// models.wrm - for AATDB, database release 1-9
// Lisa Lorenzen July 14, 1994

// ACEDB system models now in sysmodels.wrm

//ALLELES, GENES, TRAITS, and GERMPLASM

?Allele Name	Correct_name ?Allele XREF Other_name
		Other_name ?Allele XREF Other_name
	Gene ?Gene XREF Allele
	Locus ?Locus XREF Allele 
        Reference_allele ?Text
                         For ?Allele XREF Like_ref_allele
        Like_ref_allele ?Allele XREF For
        Mutagen UNIQUE ?Reagent Text	// Text is dose
        Reference_Germplasm ?Germplasm XREF Allele
        Location ?Colleague  #Lab_Location
	Date	Text
        Genetics        gMap UNIQUE ?Linkage_Group XREF Allele Float Float
                        Mapping_data    2Point ?2_point_data
                                        3Point ?3_point_data
                                        Df_Dup ?Df_Dup_data
        Phenotype       ?Text #Gene_Action
			Image ?Image XREF Allele
	                Interactions    Suppressed_by	?Allele XREF Suppresses
                                        Suppresses 	?Allele XREF  Suppressed_by
	Origin ?Text
        Molecular_nature        Probe ?Probe XREF Allele
                                Sequence ?Sequence
	Comment Text
	Reference ?Paper XREF Allele
	Information_provided_by ?Source
	First_entered Text
	Last_update UNIQUE Text


?Gene_Action		Recessive
                        Dominant
			Semi-dominant
			Codominant
			Weak
		        Temperature_Sensitive
			Amber
                        Maternal	
                        Paternal


?Gene_Class     Description ?Text
                Gene      ?Gene
		Information_provided_by


?Gene 	Gene
  	Name    Gene_class UNIQUE ?Gene_Class XREF Gene
		Correct_name ?Gene XREF Other_name
                Other_name ?Gene XREF Other_name
	Of_Enzyme ?Enzyme
        Reference_Allele ?Allele Text
        Molecular_information	Probe   ?Probe XREF Gene
				Sequence ?Sequence XREF Gene
	EC_Number ?Text 
	Phenotype ?Text
	Image ?Image XREF Gene
	Origin ?Text
        Allele  ?Allele 
        Germplasm   ?Germplasm XREF Gene
	Map ?Map XREF Gene
        Mapping_information	Locus ?Locus XREF Gene
				Physical bMap UNIQUE ?Contig XREF Gene Int Int
                        	Autopos
                		Genetic  gMap ?Linkage_Group XREF Gene Float Float
                        	In_cluster ?Gene
	Mapping_data	2Point ?2_point_data 
                        3Point ?3_point_data
			F2_data ?F2_data
        Related_genes   ?Gene XREF Related_genes
                        Gene_family ?Gene XREF Gene_family
                        Interacting_genes ?Gene XREF Interacting_genes
                        Interacting_alleles ?Allele
	Resistant_to ?Pathology #Resistance_Genes
	Comment ?Text
        Reference ?Paper XREF Gene
	Information_provided_by ?Source
	First_entered Text
	Last_update UNIQUE Text


?Trait	Name ?Trait XREF Other_name
	Other_name ?Trait XREF Name
	Description ?Text
	Reference ?Paper #Reference //Description tag (see ?Reference)
	Associated_with_QTL ?QTL_Study
	Of_Germplasm ?Germplasm
	Information_provided_by ?Source


?Trait_Information	Trait_value ?Text
			Environment ?Environment

?Germplasm 	Name ?Germplasm XREF Other_name
		Other_name ?Germplasm XREF Name 
		PVP ?PVP XREF Variety
		Species UNIQUE ?Species
		Collection_and_ID# ?Collection XREF Entries ?Germplasm XREF Other_name
		Originator ?Text
		Legal_status ?Text
		Year_released Int
		Pedigree	Female_Parent UNIQUE ?Germplasm
				Male_Parent UNIQUE ?Germplasm
				Summary_pedigree ?Text
		Generation_derived UNIQUE Text
		Selection_method ?Text
		Maturity_group ?Text
		Market_Class ?Text
		Enzymes_studied ?Enzyme
		Contains_nodulin ?Nodulin
		Allele    ?Allele XREF Germplasm
		Traits ?Trait XREF Of_Germplasm #Trait_Information  
		Phenotype UNIQUE ?Text
		Gene ?Gene XREF Germplasm
		Locus ?Locus
		Mutagen UNIQUE ?Reagent
		Developed_by ?Colleague 
		Development_site ?Text 
		Registration# ?Text     
		Molecular_information	Probe ?Probe
		Source ?Text
		Notes ?Text
		Comment ?Text
		Reference ?Paper XREF Germplasm
		Information_provided_by ?Source
		First_entered Text
		Last_update UNIQUE Text



?PVP	Variety ?Germplasm XREF PVP

?Collection	Curator ?Colleague
		Description ?Text
		Entries ?Germplasm XREF Collection 

?Environment	Evaluator ?Colleague
		Institute ?Text
		Env._Type UNIQUE ?Text
		Env._Design UNIQUE ?Text
		Location	Latitude UNIQUE Text
				Longitude UNIQUE Text
				Elevation UNIQUE Text
				Topography UNIQUE Text
				Drainage UNIQUE Text
				Soil_texture UNIQUE Text
		Irrigation 	Type UNIQUE ?Text
				Days  UNIQUE Int
				Total_amount UNIQUE Float
		Planting_date UNIQUE Text
		Testing_date	Text
		Information_provided_by  ?Source



//MAP INFORMATION

?Map	Name ?Map  
	Linkage_Group	gMap ?Linkage_Group XREF Map  UNIQUE Float
	Locus ?Locus XREF Map 
	Gene ?Gene XREF Map

?Linkage_Group	Non_graphic  // Prevents a graphic display of a chromosome //Lisa changed Chromosome to Linkage_Group
            	Centre Float Float  // Overrules default Initial centre and width
	    	Map ?Map XREF gMap 
		Image ?Image
            	Gene ?Gene 
            	Locus ?Locus 
		Information_provided_by ?Source
		First_entered Text
		Last_update UNIQUE Text

?Locus  Type	RFLP
		Gene
		PCR
        Mapping_information	Physical bMap UNIQUE ?Contig XREF Locus Int Int
                         	Autopos
                		Genetic  gMap ?Linkage_Group XREF Locus Float Float
				2Point ?2_point_data
	Has_Restriction_map	?Locus
	Map ?Map XREF Locus
	Molecular_information	Probe   ?Probe XREF Locus
				Sequence ?Sequence XREF Locus
	Associated_with_Gene ?Gene XREF Locus 
	Associated_with_Allele ?Allele XREF Locus 
	Associated_with_QTL ?QTL_Study
	Germplasm ?Germplasm XREF Locus #Pattern
	Image ?Image XREF Locus 
	Data ?F2_data
	Remarks Text
        Polymorphic_for ?Restriction REPEAT
	Not_used ?Restriction REPEAT
	Not_polymorphic_for ?Restriction REPEAT
	Information_provided_by ?Source
	First_entered Text
	Last_update UNIQUE Text


?Probe  Type	#Probe_Type
	Gene    ?Gene XREF Probe
        Locus   ?Locus XREF Probe
        Position  pMap UNIQUE ?Contig XREF Probe Int Int 
		  bMap UNIQUE Int Int	
		  Autopos
	PCR_primers ?Sequence
	Amplification_conditions ?Text
	Sequence	?Sequence XREF Probe
	Insert	Size Int 
		Insert_sequence ?Sequence 
	Polymorphism	Present	?Restriction 
			Absent	?Restriction 
       	Map ?Map 
	Linkage_Group ?Linkage_Group
	Germplasm ?Germplasm XREF Probe #Pattern
	Origin	Vector   ?Text 
		Vector_enzyme ?Restriction 
		Insert_enzyme ?Restriction 
		Excision_enzyme ?Restriction 
		cDNA 
		Genomic 
		Derived_from ?Germplasm
		Tissue_source ?Text
		Vector_PCR_primers ?Sequence 
	Subcloned_in ?Probe XREF Subclone_of
	Subclone_of ?Probe XREF Subcloned_in
	Location ?Colleague
	Image ?Image XREF Probe 
	Information_provided_by ?Source
	First_entered Text
	Last_update UNIQUE Text


?Probe_Type	RFLP
		SSCP
		RAPD
		VNTR

?Pattern	Enzyme ?Restriction #Bands

?Bands	Bands_detected Text

?2_point_data	a Gene1 ?Gene XREF 2Point Unique Int
		b Gene2 ?Gene XREF 2POint Unique Int 
		Germplasm ?Germplasm #Germ_Info
         	Phase UNIQUE  Text
		Map ?Map
		Linkage_Group ?Linkage_Group
		Generation UNIQUE Text
		Number_of_individuals UNIQUE Int
  		Method UNIQUE ?Text 
		Temperature UNIQUE Text
		Date  UNIQUE Text
		Mapper ?Author
		Laboratory UNIQUE ?Colleague
		Results	Min Float
     			Distance Float
			Independent
			Linked
                        Max Float
                        Error Float
		  	Standard_error Float
		Reference ?Paper XREF 2_point_data
		Comment Text             
		Reviewed_by ?Colleague
		Information_provided_by ?Source
		First_entered Text
		Last_update UNIQUE Text

?Germ_Info	Female_Parent
		Male_Parent
		Allele ?Allele
		Species ?Species


?Restriction	Site UNIQUE Text
		Offset Text
		Cleavage Text
		Overhang Text
		Isoschizomers ?Restriction REPEAT
		Company ?Source
		Reference ?Paper
		Remark Text
		Information_provided_by ?Source
		First_entered Text
		Last_update UNIQUE Text


?Sequence	Name ?Sequence XREF Other_name
		Other_name ?Sequence XREF Name
		Database ?Text
		Description ?Text
		Information_provided_by ?Colleague
		First_entered Text
		Last_update UNIQUE Text


//IMAGES

?Image  Probe ?Probe XREF Image
	Locus ?Locus XREF Image
	Pathology ?Pathology XREF Image
	Author ?Author XREF Image
	Paper  ?Paper  XREF Image
	Gene   ?Gene XREF Image 
	Pick_me_to_call  UNIQUE Text Text   // A program name followed by a file name
	Secret  Text  // If set prevents display except by owner (uid == Text)
	Information_provided_by ?Source
	Comment ?Text
	First_entered Text
	Last_update UNIQUE Text



//A SERIES OF UNUSED CLASSES


?Probe_Grid

?Contig bMap

?Rearrangement 
		
?Df_Dup_data 	      

?3_point_data    

?Protein

?Search_Method	

?Homology 

?Seg_Set

?Octamer_Table
	
?F2_data

?Pool	

?Chrom_Band

?Lab_Location



//COLLEAGUES, REFERENCES, and SOURCE    

?Colleague	Other_name ?Colleague
		Collection Text
		Position Text
		Profession Text
		Address Mail Text
			Institution Text
			City Text
			State Text
			Country Text
			ZipCode Text
                        Phone Text	
			Mobile_phone Text
                        E_mail Text
			       Bitnet Text
                               Internet Text
			Fax Text
			Telex Text
		Research_interest ?Text
		Keyword ?Keyword
     		Publishes_as ?Author XREF Full_name
		Associate ?Colleague XREF Associate
		Information_provided_by ?Source
		First_entered Text
		Last_update UNIQUE Text



?Author Full_name ?Colleague XREF Publishes_as
        Paper ?Paper XREF Author

?Journal Paper ?Paper XREF Journal

?Paper  Reference       Title UNIQUE ?Text
                        Original_title ?Text
			Source ?Text
			Journal UNIQUE ?Journal XREF Paper
			Book ?Text
			Meeting Text
			Editor ?Colleague
			Publisher UNIQUE Text
                        Year UNIQUE Int
                        Volume UNIQUE Int Text
			Edition	Text
                        Page  UNIQUE Int Int
	Institution Text
        Author ?Author XREF Paper
	Type UNIQUE Text
	Language Text
	Abstract Text
        Refers_to	Gene ?Gene XREF Reference
			Allele ?Allele XREF Reference
			Sequence ?Sequence XREF Reference
			Germplasm ?Germplasm
			2_point_data ?2_point_data //Lisa
			Gene_Product ?Gene_Product
        Keyword ?Keyword
	Comment ?Text
	Information_provided_by ?Source
	First_entered Text
	Last_update UNIQUE Text


?Reference	Reference ?Paper
		Comment ?Text
		Species ?Species
		Description ?Text //For trait information

?Source		Other_name ?Text // Full name
		Contents Text // Description of collection
		Remarks Text // other descriptions
		Reference ?Paper
		Contact ?Colleague
		Address Mail Text
                        Phone Text
                        E_mail Text
			Fax Text


//PATHOLOGY SECTION

?Pathology	Other_name ?Pathology 	
		Related_organism ?Pathology
		Organism_type #Organism_type
		Genus_Species UNIQUE ?Species 
		Virus_group ?Text
		Forma_specialis ?Text
		Variety Text
		Authority ?Colleague
		Differential_information_for ?Differentials
		Races ?Race REPEAT
		Strain_groups ?Race REPEAT
		Reference ?Paper
		Comment ?Text
		Contact ?Colleague
		Disease ?Disease
		Soybean_Defense ?Pathology_reactions
		Resistance_Locus ?Gene REPEAT
		Image ?Image XREF Pathology
		Information_provided_by ?Source
		Reviewed_by ?Colleague
		First_entered Text
		Last_update UNIQUE Text



?Organism_type  Nematode
		Disease
		Virus
		Bacterial
		Fungus

?Race	Differential_value ?Germplasm ?Text
	Soybean_Resistance ?Text
	Contact ?Colleague
	Source_of_Resistance ?Germplasm
	Resistance_Gene ?Allele
	Reference ?Paper
	Comment Text
	Information_provided_by ?Source
	First_entered Text
	Last_update UNIQUE Text

//?Differential_Value	Susceptible
//			Resistant
//			?
//			Symptomless
//			Necrotic
//			Mosaic
//			Not_tested
		     	            		
?Disease 	Diagnostic_symptom ?Text
		Geographical_distr._(USA_&_Canada) Text #Reference
		Geographical_distr._(World) Text #Reference
		Species_host_range Text #Reference
		Genus_host_range Text #Reference
		Family_host_range Text #Reference
		Comment ?Text
		Reference ?Paper

?Pathology_reactions	Resistance_type ?Text
			Resistance_reaction ?Text
			Tolerance_Description ?Text #Reference
			Location ?Text #Tolerance
			Protocol ?Text #Reference
			Comment Text
			Reference ?Paper

?Tolerance	Protocol ?Text
		Tolerance_Rating ?Text
		Reference ?Paper

?Resistance_Genes	Allele ?Allele #Resistance_Source

?Resistance_Source	Source ?Germplasm
			Reference ?Paper

?Species	Name ?Species

?Differentials	Differential_Reaction Text
		Differentials ?Germplasm XREF Differential_for 
		Standard_Suscept._Germplasm ?Germplasm
		Protocol  Text #Reference
		Reference ?Paper
		Information_provided_by ?Source

//QTL SECTION

?QTL_Study	Trait_Evaluated ?Trait XREF Associated_with_QTL
		Reference ?Paper #Comp_QTL	
		Other_QTL's_evaluated ?QTL_Study
		Parent ?Germplasm #Parent_Info
		Heritability UNIQUE Float
		Population_size Int
		Population_type Text
		Analysis_method Text
		No._plants_bulked Int //for bulk analysis
		High Text //for bulk analysis
		Low Text //for bulk analysis
		No._loci_tested Int
		No._loci_associated Int 
		Interval ?Locus #Interval XREF Associated_with_QTL //for interval mapping
		Locus ?Locus XREF Associated_with_QTL #QTL_Info
		Phenotypic_R2 Float
		Genotypic_R2 Float
		R2_Definition ?Text

		Comment Text
		Information_provided_by ?Colleague
		First_entered Text
		Last_update UNIQUE Text

?Interval	To ?Locus
		Interval_length Float
		R2 Float
		LOD_Score Float

?Comp_QTL	Other_traits_evaluated ?QTL_Study

?Parent_Info	Trait_value ?Text

?QTL_Info	Mean_trait_value	Homozygous_female Text
					Homozygous_male Text
					Heterozygous Text
					R2 Float
					P_value Float
					LOD_score Float

//METABOLIC SECTION

?Reaction_or_Pathway	Name ?Reaction_or_Pathway XREF Other_name #Reference
			Other_name ?Reaction_or_Pathway XREF Name
			Image ?Image
			Type #PathType
			Components ?Reaction_or_Pathway XREF In_Pathway #EnzymeInfo
			In_Pathway ?Reaction_or_Pathway
			Enzyme	?Enzyme XREF Catalyzes #Reference
			Major_Reactant ?Metabolite XREF Consumed_by #ReactantInfo
			Minor_Reactant ?Metabolite XREF Consumed_by #ReactantInfo
			Major_Product ?Metabolite XREF Produced_by #ReactantInfo
			Minor_Product ?Metabolite XREF Produced_by #ReactantInfo
			Cofactor_Reactant ?Metabolite XREF Consumed_by #ReactantInfo
			Cofactor_Product ?Metabolite XREF Produced_by #ReactantInfo
			Additional_Cofactor_Reactant ?Metabolite XREF Consumed_by #ReactantInfo
			Additional_Cofactor_Product ?Metabolite XREF Produced_by #ReactantInfo
			Ancillary_Rx	Reactants ?Metabolite #ReactantInfo
					Products ?Metabolite #ReactantInfo //i.e. for transport. . 
					Anc_Enzyme ?Enzyme #Reference
			pH_optimum Text #Reference
			Temp._optimum Text #Reference
			Next_Step	?Reaction_or_Pathway #InPW
			Previous_Step	?Reaction_or_Pathway #InPW
			Species_studied ?Species
			Activator ?Metabolite XREF Activates #InhibitorInfo
			Cooperativity ?Text #Reference
			Inhibitor ?Metabolite XREF Inhibits #InhibitorInfo
			Catalytic_mechanism ?Text #Reference
			Location ?Text #Reference
			Regulation #RegulationType
			Diagram	?PathwayDiagram XREF Pathway
			Comment ?Text
			Reviewed_by ?Colleague
			Information_provided_by	?Colleague
			First_entered ?Text
			Last_update UNIQUE ?Text

?PathType	Pathway
		Partial_Pathway
		Reaction
		Translocation

?RegulationType	Induction ?Text #Reference
		Repression ?Text #Reference
		Developmental ?Text #Reference
		Hormonal ?Text #Reference
		Environmental ?Text #Reference
		Genetic ?Text #Reference

?InhibitorInfo	Type #InhibitorType  //for inhibitor
		Ki Text  //for inhibitor
		Comment ?Text
		Reference ?Paper

?InhibitorType	Active_site

?EnzymeInfo

?ReactantInfo	Major_Role
		Minor_Role
		Cofactor
		N Int // etc.
		Km Text #Reference
		Vmax Float #Reference
		Substrate_specificity ?Text #Reference
		Comment ?Text
		Reference ?Paper
	
?InPW	In ?Reaction_or_Pathway

?Enzyme		Name ?Enzyme XREF Other_name #Reference 
		Other_name ?Enzyme XREF Name #Reference
		Isozyme ?Enzyme #Reference
		EC_Number ?EC_Number #Reference  //probably should be under reaction
		Gene_symbol ?Gene XREF Of_enzyme #Reference
		Mutants ?Text #Reference
			Heterologous_mutants ?Text #Reference
			Mutant_Gene_symbol ?Gene #Reference
		Isoelectric_point ?Text #Reference
		Sequence ?Text #Reference
		Prosthetic_groups ?Metabolite #Reference
		Properties	Native_Mr ?Text #Reference
				Subunits ?Metabolite XREF Subunit_of
				Subunitation ?Text #Reference
				Subunit_Mr ?Text #Reference
				3D_structure ?Text #Reference
		Purification ?Text #Reference
		Catalyzes ?Reaction_or_Pathway
		Source	Species ?Species #Reference
			Cultivar ?Germplasm XREF Enzymes_studied #Reference
			Tissue ?Tissue XREF Enzyme #Reference
			Organelle ?Organelle XREF Enzyme #Reference
		Availability	DNA_probe ?Text #Reference
				Heterologous_probe ?Text #Reference
				cDNA_clone ?Text #Reference
				Heterologous_cDNA ?Text #Reference
				Genomic_clone ?Text #Reference
				Heterologous_clone ?Text #Reference
				RFLP_probe ?Text #Reference
				Heterologous_RFLP_probe ?Text #Reference
				Antibody_probe ?Text #Reference
				Heterologous_antibody_probe ?Text #Reference
		Chromosomal_Location ?Text #Reference
		Membrane_Associated #Reference//boolean
		Contains_nodulin ?Nodulin XREF Enzyme
		Comment ?Text
		Reference ?Paper
		Reviewed_by ?Colleague
		Information_provided_by ?Colleague
		First_entered ?Text
		Last_update UNIQUE ?Text

?EC_Number	EC_Number ?EC_Number
		Corresponds_to	IUB_number ?Text

?Metabolite	Name ?Metabolite XREF Other_name
		Other_name ?Metabolite XREF Name
		Subunit_of ?Enzyme XREF Subunits
		Consumed_by	?Reaction_or_Pathway
		Produced_by	?Reaction_or_Pathway
		Activates	?Reaction_or_Pathway
		Inhibits ?Reaction_or_Pathway XREF Inhibitor
		Contains_nodulin ?Nodulin
		Comment ?Text		

?PathwayDiagram	Name
		Pathway ?Reaction_or_Pathway		
		Node	Int Float Float Int ?Metabolite // ID X Y LabelID Metabolite
		Arc   Int Int   Int  Int Int       Float  ?Reaction_or_Pathway
		   // ID  Label From To  Curvature Radius Step
		TangentArc Int Int
		   //      Arc Tangent
		Label Int Float Float Text // ID X Y Label

		
?Nodulin	Name ?Nodulin XREF Other_name #Reference
		Other_name ?Nodulin XREF Name #Reference
		Gene_symbol ?Gene XREF Contains_nodulin #Reference
		Mutants ?Text #Reference
		Isoelectric_point ?Text #Reference
		Sequence ?Text #Reference
		Related_Sequence ?Nodulin #Reference
		Gene_product ?Metabolite XREF Contains_nodulin #Reference
		Enzyme ?Enzyme XREF Contains_nodulin #Reference
		Function Text #Reference	 	 
		Time_of_initiation Text #Reference
		Regulation #RegulationType
		Nodulin_family ?Text #Reference
		Nodulin_subfamily ?Text #Reference
		Related_member ?Nodulin #Reference
		Conservation Text #Reference
		Properties	Native_Mr ?Text #Reference
				Subunit_Mr ?Text #Reference
				3D_structure ?Text #Reference
		Source  Species ?Species #Reference		 
			Cultivar ?Germplasm XREF Contains_nodulin #Reference
			Tissue ?Tissue XREF Contains_nodulin #Reference
			Organelle ?Organelle XREF Contains_nodulin #Reference
			Bacterium ?Bacterium XREF Contains_nodulin #Reference
			Cell_type ?Cell_type XREF Contains_nodulin #Reference
		Availability	DNA_probe ?Text #Reference
				Heterologous_probe ?Text #Reference
				cDNA_clone ?Text #Reference
				Heterologous_cDNA ?Text #Reference
				Genomic_clone ?Text #Reference
				Heterologous_clone ?Text #Reference
				RFLP_probe ?Text #Reference
				Heterologous_RFLP_probe ?Text #Reference
				Antibody_probe ?Text #Reference
				Heterologous_antibody_probe ?Text #Reference
				Transgenic_plant ?Text #Reference
		Linkage_data ?Text #Reference
		Fine_structure_map ?Text #Reference
		Special_features Text #Reference
		Signal_peptide #Reference//boolean
		Membrane_Associated #Reference//boolean
		Comment ?Text
		Reference ?Paper
		Information_provided_by ?Colleague
		First_entered ?Text
		Last_update UNIQUE ?Text
				
		
?Tissue	Name ?Tissue XREF Other_name
	Other_name XREF Name
	Contains_nodulin ?Nodulin
	Enzyme ?Enzyme

?Organelle	Name ?Organelle XREF Other_name
		Other_name XREF Name
		Contains_nodulin ?Nodulin
		Enzyme ?Enzyme

?Bacterium 	Name ?Bacterium XREF Other_name
		Other_name XREF Name
		Contains_nodulin ?Nodulin

?Cell_type 	Name ?Cell_type XREF Other_name
		Other_name XREF Name
		Contains_nodulin ?Nodulin