All OA tables

To OA form summaries

• all in Tab column means the field exists in all tabs, or that there is only one tab in the OA.
• all fields have a corresponding postgres history table
• ontology type "obo" refers to all three obo_name_<>, obo_syn_<>, and obo_term_<> tables

abp_tables Antibody

postgres tables for the Antibody class
dumper on tazendra at /xiaodong/antibody/use_package.pl

Model tag	table	type	OA label	tab	ontology_type	ontology_table	cross table population script	comment
pgonly	abp_id	not a table	pgid	all*	-	-	-
pgonly	abp_timestamp	not a table	none		-
pgonly	abp_curator	dropdown	Curator	all	-	-	-
Antibody	abp_name	text	Name	all
Summary	abp_summary	bigtext	Summary	all
Other_name	abp_other_name	bigtext	Other Name	all
Gene	abp_gene	multiontology	Gene	all	WBGene	gin_tables
Original_publication	abp_original_publication	ontology	Original Publication	all	WBPaper	pap_tables
Person (not used??)
Laboratory	abp_laboratory	multiontology	Laboratory	all	obo	laboratory
Clonality	abp_clonality	dropdown	Clonality	all
Antigen	abp_antigen	dropdown	Antigen	all
Peptide	abp_peptide	bigtext	Peptide	all
Protein	abp_protein	bigtext	Protein	all
Source	abp_source	dropdown	Source	all
Animal	abp_animal	dropdown	Animal	all
Other_animal	abp_other_animal	bigtext	Other Animal	all
Other_antigen	abp_other_antigen	bigtext	Other Antigen	all
Possible_pseudonym	abp_possible_pseudonym	bigtext	Possible Pseudonym	all
Expr_pattern	exp_antibody	multiontology	Antibody_info	EXPRPAT tab2	Antibody	abp_tables
Gene_regulation	grg_antibody	multiontology	Antibody_info	GENEREG tab2	Antibody	abp_tables
Reference	abp_paper	multiontology	Reference	all	WBPaper	pap_tables
Remark	abp_remark	bigtext	Remark	all

app_tables Phenotype

Model tag	table	type	OA label	tab	ontology_type	ontology_table	cross table population script	comment
pgonly	app_legacy_info	bigtext	Legacy Info	1				NO DUMP field
pgonly	app_curator	dropdown	Curator	1	-	-	-
pgonly	app_allele_status	dropdown	Allele Status	1			used to trigger population a form for Mary Ann	necessary?
pgonly	app_curation_status	dropdown	Curation Status	1				NO DUMP field
Phenotype_info- Person_evidence	app_person	multiontology	Person	1	WBPerson	?
pgonly	app_id	not a table	pgid	1	-	-	-
Rearrangement	app_rearrangement	ontolog	Rearrangement	1	obo	rearrangement
Phenotype_info- Paper_evidence	app_paper	ontology	Pub	1	WBPaper	pap_tables
Variation	app_variation	ontology	Variation	1	obo	variation
Transgene	app_transgene	ontology	Transgene	1	Transgene	trp_tables
Phenotype_info- Caused_by ?Gene	app_caused_by	ontology	Caused by	1	WBGene	gin_tables
Strain	app_strain	text	Strain	1
pgonly	app_obj_remark	text	Object Remark	1				for Mary Ann- information displayed on ~postgres/cgi-bin/new_objects.cgi for a queried allele
Phenotype_info- Caused_by	app_caused_by_other	text	Caused by Other	1
Phenotype_info Remark	app_phen_remark	bigtext	Phenotype_remark	2				columnWidth=600
Phenotype_info Ease_of_scoring	app_easescore	dropdown	ES	2
Variation Mating_efficiency	app_mmateff	dropdown	ME	2
Variation Mating_efficiency	app_hmateff	dropdown	HME	2
Phenotype_info Affected_by	app_molecule	multiontology	Molecule	2	Molecule	mop_tables
Phenotype_info Anatomy_term	app_anat_term	multiontology	Anatomy	2	obo	anatomy
Phenotype_info Phenotype_assay Life_stage	app_lifestage	multiontology	Life Stage	2	obo	lifestage
Rescued_by_transgene	app_rescuedby	multiontology	Rescued By	2	Transgene	trp_tables
?Variation Phentoype	app_term	ontology	Phenotype	2	obo	phenotype
Phenotype_info- Not_in tags	app_not	toggle	NOT	2
Phenotype_info Phenotype_assay Temperature	app_treatment	bigtext	Treatment	3
Phenotype_info Penetrance text	app_percent	bigtext	Penetrance Remark	3
Phenotype_info by value	app_nature	dropdown	Allele Nature	3
Phenotype_info Loss_of_function/Gain_of_function	app_func	dropdown	Functional Change	3
Phenotype_info Penetrance	app_penetrance	dropdown	Penetrance	3
Phenotype_info Maternal	app_mat_effect	dropdown	Maternal Effect	3
Phenotype_info Phenotype_assay Temperature	app_temperature	text	Temperature	3
Phenotype_info Phenotype_assay ?	app_control_isolate	text	Control Isolate	3				needs to be added to model, used for parasitic nematodes
Phenotype_info Cold_sensitive	app_cold_degree	text	Cold Sensitive Degree	3
Phenotype_info Heat_sensitive	app_heat_degree	text	Heat Sensitive Degree	3
Phenotype_info Paternal	app_pat_effect	toggle	Paternal Effect	3
Phenotype_info Haplo_insufficient	app_haplo	toggle	Haploinsufficient	3
Phenotype_info Cold_sensitive	app_cold_sens	toggle_text	Cold Sensitive	3
Phenotype_info Heat_sensitive	app_heat_sens	toggle_text	Heat Sensitive	3
pgonly	app_suggested_definition	bigtext	Suggested Definition	4			Cross posts on http://tazendra.caltech.edu/~postgres/cgi-bin/new_objects.cgi
pgonly	app_child_of	multiontology	Child of	4	obo	phenotype	Cross posts on http://tazendra.caltech.edu/~postgres/cgi-bin/new_objects.cgi
pgonly	app_suggested	text	Suggested	4			Cross posts on http://tazendra.caltech.edu/~postgres/cgi-bin/new_objects.cgi
Phenotype_assay Genotype	app_genotype	bigtext	Genotype	5
pgonly	app_intx_desc	bigtext	Genetic Intx Desc	5
pgonly	app_nbp	bigtext	NBP	5
Phenotype #Evidence	app_laboratory	multiontology	Laboratory Evidence	5	obo	laboratory
pgonly	app_entity	ontology	Entity	5	obo	Entity		PATO
pgonly	app_quality	ontology	Quality	5	obo	quality		PATO
pgonly	app_filereaddate	text	NBP / File Date	5
pgonly	app_timestamp	not a table	none		-

con_tables Concise description

postgres tables for Concise descriptions
dumper on tazendra at /kimberly/citace_upload/concise/wrapper.pl and /home/postgres/work/citace_upload/concise/dump_concise.pl

Model tag	table	type	OA label	tab	ontology_type	ontology_table	cross table population script	comment
pgonly	con_id	not a table	pgid	all*	-	-	-
pgonly	con_timestamp	not a table	none		-
pgonly	con_curator	dropdown	Curator	all	-	-	-
Gene	con_wbgene	ontology	WBGene	all	WBGene	gin_tables
	con_curhistory	ontology	Curator History	all	Concurhst
Structured_description	con_desctype	dropdown	Description Type	all
	con_desctext	textarea	Description Text	all				cols_size =90, rows_size=12
	con_paper	multiontology	Reference	all	WBPaper	pap_tables
	con_accession	text	Accession Evidence	all
	con_lastupdate	text	Last Updated	all
	con_comment	bigtext	Comment	all
	con_nodump	toggle	NO DUMP	all
	con_person	multiontology	Person	all	WBPerson	?
	con_exprtext	text	Expression Pattern	all
	con_rnai	text	RNAi	all
	con_microarray	text	Microarray	all

cnstr_tables Construct

postgres tables for the Construct class
dumper on tazendra at XXXXXXX

Model tag	table	type	OA label	tab	ontology_type	ontology_table	cross table population script	comment
pgonly	cnstr_id	not a table	pgid	all*	-	-	-
pgonly	cnstr_timestamp	not a table	none		-
pgonly	cnstr_curator	dropdown	Curator	all	-	-	-
Name	cnstr_name		Name	all*	-	-	-	WBMol: $molId = &pad8Zeros($newPgid)//assigned WBConstructID mop_id
Public_name ?Text
Other_name ?Text
Summary ?Text //genotype like [Pmyo-2::GFP]
Sequence_feature ?Feature XREF Construct
Driven_by_gene ?Gene XREF Drives_transgene
Gene ?Gene XREF Transgene_product
Fusion_reporter ?Text //fluorescent proteins GFP, RFP, mCherry, etc.
Other_reporter ?Text //to add reporters, tags that aren’t included in model
Purification_tag ?Text //FLAG, HA, Myc, TAP, etc.
Recombination_site ?Text //LoxP, FRT
Type_of_construct	Chimera Domain_swap Engineered mutation Fusion Complex // complex changes (e.g. GFP fusion plus point mutations) Transcriptional_fusion Translational_fusion N-terminal_translational_fusion C-terminal_translational_fusion Internal_coding_fusion
Selection_marker ?Text //for elements stitched into contiguous sequence, coinjected elements will get their own construct ID, these will be joined together to create transgene
Construction_summary ?Text //Backbone vector, mol bio
DNA_text ?text // for mapping to genome, can include entire construct sequence
Clone ?Clone XREF Clone
Used_for Transgene_construct ?Transgene XREF Construct Transgene_coinjection ?Transgene XREF Coinjection Engineered_variation ?Variation XREF Derived_from Topic_output_indicator ?WBProcess XREF marker_construct Expression_pattern ?Expr_pattern XREF Construct
Reference ?Paper XREF Construct
Person ?Person XREF Construct
Laboratory ?Laboratory #Lab_Location
Historical_gene ?Gene #Evidence
Remark ?Text #Evidence

mop_tables Molecule

postgres tables for the Molecule class
dumper on tazendra at karen/Molecule/dump_molecule_ace.pl

Model tag	table	type	OA label	tab	ontology_type	ontology_table	cross table population script	comment
pgonly	mop_id	not a table	pgid	all*	-	-	-	WBMol: $molId = &pad8Zeros($newPgid)
pgonly	mop_timestamp	not a table	none	-	-	-	-
pgonly	mop_curator	dropdown	Curator	all	-	-	-	same values in all OA curation tables
Name	mop_name	text	Name	all	-	-	-	WBMolID -added after tables were built
Public_name	mop_publicname	bigtext	Public_name	all	-	-	-
Synonym	mop_synonym	bigtext	Synonyms	all	-	-	-
DB_info	mop_molecule	text	MeSH / CTD or default	all	-	-	-	use MeSh ID here originally used as Name
DB_info	mop_chemi	text	CasRN	all	-	-	-
DB_info	mop_chebi	ontology	ChEBI_id	all	obo	chebi
DB_info	mop_kegg	text	Kegg compound (Acc#)	all	-	-	-
Remark	mop_remark	bigtext	Remark	all	-	-	-
Reference	mop_paper	multiontology	WBPaper	all	WBPaper	pap_tables	-
Molecule_use	mop_moleculeuse	bigtext	Molecule use	all	-	-	-
Not in model	mop_gotarget	multiontology	GO target	all	obo	goid	-
Not in model	mop_genetarget	multiontology	Gene target	all	WBGene	gin_tables	-
DB_info	mop_smmid	text	SMID-DB	all	-	-	-
Gene_regulation	grg_moleculeregulator	multiontology	Molecule Regulator	GENEREG tab3	Molecule	mop_tables	-
WBProcess	pro_molecule	multiontology	Molecule	PROCESS tab1	Molecule	mop_tables	-
Phenotype	app_molecule	multiontology	Molecule	PHENOTYPE tab2	Molecule	mop_tables	-
RNAi	rna_molecule	multiontology	Molecule	RNAi tab2	Molecule	mop_ tables	-
Interaction	int_otheronetype int_othertwotype	dropdown	Effected other type Affected other type	INTERACTION tab4	-	-	-

trp_tables Transgene

Model tag	table	type	OA label	tab	ontology_type	ontology_table	cross table population script	comment
Summary	trp_summary	bigtext	Summary	1
Construction_summary	trp_constructionsummary	bigtext	Construction Summary	1
pgonly	trp_cgcremark	bigtext	CGC remarks	1
Reporter_type	trp_reporter_type	dropdown	Reporter type	1
Reporter Reporter_product	trp_reporter_product	multidropdown	Reporter Product	1
Promoter Driven_by_gene ?Gene	trp_driven_by_gene	multiontology	Driven by Gene	1	WBGene	gin_tables
Reporter ?Gene	trp_gene	multiontology	Gene	1	WBGene	gin_tables
3_UTR	trp_threeutr	multiontology	3 UTR	1	WBGene	gin_tables
pgonly	trp_id	not a table	pgid	1	-	-	-
pgonly	trp_mergedinto	ontology	Merged Into	1	Transgene
?Transgene	trp_name	text	Name	1			expression pattern/textpresso
Public_name	trp_public_name	text	Public Name	1			transgene.pl parses results from transgenes_in_ocr_papers.out and transgenes_in_regular_papers.out and enters them into the trp_tables
Synonym	trp_synonym	text	Synonym	1			expression pattern see wiki
Reporter Reporter_product	trp_other_reporter	text	Other reporter	1
Coinjection_marker	trp_coinjection	text	Coinjection	1
Integration_method	trp_integration_method	dropdown	Integration Method	2
Map ?Map #Map_position	trp_map	multidropdown	Map	2
Associated_with Clone	trp_clone	multiontology	Clone	2	obo	clone
#Map #Evidence	trp_map_person	multiontology	Map person	2	WBPerson	person_tables?
#Map #Evidence	trp_map_paper	multiontology	Map Paper	2	WBPaper	pap_tables
Laboratory	trp_laboratory	multiontology	Laboratory	2	obo	laboratory
Associated_with_strain	trp_strain	text	Strain	2
Remark	trp_remark	bigtext	Remark	3			expression pattern see wiki
pgonly	trp_curator	dropdown	Curator	3			expression pattern/ textpresso
Reference	trp_paper	multiontology	Paper	3	WBPaper	pap_tables
Evidence	trp_person	multiontology	Map person	3	WBPerson	person_tables?
Used_for Marker_for #Evidence	trp_marker_for_paper	multiontology	Marker for Paper	3	WBPaper	pap_tables
Used_for Marker_for	trp_marker_for	test	Marker for	3
Species	trp_species	text	Species	3
Promoter Driven_by_construct	trp_driven_by_construct	text	Driven by Construct	3
pgonly	trp_timestamp	not a table	none		-

PROPOSED OA tables

dbs_tables Database

postgres tables for the Database class
dumper on tazendra at /karen/database/

Model tag	table	type	OA label	tab	ontology_type	ontology_table	cross table population script	comment
pgonly	dbs_id	not a table	pgid	1	-	-	-
pgonly	dbs_timestamp	not a table	none		-
pgonly	dbs_curator	dropdown	Curator	1	-	-	-
Database	dbs_database	text	Database	1			(main label)
Database	dbs_name	text	Public name	1			description
github only	dbs_person	text	Database maintainer	1			maintainer
Email	dbs_email	text	Contact e-mail	1			email
Description	dbs_description	bigtext	Description	1
URL	dbs_url	text	Database URL	1			base	cols_size=90
URL_constructor	dbs_urlconstructor	bigtext	URL constructor	1			search
pgonly	dbs_remark	bigtext	Remark	1
github only	dbs_otherurl	text	Database page URL	2			for git file output use name from URL page name*
github only	dbs_otherurl	text	Database page URL	2			for git file output use name from URL page name
github only	dbs_otherurl	text	Database page URL	2			for git file output use name from URL page name
github only	dbs_otherurl	text	Database page URL	2			for git file output use name from URL page name
github only	dbs_otherurl	text	Database page URL	2			for git file output use name from URL page name
github only	dbs_otherurl	text	Database page URL	2			for git file output use name from URL page name
github only	dbs_otherurl	text	Database page URL	2			for git file output use name from URL page name

• for example in git file output, the URL http://www.signalink.org/protein/%s
  should be written as
  

protein = 'http://www.signalink.org/protein/%s' --kjy 20:57, 11 October 2013 (UTC)