// RiceGenes
// 19930812 EMP added RFLPr class to split out rf-lengths from probe.  add
// ability to tag polymorphic enyzme/probe combos
// stole from solgenes 1.10 version.
// models.wrm for Spudgenes 1.4 19930326 EMP, incorporated gg model and
//   existing spudgenes, which had changes in colleague and locus
// EMP added rf_length to probe to include MW info
// EMP added RF_bands to locus for MW of mapped bands, also Info fields
// in both linkage group and locus. 19930520
// EMP - mods for adding germplasm info provided by Rick/Chetelat
// EMP 19930805 mods to gene for other names/phenotypic classes
// EMP 19930920 added locus-mapped to polymorphism record
// EMP 19940107 changed valid locus types
// models.wrm - main file defining tree class structures
// This file is read only at run time, and furthermore
// only when you select 
// "Read Models" or "Add Update File"
// from the main menu.
//
// all tags must appear in tags.wrm or systags.wrm
//
// format for non-CGC literature references is
//	Foreign_Reference Text
//   where several Text entries can give authors, title, and 
//   reference (in EMBL/GenBank format if possible - i.e.
//    "Journal Volume:page1-pageN(Year)").
//


//?Allele - added Map_Enz_Sizes to indicate bands used
//   in a particular cross.
//EMP 19931029 add subspecies_class/code, and MW_of_band to handle gerards
//EMP 19940802 add Polymorphism and Molecular phenotype, remove subspecies
// code.  get rid of MW of band.
?Allele Name	Correct_name ?Allele XREF Other_name
		Other_name ?Allele XREF Other_name
	Gene UNIQUE ?Locus XREF Allele
        Locus UNIQUE ?Locus XREF Allele
	MW_of_band ?Restriction Float ?Colleague //change for gerard
	Subspecies_classification ?Text //EMP added for gerard data
        Polymorphism ?Polymorphism XREF Allele
	Absent_in ?Germplasm //EMP add for gerard
	Present_in ?Germplasm //EMP add for gerard
        Phenotype       ?Text
	Remark	?Text
        Mutagen UNIQUE ?Text
        Location Map ?Map XREF Allele #map_location //add map position
	Author	?Author
	Date	Text
	Pathology ?Pathology XREF Resistant_allele
	Other_information ?Text
	Origin ?Text
        Probe ?Probe XREF Allele
        Sequence ?Sequence
	RFLP ?Locus XREF Allele
	Reference ?Paper XREF Allele
	Acknowledgement ?Colleague
	Last_update	Text
	Image ?Image XREF Allele

?Gene_Class     Phenotype ?Text
                Gene      ?Locus

?Rearrangement  Name    Correct_name ?Rearrangement XREF Other_name
                	Other_name ?Rearrangement XREF Other_name
	        Reference_germplasm ?Germplasm  Text
		Remark ?Text
		Variant Text
		Mutagen ?Text	// remove reagent
		Phenotype	?Text
		Qualifier Text
		Author Text
		Date Text
		2_Point ?2_point_data
		Germplasm ?Germplasm XREF Rearrangement //approx=line 122
        	Reference ?Paper XREF Rearrangement

//?Locus
// 19940107 EMP removed pcr, gene, added cloned_gene, morph as types
// 19931216 EMP removed mapped-name and changed preferred name because 
// no longer using the () ++ # etc. in the locus names.  Added QTL type.
// also removed Loci and In_low_lod_group fields, no longer used.
// 19931025 EMP added Mapped_name and 
// 19930812 EMP added label and bands-mapped
// Add In_low_LOD_group - points to the loci in this contrived group
// Add Loci - individual true locus names, points to contrived name ()
// Add Low_LOD_group - boolean to indicate larger group
// This was done to make map correspond to published version - EMP
// Added PCR, Microsatellite, VNTR and Isolzyme as locus types - EMP
// Added band-data EMP 19930517.
// 19930810 EMP combined gene/locus and made several subclasses from
// locus record (rflp, rapd, gene, pcr, microsatellite, vntr, isozyme)
?Locus	Type	RFLP
		RAPD
		Cloned_gene
		Morph
		Microsatellite
		VNTR
		Isozyme
                QTL
                PCR //emp - add per sm for jmap
	        Low_LOD_group  ?Map_Data //Edie - point to which map
                Framework_marker  ?Map_Data //EMP - point to which map
	Name    Full_name ?Text  //EMP added for Roger
		Gene_class UNIQUE ?Gene_Class XREF Gene
	Germplasm ?Germplasm XREF Gene //EMP
        Allele  ?Allele XREF Locus
 	Phenotype ?Text
	Pathology ?Pathology XREF Resistance_gene //DEM
        Related_loci ?Text ?Locus //text is nature of relationship
        Reference ?Paper XREF Locus
        Acknowledgement ?Colleague
	Location Map ?Map XREF Locus #map_location //add map position
	Map_data ?Map_Data XREF Locus //EMP moved up to here
	2_Point ?2_point_data //EMP added
	Probe   ?Probe XREF Locus
	Sequence ?Sequence XREF Locus
	Image ?Image XREF Locus //Lisa added the XREF
	Remarks Text
	Other_information ?Text
	Info Text //EMP added for help object
	Label Text //EMP
	Mapped_bands ?Restriction ?Germplasm Float //EMP changed from rf-bands


//?Germplasm
//DEM 25 Feb 93 Removed the dumb "Pedigree" indentation pseudotag, but no
//  effect on data display even after "Read models",quit,restart; must 
//  rebuild database.
//  Added tags for describing genetic stocks.
//  Removed the XREF from Collection_and_ID ?Collection
//  Added XREF for Other_name
//  Changed Summary_pedigree to Pedigree, and made UNIQUE
//  Made Species ?Species instead of ?Text
//EMP - 19930607 Added Origin group of fields, also mating_system
//  done to accomodate germplasm data from Rick/Chetelat.  also added
//  gene-isogeni, background.
//EMP 19931029 added IRRI_accession field
?Germplasm 	Other_name ?Germplasm XREF Other_name // Put data in only one.
		IRRI_accession ?Text //EMP for gerard data
		Species UNIQUE ?Species
		Donor_species ?Text // For addition chromosomes
		Collection_and_ID ?Collection ?Germplasm XREF Other_name
		Developed_by ?Colleague //lisa 
		Development_site ?Text  //lisa
		Background_genotype ?Germplasm ?Germplasm
		Type #Germplasm_type
		Origin	Collector ?Colleague 
			Site ?Text //specific local
			Elevation_meters Text //not int so can take range
			Province ?Text //or department, county etc
			Country ?Text
			Year Int  //4 digit year
			Population_size Text //can be "small",10,etc
			Sample_size Text //same as above
			Habitat ?Text
			Associated_biota ?Text
			Vegetation_type ?Text
			Field_notes ?Text
		Mating_system ?Text
		Abbreviation ?Text
		Sporophytic_chrom_num ?Text //Not Int. "42tt" = ditelosomic substn.
 	        Female_Parent UNIQUE ?Germplasm
		Male_Parent UNIQUE ?Germplasm
		Pedigree UNIQUE ?Text
	 	Band_pattern ?Polymorphism ?Text //EMP -gerard.  text has MWs
		Generation_derived UNIQUE Text
		Selection_method ?Text
		Maturity_group ?Text
		Market_Class ?Text
		Traits ?Trait 
		Pathology ?Pathology XREF Resistant_line
		Phenotype ?Text
	   	Characteristics ?Text /EMP for geneva data
		Gene ?Locus XREF Germplasm Text //EMP for TGRC data
		Allele    ?Allele XREF Germplasm
		Rearrangement	 ?Rearrangement XREF Germplasm
		Reference_Allele Text
		Genotype Text	
		Growth_Req UNIQUE Text
		Mutagen ?Text
		Derived_from ?Germplasm  //DEM: should XREF?
		Registration_No ?Text     //lisa
		Remarks ?Text
		Source ?Text
		Reference ?Paper XREF Germplasm
		Mapping_data ?Map_Data
		Image ?Image XREF Germplasm

//?Germplasm_type
// DEM 2/93  Controlled vocabulary for ?Germplasm Type tag.
// EMP 19930607 added wild_species thru Allozyme_marker
?Germplasm_type	Cultivar
		Germplasm
		Wild_species
		Land_race
		Translocation
		Monogenic
		Misc_markers
                Autotetraploid
                Disease_resistant
                Linkage_screener
                Male_sterile
                Prebred
                Provisional_mutant
                Stress_tolerant
                Chromosome_marker
		Allozyme_marker

?Trait	Name ?Trait 
	Trait_value ?Text
	Environment ?Environment

?Environment	Evaluator ?Colleague
		Institute ?Text
		Environment ?Text


//?Linkage_Group
//Lisa changed Chromosome to Linkage_Group
//19930429 - added a Remarks fields to load an About_linkage_groups 
//occurrence for a help feature.  EMP
//EMP remove - now use ?map class
//?Linkage_Group	Non_graphic  // Prevents a graphic display 
//            	Centre Float Float  // Overrules default Initial centre, width


//?Probe - added field RF_length which contains vector of germplasm, enzyme, 
// EMP remove #type, add PCR and cloned_gene
//  MW band sizes and intensity indicator.  (dark, medium, faint).  sizes
//  are in kbs.  data comes from HyperBlot.  field will contain a lot of
//  data.  also add repeat to various types of enzymes.  EMP
//  19930812 EMP split rf-lengths into new class, morphism
// 19940110 EMP remove probe-type, add PCR and cloned_gene
?Probe  Locus   ?Locus XREF Probe
        Gene   ?Locus XREF Probe
	Allele ?Allele XREF Probe
	Reference ?Paper  //DEM Added
        Remark  General_Remark ?Text
		Y_Remark Text
		PCR_Remark ?Text
        Position  In_situ  UNIQUE Int Int
		  Chrom_Band ?Chrom_Band XREF Probe
		  Hybridizes_to ?Probe_Grid ?Probe XREF Positive_probe ?Text
		  Positive_probe ?Probe
		  Positive_pool_probe ?Pool
	PCR_primers ?Text //EMP change to text from ?sequence
	Amplification_conditions ?Text
	Sequence	?Sequence XREF Probe
	Insert	Size Float //Lisa  ...DEM changed from Int
		Insert_sequence ?Sequence //Lisa
       	Map_data ?Map_Data 
	Germplasm ?Germplasm XREF Probe 
	Origin	Vector   ?Text //Lisa changed this from ?Probe
		Vector_enzyme ?Restriction Repeat //Lisa
		Insert_enzyme ?Restriction Repeat //Lisa
		Excision_enzyme ?Restriction Repeat //Lisa  I removed Cutter_used
                Drug_resistance ?Text //drug resist, e.g. TET, AMP EP 4/16
		cDNA //boolean
		Genomic //boolean
                PCR //boolean
                Cloned_gene //boolean
		DNA_Origin ?Text
		Derived_from ?Germplasm
		Tissue_source ?Text
		Source_species ?Species //added to link to species EP 4/16
		Vector_PCR_primers ?Sequence  //lisa
	Subcloned_in ?Probe XREF Subclone_of
	Subclone_of ?Probe XREF Subcloned_in
	Laboratory ?Colleague
	Authority ?Colleague
	Image ?Image XREF Probe //Lisa
        Cant_map_as_RFLP ?Text //edie as per srm for jmap
	Polymorphism ?Polymorphism ?Text 
//EMP  ?Text holds polymorphic, possibly_polymorphic, not_poly, used_to_map


//?Polymorphism  EMP -  holds probe/enzyme/germplasm/MW/intensity info
//  for given probe/enzyme combos
//19930920 EMP - added Locus-mapped to link back to locus
//
?Polymorphism	Probe UNIQUE ?Probe XREF Polymorphism
		Enzyme UNIQUE ?Restriction
                Locus_mapped ?Locus
		Allele ?Allele XREF Polymorphism
		Image ?Image XREF Polymorphism
		Label Text
		Size ?Germplasm Text Float ?Text
                Band_MW ?Text //EMP add for gerard
                Pattern Text ?Germplasm //EMP add for gerard
		Remarks ?Text

?Probe_Grid	Title	?Text
		Layout	Columns	Int
			Lines_at	Int Int	// x, y spacing
			Space_at	Int Int	// x, y spacing
			No_stagger	// default is with alternate lines staggered
			A1_labelling	// label spaced blocks a-h down LHS, 1-12 across top
		Row Int ?Probe XREF Gridded REPEAT


//?2_point_data EMP changed to look more like aatdb, to incorporate data from 
//              M. Koornneef 19930713
//              Linkage_Group ?Linkage_Group Float - removed this line, 
//		replaced with one below to work around bug Dave found.

?2_point_data	a Gene1  ?Locus XREF 2_Point UNIQUE Int //EMP copy from aatdb
		b Gene2 ?Locus XREF 2_Point UNIQUE Int  //EMP copy from aatdb
                Results   Min      Float
                          Distance Float //EMP changed back to Float
                          Max      Float
                          Error    Float
		          Standard_error Float
                          Linkage  Text
		Map_data ?Map_Data XREF 2_point
		Location ?Map XREF Mapping_data #map_location //change from LG
                Date  UNIQUE Text
                Laboratory UNIQUE ?Colleague
                Reference ?Paper XREF 2_point
		Remark Text             

//?Colleague
// New version from Edie Paul, 3/93
?Colleague      Position Text
                Institution // Boolean, = "not_person"
                Address Mail Text //EMP: for Street,City,State,Zip together
                        Street Text //EMP - separate out address
                        City ?Text //EMP - separate city, make text object
                        State ?Text //EMP - separate, make text object
                        Postal_code ?Text //EMP - separate, make text object
                        Country ?Text //EMP - make text object
                        Phone Text
                        E_mail Text //EMP - deleted bitnet and internet
                        Fax Text
                Research_interest ?Text
                Keyword ?Keyword
                Last_update Text
                Comment Text //EMP add for gerard

//?Author
//DEM: On R.Durbin's advice, 11 Mar 93 (~/Mail/acedb), removed the 
//    "XREF Author" after "Paper ?Paper".  To avoid scrambled Author orders
//    in papers loaded from dump files.
?Author Full_name ?Colleague
        Paper ?Paper

?Journal Paper ?Paper XREF Journal

//?Paper
?Paper  Reference       Title UNIQUE ?Text
			Journal UNIQUE ?Journal XREF Paper
			Publisher UNIQUE Text
			So UNIQUE Text
			Contained_in ?Paper XREF Contains
                        Year UNIQUE Int
                        Volume UNIQUE Int Text
                        Page  UNIQUE Int Int
	Institution Text
        Author ?Author XREF Paper
	Type UNIQUE Text
	Language Text

	Abstract Text
	Contains ?Paper XREF Contained_in
        Refers_to	Locus ?Locus XREF Reference
			Gene ?Locus XREF Reference
			Allele ?Allele XREF Reference
			Rearrangement ?Rearrangement XREF Reference
			Sequence ?Sequence XREF Reference
			Germplasm ?Germplasm XREF Reference
			Mapping_data ?Map_Data XREF Reference
			2_point ?2_point_data //Lisa
        Keyword ?Keyword
	Image ?Image XREF Paper

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

//?Sequence 19941004 EMP add external_db_key for EMBL links
?Sequence Title UNIQUE ?Text
	  Other_name ?Text	// for repeats
          External_DB_key ?Colleague  ?Text //EMP add for ddbj or embl etc.
	  DNA UNIQUE ?DNA	// only one or the other of these
	  Peptide UNIQUE ?Peptide	// if there is DNA then derive from that
          RNA			// if this tag is set display AUGC
	  Length UNIQUE Int
	  Library	?Source Text Text // ID  Accession_number
	  Origin  From_Library ?Source
		  From_Author ?Author
		  From_Laboratory ?Colleague
		  Date Text
	  General	cDNA
		  	Probe ?Probe XREF Sequence 
			Gene ?Locus XREF Sequence
			Gene_product ?Gene_Product XREF Sequence
          	        Locus    ?Locus XREF Sequence
		        Related_Sequence ?Sequence XREF Related_Sequence
			Keyword ?Keyword
	  		Remark ?Text
			DB_remark ?Text
	  		Reference ?Paper XREF Sequence
			DB_searched ?Source Int // number of homologues found
	  Properties    Pseudogene Text
			Transposon
			Coding	CDS UNIQUE Int Int
				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

	  Features	polyA_signal Int Int // putative
			promoter Int Int ?Text
			polyA_site Int Int Text
			misc_signal Int Int ?Text
			misc_feature Int Int ?Text
			repeat_region Int Int Text
			repeat_unit Int Int Text
			mutation Int Int ?Text
			sig_peptide Int Int Text
			mat_peptide Int Int Text
			old_sequence Int Int Text
			modified_base Int Int Text
	  Structure	Pep_homol ?Sequence Float Int Int Int Int Text Text
			DNA_homol ?Sequence Float Int Int Int Int Text Text

?Gene_Product	Other_name ?Text
		Type ?Text ?Paper Text //Enzyme, Protein, etc
		Function ?Text
		Gene ?Locus ?Paper ?Text
		Source	Species UNIQUE ?Text ?Paper
			Cultivar ?Germplasm ?Paper ?Text
			Tissue ?Text ?Paper ?Text
			Organelle ?Text ?Paper ?Text
		Substrate_specificity ?Text ?Paper ?Text
		pH_optimum Float ?Paper ?Text
		Temp_optimum(C) Text ?Paper ?Text
		Regulation ?Text	
		Catalytic_mechanism ?Text
		Prosthetic_group ?Text
		Isozymes ?Gene_Product
		3D_structure Text //boolean with comment
		Purification Text 
		Isoelectric_point Float
		Biochemistry Text //
		Remarks Text //
		Reference ?Paper //
		Contact ?Colleague //
		Sequence ?Sequence //


?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


?Homology   Title UNIQUE ?Text

//?Image
?Image  Author ?Author XREF Image
	Reference  ?Paper  XREF Image
        Contact ?Colleague //EMP added for supplier of image
	Gene   ?Locus XREF Image 
	Locus ?Locus XREF Image
        Allele ?Allele XREF Image //EMP added for mutant images from TGRC
	Germplasm ?Germplasm XREF Image
	Species ?Species XREF Image
	Map_data ?Map_Data XREF Image
	Polymorphism ?Polymorphism XREF Image
	Pathology ?Pathology XREF Image //DEM added
	Probe ?Probe XREF Image //DEM
        Image ?Image //EMP add
	Caption Text //DEM
	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)


?Pool	Contains	Probe ?Probe XREF In_pool
			Subpool ?Pool XREF In_pool
	In_pool ?Pool
	Map	Hybridizes_to ?Probe_Grid ?Probe XREF Positive_pool_probe ?Text
		Chrom_Band ?Chrom_Band XREF Positive_pool_probe
	Reference ?Paper

//?Chrom_band  EMP added remarks field.  Use this to model hatch areas on
// the pepper map, showing synteny with tomato
?Chrom_Band     Type	Centromere	// special flag for waisted drawing
                        p_Telomere //left end of chrom
                        q_Telomere //right end of chrom
		Position UNIQUE Map ?Map XREF Chrom_Band #map_location
		Drawing Colour	#Colour
 		        Dark
		        NOR
		Contains ?Chrom_Band XREF Contained_in
		Contained_in ?Chrom_Band XREF Contains
                Locus Inside ?Locus XREF Chrom_Band
		Probe ?Probe XREF Chrom_Band
                Remarks ?Text //EMP added for pepper map


//?Collection     lisa added the Collection class
// DEM removed the  "Collection_and_ID ?Collection XREF Entries" from 
//     ?Germplasm, so ?Collection no longer contains an automatic list of
//     all its entries.
?Collection	Curator ?Colleague
		Description ?Text
		Acc_per_species ?Species Int
		
//?Pathology   Lisa added the pathology class
// 2/93 Dave extended
?Pathology	Other_name ?Pathology //Choose one, put the data in that
		Type	Fungus
			Bacterium
			Virus
			Nematode
			Insect
			Abiotic
		Host_species ?Species XREF Disease
		Causal_organism ?Species XREF Causes
		Resistance_gene ?Locus XREF Pathology
		Resistant_allele ?Allele XREF Pathology
		Resistant_line ?Germplasm XREF Pathology
		Symptoms Text
		Image ?Image XREF Pathology

//?Species 2/93 DEM, based on the PGD schema
//         3/6/93 KDK,DEM refined
// Object's id is of the form "T. turgidum var. durum", no authority.
// Correct_name is not XREF'd as Synonym.  This allows two classes of wrong
// names: dumb ones like "A. squarrosa" that aren't even listed as Synonyms,
// and valid (common or historical) ones like "Ae. squarrosa L.".
?Species   Correct_name UNIQUE ?Species //If object is a Synonym, say only this
           Full_name UNIQUE ?Text //Genus not abbreviated, with Authority
           Genus UNIQUE ?Text
           Species ?Text
	   Variety ?Text
           Authority ?Text
           Synonym ?Species XREF Correct_name
           Common_name ?Text
           Haploid_chromosome_number UNIQUE Int
	   Mapping_data ?Map_Data
	   Disease ?Pathology XREF Host_species // diseases of this species
	   Causes ?Pathology XREF Causal_organism // diseases caused by it
	   Reference ?Paper
	   Image ?Image XREF Species

//?Map_Data:  A result of a particular mapping study, or perhaps a summary map.
// Added by Lisa, extended by Dave Matthews
// v1.5: Now contains what used to be ?F2_data
?Map_Data	Species ?Species XREF Mapping_data // If interspec, give both.
		Female_parent UNIQUE ?Germplasm XREF Mapping_data
		Male_parent UNIQUE ?Germplasm XREF Mapping_data 
		Parent ?Germplasm XREF Mapping_data // for reciprocal, multiparental...
		Type 	Genetic
			Cytogenetic
			Physical
		Map_units Text // e.g. centiMorgans, microns, KB
		Reference ?Paper XREF Mapping_data
		Contact ?Colleague
		Image ?Image XREF Map
		Remarks Text  // Number of progeny, markers; kind of mapping population
		Linkage_Group ?Map XREF Map_data #map_location
		Locus ?Locus XREF Map_data Text //Text is raw Mapmaker data.
		2_point ?2_point_data XREF Map_data

//EMP add new MAP class, which will be like old linkage group
?Map	Type UNIQUE Genetic  //can use flag to define subclasses
		    Cytogenetic
                    Physical
	Display	Non_graphic // prevents graphic display
	        Title UNIQUE ?Text
	        Remark Text //Will appear in top right corner
	        Flipped //coordinates go upwards
	        Map_units Text // kb, cM, etc
		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 locally edit
			Author Text   //login name of who edited it
			Date Text	
	Main_Marker ANY  //appear left of scroll bar
	Contains	Locus ?Locus XREF Map
                        Chrom_Band ?Chrom_Band XREF Map
			Map ?Map XREF Map #map_location
			Allele ?Allele XREF Map
	Mapping_data ?Map_Data XREF Linkage_Group //lisa
	Info Text //EMP added for descriptions of lg conventions


?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