OA forms, tables, scripts, etc

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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_
abp_tables
/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
wiki
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
Topic wiki
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
Process_term wiki
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

Back to Caltech documentation