either obo tables or taken from other OA datatype tables. obo tables are obo_data_<datatype>, obo_syn_<datatype> or obo_name_<datatype>. Other OA datatype tables include trp_<tables>, mop_, grg_, abp_. Exceptions are person, paper, gene data as these are not curated through an OA.
Last updated | Ontology/Autocomplete | postres table | Source(s) | Updating scripts | Used in OA |
WBPaper | pap_tables (non OA) | NCBI pap_tables paper editor |
/home/postgres/work/pgpopulation/pap_papers/new_papers/pap_match.pm the paper editor uses this module to look at NCBI to populate pap_tables |
All | |
201309 | Gene | gin_tables (non OA) | genename server (for most info)/WS (for CDS etc) |
WBGene_information_and_status_pipeline : /home/acedb/cron/populate_gin_locus.pl - updates information from nameserver nightly dumps /home/acedb/cron/populate_gin.pl - updates information from WS releases |
Most |
Person | two_tables (non OA) | cecilia person editor | manual for author, on-the-fly scripts for abstracts | Most | |
201310 | Variation object and term info | obo_name_variation obo_data_variation |
geneace nightly dumps and obo_tempfile_variation flat file | nightly_geneace.pl generic.cgi |
Phenotype GeneReg Interaction GO Movie |
GO | obo_name_goid and obo_syn_goid | http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo | /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl | Process GO Expression | |
Phenotype | phenotype_ontology_obo (from CVS on spica?) | /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl | Phenotype Interaction Process | ||
Molecule | molecule.obo from mop tables | Phenotype Process Gene regulation RNAi | |||
Anatomy | https://github.com/raymond91125/Wao/raw/master/WBbt.obo | /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl | Phenotype Process Expression | ||
Lifestage | https://raw.github.com/draciti/Life-stage-obo/master/worm_development.obo | /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl | Phenotype Process Expression | ||
201310 | Expression cluster | latest WS (cronjob) | /home/acedb/cron/update_ws_tazendra.pl /home/acedb/cron/dump_from_ws.sh; # dump .ace files and update postgres tables writes to a timestamp file my $dateOfWsDumpFile = '/home3/acedb/cron/dump_from_ws/files/latestDate'; `echo "$date" >> $dateOfWsDumpFile`; /home/postgres/work/pgpopulation/obo_oa_ontologies/ws_updates/populate_pg_from_ws.pl generates files to populate postgres tables for obo_ tables for exprcluster when the date in the timestamp file is more recent than the latest timestamp in gin_molname |
Process | |
Taxon | /home/acedb/karen/processOA/wbspecies.txt (manually updated) | /home/acedb/karen/processOA/update_obo_taxon.pl | Process | ||
Picture | Process | ||||
2011? | Transgene | from trp_tables | Expression Phenotype Gene regulation Interaction | ||
201309 | Rearrangement object and term info | geneace nightly dump | nightly_geneace.pl | Phenotype Interaction | |
Process | prc tables | Interaction | |||
<2012 | Laboratory | geneace nightly dump | nightly_geneace.pl | Transgene Expression pattern Interaction Phenotype /data1/Users/arunr/Curator_related/Alleles/scripts (for Mary Ann's alleles) | |
201309 | Clone object and term info | geneace nightly dumps | nightly_geneace.pl | Expression pattern Transgene | |
201309 | Strain object and term info | geneace nightly dumps | nightly_geneace.pl | Expression pattern Phenotype | |
ChEBI | ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/chebi.obo | /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl | Molecule | ||
Human Disease DO (humando) | https://diseaseontology.svn.sourceforge.net/svnroot/diseaseontology/trunk/HumanDO.obo | /postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl | Human disease |
OA form dropdown lists
These are the values associated with the dropdown lists in the fields of the OAs. These values are all hardcoded in the wormOA.pm on tazendra.
Controlled vocabulary lists associated with model tags (non-onotological vocabularies)
Last updated | OA | postgres table | ?Class tag |
Values (id - name) | Controlled vocab in model? |
Antibody | abp_clonality | ?Antibody Clonality |
Monoclonal Polyclonal |
yes | |
Antibody | abp_animal | ?Antibody Animal |
Goat Guinea-pig Rat Mouse Other_animal Rabbit Chicken |
yes | |
Antibody | abp_antigen | ?Antibody Antigen |
Peptide Protein other_antigen |
yes | |
Antibody | abp_source | ?Antibody Source |
No_orginal_reference Original_publication |
yes | |
Concise(description) | con_desctype | ?Gene Structured description |
Provisional_description Sequence_features Functional_pathway Functional_physical_interaction Biological_process Molecular_function Expression Other_description |
yes | |
Disease | dis_species | ?Species |
Pristionchus pacificus Homo sapiens Caenorhabditis japonica Caenorhabditis briggsae Cruznema tripartitum Caenorhabditis sp.3 Brugia malayi Caenorhabditis brenneri Caenorhabditis remanei Panagrellus redivivus Caenorhabditis elegans |
||
Expression pattern | exp_qualifier | Certain Partial Uncertain |
yes | ||
Expression pattern | exp_exprtype | Antibody Reporter_gene In_Situ RT_PCR Northern Western |
yes | ||
Expression pattern | exp_species | ?Species | Pristionchus pacificus Homo sapiens Caenorhabditis japonica Caenorhabditis briggsae Cruznema tripartitum Caenorhabditis sp.3 Brugia malayi Caenorhabditis brenneri Caenorhabditis remanei Panagrellus redivivus Caenorhabditis elegans |
no | |
GO | go_project | Reference Genomes PAINT Variation phenotype2GO Human Disease Gene Ortholog |
|||
GO | go_goontology | F(Molecular_function) P(Biological_function) C(Cellular_component) |
|||
GO | go_goinference | IDA IEA IEP IGI IMP IPI ISS NAS ND IC TAS RCA EXP ISA ISO ISM IGC |
|||
GO | go_accession | GO_REF:0000011 GO_REF:0000012 GO_REF:0000015 GO_REF:0000033 GO_REF:0000024 |
|||
GO | go_qualifier | NOT contributes_to colocalizes_with |
|||
GO | go_dbtype | protein gene transcript complex protein_structure |
|||
Gene regulation | grg_type | ?Interaction Regulatory |
Change_of_localization Change_of_expression_level |
yes | |
Gene regulation | grg_regulationlevel | ?Interaction Regulation_level |
Transcriptional Post_transcriptional Post_translational |
yes | |
Gene regulation | grg_result | ?Interaction Regulation_result |
Positive_regulate Negative_regulate Does_not_regulate |
yes | |
Interaction | int_type | ?Interaction Interaction_type |
Physical Predicted Genetic - Genetic Interaction Genetic - Negative genetic Genetic - Synthetic Genetic - Enhancement Genetic - Unilateral enhancement Genetic - Mutual enhancement Genetic - Positive genetic Genetic - Suppression Genetic - Complete suppression Genetic - Partial suppression Genetic - Unilateral suppression Genetic - Complete unilateral suppression Genetic - Partial unilateral suppression Genetic - Mutual suppression Genetic - Complete mutual suppression Genetic - Partial mutual suppression Genetic - Asynthetic Genetic - Suppression/Enhancement Genetic - Epistasis Genetic - Positive epistasis Genetic - Maximal epistasis Genetic - Minimal epistasis Genetic - Neutral epistasis Genetic - Qualitative epistasis Genetic - Opposing epistasis Genetic - Quantitative epistasis Genetic - Neutral genetic Genetic - Oversuppression Genetic - Unilateral oversuppression Genetic - Mutual oversuppression Genetic - Oversuppression/Enhancement Genetic - Phenotype bias Genetic - No_interaction |
yes | |
Interaction | int_detectionmethod | ?Interaction Detection_method |
Affinity_capture_luminescence Affinity_capture_MS Affinity_capture_RNA Affinity_capture_Western Cofractionation Colocalization Copurification Fluorescence_resonance_energy_transfer Protein_fragment_complementation_assay Yeast_two_hybrid Biochemical_activity Cocrystal_structure Far_western Protein_peptide Protein_RNA Reconstituted_complex Yeast_one_hybrid Directed_yeast_one_hybrid Electrophoretic_mobility_shift_assay |
yes | |
Interaction | int_neutralityfxn | ?Interaction Neutrality_function |
Multiplicative Additive Minimal |
yes | |
Interaction | int_otheronetype | ?Interaction | Transgene Chemical |
no | |
Interaction | int_othertwotype | ?Interaction | Transgene Chemical |
no | |
Phenotype | app_easescore | #Phenotype_info Ease_of_scoring |
ES0_Impossible_to_score #Evidence ES1_Very_hard_to_score #Evidence ES2_Difficult_to_score #Evidence ES3_Easy_to_score #Evidence |
yes | |
Phenotype | app_mmateff | ?Variation Mating_efficiency Male |
Male UNIQUE ME0_Mating_not_successful ME1_Mating_rarely_successful ME2_Mating_usually_successful ME3_Mating_always_successful |
yes | |
Phenotype | app_hmateff | ?Variation Mating_efficiency Hermaphrodite |
HME0_Mating_not_successful HME1_Mating_rarely_successful HME2_Mating_usually_successful HME3_Mating_always_successful |
yes | |
Phenotype | app_nature | #Phenotype_info | Recessive Semi_dominant Dominant |
yes | |
Phenotype | app_func | #Phenotype_info Loss_of_function/Gain_of_function |
Hypomorph Amorph Uncharacterised_loss_of_function Dominant_negative Hypermorph Neomorph Uncharacterised_gain_of_function |
yes | |
Phenotype | app_penetrance | #Phenotype_info Penetrance |
Incomplete Low High Complete |
yes | |
Phenotype | app_mat_effect | ?Phenotype_info Maternal |
Strictly_maternal With_maternal_effect |
yes | |
RNAi | rna_deliverymethod | ?RNAi Delivered_by |
Bacterial_feeding Injection Soaking Transgene_expression |
yes | |
RNAi | rna_species | Pristionchus pacificus Homo sapiens Caenorhabditis japonica Caenorhabditis briggsae Cruznema tripartitum Caenorhabditis sp.3 Brugia malayi Caenorhabditis brenneri Caenorhabditis remanei Panagrellus redivivus Caenorhabditis elegans |
|||
RNAi | rna_penetrance | ?Phenotype_info Penetrance |
Incomplete Low High Complete |
yes | |
Transgene | trp_reporter_product | ?Transgene | 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 Histone H2B His-tag FLAG HA-tag MYC/c-myc Stag |
no | |
Transgene | trp_integration_method | ?Transgene Integration_method |
Gamma_irradiation X-ray Spontaneous UV UV_TMP MMS_mutagenesis Single_copy_insertion Particle_bombardment EMS_mutagenesis |
no | |
Transgene | trp_reporter_type | ?Transgene Reporter_type |
Transcriptional fusion Translational fusion |
no | |
Transgene | trp_map | ?Transgene Map ?Map #Map_position |
I II III IV V X |
no |
Caltech use only
Last updated | OA | postgres table | ?Class tag |
Values (id - name) | Controlled vocab in model? |
ALL | <OA_table>_curator | Caltech use only | two1823 - Juancarlos Chan two101 - Wen Chen two1983 - Paul Davis two2021 - Jolene S. Fernandes two2987 - Chris two12884 - Snehalata Kadam two324 - Ranjana Kishore two363 - Raymond Lee two1 - Cecilia Nakamura two480 - Tuco two12028 - Daniela Raciti two1847 - Anthony Rogers two557 - Gary C. Schindelman two567 - Erich Schwarz two625 - Paul Sternberg two2970 - Mary Ann Tuli two1843 - Kimberly Van Auken two736 - Qinghua Wang two1760 - Xiaodong Wang two712 - Karen Yook |
no, not dumped | |
Phenotype | app_allele_status | Caltech use only | other lost new_gene_assignment |
no | |
Phenotype | app_curation_status | Caltech use only | happy not_happy down_right_disgusted |
no | |
Gene class | glc_type | molecular phenotype phenotype-function other |
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