OA forms, tables, scripts, etc

OA form summaries

OA form	Function (Datatype)	Postgres Tables	Dumper Script	Ontologies used	Other dependencies	Curator	Other remarks
antibody	Antibody objects		/home/acedb/xiaodong/antibody/use_package.pl	Paper Gene Laboratory		Xiaodong Wang
concise	Concise Description	con_	/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
disease	Worm models of human disease	dis_				Ranjana Kishore
exprpat	Expression pattern of genes	expr_	/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	Concise description of gene classes			Gene Paper		Karen Yook
go	Gene ontology annotation					Kimberly Van Auken, Ranjana Kishore	GO pipeline is currently in flux as we migrate to using Protein2GO
genereg	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
interaction	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	Drug/Chemical/Small molecule objects	mop_	acedb/karen/Molecule/dump_molecule_ace.pl acedb/karen/Molecule/database.ace	Paper Chebi		Karen Yook
movie	Movies	mov_	/home/acedb/draciti/oa_movie_ace_dumper use_movie_package.pl	Paper Expr_pattern Variation		Daniela Raciti
phenotype	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
picture	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
process	Process curation	prc_	/home/acedb/karen/process/use_process_curation_package.pl	Paper Person GO Phenotype Gene Molecule Anatomy Lifestage Expression cluster Taxon Picture		Karen Yook
process term	Creation of process names	pro_	/home/acedb/karen/process/use_process_package.pl	Paper		Karen Yook
rnai	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 object curation	trp_ trp_tables	acedb/karen/transgene ./use_package.pl	Gene Paper Laboratory Person	/postgres/work/pgpopulation/textpresso/transgene/update_textpreso_transgene.pl which makes http://textpresso-dev.caltech.edu/transgene/ /home/citpub/Karen/TgSummary/getNewTg.pl parses results into trp_tables	Karen Yook

OA form ontology/dependency and sources

Ontology	Source(s)	Script(s) updating information from source	Used in OA form
Paper	paper.obo		All
Gene	Gene name server		All?
Person			All?
Variation	/home/acedb/jolene/WS_AQL_queries/Variation_gene.txt queried from the latest release for variation-gene mappings and http://www.sanger.ac.uk/cgi-bin/Projects/C_elegans/nameserver_json.pl?domain=Variation -Variation Name Server for immediate variation updates (no gene mappings)	http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo	Phenotype GO Interaction
GO	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	http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_ontology_obo.cgi (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
Expression cluster	/home/acedb/jolene/WS_AQL_queries/expr_cluster.txt manually queried from latest release	http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo?	Process
Taxon	/home/acedb/karen/processOA/wbspecies.txt (manually updated)	/home/acedb/karen/processOA/update_obo_taxon.pl	Process
Picture			Process
Transgene	/home/acedb/jolene/WS_AQL_queries/transgene_summary.txt manual query of latest release for term info in OA, trp_transgenes(?)	http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo?
Rearrangements	/home/acedb/jolene/WS_AQL_queries/rearr_simple	http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo?	Phenotype Interaction
Process	prc tables		Interaction
Laboratory	obo_data_laboratory	/home/acedb/cron/populate_gin.pl	Transgene Expression pattern Interaction Phenotype
Clone	/home/acedb/jolene/WS_AQL_queries/clone_info.txt manually queried from latest release	http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo?	Expression pattern
Strain	/home/acedb/jolene/WS_AQL_queries/strains.txt manually queried from latest release	http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=UpdateVariationObo?	Expression pattern
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

app_tables

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