// models.wrm - main file defining tree class structures
// This file is read only when starting a new database or when you select 
// "Read Models" or "Add Update File" from the main menu.
//
// all tags must appear in tags.wrm or systags.wrm


?Map	Type UNIQUE Genetic  // this flag can be used to define subclasses
                    Cytogenetic // Chromosome could be Map, filtered Cytogenetic
                    Physical
        Display Non_graphic  // Prevents a graphic display 
                Title UNIQUE ?Text
                Remark Text // Will appear in top right corner  
		Flipped // Then coordinates go upwards
                Unit   Text // i.e. kb, centiMorgan, MegaParsec
		Centre UNIQUE Float UNIQUE Float  // centre, width - else 0, 10
	    	Extent UNIQUE Float UNIQUE Float  // min, max - else min, max gene/locus
                Error_scale UNIQUE Float  // To position loci on x axis, default = 10
        Inherits  From_map ?Map 	  // To loaclly edit
		  Author Text             // login name of who edited it
		  Date Text
 	Main_Marker ANY       // Appear left of scroll bar
        Contains Locus ?Locus XREF Map
                 YAC ?YAC XREF Map
                 Fragment ?Fragment XREF Map
                 Clone ?Clone XREF Map
                 Map ?Map XREF Map #map_location

?Map_Data	Name ?Text XREF Map_Data
		Female_parent UNIQUE ?Text 
		Male_parent UNIQUE ?Text
		Parent ?Germplasm XREF Map_Data // For reciprocal, multiparental
		Type	Genetic
			Cytogenetic
			Physical
			RFLP
			RAPD
		Map_units Text
		Paper ?Paper XREF Map_Data
		Author ?Author
		Remark Text
		Image ?Image XREF Map
		Map ?Map XREF Map_Data
		MultiMap ?MultiMap XREF Map_Data
		Contributed_by ?Colleague XREF Map_Data
	

?map_location UNIQUE Position UNIQUE Float #map_error
                     Multi_Position  Float #map_error
                     Ends Left UNIQUE Float #map_error
                          Right UNIQUE Float #map_error

?map_error Error UNIQUE Float

?MultiMap Map ?Map

?Clone  Position  Map ?Map XREF Clone #map_location  // position on vertical maps
	Name UNIQUE ?Text
	Type Text
	Size Text
	Restriction_Enzyme Text
        Inside    Links ?Fragment XREF Link
        Contains  Locus   ?Locus XREF Clone
	Contributed_by ?Colleague XREF Clone

?Colleague	Full_name ?Colleague XREF Colleague 
		Position ?Text
		Profession ?Text
		Organization ?Text               
		Address Mail ?Text 
			Country ?Text
			Phone ?Text
			Fax ?Text
			Telex ?Text
			E_mail ?Text
		Research_interest ?Text
		Publishes_as ?Author XREF Colleague 
		Obtained_from ?Text
		Contributed_by ?Colleague XREF Colleague
		Last_update UNIQUE ?Text

?YAC    Location 	Position  UNIQUE Map ?Map XREF YAC #map_location
        Contains        Locus ?Locus XREF Inside_YAC
        Inside          Inside_Fragment ?Fragment XREF YAC
        Size UNIQUE Int Int // length , range in kb
        Status UNIQUE Chimeric
                      Non_Chimeric
       
?Fragment   Position  UNIQUE Map ?Map XREF Fragment #map_location
            Contains Locus ?Locus XREF Inside_Fragment Int // offset in fragment
                     Link ?Clone XREF Links Int
                     YAC ?YAC XREF Inside_Fragment Int 
            Length UNIQUE Int // kb
      	    Contributed_by ?Colleague XREF Fragment 
  
?Motif	Site UNIQUE Text // AA or DNA or some more elaborate descriptor
	Oligo
	Restriction_Enzyme	Isoschizomers ?Motif XREF Isoschizomers REPEAT
		                Offset Int   
	        		Cleavage Text  // will show the cleavage points ex: G_AC
		                Overhang  Text // was Int
                		Company  Text
                                Paper   Text
                                Remark  Text


?Enzyme Locus ?Locus XREF EC_enzyme

?Probe  General Name ?Text
		Other_name ?Text 
                Locus ?Locus XREF Probe
                DNA_type Text
                Clone ?Clone
                Pick_me_to_call Text Text
                Location Text
                Type ?Keyword
                Polymorphism ?Keyword
                Availability Text
                Description  Text
		Annotation  Text
                Cosmid_clones ?Clone ?Keyword
        Vector_type Text
        Excision_Data  Text
        Polymorphism_Data Text
        Originator Text
        GenBank_ref ?Text
        ATCC_ref    ?Text
        EC_ref      ?Text
        HGML_ref    ?Text
        Reference ?Source XREF Probe
        Contact   ?Contact XREF Probe
        Paper     ?Paper
	Created Text
	Modified  Text
	Approved Text

?Source Name ?Text
        Address Text
        Probe ?Probe XREF Reference

?Reference	Title UNIQUE ?Text
		Type	Paper
			Book
			Thesis
		Journal UNIQUE ?Journal XREF Reference
		Publisher UNIQUE Text
		Year UNIQUE Text 
		Volume UNIQUE Text Text 
		Page Text
		Pages UNIQUE Text UNIQUE Text
		Author ?Author XREF Paper 
		Abstract ?LongText
		Image ?Image XREF Reference
		Keyword ?Keyword
		
?Locus  Description  Name     UNIQUE Text 
                     Other_name        Text
                     Type              UNIQUE Text
                     Current_symbol    UNIQUE Text
                     Previous_symbol   Text
                     Assign_mode       Text
                     Annotation        Text
                     Polymorphism         UNIQUE Text
                     Max_heterozygosity   UNIQUE Float
                     Add_date          UNIQUE Text
                     Modification_date UNIQUE Text
                     Approval_date     UNIQUE Text
        Location     Cytogenetic_location Text
                     Map ?Map XREF Locus #map_location
                     Main_Marker ?Map XREF Main_Marker
        Inside       Inside_YAC  ?YAC XREF Locus
                     Inside_Fragment ?Fragment XREF Locus
        Links_to     Probe          ?Probe    XREF Locus
                     Sequence       ?Sequence XREF Locus
                     Clone          ?Clone    XREF Locus
                     EC_enzyme      ?Enzyme   XREF Locus
	Marker_distance ?Text
      	Trait ?Text
        Phenotype ?Text 
	Reference ?Reference XREF Locus
        Paper ?Paper XREF Locus 
        Remark ?Text
        Contributed_by ?Colleague XREF Locus

?Author Full_name ?Author XREF Paper 
	Laboratory ?Laboratory XREF Staff
        Address Mail Text
		Country ?Text 
                Phone Text
		Fax   Text
		E_mail ?Text
        Paper ?Paper XREF Author
	Image ?Image XREF Author
	Contributed_by ?Colleague XREF Author 

?Journal Paper ?Paper XREF Journal

?Paper  Reference       Title UNIQUE ?Text
			Author ?Author XREF Paper
                        Journal UNIQUE ?Journal XREF Paper
			In ?Text
			Type UNIQUE Text
			Remark ?Text
			Language ?Text
			Editor ?Colleague XREF Paper
			Publisher UNIQUE Text
			Cited_in ?Paper XREF Contains
                        Year UNIQUE Text
                        Volume UNIQUE Text Text
                        Page  UNIQUE  Text UNIQUE Text
			Pages UNIQUE Text
			Accession_number ?Text
			Call_number ?Text
	Institution ?Text
        Abstract ?Text
	Contains ?Paper XREF Cited_in
        Image ?Image XREF Paper
        Keyword ?Keyword
	Contributed_by ?Colleague XREF Paper

?Pathology	Diseases ?Diseases XREF Pathology
		Other_name ?Pathology
                Type    Fungus
                        Bacterium
                        Virus
                        Nematode
                        Insect
                        Abiotic
                        Mycoplasma
                        Parasitic_plant
                        Mollusk
                Host_species ?Text 
                Causal_organism ?Pathogens XREF Causes
                Vector ?Pathogens 
                Resistant_allele ?Allele XREF Pathology 
                Resistant_line ?Germplasm XREF Pathology 
                Symptoms ?Text
                Control ?Text
                Data_Source ?Colleague XREF Pathology 
                Image ?Image XREF Pathology 
                Paper ?Paper XREF Pathology 
                Contributed_by ?Colleague Pathology 

?Diseases	Other_name ?Diseases 
		Type	Fungus
			Bacterium
			Virus
			Nematode
			Insect
			Abiotic
			Mycoplasma
			Parasitic_plant
			Mollusk
		Host_species ?Text
		Causal_organism ?Pathogens XREF Causes
		Vector ?Pathogens
		Resistant_allele ?Allele XREF Diseases 
		Resistant_line ?Germplasm XREF Diseases 
		Symptoms ?Text
		Control ?Text
		Data_Source ?Colleague XREF Diseases 
		Image ?Image XREF Diseases
		Paper ?Paper XREF Diseases
		Contributed_by ?Colleague Diseases 

?Pathogens	Bacterial_Species ?Bacterial_Species XREF Pathogens 
		Fungal_Species ?Fungal_Species XREF Pathogens
		Viral_Groups ?Viral_Groups XREF Pathogens
		Classification  Full_name ?Pathogens XREF Pathogens
                                Authority ?Text
                                Genus UNIQUE ?Text
                                Species_epithet ?Text
				Asexual_State ?Text
				Sexual_State ?Text
                                Synonym ?Bacterial_Species XREF Synonym
                                Common_name ?Text
                Haploid_chromosome_number Int
                Description ?Text
                Disease ?Diseases XREF Diseases
                Causes ?Diseases
                Paper ?Paper XREF Pathogens 
                Image ?Image XREF Pathogens
                Contributed_by ?Colleague XREF Pathogens


?Taxonomy	Classification	Family ?Text
				Tribe ?Text
				Sub_Tribe ?Text
				Genus ?Text
				Section ?Text 
				Species ?Sorghum_Species XREF Taxonomy
		Description ?Text
		Remark ?Text

?Bacterial_Species	Classification	Full_name ?Bacterial_Species
          		      		Authority ?Text 
					Genus UNIQUE ?Text
					Species_epithet ?Text
					Synonym ?Bacterial_Species XREF Synonym
					Common_name ?Text
			Haploid_chromosome_number Int
			Description ?Text 
			Disease ?Diseases XREF Diseases 
			Causes ?Diseases 
			Paper ?Paper XREF Bacterial_Species
			Image ?Image XREF Bacterial_Species
			Contributed_by ?Colleague XREF Bacterial_Species

?Fungal_Species		Classification	Full_name ?Fungal_Species
       		                        Authority ?Text
                              		Genus UNIQUE ?Text
                      			Species_epithet ?Text
					Asexual_State ?Text
					Sexual_State ?Text
                                	Synonym ?Fungal_Species XREF Synonym
                              		Common_name ?Text
                	Haploid_chromosome_number Int
                	Description ?Text
                	Disease ?Diseases XREF Diseases
                	Causes ?Diseases 
                	Paper ?Paper XREF Fungal_Species
                	Image ?Image XREF Fungal_Species
                	Contributed_by ?Colleague XREF Fungal_Species

?Viral_Groups		Classification	Full_name ?Viral_Groups
      		                    	Authority ?Text
               		            	Genus UNIQUE ?Text
					Species_epithet ?Text
                       			Synonym ?Viral_Groups XREF Synonym
                                	Common_name ?Text
                	Haploid_chromosome_number Int
                	Description ?Text
                	Disease ?Diseases XREF Diseases
                	Causes ?Diseases 
                	Paper ?Paper XREF Viral_Groups
                	Image ?Image XREF Viral_Groups
                	Contributed_by ?Colleague XREF Viral_Groups

?Sorghum_Species	Classification	Full_name ?Sorghum_Species
                                	Authority ?Text
                                	Genus UNIQUE ?Text
                                	Species_epithet ?Text
                                	Synonym ?Sorghum_Species XREF Synonym
                                	Common_name ?Text
                                	Sub_species ?Sub_species XREF Sorghum_Species
                	Haploid_chromosome_number Int
                	Description ?Text
                	Paper ?Paper XREF Sorghum_Species
                	Image ?Image XREF Sorghum_Species
                	Contributed_by ?Colleague XREF Sorghum_Species


?Sub_species    Classification  Full_name ?Sub_species
                                Authority ?Text
                                Synonym ?Sub_species XREF Synonym
                                Common_name ?Text
                                Race ?Race XREF Sub_species
				Intermediate_Race ?Text 
                Haploid_chromosome_number Int    
                Description ?Text 
                Paper ?Paper XREF Sub_species
                Image ?Image XREF Sub_species
                Contributed_by ?Colleague XREF Sub_species

?Race		Race ?Race XREF Sub_species 
		Intermediate_Race ?Text
		Description ?Text

?Germplasm 	Cultivars ?Cultivars XREF Germplasm
		Germplasms ?Germplasms XREF Germplasm
		Parental_Lines ?Parental_Lines XREF Germplasm
		Genetic_Stocks ?Genetic_Stocks XREF Germplasm
		Name ?Germplasm XREF Germplasm 
                Other_name ?Germplasm XREF Germplasm 
		Other_Identities ?Text
                Type    Registered_Cultivar
			Registered_Germplasm
			Registered_Parental_Line
			Registered_Genetic_Stock
                Registration_Number UNIQUE ?Text
                Accession_ID ?Text
                Female_Parent ?Text
                Male_Parent ?Text
                Pedigree ?Text
                Features ?Text
                Locus ?Locus XREF Germplasm 
                Allele ?Allele XREF Germplasm
                Panicle_Type ?Text
                Glume_Color ?Text
                Pericarp_Color ?Text
                Awns ?Text
                Seed_Color ?Text
                Plant_Height ?Text
                Maturity ?Text
                Fertility ?Text
                Organization ?Text
                Development_Site ?Text
                Developed_by ?Colleague XREF Germplasm
                Date_of_Release ?Text
                Contributed_by ?Colleague XREF Germplasm
                Remark ?Text
                Image ?Image XREF Germplasm
                Paper ?Paper XREF Germplasm

?Cultivars	Name ?Cultivars XREF Cultivars 
		Other_name ?Cultivars XREF Cultivars 
		Other_Identities ?Text
		Type 	Registered_Cultivar
	    	Registration_Number UNIQUE ?Text
	    	Accession_ID ?Text
		Female_Parent ?Text
		Male_Parent ?Text    
		Pedigree ?Text
		Features ?Text
		Locus ?Locus XREF Cultivars
		Allele ?Allele XREF Cultivars 
		Panicle_Type ?Text
		Glume_Color ?Text
		Pericarp_Color ?Text
		Awns ?Text
		Seed_Color ?Text
		Plant_Height ?Text
		Maturity ?Text
		Fertility ?Text
		Organization ?Text
		Development_Site ?Text
		Developed_by ?Colleague XREF Cultivars 
		Date_of_Release ?Text
		Contributed_by ?Colleague XREF Cultivars 
		Remark ?Text
		Image ?Image XREF Cultivars 
	    	Paper ?Paper XREF Cultivars

?Germplasms	Name ?Germplasms XREF Germplasms
                Other_name ?Germplasms XREF Germplasms
                Other_Identities ?Text
                Type       Registered_Germplasm
                Registration_Number ?Text
                Accession_ID ?Text
                Female_Parent ?Text
                Male_Parent ?Text
                Pedigree ?Text
                Features ?Text
                Locus ?Locus XREF Germplasms
                Allele ?Allele XREF Germplasms
                Panicle_Type ?Text
                Glume_Color ?Text
                Pericarp_Color ?Text
                Awns ?Text
                Seed_Color ?Text
                Plant_Height ?Text
                Maturity ?Text
                Fertility ?Text
                Organization ?Text
                Development_Site ?Text
                Developed_by ?Colleague XREF Germplasms
                Date_of_Release ?Text
                Contributed_by ?Colleague XREF Germplasms
                Remark ?Text
                Image ?Image XREF Germplasms
                Paper ?Paper XREF Germplasms

?Parental_Lines	Name ?Parental_Lines XREF Parental_Lines 
                Other_name ?Parental_Lines XREF Parental_Lines 
                Other_Identities ?Text
                Type       Registered_Parental_Line
                Registration_Number ?Text
                Accession_ID ?Text
                Female_Parent ?Text
                Male_Parent ?Text
                Pedigree ?Text
                Features ?Text
                Locus ?Locus XREF Parental_Lines
                Allele ?Allele XREF Parental_Lines
                Panicle_Type ?Text
                Glume_Color ?Text
                Pericarp_Color ?Text
                Awns ?Text
                Seed_Color ?Text
                Plant_Height ?Text
                Maturity ?Text
                Fertility ?Text
                Organization ?Text
                Development_Site ?Text
                Developed_by ?Colleague XREF Parental_Lines
                Date_of_Release ?Text
                Contributed_by ?Colleague XREF Parental_Lines
                Remark ?Text
                Image ?Image XREF Parental_Lines 
                Paper ?Paper XREF Parental_Lines

?Genetic_Stocks	Name ?Genetic_Stocks XREF Genetic_Stocks 
                Other_name ?Genetic_Stocks XREF Genetic_Stocks 
                Other_Identities ?Text
                Type       Registered_Genetic_Stock
                Registration_Number ?Text
                Accession_ID ?Text
                Female_Parent ?Text
                Male_Parent ?Text
                Pedigree ?Text
                Features ?Text
                Locus ?Locus XREF Genetic_Stocks 
                Allele ?Allele XREF Genetic_Stocks
                Panicle_Type ?Text
                Glume_Color ?Text
                Pericarp_Color ?Text
                Awns ?Text
                Seed_Color ?Text
                Plant_Height ?Text
                Maturity ?Text
                Fertility ?Text
                Organization ?Text
                Development_Site ?Text
                Developed_by ?Colleague XREF Genetic_Stocks
                Date_of_Release ?Text
                Contributed_by ?Colleague XREF Genetic_Stocks
                Remark ?Text
                Image ?Image XREF Genetic_Stocks
                Paper ?Paper XREF Genetic_Stocks

?Cell_Culture	Study_of ?Cell_Culture XREF Cell_Culture
		Species_epithet ?Text
		Paper ?Paper XREF Cell_Culture
		Remark ?Text
		Contributed_by ?Colleague
			

?Allele		Reference ?Reference XREF Allele
		Contributed_by ?Colleague XREF Allele

?Image  Title Text
	Paper ?Paper  XREF Image
	Remark ?Text
	Contributed_By ?Colleague XREF Image
	Pick_me_to_call  UNIQUE Text Text   // A program name followed by a file name

?Sequence Name ?Sequence XREF Sequence
	  Other_name ?Text	// for repeats
	  Type UNIQUE DNA UNIQUE ?DNA UNIQUE Int	// Int is the length
		      Peptide UNIQUE ?AA
          RNA			// if this tag is set display AUGC
	  Structure  Length UNIQUE Int
		     From	Source UNIQUE ?Sequence
				Source_Exons Int UNIQUE Int // start at 1
	                        Assembled_into ?Sequence
		     Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int
		     Assembled_from ?Sequence XREF Assembled_into UNIQUE Int UNIQUE Int
	  Library	?Library Text Text // ID  Accession_number
	  Origin  From_Library ?Library
		  From_Author ?Author
		  From_Laboratory ?Laboratory
		  Date Text
	  Visible	cDNA 
			Genomic_Canonical UNIQUE Float // from the project: order
			Matching_Genomic ?Sequence XREF Matching_cDNA
			Matching_cDNA ?Sequence XREF Matching_Genomic
			Corresponding_DNA ?Sequence XREF Corresponding_peptide
			Corresponding_peptide ?Sequence XREF Corresponding_DNA
		  	Clone ?Clone XREF Sequence 
          	        Locus ?Locus XREF Sequence
		        Related_Sequence ?Sequence XREF Related_Sequence
			Keyword ?Keyword
	  		Remark ?Text
			DB_remark ?Text
			Brief_identification ?Text
	  		Reference ?Paper XREF Sequence
			Foreign_Reference ?Text
			DB_searched ?Library Int // version
			Expression_construct ?Clone
	  Properties    Pseudogene Text
			Transposon Text
			Coding	CDS UNIQUE Int UNIQUE Int
				CDS_predicted_by ?Method Float // score of method
				Precursor
			Transcript	End_not_found
				 	Start_not_found Int // Int is frame of base 1
					mRNA	Processed_mRNA
						Unprocessed_mRNA
					tRNA Text
					rRNA Text
					snRNA Text
			Status UNIQUE	Shotgun
					Contiguous
					Finished
	  Repeats	Inverted	Int UNIQUE Int #Match
			Tandem		Int UNIQUE Int #Match
			Direct		Int UNIQUE Int #Match
          Assembly_tags Comment Int Int Text
                        Compression Int Int Text
                        Stop Int Int Text
                        Assembly_repeat Int Int Text
                        Cosmid_vector Int Int Text
                        Alu_segment Int Int Text
                        Sequencing_vector Int Int Text
                        Cloning_vector Int Int Text
                        Oligo Int Int Text
			A_Repeat Int Int Text
	  Features	TSL_site Int UNIQUE Int Text // Trans-spliced leader
			TSL Int UNIQUE Int Text
			Possible_exon Int UNIQUE Int UNIQUE Int ?Method UNIQUE Float // 3rd Int is frame
			promoter Int UNIQUE Int ?Text
			polyA_site Int UNIQUE Int Text
			polyA_signal Int UNIQUE Int Text  // AATAA
			misc_signal Int UNIQUE Int ?Text
			misc_feature Int UNIQUE Int ?Text
			repeat_region Int UNIQUE Int Text
			repeat_unit Int UNIQUE Int Text
			mutation Int UNIQUE Int ?Text
			sig_peptide Int UNIQUE Int Text
			mat_peptide Int UNIQUE Int Text
			old_sequence Int UNIQUE Int Text
			modified_base Int UNIQUE Int Text
			TATA_signal Int UNIQUE Int Text
	  Similarity	Homol ?Sequence XREF Homol ?Method Float Int UNIQUE Int Int UNIQUE Int

// ?Species Sequence ?Sequence XREF Species	// much more to do here

?Match	Percent_Identity UNIQUE Int
	Score ?Method UNIQUE Float
	N_gaps UNIQUE Int
	Loop UNIQUE Int UNIQUE Int	// rel start, stop
	Unit_Length UNIQUE Int

?Library	Name Text // Full name
		Contents ?Text // Description of material included

?Method	Function ?Text	// what does it do?
	Variant_of UNIQUE ?Method XREF Variant
	Variant ?Method
	Version	Text
	Parameters 	Float_Params UNIQUE Text Float REPEAT 
			Int_Params UNIQUE Text Int REPEAT
			Text_Params UNIQUE Text Text REPEAT
	Min_score UNIQUE Float	// used in plotting
	Remark ?Text
	Reference ?Paper XREF Search_Method