OA forms, tables, scripts, etc

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

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