OA forms, tables, scripts, etc

OA form summaries

OA form	Function (Datatype)	Postgres Tables	Scripts	Ontologies used	Other dependencies	Curator	Other remarks
antibody	Antibody objects					Xiaodong Wang
concise	Concise Description					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
genereg	Gene regulation					Xiaodong Wang
interaction	Genetic and physical interactions	int_		Paper Gene Variation Phenotype Person Laboratory Antibody Rearrangement Transgene RNAi		Chris Grove, Gary Schindelman, Kimberly Van Auken, Karen Yook
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					Chris Grove, Gary Schindelman, Wen Chen
transgene	Transgene object curation	trp_ trp_tables	acedb/karen/transgene ./use_package.pl	Gene Paper Laboratory Person		Karen Yook

OA form ontology/dependency sources

Ontology	Source	Script updating information from source	Used in OA form
Paper	paper.obo		All
Gene	Gene name server		All?
Person			All?
Variation	Variation Name Server	/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl	Phenotype GO Interaction
GO			Process GO Expression
Phenotype	phenotype.obo		Phenotype Interaction Process
Molecule	molecule.obo from mop tables?		Phenotype Process Gene regulation, RNAi
Anatomy	WBbt.obo		Phenotype Process Expression
Lifestage	worm_development.obo		Phenotype Process Expression
Expression cluster	flat file	manual update to	Process
Taxon	/home/acedb/karen/processOA/wbspecies.txt (manually updated)	/home/acedb/karen/processOA/update_obo_taxon.pl	Process
Picture			Process
Transgene	trp tables	/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl ?
Rearrangements	obo_oa_ontology	/postgres/work/pgpopulation/obo_oa_ontologies/update_obo_oa_ontologies.pl	Phenotype Interaction
Process	prc tables		Interaction

app_tables

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