// more updates GRL
// ~sbeer/AllWheat/Roeder/models.wrm 3feb99 SCB
// for testing models for ?Breakpoint_interval and ?Breakpoint

// Indexed 1077 tags in 943 objects totalling 891 nodes

// testing model; imported tags for ACEDB 4.6a 23nov98 GRL
// models.wrm 2.7, for GrainGenes 1.8, from GRL 18mar98, ex:
// models.wrm 2.6, for GrainGenes 1.8, ex:
// models.wrm 2.5, for GrainGenes 1.7, ex:
// models.wrm 2.4, for GrainGenes 1.6, ex:
// models.wrm 2.3, for GrainGenes 1.5, ex:
// models.wrm 2.2, enhanced 28 Aug 95 for ace4_1, ex:
// models.wrm v. 1.9, 28 Oct 1994, for GrainGenes 1.4.  ex:...
// models.wrm for Soybase, from Lisa Lorenzen, 10 Sep 1992, based on:
// models.wrm - for AATDB, database release 1-6

// DEM 4/94 Removed some fossil tags and classes that weren't in use.
//	    Added ?Help
// DEM 10/94 Changed Comment Text to Comment ?Text in ?Gene, ?Gene_Class and
//	and ?Gene_Set, thus squashing a big bad bug of long standing.
//           Also changed ?Colleague Mail Text to ?Text, so Text Search's by 
//	city name etc. will work.
// v2.1, DEM 6/95: Patched errors reported by xace4_0b4 (mainly dangling XREFs)
// DEM 7/95 Added Orthologous_gene_set, Current_name, Alien_species to ?Gene
//	and ?Allele
// JMW, 6-15-95:  Added Candidate_orthology_group and Possible_orthologues
// tags from mapdb models.wrm to ?Locus
//
// JMW, 6-15-95:  Added anchoring to ?MultiMap copying from mapdb models.wrm. 
// 
// JMW 6-15-95: Added tags to Trait_study and Trait_scores classes and an XREF
// to the Environment class (for R.Line stripe rust data). 
//
// JMW 7/31/95: Added Gale_orthology_group and Gale_orthologues tags to ?Locus.
// JMW 8/01/95: Adding Translocation_break_point as a possible type to Type tag
// of Class ?Locus.
// JMW 8/04/95: Added Type STS to Locus data object model.
// DEM 3 Apr 95, version 2.4: Added Tom De Stein's ?Sequence modifications for
//	Genbank data

// 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
//

//DEM 11/94 First use.  Based on current SolGenes + old Soybase
//    11/95 'Results' -> 'Simple_distance', to allow 'Gmap data' display
//	    Removed 'Standard_error'.
?2_point_data  Gene ?Gene  // remove XREF GRL
	       Genotype  UNIQUE Text
               Species ?Species // Give this even if parents also given.
	       Female_Parent ?Germplasm	XREF 2_point_data
	       Male_Parent ?Germplasm XREF 2_point_data
               Parent ?Germplasm XREF 2_point_data // If cross was reciprocal,
						   //  or unknown
	       Population ?Text // If parents not known
               Generation ?Text // e.g. "BC1F2"
	       Results  UNIQUE Text
	       Number_of_individuals Int
	       Method ?Text
               // for raw segregation data:
	       Experiment	Mapper ?Author
				Laboratory ?Laboratory
				Date  UNIQUE DateType
				Temperature UNIQUE Text
               Map_data ?Map_Data XREF 2_point_data
               Linkage_data ?Linkage_data XREF 2_point_data
	//Mapped_by ?Colleague // DEFUNCT, EXPUNGED 2/96
	// A convenience link for querying from the Gene side.  ?Locus values are still required.
	       Point_1 UNIQUE Locus_1 UNIQUE ?Locus XREF 2_point_data UNIQUE ?Allele XREF In_2_point
			      Allele_1 UNIQUE ?Allele XREF 2_point_data
			      Rearrangement_1 UNIQUE ?Rearrangement XREF 2_point_data
	       Point_2 UNIQUE Locus_2 UNIQUE ?Locus XREF 2_point_data UNIQUE ?Allele XREF In_2_point
			      Allele_2 UNIQUE ?Allele XREF 2_point_data
			      Rearrangement_2 UNIQUE ?Rearrangement XREF 2_point_data
			// Point_1 and Point_2 are tag2 for the mapped loci
			// for now to use this on a map both must be on it with Position type Map info.
	       Calculation UNIQUE Full UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int // WT X Y XY
				  One_recombinant UNIQUE Int UNIQUE Int // WT X
				  Selected UNIQUE Int UNIQUE Int // X XY
				  One_all UNIQUE Int UNIQUE Int // X ALL
				  Tested UNIQUE Int UNIQUE Int // X H
				  Selected_trans UNIQUE Int UNIQUE Int // X XY
				  Backcross UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int // WT X Y XY
				  Dom_one UNIQUE Int UNIQUE Int // WT nonWT
				  Dom_selected UNIQUE Int UNIQUE Int // WT X
				  Dom_semi UNIQUE Int UNIQUE Int // XD ALL
				  Direct UNIQUE Int UNIQUE Int // R T
				  Complex_mixed UNIQUE Int UNIQUE Int // X ALL
			// calculation fields can be used for full likelihood calculations
	       Calc  Calc_distance UNIQUE Float
	             Calc_lower_conf UNIQUE Float
	             Calc_upper_conf UNIQUE Float
			// these fields are filled in by software from the Calculation data
	       Simple_distance	Min      UNIQUE Float 
                                Distance UNIQUE Float
                                Distance_units Text
                                Max      UNIQUE Float
                                Error    UNIQUE Float
                                Linkage  UNIQUE Text
			// some of these are used for drawing in the absence of Calculation data
	       Trait_marker	//== Locus_1 is a gene or qtl and Locus_2 is 
				// a molecular marker for it.
	       QTL
	       Contact ?Colleague // Replaces Mapped_by, for Penner & Sorrells
	       Reference ?Reference
	       Remark ?Text
	       Data_source ?Colleague ?Text // Text is date, 94.11.30 e.g.     
	// code uses Point_1, Point_2, Calculation and all its subtags, all the Calc subtags,
	// and most of the Simple_distance subtags.

?3_point_data          Gene1 UNIQUE ?Gene XREF 3_point_data ?Allele XREF 3_point_data
                       Allele1 UNIQUE  ?Allele XREF 3_point_data
                       Gene2 UNIQUE ?Gene XREF 3_point_data ?Allele XREF 3_point_data
                       Allele2 UNIQUE  ?Allele XREF 3_point_data
                       Gene3 UNIQUE ?Gene XREF 3_point_data ?Allele XREF 3_point_data
                       Allele3 UNIQUE  ?Allele XREF 3_point_data
		       Linker ?3_point_data XREF Linker
                       Linkage_group ?Map
                       Temperature UNIQUE Text
                       Date  UNIQUE Text
                       Mapper ?Author
                       Genotype  Text
                       Results Text
                       Result_type ABC
                                   AB_C
                                   A_BC
                       Recombinant_1 Text
                       Recombinant_2 Text
                       Recombinant_3 Text
                       Counts UNIQUE Int Text Int Text Int Text Int Text
                       CGC   Laboratory UNIQUE ?Colleague

//ACE
?Alignment Description ?Text
	   Consensus UNIQUE Verbatim UNIQUE Text
	   Alignment	Sequence ?Sequence XREF In_alignment Int UNIQUE Int #Align_component  // Member_Alignment
			Protein ?Protein XREF In_alignment Int UNIQUE Int #Align_component
			Include_alignment ?Alignment XREF In_alignment UNIQUE Int UNIQUE Int #Align_component
	   In_alignment #Alignment
	   Parent ?Alignment XREF Child
	   Child ?Alignment XREF Parent Int UNIQUE Int #Align_component
	   Is_subalign
	   Homol Pep_homol ?Protein XREF Align_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info

//ACE
?Align_component  Verbatim UNIQUE Text				// use this not extracted seq if present
		  Extract UNIQUE DNA #Extract_info
				 Peptide #Extract_info
				 Translate #Extract_info
				 Alignment #Extract_info
		  Partial UNIQUE Int UNIQUE Int			// start, end of self
		  Properties  Is_frame_shifted
			      Has_introns
			      Checked
			      Core
	
//?Allele:  DEM 5/93 Modified to load Cat. Gene Symb. for Wheat
//lines deleted or changed:
//?Allele Name	Correct_name ?Allele XREF Other_name
//		Other_name ?Allele XREF Other_name
//  	Reference_Germplasm ?Germplasm XREF Allele
//	Origin ?Text
//10/93 Added link to ?Gene_Product
// Gary Hart, email of 11/16/93: v, tv, dv, al, and i stocks should be
//	?Germplasm; ad, s, su and tr should be ?Text
// Gary Hart, email of 1/5/94: For stocks OTHER than the reference stocks that
//  are also known to bear a particular allele, use label "Other_stock".

?Allele Reference ?Reference XREF Allele
	Correct_name UNIQUE ?Allele XREF Other_name
	Other_name ?Allele XREF Correct_name ?Reference XREF Allele
	Qualifier Text	    // sd, sm, ts etc.  Not systematic just now
	Rearrangement ?Rearrangement XREF Allele
        Previous_name ?Allele ?Reference //DON'T XREF.  For the case of two
                //old names whose meanings are now swapped. XREF -> confusion!
        Current_name ?Allele ?Reference //DON'T XREF.
	Synonym ?Allele XREF Synonym ?Reference //For two valid names for same
		//allele, e.g. wheat "Aco-H1a (Hordeum)" vs. barley "Aco-1a"
	Compound_allele ?Allele XREF Component_allele ?Reference
	Component_allele ?Allele XREF Compound_allele ?Reference
	Gene UNIQUE ?Gene XREF Allele //Put the Reference in the ?Gene record
	Gene_class ?Gene_Class XREF Allele
	Gene_product ?Gene_Product XREF Allele ?Reference
	Hexaploid_stock ?Germplasm XREF Allele ?Reference
	Tetraploid_stock ?Germplasm XREF Allele ?Reference
	Diploid_stock ?Germplasm XREF Allele ?Reference
	Alien_species ?Germplasm XREF Allele ?Reference
	Near_isogenic_stock ?Germplasm XREF Allele ?Reference
	Unnamed_synthetic_stock ?Germplasm XREF Allele ?Reference
	Homologous_chromosome_substitution_line ?Text ?Reference
	Alien_chromosome_addition_line ?Text ?Reference
	Alien_chromosome_substitution_line ?Text ?Reference
	Translocation_line ?Text ?Reference
	Sequence ?Sequence		//Use only for ?Probe or ?Clone
        Reference_Allele
	Origin ?Text ?Reference	//for non-germplasms like "Ace*4/CS"
	Isolation	Author	Text	// Isolator - should be ?Author
			Date	DateType
		        Mutagen UNIQUE ?Reagent Text	//Text is dose, other conditions.
			Procedure Text
			Transposon_insertion Text  // Text Transposon type
			Derived_from ?Allele XREF Derivative
		// for revertants and deletions from Transposon alleles
			Isolated_for ?Author  
		// person requesting allele -- for transposon insertion
        Location ?Laboratory #Lab_Location
	Derivative ?Allele XREF Derived_from
        Genetics        Map ?Map #Map_position
                        Mapping_data    3_point_data ?3_point_data
               	      			Df_Dup ?Df_Dup_data
               	      			2_point_data ?2_point_data
                                        Multi_point ?Multi_pt_data
	                                Pos_neg_data ?Pos_neg_data
				// above three are for mapping on its own behalf
                        		In_3_Point ?3_point_data
               	      			In_Df_Dup ?Df_Dup_data
	                                In_2_point ?2_point_data
                                        In_multi_point ?Multi_pt_data
	                                In_pos_neg_data ?Pos_neg_data
				// these are for when the locus is mapped
			Covers Text // from MRC allele list
	Germplasm ?Germplasm XREF Allele ?Reference //for germplasms in which
		// the allele is present but which aren't the Stock for it
	Comment	?Text
	Pathology ?Pathology XREF Resistant_allele
        	//Some of these properties should be dropped or done another way.
	Properties	Phenotype ?Text
			Recessive
			Intragenic_revertant_of_dominant
                        Dominant
			Semi_dominant
			Codominant 
			Weak
		        Temperature_Sensitive	Thermo_sensitive
						Cryo_sensitive
			Amber
                        Maternal	Strictly_Maternal
					Maternal_and_Zygotic
					With_Maternal_effect
                        Paternal
	Image ?Image XREF Allele
	Interactions ?Text 	//Text says what kind of interaction.
        Probe ?Probe XREF Source_allele
	Numbered_reference Int ?Reference XREF Allele //Int is a numbered reference
						  //citation used in a Comment.
	Data_source ?Colleague ?Text 	//Text is date, eg 94.04.28
	Information_source ?Reference // If source is a reference
	Data_curated ?Colleague ?Text   //Who validated and converted to .ace
	Last_update ?Text		//PGD wants this for all our data.
	Clone_of_allele ?Clone  		//clones derived from this allele
	Molecular_phenotype ?Gel_pattern  	//MWs of bands for this allele
	External_DB_keys ?Text ?Text  	//links to external databases

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

?Balancer From_left_end
          To_right_end
          Locus ?Locus

//10/97, for Kleinhofs' bins
?Bin Locus ?Locus XREF Bin
     Bin_marker ?Locus XREF Bin_marker_for
     Data_source ?Colleague Text	// Text is date, eg 97.09.23

// ?Breakpoint added 3feb99 SRB
?Breakpoint  	Correct_name ?Breakpoint XREF Other_name
                Other_name ?Breakpoint XREF Other_name
		Map_data ?Map_Data XREF Breakpoint
 		Map ?Map XREF Breakpoint #map_position
		Positive In_chrom_band ?Chrom_Band XREF Contains_breakpoint
		Negative Not_in_chrom_band ?Chrom_Band XREF Does_not_contain_breakpoint
		Fraction_length	UNIQUE Float UNIQUE ?Reference
		Germplasm ?Germplasm XREF Contains_breakpoint
		Distal_deletion_in ?Germplasm XREF Deletion_distal_to
		Distal_interval ?Breakpoint_interval XREF Proximal_breakpoint
		Proximal_interval ?Breakpoint_interval XREF Distal_breakpoint
		Distal_rearrangement ?Rearrangement XREF Proximal_breakpoint
		Proximal_rearrangement ?Rearrangement XREF Distal_breakpoint
		Reference ?Reference XREF Breakpoint
		Remark ?Text

// ?Breakpoint_interval added 3feb99 SRB
?Breakpoint_interval	Correct_name ?Breakpoint_interval XREF Other_name
                 	Other_name ?Breakpoint_interval XREF Other_name
			Map_data ?Map_Data XREF Breakpoint_interval
 			Map ?Map XREF Breakpoint_interval #map_position
			Proximal_breakpoint ?Breakpoint XREF Distal_interval
			Distal_breakpoint ?Breakpoint XREF Proximal_interval
			Positive Contains ?Locus XREF In_interval
			Negative Does_not_contain ?Locus XREF Not_in_interval
 	        	Reference_stocks ?Germplasm ?Germplasm //15feb99
 			Phenotype	?Text
         		Reference ?Reference
 			Location ?Colleague
 			Remark ?Text

// 5/94, modified for acedb 3.0
?Chrom_Band 	Type	Centromere	// special flag for waisted drawing
		Drawing Dark
                      	NOR
                      	Colour #Colour
	                p_Telomere	// special flag for drawing // Left end of chromosome
        	        q_Telomere	// special flag for drawing // Right end of chromosome
                Symbol Text //jld
                Species ?Species //jld
		Position  UNIQUE Map ?Map XREF Chrom_Band #map_position
		Contains ?Chrom_Band XREF Contained_in
		Contained_in UNIQUE ?Chrom_Band XREF Contains
		Positive Contains_breakpoint ?Breakpoint XREF In_chrom_band // 3feb99
		Negative Does_not_contain_breakpoint ?Breakpoint XREF Not_in_chrom_band // 3feb99
		Locus Inside ?Locus XREF Chrom_Band
		Positive_pool_probe ?Pool XREF Chrom_Band
		Reference ?Reference

//ACE
?Clone  Remark  General_remark ?Text
		Y_remark ?Text
		PCR_remark ?Text
	Position  Map ?Map XREF Clone #Map_position
        	  pMap UNIQUE  ?Contig XREF Clone  UNIQUE Int UNIQUE Int 
						// pMap units are bands
		  Clone_as_locus ?Locus XREF Clone_as_locus
		  Clone_left_end ?Sequence	// filled by XREF
		  Clone_right_end ?Sequence	// filled by XREF
		  Pos_neg_data ?Pos_neg_data
	Positive  Inside_rearr ?Rearrangement XREF Clone_inside ?Author
		  Positive_locus ?Locus XREF Positive_clone ?Author
		  Hybridizes_to ?Clone XREF Positive_probe ?Grid
		  Hybridizes_weak ?Clone XREF Pos_probe_weak ?Grid
		  Positive_probe ?Clone XREF Hybridizes_to ?Grid
		  Pos_probe_weak ?Clone XREF Hybridizes_weak ?Grid
	Negative  Negative_locus ?Locus XREF Negative_clone ?Author
		  Outside_rearr ?Rearrangement XREF Clone_outside ?Author
		  Negative_probe ?Clone XREF Does_not_hybridize_to ?Grid
		  Does_not_hybridize_to ?Clone XREF Negative_probe ?Grid
	Sequence    ?Sequence XREF Clone
	Length	Seq_length UNIQUE Int 			// bp
		Gel_length UNIQUE Float			// Kb
	Location ?Laboratory #Lab_Location
	Gridded ?Grid
	Grid_data ?Grid_data 
	In_pool ?Pool XREF Clone
        FingerPrint     Gel_Number UNIQUE Int
                        Approximate_Match_to UNIQUE ?Clone XREF Canonical_for
                        Exact_Match_to UNIQUE ?Clone XREF Canonical_for 
                        Funny_Match_to UNIQUE ?Clone XREF Canonical_for 
                        Canonical_for ?Clone UNIQUE Int UNIQUE Int 
				// start and stop offsets from self start
                        Bands   UNIQUE Int UNIQUE Int	// not used
                        Gel ?Motif  #Lane               // Magic tag2 construct
	Contig9	Chromosome UNIQUE ?Map 
                Vaxmap UNIQUE Float
		In_Situ  UNIQUE Int UNIQUE Int // percent of physical chromosome
		Cosmid_grid
                Canon_for_cosmid
	        Flag    UNIQUE Int
		Autopos
	Expression_construct	Pattern ?Text	// archaic
  	Reference ?Reference XREF Clone
        cDNA_group Contains ?Clone XREF Contains Text
                   Contained_in ?Clone XREF Contained_in
                   Best_match UNIQUE ?Text
	Sequence_status	Shotgun	UNIQUE DateType
			Finished UNIQUE DateType
			Accession_number UNIQUE Text

//?Colleague
// New version from Edie Paul, 3/93
// DEM 10/93 Added Image
?Colleague      Position Text
                Profession Text
                Institution // Boolean, = "not_person"
                Address Mail ?Text 
                        Country ?Text 
                        Phone Text
                        Fax Text
                        E_mail Text
                        Telex Text
		WWW_page Text
		Laboratory ?Laboratory
		Background Text	// Training, experience, degrees
                Research_interest ?Text
		Image ?Image XREF Colleague
                Publishes_as ?Author XREF Full_name
		Remark Text   // Note uncertainties, possible other_names etc.
                Last_update UNIQUE ?Text // For info direct from source, yy.mm 
                Obtained_from ?Source Text // Text is date, e.g. 95.10.27

//?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.
// DEM 1/96 added new fields for IPGRI database of collections.  Previous
//	records should have their addresses moved from Description to Mail
?Collection Curator ?Colleague
	    Address Mail Text
		    Country Text
		    Phone Text
		    Fax Text
		    E_mail Text
		    Cable Text
		    Telex Text
	    Description ?Text
	    Please_see ?Collection // For the GrainGenes name_of_record.
	    Contained_in ?Collection XREF Contains
	    Contains ?Collection XREF Contained_in
	    IPGRI_code Text
	    Species ?Species Int   // Int is number of entries.
	    Entries ?Germplasm XREF Collection_and_ID
	    Update ?Source Text // When our source was last updated, e.g. 
				// IPGRI 94.11.07
	    Data_source ?Source Text   // Text is date.

?Column	UNIQUE	Scale Scale_unit UNIQUE Float	// minimum increment
		      Cursor Cursor_on
			     Cursor_unit UNIQUE Float
		Locator Magnification UNIQUE Float
			Projection_lines_on
		Marker_points
		Marker_intervals
		Contigs
		Reversed_physical
		Physical_genes
		Two_point
		Multi_point
		Likelihood
		Points	Point_query UNIQUE Text
			Point_yellow UNIQUE Text
                        Point_colour Text #Colour // to replace above
			Point_width UNIQUE Int	// max width if not at RHS
                        Point_error_scale UNIQUE Float
			Point_segregate_ordered
                        Point_show_marginal
			Point_pne #Colour // positive, no error
			Point_pe  #Colour // positive, error
			Point_nne #Colour // negative, no error
                	Point_ne  #Colour // negative, error
			Point_symbol UNIQUE Text // can now have more than one of these
		Interval_JTM	#Interval_col_conf
		Interval_RD	#Interval_col_conf
               	Interval_SRK 	#Interval_col_conf
		Derived_tags	DT_query UNIQUE Text
				DT_width UNIQUE Int
				DT_no_duplicates
                                DT_neighbours
                                DT_parents
				DT_follow_parent
                                DT_symbol_query
                                DT_tag Text
                                DT_hide
 		Spacer          Spacer_colour #Colour
                                Spacer_width Float
		RH_data		RH_query UNIQUE Text
				RH_spacing UNIQUE Float
				RH_show_all
				RH_positive #Colour
				RH_negative #Colour
				RH_contradictory #Colour
		pepSequence	PS_Highlight_residue   // il all needed for colomn display of peptides
				PS_Residues_per_wrap Int
				PS_Colours Text #Colour
		Hydrophobicity	HP_Show_Zero_bar
				HP_Fixed_Scaling
				HP_Calculation_window Int
				HP_Display_width Int
                Homol           HOM_bump
                pepFeature      FEA_bump
                                FEA_Query Text
                Homol_Name      HOM_NAME_bump
				HOM_NAME_width Int
                pepActiveZone
	        Submaps         Loci_Query UNIQUE Text		// ACE
				Interval_Query UNIQUE Text	// ACE
				Show UNIQUE Int			// ACE
				Tolerance UNIQUE Int		// ACE
				Pos_By_Loci			// ACE
	
?Components	Reaction ?Reaction
		Reactant ?Text
		Km Text
		Product ?Text

//4/94: Unused, possibly unusable in acedb3.0
?Contig bMap	Length UNIQUE Int	// in base units
		Position UNIQUE Int	// left extremity in bases
		b2g	UNIQUE	Float Float // gMap = ax + b
	gMap	UNIQUE ?Map XREF Contig Float Float	// extremities on gMap
        pMap    UNIQUE Int Int         // extremities in pMap units
	Map 	?Map XREF Contig #Map_position
//	Probe	?Probe XREF Contig
//      Locus	?Locus XREF bMap
	Clone ?Clone XREF pMap

?Database	Name Text // Full name
		Contents ?Text // Description of material included
		WWW	Arg1_URL_prefix UNIQUE Text
			Arg1_URL_suffix UNIQUE Text
			Arg2_URL_prefix UNIQUE Text
			Arg2_URL_suffix UNIQUE Text

?Df_Dup_data 	       Rearrangement ?Rearrangement XREF Df_Dup
		       Allele1 Text  // when the def is also known as allele
		       Gene UNIQUE ?Gene XREF Df_Dup
                       Allele UNIQUE  ?Allele XREF Df_Dup
                       Linkage_Group ?Map
                       Temperature UNIQUE Text
                       Date  UNIQUE Text
                       Mapper ?Author
                       Genotype UNIQUE Text
                       Results UNIQUE Text
                       CGC   Flag Text
                             Laboratory UNIQUE ?Colleague
			     Linkage Text
                       AATDB   Note UNIQUE Text
         		       Total UNIQUE  Int
		               A_deletes_B  UNIQUE Text Text
         		       A_does_not_delete_B UNIQUE  Text Text
		               A_includes_B UNIQUE  Text Text
         		       A_does_not_include_B UNIQUE   Text Text

//ACE
?Doc              Reference ?Reference
                  Type    Protein
                          Sequence
                          RFLP
                          Other

#EMBL_dump_info	EMBL_dump_method UNIQUE ?Method
		ID_template UNIQUE Text
		ID_division UNIQUE Text
		DE_format UNIQUE Text  
		OS_line UNIQUE Text    
		OC_line Text           
		RL_submission Text     
		EMBL_reference ?Reference  
		CC_line Text           
		source_organism UNIQUE Text   

?EMBL_info	Location UNIQUE Text	// full location if non-trivial
		Qualifier Note Text	// all qualifiers correctly
			  Product Text
	// We could have in #EMBL_info a more complete representation of
	// feature table qualifiers/syntax.  I doubt this is worth it.

//?Environment:  Location and experimental conditions for a (field) test of
//    a trait.
// DEM 5/93, built on Lisa's version
?Environment Year UNIQUE Text    	//eg 1993-4
	     Location UNIQUE ?Text	//eg "Ketola Farm, Ithaca, NY, USA"
	     Latitude UNIQUE Text
	     Longitude UNIQUE Text
	     Elevation UNIQUE Text
	     Experimental_design ?Text	//eg "Randomized Complete Block"
	     Replications UNIQUE Int	//How many replications here?
	     Evaluator ?Colleague	
	     Institute ?Text
	     Topography UNIQUE Text
	     Drainage UNIQUE Text
	     Soil_texture UNIQUE Text
	     Irrigation Text		//Type, number of days, total amount
	     Moisture Text		//Amount, units; eg 455 mm
	     Planting_date UNIQUE Text  //Format: 88.04.16
	     Harvest_date UNIQUE Text
	     Testing_date Text
	     N_applied Text		//Nitrogen fertilizer used, units
	     P2O5_applied Text		//Phosphorus, in units of P2O5
	     K2O_applied Text		//Potassium, in units of K2O
	     Remarks Text		//Special conditions or events here
	     Trait_study ?Trait_Study XREF Environment //What study(ies) were
	         //performed at this Environment.  (Usually only one.)
	     Trait_scores ?Trait_scores XREF Environment //Scores obtained here
	     QTL ?QTL XREF Environment

?Enzyme		Other_name ?Text
		EC_Number ?Text #Reference  // probably should be under reaction
		Corresponds_to	Locus ?Locus XREF Enzyme
				DNA ?Sequence XREF Enzyme
				Protein ?Protein XREF Enzyme
		Catalyzes ?Pathway
		Remark ?Text
		Reference ?Reference

//ACE
?Extract_info UNIQUE Gap UNIQUE Int #Extract_info
		     Seg UNIQUE Int UNIQUE Int #Extract_info
		     Insert UNIQUE Int #Extract_info		// add X's, not .'s

?Feature_info	EMBL_dump UNIQUE EMBL_dump_YES
				 EMBL_dump_NO
			// overrides for embl dump based on method
		Bury

//DEM 8/93 New
//Information about a gel electrophoretogram or autoradiogram (DNA, protein...)
//A blot or film is also a ?Gel.
//Better name for this class?  "Phoretogram"?
?Gel	Probe ?Probe XREF Gel	
	Date ?Text  // Date of gel or blot or autorad, then what procedure
		    // E.g. "93.08.05 DNA extraction"
		    // Standard date format: "93.08.05" (5 Aug 93)
	Run_by ?Colleague	// Who did the lab work
	Conditions ?Text	// Stringency, exposure time,...
	Polymorphism ?Polymorphism  //LOAD AS ?POLYMORPHISM XREF, NOT DIRECTLY
	Germplasm ?Germplasm	// Source of sample.
	Image ?Image		
	TABLE Text REPEAT 	// Column headings for Band table.
        Band ?Restriction Float UNIQUE Int UNIQUE Text // Kb, Intensity, Chrom
	Data_source ?Colleague Text  // Text is date, e.g. 97.11

//?Gene:  DEM May 93 Modified to load the Catalogue of Gene Symbols for Wheat
//lines removed or changed:
//?Gene Name	Gene_class UNIQUE ?Gene_Class XREF Gene
//		Correct_name ?Gene XREF Other_name
//              Other_name ?Gene XREF Other_name
//      Reference_Allele ?Allele XREF Gene Text
//      Allele  ?Allele XREF Gene
//	Origin ?Text
//    New:
//	Hexaploid_stock ?Germplasm XREF Gene ?Reference, etc.
//10/93 Added link to ?Gene_Product.  Moved Reference to top of model.
// Gary Hart, email of 11/16/93: v, tv, dv, al, and i stocks should be
//  ?Germplasm; ad, s, su and tr should be ?Text.
// Gary Hart, email of 1/14/94: Add Previous_name and Synonym for the special
//  usages indicated below.
// 6/94: Expanded Tab's to Space's in this model.
?Gene   Full_name ?Text //Barley uses full names a lot.
        Reference ?Reference XREF Gene //The standard reference for this gene
        Gene_class ?Gene_Class XREF Gene
	Orthologous_gene_set ?Gene_Set XREF Gene
        Other_name ?Gene XREF Correct_name ?Reference  
        Correct_name ?Gene XREF Other_name ?Reference
        Previous_name ?Gene ?Reference //DON'T XREF.  For the case of two
                //old names whose meanings are now swapped. XREF -> confusion!
        Current_name ?Gene ?Reference //DON'T XREF.
        Synonym ?Gene XREF Synonym ?Reference //For two valid names for same
                //gene, e.g. wheat and barley names Aco-H1(Hordeum) vs. Aco-1
		//Use instead of Other_name<->Correct_name for ALL barley genes
        Compound_gene ?Gene XREF Component_gene ?Reference
        Component_gene ?Gene XREF Compound_gene ?Reference
	QTL ?QTL XREF Associated_gene
        Gene_product ?Gene_Product XREF Gene ?Reference
        Chromosome ?Text ?Reference
        Chromosome_arm ?Text ?Reference
        Hexaploid_stock ?Germplasm XREF Gene ?Reference
        Tetraploid_stock ?Germplasm XREF Gene ?Reference
        Diploid_stock ?Germplasm XREF Gene ?Reference
	Alien_species ?Germplasm XREF Gene ?Reference
        Near_isogenic_stock ?Germplasm XREF Gene ?Reference
	Unnamed_synthetic_stock ?Germplasm XREF Gene ?Reference
        Homologous_chromosome_substitution_line ?Text ?Reference
        Alien_chromosome_addition_line ?Text ?Reference
        Alien_chromosome_substitution_line ?Text ?Reference
        Translocation_line ?Text ?Reference
        Origin ?Text ?Reference //for non-germplasms like "Ace*4/CS"
        Reference_allele UNIQUE ?Allele XREF Gene ?Reference
        Allele ?Allele XREF Gene ?Reference
        Comment ?Text
        Molecular_information   Clone ?Probe XREF Source_gene //3/94
                                Sequence ?Sequence XREF Gene
        Pathology ?Pathology XREF Resistance_gene //DEM
        Image ?Image XREF Gene
        Mapping_information Locus ?Locus XREF Associated_gene
			    Candidate_locus ?Locus XREF Candidate_gene
        Mapping_data    2_point_data ?2_point_data
                        3_point_data ?3_point_data
                        Df_Dup ?Df_Dup_data
        Related_genes   ?Gene XREF Related_genes ?Text //4/94: Text describes
                                //kind of relationship.
        Numbered_reference Int ?Reference XREF Gene //Int is a numbered 
                                //reference citation used in a Comment.
	Data_source ?Colleague ?Text 	 //Text is date, eg 94.04.28
	Information_source ?Reference // If source is a reference.
	Data_curated ?Colleague ?Text   //Who validated and converted to .ace

//?Gene_Class:  DEM extended, 5/93
//see abbreviation list in Catalogue of Gene Symbols for Wheat, 1988, p.1295
//DEM 9/93 Added Trait_affected
//DEM 11/93 removed (should link to Allele instead, maybe Gene):
//		Gene_product ?Gene_Product
//  Should change Abbreviation from ?Text to Text.  It's picking up values from
//  the Germplasm Abbreviation ?Text, which are ALL CAPs.  Or, change the 
//  name to 'Symbol'?
//DEM 2/94 Abbreviation ?Text -> Text (collided with Germplasm Abbreviation)
//	   Changed Character_affected from ?Text to ?Trait
//DEM 3/94 Appending "XREF Affected_by" to Character_affected caused ACEDB 
//           death, until database reinitialized.
//DEM 6/94 Gene <-> Gene_Class links are now routinely causing database death.
//	     There's some nonuniformity in Space vs. Tab alignment of tags
//	     in the model here; expanded to all Space's.
?Gene_Class Phenotype ?Text
	    Reference ?Reference XREF Gene_class
            Abbreviation Text //eg "Adh". 
            See_also ?Gene_Class XREF See_also
            Character_affected ?Trait XREF Affected_by
	    Pathology ?Pathology XREF Gene_class
            Orthologous_gene_set ?Gene_Set XREF Gene_class	//e.g. Adh-1
            Gene ?Gene XREF Gene_class				//e.g. Adh-A1, Adh-B1...
            Gene_product ?Gene_Product XREF Gene_class		// GRL
	    Locus ?Locus XREF Gene_class
            Clone ?Probe XREF Source_gene_class			//DEM 3/94
            Sequence ?Sequence XREF Gene_Class			// GRL
            Comment ?Text
            Numbered_reference Int ?Reference XREF Gene_class //Int is a  
                        //numbered reference citation used in a Comment.
	    Designating_laboratory UNIQUE ?Laboratory XREF Gene_classes
	    Allele ?Allele	XREF Gene_class

?Gene_Product	Other_name ?Text
		Type ?Text ?Reference Text //Enzyme, Protein, etc
		Function ?Text
		RNA_type
		IUB_number UNIQUE ?Text ?Reference
		EC_number UNIQUE ?Text
		Gene ?Gene XREF Gene_product
		Gene_class ?Gene_Class XREF Gene_product  // GRL
		Allele ?Allele XREF Gene_product
		Source	Species ?Species ?Reference
			Germplasm ?Germplasm XREF Gene_product ?Reference ?Text
			Tissue ?Text ?Reference ?Text
			Organelle ?Text ?Reference ?Text
			Membrane_Associated ?Reference //boolian +ref.
		Pathway ?Pathway #Components
		Substrate_specificity ?Text ?Reference ?Text
		pH_optimum Float ?Reference ?Text
		Temp_optimum(C) Text ?Reference ?Text
		Regulation #Regulators	
		Ancillary_enzyme ?Gene_Product
		Catalytic_mechanism #Mechanism
		Prosthetic_group ?Text
		Isozymes ?Gene_Product
		Structure	Native_Mr Float
				3D_structure Text //boolian with comment
				Purification Text 
				Isoelectric_point Float
		Biochemistry Text //
		Remarks Text //
		Reference ?Reference //
		Contact ?Colleague //
		Sequence ?Sequence //

//DEM 11/93 created.  E.g. Aadh-1 is a homologous gene set in the Gene_Class
//Aadh.  The set includes the individuals on homoeologous chromosomes of wheat
//or other species: Aadh-A1 (Triticum), Aadh-B1 (Triticum), Adh-R1 (Secale), 
//etc.
?Gene_Set 	Reference ?Reference XREF Gene_Set
		Abbreviation ?Text		//eg "Adh-1"
		Gene_class ?Gene_Class XREF Orthologous_gene_set
		Character_affected ?Text
                Gene ?Gene XREF Orthologous_gene_set
		Comment ?Text
		Numbered_reference Int ?Reference XREF Gene_Set //Int is a  
			//numbered reference citation used in a Comment.

//?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
//v1.6: Added Image, Trait, Trait_scores
//DEM 13 Aug 94 Removed UNIQUE from Species, Pedigree, etc.  Data should be
//  loaded and then tested for COUNT > 1 to test for inconsistencies.
?Germplasm 	Other_name ?Germplasm XREF Other_name // Put data in only one.
		Species ?Species //Required.  Even if Subspecies also given.
		Subspecies ?Species //e.g. "Triticum turgidum ssp. durum"
		Donor_species ?Species 	//For addition chromosomes
		Type #Germplasm_type
		Collection_and_ID ?Collection ?Germplasm XREF Other_name
		Cross_number ?Text	//Identifier used by CIMMYT
		Chromosome_configuration ?Text
		Deletion_distal_to ?Breakpoint XREF Distal_deletion_in // 3feb99
		Contains_breakpoint ?Breakpoint XREF Germplasm // 3feb99
		Abbreviation ?Germplasm XREF Full_name //DEM 3/94
		Full_name ?Germplasm XREF Abbreviation // "   "
		Pairing_configuration ?Text
		Chromosome_number ?Text //Not Int. "42tt" = ditelosomic substn.
		Female_Parent ?Germplasm
		Male_Parent ?Germplasm
		Pedigree ?Text
		Selection_history ?Germplasm XREF Other_name
		Market_Class ?Text
		Characteristic ?Text 	//e.g. "Awn-color: blue-black"
		Pathology ?Pathology XREF Resistant_line
		Allele ?Allele XREF Germplasm 
		Gene ?Gene 	//No XREF, load only from Gene side
		Gene_product ?Gene_Product XREF Germplasm //To add Reference,
							//load from other side.
		Rearrangement	 ?Rearrangement XREF Germplasm
		Sequence ?Sequence XREF Germplasm
		Derived_from ?Germplasm  //DEM: should XREF?
		Chromosome_donor ?Text //for additions, substitutions.  May be
			// a Germplasm or Species (or any text)
		Cytoplasm ?Text
		Developed_by ?Text //changed from ?Colleague for KDK, 2/94
		Development_site ?Text //e.g. Alabama-USA
		Collection_site ?Text  //e.g. "By the road, near Tel Aviv"
		Date_collected ?Text   //e.g. 72.08.09
		Primary_collection ?Collection
		Date_of_release ?Text
		Registration_No ?Text     //lisa
		Remark ?Text
		Polymorphism ?Polymorphism #Presence //list of band sizes
		Trait_description ?Trait_Study XREF Germplasm_description ?Text ?Text 
			// First Text is coded score, second is rough 
			// translation.
		Trait_score ?Trait_Study Float ?Text 
			// Float is score, Text is units.  NOTE:  No XREF.
			// Must manually add data to
			///?Trait_Study Germplasm_score ?Germplasm Float ?Text
		Reference ?Reference XREF Germplasm
		Data_source ?Colleague ?Text //Text is date, e.g. 93.08.27
		Data_curated ?Colleague ?Text // Who converted source to .ace
		Mapping_data ?Map_Data
                Linkage_data ?Linkage_Data
		2_point_data ?2_point_data
		Trait_study ?Trait_Study
        	Image ?Image XREF Germplasm
		Trait_scores ?Trait_scores //Should be near end of model, 
			//could be a long list.
		Coefficient_of_parentage ?Germplasm Float //Must be at end of
			//model; this could be a Long list.  Should XREF, or
			//let folks query for the other matrix direction?
//DEM 5/93: Old tags expunged:
//		Traits ?Trait #Trait_Information 
//    9/93: Changed 'Remark General_remark' to 'Remark'
//DEM 4/94: Old tags expunged:
//		Generation_derived UNIQUE Text
//		Selection_method ?Text
//		Maturity_group ?Text
//		Phenotype UNIQUE ?Text  //DEM: Delete?
//		Genotype Text	//3/94: not used yet
//		Growth_Req UNIQUE Text
//		Mutagen UNIQUE ?Reagent
//		Location ?Colleague #Lab_Location
//		Source ?Text

//?Germplasm_type, DEM 2/93  
// Controlled vocabulary for ?Germplasm Type tag.
?Germplasm_type	Cultivar
		Elite_germplasm
		Germplasm
		Substitution
		Translocation
		Amphiploid
		Aneuploid
		Deletion
		Alien_addition
		Synthetic
		Recombinant_translocation_line
		Mutation
	        Isogenic
		Marker
		Alloplasmic_line

//ACE
?Grid	Title	?Text
	Layout	Columns	UNIQUE Int
		Lines_at UNIQUE Int UNIQUE Int	// x, y spacing
		Space_at UNIQUE Int UNIQUE Int	// x, y spacing
		No_stagger // default is with alternate lines staggered
		Size UNIQUE Int UNIQUE Int
			// idea is to give box size here
		Labels 	UNIQUE	A1_labelling
		    // label spaced blocks a-h down LHS, 1-12 across top
				XY_labelling UNIQUE Text UNIQUE Text
		    // X-axis and Y-axis labels in the form of
		    // 01-XX or XX-01, for ascending vs. descending.
		    // Append an 'A', eg. 01-10A, for alphabetic.
	View ?View
	Row Int #Grid_row
	Virtual_row Int UNIQUE ?Grid XREF In_grid REPEAT
	In_grid ?Grid
	// If using lazy_grid, must set XY_labelling to be able to
        // generate object names of the form <prefix><column_label><row_label>
	Lazy_grid	Prefix UNIQUE Text
			Lazy_template Clone UNIQUE ?Clone
				      PAC   UNIQUE ?Pac 
                                      YAC   UNIQUE ?Yac
                                      BAC   UNIQUE ?Bac
                                      Cosmid   UNIQUE ?Cosmid 
                                      Fosmid   UNIQUE ?Fosmid
                                      cDNA   UNIQUE ?cDNA
                                      Hybrid   UNIQUE ?Hybrid
                                      Pool   UNIQUE ?Pool
                                      Tissue   UNIQUE ?Tissue
                                      Oligo   UNIQUE ?Oligo  // Tag2

//ACE
?Grid_data	Experiment  Mapper ?Author
			    Laboratory ?Laboratory
			    Date  UNIQUE DateType
		Positive Hybridizes_to ?Clone
			 Positive_product ?Clone
		Grid_data Grid UNIQUE ?Grid
			  Probe	UNIQUE	STS UNIQUE ?STS XREF Grid_data
					Clone UNIQUE ?Clone XREF Grid_data
		// tag 2 for probe - REQUIRED
			  Default_negative
		// if set then all non-explicit elements on Grid score -ve

//ACE
?Grid_row UNIQUE Clone UNIQUE ?Clone XREF Gridded REPEAT
		 Rearrangement UNIQUE ?Rearrangement XREF Gridded REPEAT
		 Mixed #Mixed_grid_row

//?Help.  Added by DEM 4/94
?Help Intro ?Text
      Overview ?Text
      Note ?Text
      Tip ?Text
      More ?LongText
 
//4/94 Proposed:
//List of all loci that are homoeologous, i.e. homologous in function and/or
//DNA sequence, and not-non-syntenic in location.  Includes loci that are
//variant names for the same probe used by different authors.
//?Homoeology_group
//	Homoeologues ?Locus XREF Homoeology_name

//ACE
?Homology_group Type UNIQUE Pairwise ?Locus XREF Pairwise ?Locus XREF Pairwise ?Doc 
                            Fuzzy ?Locus XREF Fuzzy
                Reference ?Reference
                Remark Text

//ACE
?Homol_info Segs #Match_seg
	    Bury		// do not show on the standard display

// Constructed type used in ?Locus Data ?Map_Data #How_mapped
?How_mapped Mapped_with_probe ?Probe
            Mapped_by_function ?Gene

// models for Drawing display - not used yet
// do not use - they may well change, but I leave them here because
// they form the basis for what is in the code - no, comment them out
//
//?Image   Image #Image_file
//	 Drawing Centre UNIQUE Float UNIQUE Float
//         	 Scale UNIQUE Float		// units -> pixels
//		 Bounds UNIQUE Float UNIQUE Float UNIQUE Float UNIQUE Float
//         Display  Default_view UNIQUE ?View
//  		  View ?View
//  	 Contains  Cell ?Cell
//  		// Contains is tag2 for objects - where is under Drawing
//
//#ImageFile File_name UNIQUE Text
//  	   File_type UNIQUE GIF	// could add JPEG, TIFF etc
//  	   Colormap UNIQUE Greyscale
// 		           Color
//
//#DrawInfo UNIQUE Point UNIQUE Float UNIQUE Float
//				// x y
//	         Rectangle UNIQUE Float UNIQUE Float UNIQUE Float UNIQUE Float
//				// x1 y1 x2 y2
//		 Polygon Float UNIQUE Float
//				// column of x y pairs

// DEM v1.5: Added Pathology, Probe, Caption
//     v1.6: Added Germplasm, Species, Map, Trait; changed Paper to Reference
//   	     Added Locus, QTL
?Image  Continued_from ?Image XREF Continued_in
	Continued_in ?Image XREF Continued_from
	Gene ?Gene XREF Image
	Locus ?Locus XREF Image 
	Allele ?Allele XREF Image
	Pathology ?Pathology XREF Image 
	Probe ?Probe XREF Image 
	Polymorphism ?Polymorphism XREF Image
	//A QTL link is for an image of a particular QTL, e.g. an autorad of 
	//bulked segregant analysis of the linked marker.  See also Trait.
	QTL ?QTL XREF Image
	Germplasm ?Germplasm XREF Image
	Species ?Species XREF Image
	Map ?Map_Data XREF Image
        Linkage_data ?Linkage_Data XREF Image
	Colleague ?Colleague XREF Image	//For pix of people.  cf Author, below.
	Trait_study ?Trait_Study XREF Image
	Caption ?Text //DEM
	Author ?Author XREF Image
	Reference ?Reference XREF Image
	Pick_me_to_call  UNIQUE Text Text  //Program name followed by file name
//	Secret  Text  // If set prevents display except by owner (uid == Text). DEM deactivated.

// DEM 98apr.  For miscellaneous map intervals.
?Interval   	Position  UNIQUE Map ?Map XREF Interval #map_position
		Contains ?Interval XREF Contained_in
		Contained_in UNIQUE ?Interval XREF Contains
		Locus Inside ?Locus XREF Interval
		Remark Text

?Interval_col_conf 	Query UNIQUE Text // Query
			Names_on
			No_neighbours
			Show_multiple
			Width UNIQUE Int
			Symbol UNIQUE Text
			Colours Text #Colour // Only for chrom_bands.
			Pne #Colour // positive, no error
			Pe  #Colour // positive, error
			Nne #Colour // negative, no error
                	Ne  #Colour // negative, error

//?Isolate 5/97 DEM, based on PathoGenes
//  For all kinds of pathogen and pest "germplasm"s.
?Isolate Synonym ?Isolate XREF Synonym
	 Type Pathotype
	      Strain
	 Species ?Species
         Origin Collector ?Colleague ?Text
                Latitude ?Text
                Longitude ?Text
                Country ?Text
         Characteristic ?Text //eg "Mating type: +" "1 mM Ethirimol: Resistant"
	 Avirulence ?Text     //for formulae
         Note ?Text
         Reference ?Reference XREF Isolate
         Data_source ?Colleague ?Text // Text is date, eg. 95.03.07
         Reaction_to_host_genes ?Text ?Allele  //e.g. "2-3", "A", "V"
         Reaction_to_host_germplasm ?Text ?Germplasm

?Journal Other_name ?Journal XREF Other_name
	 Source_code ?Text
         Paper ?Reference XREF Journal

//ACE
?Laboratory     Address Mail Text
                        Phone Text
                        E_mail Text
			Fax Text
                CGC     Representative UNIQUE ?Colleague XREF Laboratory 
                        Strain_designation Text
                        Allele_designation Text
                        Gene_classes ?Gene_Class XREF Designating_laboratory
		Staff   ?Colleague XREF Laboratory

//ACE
?Lab_Location	Freezer		Text
		LiquidN2        Text
		Minus70		Text
                Remark		?Text

//ACE
#Lane UNIQUE Bands UNIQUE Float REPEAT // In base pairs: if you prefer to minimise the ace format
             Band_Lengths  UNIQUE Float REPEAT // in mm: if you prefer to minimise the ace format
             Band Float Text    // if you wish to comment single band value

//?Linkage_Data:  A subchromosomal region resulting from a particular mapping
// study (population).  Bigger than 2 or 3 markers (see ?2_point_data), and/or
// with the raw population segregation data given.
// Added by Dave Matthews, 3/96, based on ?Map_Data.
// Removed Type Chromosome_arm
?Linkage_Data Species ?Species XREF Linkage_data //If interspecies cross,
                                                 // give both parental species.
              Female_parent UNIQUE ?Germplasm XREF Linkage_data
              Male_parent UNIQUE ?Germplasm XREF Linkage_data
              Parent ?Germplasm XREF Linkage_data //for reciprocal etc.
              Type      Genetic
                        Cytogenetic
                        Physical
              Map_units Text // e.g. centiMorgans, microns, KB
              Reference ?Reference XREF Linkage_data
              Contact ?Colleague
              Remarks ?Text //Number of progeny, kind of mapping populat'n
              Image ?Image XREF Linkage_data
              Map ?Map XREF Linkage_data
              Trait_study ?Trait_Study XREF Linkage_data  //Trait analyzed for
                                                          // QTLs with this map
              QTL ?QTL XREF Linkage_data      //Each QTL found
              2_point_data ?2_point_data XREF Linkage_data
              Locus ?Locus XREF Linkage_data Text //Text is raw Mapmaker data

//?Locus
//DEM 5 Oct 92:
//	New "Type" values: RAPD, Gene
//	Removed:
//	Mapped_bands	Map ?Map_Data //Lisa
//			Enzyme ?Restriction //Lisa
//			A81-356022 float  //Lisa
//			PI468.916 float  //Lisa
//v1.5, Feb 93:
//	"Mapping_information" -> "Map"
//	Data ?F2_data -> Data ?Map_Data
// S.Tanksley 3/93 says Locus_type's should include: RFLP RAPD PCR VNTR
//      Microsatellite Isozyme Gene (Gene includes Morph, Resistance, etc.)
//v1.6: Added: QTL, Linked_QTL, Image
//	Removed:
//	Not_used ?Restriction REPEAT
//      Polymorphic_for ?Restriction REPEAT //Lisa
//	Not_polymorphic_for ?Restriction REPEAT
//4/94: Drop the Wheat_name, Published_name, GrainGenes_name business,
//	and switch to listing only under published name and Homoeology_
//	name?
//	Wheat_name ?Locus XREF GrainGenes_name//Name that follows Wheat rules
//	Published_name ?Locus XREF GrainGenes_name //Name published as
//	GrainGenes_name ?Locus  //Put gMap values only in this object
//Feb 95: Added Candidate_gene, for Gary Hart	
//JMW, 6-15-95:  Added Candidate_orthology_group and Possible_orthologues
//	tags from mapdb models.wrm
//JMW, 7-31-95:  Added Gale_orthology_group, Gale_orthologues.
//JMW, 8-04-95:  Added Type STS.
//DEM, 6 Dec 95: Removed: (old version of Candidate_orthology_group
//       Homoeology_name ?Locus	//Common name for homoeologs on all maps.
?Locus	Type	RAPD
		APPCR		//DEM added 10/95
		Microsatellite
		STS
		AFLP
		QTL
                Translocation_break_point
		Centromere
		Telomere
		C-band
		Gene	Reference_Allele ?Allele Text
			Phenotype ?Text
			Complementation_data Text
		Polymorphism    RFLP	Text
				Transposon_insertion  Text
				Detection_method Text
		PCR_product	Primers  Text
				Length   Int	// bp
		Clone_as_locus	UNIQUE ?Clone XREF Clone_as_locus
        Molecular_information	Sequence ?Sequence XREF Locus
                                Product ?Text
				Enzyme ?Enzyme XREF Locus
	//7/95: Add Other_name, Previous_name, for Wheat Gene Catalog
        Other_name ?Locus XREF Correct_name ?Reference
        Correct_name ?Locus XREF Other_name ?Reference 
        Previous_name ?Locus ?Reference //DON'T XREF.  For the case of two
                //old names whose meanings are now swapped. XREF -> confusion!
        Current_name ?Locus ?Reference //DON'T XREF.
	Synonym ?Locus XREF Synonym    //When neither name is preferred.
        Location Chromosome Text ?Species     //E.g. 3D
                 Chromosome_arm Text ?Species //E.g. 3DS, short arm of 3D
		 Map ?Map XREF Locus #map_position
                 Main_Marker ?Map XREF Main_Marker
                 Inside Chrom_Band ?Chrom_Band XREF Inside
		 	Interval ?Interval XREF Inside
	Display_map ?Map // Only display these map(s) when drawing
	Bin ?Bin XREF Locus		// for Kleinhofs' bins
	Bin_marker_for ?Bin XREF Bin_marker
        Homology Pairwise ?Homology_group //jld
                 Fuzzy ?Homology_group //jld
	Positive In_QTL ?QTL XREF Significant_marker // to draw GMAP colors
                 In_segment ?Rearrangement XREF Contains
		 Inside_rearr ?Rearrangement XREF Locus_inside ?Reference
		 Positive_clone ?Clone XREF Positive_locus ?Reference
		 In_interval ?Breakpoint_interval XREF Contains // 3feb99
        Negative Not_in_QTL ?QTL XREF Nonsignificant_marker
                 Not_in_segment ?Rearrangement XREF Does_not_contain
		 Outside_rearr ?Rearrangement XREF Locus_outside ?Reference
		 Negative_clone ?Clone XREF Negative_locus ?Reference
		 Not_in_interval ?Breakpoint_interval XREF Does_not_contain // 3feb99
	Data	?Map_Data XREF Locus #How_mapped
	Background_marker ?Map_Data //If used specially in Composite Interval
					// Mapping
        Linkage_data ?Linkage_Data XREF Locus #How_mapped
	Mapping_data 	Well_ordered // DEM 6/95 for ace4
               	     	2_point_data ?2_point_data
                        Multi_point ?Multi_pt_data
			Pos_neg_data ?Pos_neg_data
        Species ?Species ?Reference // Species in which location was determined
	Probe ?Probe XREF Locus ?Reference
	//Float is size(s) of restriction bands that were mapped at this locus:
	TABLE ?Text REPEAT //Column headings for Mapped_bands table, e.g.
		// Enzyme "Size (kb)" Germplasm Chromosome
	Mapped_bands ?Restriction Float ?Germplasm ?Text //Float in kb, ?Text 
				//is chromosome name, e.g. 6D
	Linked_QTL ?QTL XREF Nearest_marker
	Associated_gene ?Gene XREF Locus //If locus mapped by gene function.
	Candidate_gene ?Gene XREF Candidate_locus //If mapped by probe.
	Gene_class ?Gene_Class XREF Locus
        Image ?Image XREF Locus
	Reference ?Reference XREF Locus
	Data_source ?Colleague Text // Text is date, eg 95.11.10
	Remarks Text
        Candidate_orthology_group ?Locus XREF Possible_orthologues
	Possible_orthologues ?Locus XREF Candidate_orthology_group
        Gale_orthology_group ?Locus XREF Gale_orthologues
        Gale_orthologues ?Locus XREF Gale_orthology_group
        Allele  ?Allele XREF Gene
	Laboratory ?Laboratory

//ACE
?ManyMap Map ?Map UNIQUE ?View

//ACE
?ManyPep Protein ?Protein // il  multi pep maps 

// 5/94 DEM updated for acedb 3.0
// 8/95 DEM partly updated for ace4_1
?Map	No_cache // Don't cache segs for this map.	// ACE
	Type UNIQUE Genetic  // this flag can be used to define subclasses
                    Cytogenetic //Chromosome could be Map, filtered Cytogenetic
                    Physical
        Species ?Species	// GRL to assist queries
        Mapping_data ?Map_Data XREF Map
        Linkage_data ?Linkage_Data XREF Map
        Display Non_graphic  // Prevents a graphic display 
                Title UNIQUE ?Text
                Remark Text // Will appear in top right corner  
		Flipped // Then coordinates go upwards
                Unit UNIQUE Text // i.e. kb, centiMorgan, MegaParsec
		Centre UNIQUE Float UNIQUE Float  // centre, width - else 0, 10
	    	Extent UNIQUE Float UNIQUE Float  // min, max
		Default_view UNIQUE ?View
		Minimal_view UNIQUE ?View // use this when >1 map displayed
		View ?View	// Columns to display
        Inherits  From_map UNIQUE ?Map 	  // To locally edit
		  Author Text             // login name of who edited it
		  Date Text		// GG
 	Main_Marker Main_Locus ?Locus // Items shown left of locator
		    Band ?Chrom_Band
	Map ?Map XREF Map_shown #Map_position
// Include all objects in these maps (must be mapped and have extents)
	Includes ?Map
        Contains Locus ?Locus XREF Map
                 Chrom_Band ?Chrom_Band XREF Map
		 Rearrangement ?Rearrangement XREF Map
		 Interval ?Interval XREF Map
		 Breakpoint ?Breakpoint XREF Map // 3feb99
		 Breakpoint_interval ?Breakpoint_interval XREF Map // 3feb99
                 QTL ?QTL XREF Map
		 Contig ?Contig XREF Map
		 Clone ?Clone XREF Map		// ACE
		 Sequence ?Sequence XREF Map	// ACE
		 Allele ?Allele XREF Map	// ACE
		 Map_shown ?Map XREF Map	// ACE

//?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
// v1.6: Added Image, Trait, QTL
?Map_Data Species ?Species XREF Mapping_data //If interspecies cross, 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
		Chromosome_arm
		Physical
	  Map_units Text // e.g. centiMorgans, microns, KB
	  Reference ?Reference XREF Mapping_data
	  Contact ?Colleague
	  Remarks ?Text //Number of progeny, markers; kind of mapping populat'n
	  Image ?Image XREF Map
	  Map ?Map XREF Mapping_data
	  Trait_study ?Trait_Study XREF Mapping_data  //Trait analyzed for QTLs
						      //with this map
	  QTL ?QTL XREF Mapping_data      //Each QTL found
          2_point_data ?2_point_data XREF Map_data
	  Locus ?Locus XREF Data Text  	//Text is raw Mapmaker data
	  Breakpoint ?Breakpoint XREF Map_data // 3feb99
	  Breakpoint_interval ?Breakpoint_interval XREF Map_data // 3feb99

?map_error Error UNIQUE Float

// used for ?map_position With
?map_offset Offset UNIQUE Float
	    Relative #Map_position

?map_position UNIQUE Position UNIQUE Float #map_error
                     Ends Left UNIQUE Float #map_error
                          Right UNIQUE Float #map_error
                     Multi_Position  Float #map_error //2 places on same Map
       		     Multi_Ends Float UNIQUE Float
		     With UNIQUE With_locus UNIQUE ?Locus #Map_offset
				 With_clone UNIQUE ?Clone #Map_offset	// ACE
			// see probe.nalusda.gov:/acedocs/magic/map.html
				// tag2 system for "burying"

//ACE
?Map_set Map ?Map Int
         Type Species
              List

//ACE
?Match_seg UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int #Match_seg  // Start, End of Aligment;  Start, End of Subject

?Mechanism	Ping_Pong

?Metabolite	Consumed_by	?Pathway
		Produced_by	?Pathway
		Activates	?Pathway
		Inhibits ?Pathway XREF Inhibitor
		Remark ?Text

?Method	Remark ?Text
	  // the Display information controls how the column looks.
	Display Colour #Colour
		Frame_sensitive
		Strand_sensitive Show_up_strand #Colour
		Score	Score_by_offset	// has priority over width, for Jean
			Score_by_width
			Score_by_histogram UNIQUE Float	// baseline value
			Score_bounds UNIQUE Float UNIQUE Float 
				// limits for squashing
			Percent // '%' in text, + default bounds 25, 100
		Overlap_mode UNIQUE	Overlap		  // draw on top - default
					Bumpable	  // bump to avoid overlap
			     		Cluster		  // one column per homol target
		Width UNIQUE Float
		Symbol UNIQUE Text	// first char only is used
		Right_priority UNIQUE Float // the greater the more right
		Max_mag UNIQUE Float	// don't show if more bases per line
		Min_mag UNIQUE Float	// don't show if fewer bases per line
		Show_text      // only put text in right-hand column if set
	Blastn		// can calculate percent from score if blastn
	Blixem  Blixem_X
		Blixem_N
		Blixem_P
	Belvu
	Gene_assemble	Gene_assemble_method ?Method UNIQUE Float
				// Float factor to multiply score by
			Intron_min UNIQUE Int
			Exon_min UNIQUE Int
			Intron_cost UNIQUE Float UNIQUE Float UNIQUE Int
				// base cost, cost per log bp beyond min
				// Int is min for this if not Intron_min
			Inter_gene_cost UNIQUE Float
	GF_parameters	GF_range UNIQUE Int
				// +- range for genefinder feature calculation
			GF_ATG_cutoff UNIQUE Float
			GF_5_cutoff UNIQUE Float
			GF_3_cutoff UNIQUE Float
	EMBL_dump EMBL_feature UNIQUE Text		// require this
		  EMBL_threshold UNIQUE Float		// apply to score unless overridden
		  EMBL_qualifier Text UNIQUE Text REPEAT
	  // if 1 Text, it is the entire qualifier including '/'
	  // if 2 Texts, 1st is an sprintf format and 2nd is
	  //   an argument.  If this is "score", "note", "y1", "y2" or "target"
	  //   then use the corresponding field of the Feature or Homol line.
	  // multiple formats will be concatenated until one starts with '/'.
	EMBL_dump_info #EMBL_dump_info

//ACE
?Mixed_grid_row UNIQUE Clone UNIQUE ?Clone XREF Gridded #Mixed_grid_row
		       Rearr UNIQUE ?Rearrangement XREF Gridded #Mixed_grid_row

?Motif	Match_sequence  UNIQUE Text	// Text is the DNA or protein sequence
	Num_mismatch UNIQUE Int		// Allowed number of mismatches when matching
					// (default 0)
	Restriction     Isoschizomer ?Motif XREF Isoschizomer
		        Offset UNIQUE Int   
			Cleavage UNIQUE Text  // will show the cleavage points ex: G_ACGT'C
		        Overhang UNIQUE Int
		        Company UNIQUE Text
			Redundant
        Remark ?Text
	Title ?Text
	DB_info	Database ?Database Text Text // ID  Accession_number
	  	DB_remark ?Text
		DB_text ?LongText
	Substrate UNIQUE DNA
			 Peptide
	Match_table UNIQUE ?MatchTable
	Homol	DNA_homol ?Sequence XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
		Pep_homol ?Protein XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
		Motif_homol ?Motif XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info

//ACE
?Multi_counts	UNIQUE Locus UNIQUE ?Locus XREF Multi_point UNIQUE Int #Multi_counts
		       Allele UNIQUE ?Allele XREF Multi_point UNIQUE Int #Multi_counts
		       Rearrangement UNIQUE ?Rearrangement XREF Multi_point UNIQUE Int #Multi_counts

//JMW 6-15-95:  Added everything below ?MultiMap Map ?Map from mapdb
//	models.wrm to allow anchoring.
?MultiMap Map ?Map
          Min Int // keep loci appearing on at least min maps. Default = 2 
          Anchor UNIQUE Text UNIQUE Text UNIQUE Text  // Class tag1 tag2
                            // i.e Locus Homeology_group Homelogs
                            // class members on different maps with the
                            // same Anchor tag will be chained

//ACE
?Multi_pt_data	Genotype  UNIQUE Text
		Experiment  Mapper ?Author
			    Laboratory ?Laboratory
			    Date  UNIQUE DateType
		Selected A UNIQUE Locus_A UNIQUE ?Locus UNIQUE ?Allele XREF In_multi_point
				  Allele_A UNIQUE ?Allele
				  Rearrangement_A UNIQUE ?Rearrangement
			 B UNIQUE Locus_B UNIQUE ?Locus UNIQUE ?Allele XREF In_multi_point
				  Allele_B UNIQUE ?Allele
				  Rearrangement_B UNIQUE ?Rearrangement
		Locus ?Locus UNIQUE ?Allele XREF In_multi_point	    // just to pair up alleles
		Results A_non_B #Multi_counts
			B_non_A	#Multi_counts
			Combined #Multi_counts
		Old_CGC_results Text
		Remark ?Text
	// code uses all the Results subtags, and the #Multi_counts structure

?Oligo	Sequence UNIQUE Text  // verbatim sequence 
	Length UNIQUE Int
	GC UNIQUE Float
	STS STS1 UNIQUE ?STS XREF Oligo1
	    STS2 UNIQUE ?STS XREF Oligo2
        OSP  Score UNIQUE Float
             Tm UNIQUE Float
             Pairwise_scores ?Oligo XREF Pairwise_scores UNIQUE Float Float // score and Tm
        In_sequence ?Sequence XREF Oligo
        Status Temporary
               Ordered UNIQUE DateType
               Received UNIQUE DateType
               Location ?Laboratory #Lab_Location

//?Pathology   Lisa added the pathology class
// 2/93 Dave extended
// 11/93 Added fields for Ken Kephart
?Pathology	Other_name ?Pathology XREF Other_name //Choose one, 
						      //put the data in that.
		Type	Fungus
			Bacterium
			Virus
			Nematode
			Insect
			Abiotic
			Mycoplasma
			Parasitic_plant
			Mollusk
		Host_species ?Species XREF Disease
		Causal_organism ?Species XREF Causes
		Vector ?Species XREF Vector_of
		Trait ?Trait XREF Pathology
		Evaluation ?Trait_Study XREF Pathology
		Gene_class ?Gene_Class XREF Pathology
		Resistance_gene ?Gene XREF Pathology
		Resistant_allele ?Allele XREF Pathology
		Resistant_line ?Germplasm XREF Pathology
		Symptoms Text
		Image ?Image XREF Pathology
		Reference ?Reference

//
// METABOLIC SECTION - from Stan Letovsky and the Soybase project
//

?Pathway	Structure Components ?Pathway XREF In_Pathway
			  In_Pathway ?Pathway XREF Components
			  Diagram UNIQUE ?PathwayDiagram XREF Pathway
		Enzyme ?Enzyme XREF Catalyzes #Reference
		Metabolites 	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	Anc_reactants ?Metabolite #ReactantInfo
				Anc_products ?Metabolite #ReactantInfo // e.g. for transport. 
				Anc_Enzyme ?Enzyme #Reference
		Activator ?Metabolite XREF Activates #RegulatorInfo
		Inhibitor ?Metabolite XREF Inhibits #RegulatorInfo
		Remark ?Text

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

//DEM 8/93 Restructured
//Information describing an electophoretic polymorphism: RFLP, PCR, isozyme,
//seed proteins, etc.
//DEM 11/93 removed old version of table:
//	      TABLE ?Text //Column headings for the Size table, e.g.
//			  //"    Germplasm    Gel Number   Size (kb) Intensity"
//	      // Float is in Kb, ?Text is "Faint", "Medium", "Dark":
//	      Size ?Germplasm XREF Polymorphism ?Gel XREF Polymorphism Float ?Text 
//DEM 1/95 Added Band_sizes, Pattern (based on RiceGenes)
//DEM 10/95 Removed:
//	      Locus_mapped ?Locus	  // no XREF; load ?Locus Mapped_bands
?Polymorphism Probe UNIQUE ?Probe XREF Polymorphism
	      Enzyme UNIQUE ?Restriction  // For RFLPs; omit for PCR probes.
              //
	      TABLE ?Text REPEAT //Column headings for the Size table, e.g.
		  //     "    Gel Number   Size (kb) Intensity    Germplasm"
	          // or the Value table, e.g.
		  //     "Species   " "Allele" "Germplasm"
	      // Float is in Kb, ?Text is "Faint", "Medium", "Dark":
	      Size ?Gel XREF Polymorphism Float ?Text ?Germplasm XREF Polymorphism 
	      // Gale-style table.  Text is Allele letter.:
	      Value ?Species Text ?Germplasm  
	      //
	      Band_size ?Text //Column headings for the Pattern table, e.g.
                              //"14.5 12.3  4.4"
              Pattern Text ?Germplasm // Don't just XREF, say Present/Absent
	      //
	      Germplasm ?Germplasm XREF Polymorphism //Use when there are no
			  //size measurements, just an image.
	      Image ?Image XREF Polymorphism	    // Autoradiogram, gel photo
              Remarks Text
	      Reference ?Reference
	      Data_source ?Colleague Text // Text is date, eg 95.11.10

?Pool	Contains	Probe ?Probe XREF In_pool
			Clone ?Clone XREF In_pool
			Subpool ?Pool XREF In_pool
	   // etc. Contains is tag2
	In_pool ?Pool XREF Subpool
	Map	Hybridizes_to ?Probe_Grid ?Probe XREF Positive_pool_probe ?Text
		Chrom_Band ?Chrom_Band XREF Positive_pool_probe
	Location ?Colleague
	Reference ?Reference

//ACE
?Pos_neg_data	Genotype  UNIQUE Text
		Results  UNIQUE Text
		Experiment Mapper ?Author
			   Laboratory ?Laboratory
			   Date  UNIQUE DateType
		Item_1	UNIQUE	Locus_1	UNIQUE ?Locus XREF Pos_neg_data UNIQUE ?Allele XREF In_pos_neg_data
			     	Rearrangement_1 UNIQUE ?Rearrangement XREF Pos_neg_data
				Allele_1 UNIQUE ?Allele XREF Pos_neg_data
				Clone_1 UNIQUE ?Clone XREF Pos_neg_data
		Item_2	UNIQUE	Locus_2	UNIQUE ?Locus XREF Pos_neg_data UNIQUE ?Allele XREF In_pos_neg_data
			     	Rearrangement_2 UNIQUE ?Rearrangement XREF Pos_neg_data
				Allele_2 UNIQUE ?Allele XREF Pos_neg_data
				Clone_2 UNIQUE ?Clone XREF Pos_neg_data
		Calculation UNIQUE Positive
				   Negative
		Remark ?Text
	// code uses Item_1, Item_2, Positive and Negative

// ?Presence, DEM 1/95
// List of band sizes present or absent for a polymorphism in a ?Germplasm.
// Used in 
// ?Germplasm
//            Polymorphism ?Polymorphism #Presence
?Presence Present ?Text REPEAT // e.g. 14.5 6.6 4.4
          Absent ?Text REPEAT

//?Probe
//DEM 8/27/93: Added Data_source, changed Derived_from to Source_germplasm
//DEM 12/16/93: Removed the following unused and undesired tags:
//	Type	#Probe_Type	//Replaced with local booleans under Origin
//		Y_Remark Text
//		PCR_Remark ?Text
//		  Hybridizes_to_YAC ?Probe XREF Positive_probe REPEAT//obselete
//		  Vaxmap UNIQUE Float
//		Insert_sequence ?Sequence //Lisa
//	Length		Seq_length UNIQUE Int
//			Gel_length Float Float	// Kb
//			HindIII_sites UNIQUE Int
//       Map ?Map_Data 
//        FingerPrint     Gel_number UNIQUE Int
//                        Approximate_match_to UNIQUE ?Probe XREF Canonical_for
//                        Exact_match_to UNIQUE ?Probe XREF Canonical_for
//                        Funny_match_to UNIQUE ?Probe XREF Canonical_for
//                        Canonical_for ?Probe
//                        Bands   UNIQUE Int Int
//		        Flag    UNIQUE Int
//	Calcul	Session Int
//		Neighbours ?Probe UNIQUE Float
//		Cor   Int
//		Common_bands  FREE
//DEM 10/94: Added the Other_name <-> Please_see aliasing.
?Probe  Locus   ?Locus XREF Probe
	Other_name ?Probe XREF Please_see ?Reference //Please_see is the 
					  // accepted name, 
	Please_see ?Probe XREF Other_name // Other_name is for alternates.
	Synonym ?Probe XREF Synonym	  // Nov97, added for Katrien.
	Related_probe ?Help ?Probe	  // ?Help is a word for the
				// relationship, explained in the ?Help object.
	External_DB ?Text ?Text	//e.g. "Sequence L43928", for GenBank link
	Reference ?Reference XREF Probe  //DEM Added
        General_remark ?Text
	Type cDNA	//booleans
	     Genomic
	     PCR
             SSR
	PCR_primers ?Text
	AFLP_primers ?Text //e.g. "E37 5' GACTGCGTACCAATTCACG"
	Amplification_conditions ?Text
	Specificity ?Text // What genes or alleles are known to be recognized
			  // or distinguished, or not.
	Sequence	?Sequence XREF Probe
	Barley_rating Excellent
		      Good
		      Fair
		      Poor
	Copy_number Text
	Background ?Text      //Lowest is clearest. Show scale, e.g. "3/5".
	//Chromosome, Enzyme, Score.  E.g. '7A EcorI "33 (3/13)"'
	Wheat_polymorphism ?Text ?Restriction ?Text
        //Chromosome, Enzyme, Score.  E.g. '2D EcoRI "15 (2/15)"'
	Barley_polymorphism ?Restriction ?Text
	// Band sizes for this probe, a different ?Polymorphism for each
	//  restriction enzyme.  Each one contains data for all germplasms.
	// ?Text is "Polymorphic", "Not", "Maybe", "Mapped"
	Cross_hybridizes_to ?Species Text
	Polymorphism ?Polymorphism XREF Probe ?Text
	Gel ?Gel XREF Probe  //Electrophoretogram, autoradiogram...
	Linkage_Group ?Text  //Deprecated by DEM, but Gale likes it.
	//DEM: Insert_enzyme is the enzyme used to cut the insert DNA before
	//  inserting into the vector.  Is there a better name?  "Cloning_
	//  enzyme"?  "DNA_enzyme"?
	Origin	Insert_enzyme ?Restriction ?Restriction
		Source_gene_class ?Gene_Class XREF Clone //if Gene not known
		Source_gene ?Gene XREF Clone 		 //3/94
        	Source_allele ?Allele XREF Probe
		Source_species ?Species
		Source_germplasm ?Germplasm
		Source_tissue ?Text 
		DNA_Origin ?Text //eg Hydroxylapatite-PERT-genomic (Bad label)
	Insert	Size Float ?Text // Text: additional bands, notes
		PCR_size Float //size using Vector_PCR_primers
	Clone   Vector   ?Text
		Vector_enzyme ?Restriction //enzyme used to open the vector
		Excision_enzyme ?Restriction ?Restriction // enzyme(s) used
			              // to remove insert from the vector
		Vector_PCR_primers ?Text
		Vector_amplification ?Text
		Bacterial_strain ?Text
		Antibiotic ?Text
		Subcloned_in ?Probe XREF Subclone_of
		Subclone_of ?Probe XREF Subcloned_in
		Location ?Colleague
		Authority ?Colleague
		In_pool ?Pool XREF Probe
        	Gridded ?Probe_Grid
	Position  Hybridizes_to ?Probe_Grid ?Probe XREF Positive_probe ?Text
		  Positive_probe ?Probe
		  Positive_pool_probe ?Pool
	Image ?Image XREF Probe //Lisa
	Data_source ?Colleague ?Text //Text is date, e.g. 93.08.27
        Information_source ?Reference   //If source is a Reference, other than
					// the primary reference.
	Note ?LongText
//4/94 Old tags expunged:
//      Position  In_situ  UNIQUE Int Int
//		  Chrom_Band ?Chrom_Band XREF Probe
//                pMap UNIQUE ?Contig XREF Probe Int Int // bands pMap units
//		  bMap UNIQUE Int Int	// base units
//		  Autopos

?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

?Protein  Title UNIQUE ?Text
	  Other_name ?Text	// for repeats
	  Peptide UNIQUE ?Peptide UNIQUE Int UNIQUE Int // Length + checksum
	  View ?View
	  Default_view UNIQUE ?View
	  DB_info	Database ?Database Text Text // ID  Accession_number
		  	DB_remark ?Text		// Swissprot CC entries
			Keyword ?Keyword	// Swissprot
	  		DB_searched ?Database Text // Version
	  Origin  From_Database ?Database UNIQUE Int	// release number
		  Date DateType Text			// Text for comments on operation
		  Species ?Species
		  Wormpep Replaces ?Protein XREF Replaced_by
			  Inactive Replaced_by ?Protein XREF Replaces
		// inactive wormpep entries won't be output in standard wormpep dumps
	  Visible	Corresponding_DNA ?Sequence XREF Corresponding_protein
		        Related_DNA ?Sequence XREF Related_protein
		        Related_protein ?Protein XREF Related_protein
			Enzyme ?Enzyme XREF Protein
			Reference ?Reference XREF Protein
		// tag2 system.  For now I have not populated this column.  For C. elegans
		// wormpep we want to get the information from the ?Corresponding_DNA 
		// object.  Because those objects have long term continuity, while wormpep
		// objects are one per protein sequence.  At least that is the current 
		// plan.
	  Swiss_feature	Text Int Int Text // feature name, start, stop, note
	  Match_table UNIQUE ?MatchTable
	  Homol	DNA_homol ?Sequence XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
		Pep_homol ?Protein XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
		Motif_homol ?Motif XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
		Align_homol ?Alignment XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info
	  Feature ?Method Int Int UNIQUE Float	// display according to method
					// double-click shows the method
	  In_alignment ?Alignment XREF Protein Int UNIQUE Int

//?QTL:  An individual Quantitative Trait Locus for a particular trait.  
//  DEM 5/93
//  5/20: Changed Type_I_error_per_locus to Significance_level
//		  Effect_on_score to Size_of_allelic_effect
//		  Positive_allele_from to Higher_scoring_allele_from
//		  Type_I_error_x_Environment to Significance_x_Environment
//  6/8:  Changed Size_of_allelic_effect to Effect_of_allele_substitution
//  6/24: Added Image
?QTL Trait_affected UNIQUE ?Trait XREF QTL	
     Trait_study ?Trait_Study XREF QTL
     Environment ?Environment XREF QTL
     Mapping_data UNIQUE ?Map_Data XREF QTL //Molecular markers used to map it
     Linkage_data Linkage ?Map_Data XREF QTL
     Chromosome_arm ?Text		    //eg 3BL, long arm of chromosome 3B
     Associated_gene ?Gene XREF QTL
     Nearest_marker UNIQUE ?Locus XREF Linked_QTL 
     Significance_level UNIQUE Float    //Significance of marker. P < 0.what?
     Positive Significant_marker ?Locus XREF In_QTL Text   // Text is 
                                 // significance level, e.g. "alpha < .01"
     Negative Nonsignificant_marker ?Locus XREF Not_in_QTL
     Position UNIQUE Map ?Map XREF QTL #map_position // to draw a bar on Map
     Map_label ?Text                                 // label for the bar
     LOD_peak_location UNIQUE ?Locus XREF QTL //? Or gMap position?
     LOD_peak_height Float 		//LOD value at this position
     Significant_LOD_interval gMap ?Map Float Float //Endpoints of
 		//region (eg in cM) where LOD exceeds value of LOD_threshold.
     LOD_threshold Float        //Threshold value for Significant_LOD_interval
     Phenotypic_R2 UNIQUE Float	//Phenotypic variance explained by this QTL
     Genetic_R2 UNIQUE Float	//Genetic       "         "     "   "    "
     Effect_of_allele_substitution UNIQUE Float Text//Magnitude of allelic 
	// effect.  Text is units.
     Additivity_Dominance_ratio UNIQUE Float
     Higher_scoring_allele_from ?Germplasm //Which parent's allele gives higher
				 	   //scores
     Interactions Text		     //Epistasis, interaction with environment
     Significance_x_Environment Float ?Environment //QTL x Env.  P < 0.what?
     Comment Text		     //Eg R-squared of nearby markers
     Image ?Image XREF QTL	     //Eg for blot of bulk segregant analysis.

?ReactantInfo	Major_Role
		Minor_Role
		Cofactor
		N Int // etc.
		Km Text #Reference
		Vmax Text #Reference
		Substrate_specificity ?Text #Reference
		Remark ?Text
		Reference ?Reference

?Reagent        Other_name ?Reagent XREF Other_name
		Description Text
		Remark Text
		Reference ?Reference
		Source ?Source
		Contact ?Colleague

?Rearrangement  Name    Correct_name ?Rearrangement XREF Other_name
                	Other_name ?Rearrangement XREF Other_name
	        Reference_germplasm ?Germplasm  Text
		Remark ?Text
		Allele ?Allele
	        Molecular_Information  Polymorphism Found  ?Probe
					            Absent ?Probe
		Mutagen ?Reagent Text	// Text is dose
	        Dosage_effects  Haplo_insufficiency
		Qualifier Text
		Author Text
		Date Text
		Type    Deletion Uncovers Text
        	        Duplication Covers Text
//			Duplication	Free_dup
			Translocation
			Compound Text   // More types needed?
                        Phenotype ?Text
		Balances ?Map #Balancer
		Map ?Map XREF Rearrangement #map_position
		Proximal_breakpoint ?Breakpoint XREF Distal_rearrangement // 3feb99
		Distal_breakpoint ?Breakpoint XREF Proximal_rearrangement // 3feb99
		Positive Proximal_marker ?Locus
                         Contains ?Locus XREF In_segment
			 Locus_inside ?Locus XREF Inside_rearr ?Author
			 Clone_inside  ?Clone XREF Inside_rearr ?Author
                Negative Distal_marker ?Locus
                         Does_not_contain ?Locus XREF Not_in_segment
			 Locus_outside ?Locus XREF Outside_rearr ?Author
			 Clone_outside ?Clone XREF Outside_rearr ?Author
		Mapping_data	2_point_data ?2_point_data
				3_point_data ?3_point_data
				Df_Dup ?Df_Dup_data
        	                Multi_point ?Multi_pt_data
				Pos_neg_data ?Pos_neg_data
	        In_situ  UNIQUE ?Map Float Float
		Gridded ?Grid
		Display	Hide_under UNIQUE ?Rearrangement XREF Hides
			Hides ?Rearrangement	// no XREF on purpose
		Location ?Laboratory #Lab_Location
			// ?Colleague
	        Germplasm	?Germplasm XREF Rearrangement //approx=line 122
        	Reference ?Reference XREF Rearrangement

//?Reference
//DEM Jan 94 Added Agricola_code, Gene_Catalogue_number, Cited_in.
//    Feb 94 Added Series
?Reference  Reference   Title UNIQUE ?Text
                        Original_title Text
			Journal UNIQUE ?Journal XREF Paper
			Publisher UNIQUE Text
			Series ?Text  // for named series of named volumes
			Contained_in ?Reference XREF Contains
                        Year Int      // Pers.Comm.s might have more than one. 
                        Volume UNIQUE Int Text  //Text when Int isn't complete
                        Page  UNIQUE Int Int
			Remark Text   //e.g. when page numbers aren't Int's
			URL UNIQUE Text         //for WWW hrefs
	    Institution Text
	    Author ?Author XREF Paper
	    Editor ?Author XREF Paper
	    Type UNIQUE Text 	     //Article, Book, Proceedings, Abstract,
			     	     //Dissertation, Bulletin, or Report
	    Language Text	     //English, Spanish, ...
	    Image ?Image XREF Reference
	    Abstract Text
	    Contains ?Reference XREF Contained_in
	    Refers_to	Gene_class ?Gene_Class XREF Reference	
			Gene_set ?Gene_Set XREF Reference
			Gene ?Gene XREF Reference
			Allele ?Allele XREF Reference
			Locus ?Locus XREF Reference
			Rearrangement ?Rearrangement XREF Reference
			Breakpoint ?Breakpoint XREF Reference // 3feb99
			Clone ?Clone XREF Reference
			Probe ?Probe XREF Reference
			Sequence ?Sequence XREF Reference
			Protein ?Protein XREF Reference
			Germplasm ?Germplasm XREF Reference
			Species ?Species XREF Reference
			Mapping_data ?Map_Data XREF Reference
                        Linkage_data ?Linkage_Data XREF Reference
			2_point_data ?2_point_data //Lisa
			Trait_study ?Trait_Study XREF Reference
			Isolate ?Isolate XREF Reference
	    Keyword ?Keyword
	    Agricola_code ?Text
	    Gene_Catalogue_number Int	//Ref number in 1993 Wheat Gene Catalog
	    Cited_in ?Reference		//4/94 DEM changed from ?Text
	    Summary_of ?Reference XREF Summarized_in	//e.g. Plant Breeding 
							//Abstracts
	    Summarized_in ?Reference XREF Summary_of	

?Regulators	Activator ?Text
		Vmax Text
		Cooperativity //boolian
		Inhibitor ?Text
		Ki Text
		Developmental ?Reference Text
		Hormonal Text
		Environmental ?Reference Text
		Genetic ?Reference Text
		Inducer ?Text
		Repressor ?Text

?RegulatorInfo	Type UNIQUE Active_site
		Ki Text  //for inhibitor
		Remark ?Text
		Reference ?Reference

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

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

// DEM 4/95 Added External_DB_key, like RiceGenes's
// 4/96: This version replaced by the TPD (Tom De Stein) revision below.
// ?Sequence Title UNIQUE ?Text
// 	  Other_name ?Text	// for repeats
// 	  External_DB ?Text ?Text //e.g. "Sequence" "X63202". "Sequence" makes					 
//        link to EMBL, Genobase etc. via WWW
// 	  Sequence Text // To show sequence in this Tree window instead of fMap
// 	  Type UNIQUE DNA UNIQUE ?DNA UNIQUE Int	// Int is the length
// 		      Peptide UNIQUE ?AA
//           RNA			// if this tag is set display AUGC
// 	  Length UNIQUE Int
// 	  Library	?Source Text Text // ID  Accession_number
// 	  Subsequence_of	Source UNIQUE ?Sequence
// 				Source_Exons Int Int // sequence of positions in genomic
// 	  General	cDNA
// 		  	Probe ?Probe XREF Sequence 
// 			Gene ?Gene XREF Sequence
// 			Gene_product ?Gene_Product XREF Sequence
// 		        Related_Sequence ?Sequence XREF Related_Sequence
// 			Keyword ?Keyword
// 	  		Remark ?Text
// 			DB_remark ?Text
// 	  		Reference ?Reference XREF Sequence
// 			DB_searched ?Source Int // number of homologues found
// 	  		Data_source ?Colleague ?Text // ?Text is date.
// 	  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
// 	  Contains	Has_CDS ?Sequence XREF Source Int Int
// 			Has_Transcript ?Sequence XREF Source Int Int
// 			Has_Pseudogene ?Sequence XREF Source Int Int
// 			Has_Structural_RNA ?Sequence XREF Source Int Int
// 			Has_Transposon ?Sequence XREF Source Int Int
// 			Has_Subsequence ?Sequence XREF Source Int Int
// 			Has_Other_Subsequence ?Sequence XREF Source Int Int
// 	  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
// 			protein_bind Int Int Text
// 			modified_base Int Int Text

// Start copy from SAMPLEDB
?Sequence DNA UNIQUE ?DNA UNIQUE Int		// Int is the length
          Peptide UNIQUE ?Peptide UNIQUE Int    // GRL
		// if you want to register a length without a DNA sequence, then use
		// a dummy sequence object, say "-".  This ensures that when a real
		// sequence appears, its length dominates.
	  Structure  From	Source UNIQUE ?Sequence
				Source_Exons Int UNIQUE Int // start at 1
		     Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int
                     Sequence Text // TPD
		     Overlap_right UNIQUE ?Sequence XREF Overlap_left UNIQUE Int
			// potentially use Overlap_right integer for auto-linking
		     Overlap_left UNIQUE ?Sequence XREF Overlap_right
		//     Clone_left_end ?Clone XREF Clone_left_end UNIQUE Int // TPD
		//     Clone_right_end ?Clone XREF Clone_right_end UNIQUE Int // TPD
	  DB_info	Database ?Database Text Text // ID  Accession_number // GRL
	                External_DB Text Text // TPD
			Blast_hits ?Database Text Text	// GRL database-geneid-accession
		  	DB_remark ?Text		// EMBL/Genbank
			DB_xref ?Text // GRL
                        AC_number Text
			NI_number UNIQUE Text
			EC_number ?Text // GRL
			Keyword ?Keyword	// EMBL/Genbank
	  Origin  Species ?Species XREF Sequence // TPD
                  Germplasm ?Germplasm XREF Sequence // GRL
                  Chromosome Text // GRL
                  Clone_lib ?Text // GRL
                  Tissue ?Text // GRL
                  Dev_stage ?Text // GRL
                  Sex ?Text // GRL
                  Length Int // TPD
		  Date Text  // TPD
	// TPD	  Date DateType Text			// Text for comments on operation
                  Data_source ?Colleague Text // TPD  Text is date from Genbank
		  From_Database UNIQUE ?Database UNIQUE Int	// release number
		  From_Reference ?Reference XREF Sequence
		  From_Laboratory ?Laboratory
	  Map ?Map // TPD XREF Sequence #Map_position	// use in particular for Genomic_canonical
	  Visible	Title UNIQUE ?Text
	  		Other_name ?Text	// for repeats
			Matching_Genomic ?Sequence XREF Matching_cDNA
		 	Matching_cDNA ?Sequence XREF Matching_Genomic
			Corresponding_protein UNIQUE ?Protein XREF Corresponding_DNA  // GRL
			Strain ?Text // GRL
			Clone ?Text // GRL
		  	Probe ?Probe XREF Sequence // TPD
          	        Locus ?Locus // TPD XREF Sequence
			Enzyme ?Enzyme // TPD XREF DNA
                        Gene ?Gene XREF Sequence
		        Related_DNA ?Sequence XREF Related_DNA
			Related_protein ?Protein XREF Related_DNA
			Gene_class ?Gene_Class		// GRL
			Gene_product ?Gene_Product	// GRL
			Remark ?Text
			Confidential_remark ?Text
			Brief_identification UNIQUE ?Text
	  		Reference ?Reference XREF Sequence
		// tag2 system: names of all objects following next tag are shown in the 
		//   general annotation display column as "tag:objname"
	  Contains	Has_CDS ?Sequence XREF Source Int Int // TPD
			Has_Transcript ?Sequence XREF Source Int Int // TPD
			Has_Pseudogene ?Sequence XREF Source Int Int // TPD
			Has_Structural_RNA ?Sequence XREF Source Int Int // TPD
			Has_Transposon ?Sequence XREF Source Int Int // TPD
			Has_Subsequence ?Sequence XREF Source Int Int // TPD
			Has_Other_Subsequence ?Sequence XREF Source Int Int // TPD
	  Properties    Pseudogene Text		// explanation
			pseudo // GRL
			Transposon Text		// transposon type
			virion // GRL
			chloroplast // GRL
			mitochondrion // GRL
			germline // GRL
			macronuclear // GRL
			Genomic_canonical
			cDNA cDNA_EST
			RNA	// if set then use U in place of T
			Coding	CDS UNIQUE Int UNIQUE Int
		// TPD		CDS_predicted_by ?Method Float // score of method
				Precursor
			End_not_found
			Start_not_found
			Codon_start Int // GRL
			Transcript	UNIQUE	mRNA	UNIQUE  Processed_mRNA
								Unprocessed_mRNA
//						tRNA UNIQUE Text
//						rRNA UNIQUE Text // GRL commented out
						snRNA UNIQUE Text
						scRNA UNIQUE Text
//						misc_RNA UNIQUE Text // GRL commented out
			Status	Received UNIQUE DateType
				Library_construction UNIQUE DateType
				Shotgun	UNIQUE DateType
				Shotgun_complete UNIQUE DateType
				Contiguous UNIQUE DateType
				Finished UNIQUE DateType
				Submitted UNIQUE DateType
				Archived UNIQUE DateType UNIQUE Text // Date Disk
			Match_type  UNIQUE Match_with_function
					   Match_without_function
				// These are designed specifically for measuring 
				// statistics.  What you match should be listed in 
				// Brief_id, Remark etc.  The aim now is to use Brief_id
				// exactly for what you would like a half-line summary to
				// contain, for making tables etc.
// TPD          ABI Clipping UNIQUE Int UNIQUE Int
// TPD              SCF_File UNIQUE Text
	  Quality UNIQUE ?BaseQuality UNIQUE Int
	  SCF_Position UNIQUE ?BasePosition UNIQUE Int
	  Assembly  Total_contig_length Int
		    Nbr_gel_readings Int
		    Nbr_contigs Int			// total number
		    Nbr_large_contigs Int		// number > 750bp
		    Large_contig_length Int		// lengths > 750bp
		    Pads_in_large_contigs Int
		    Ns_in_large_contigs Int
		    Double_strand Int	// amount of sequence left to double strand
		// Should most of these be UNIQUE, giving the current status, or is
		// the idea that they will show the time progression?
// TPD	  Splices	Confirmed_intron  Int Int #Splice_confirmation
// TPD			Predicted_5 ?Method Float Int Int // (x, x+1) or (x, x-1)
// TPD			Predicted_3 ?Method Float Int Int // (x, x+1) or (x, x-1)
	  Oligo ?Oligo XREF In_sequence Int UNIQUE Int	// for OSP and human mapping mostly
	  Assembly_tags	Text Int Int Text // type, start, stop, comment
	  Allele ?Allele // TPD XREF Sequence UNIQUE Int UNIQUE Int UNIQUE Text
		// start, stop, replacement sequence
		// if an insertion point Text is transposon name (distinguished
		// by containing non ACTG letters), and (n, n+1) = T A, so indicates 
		// direction (if known).
		// if a deletion, put '-' as the replacement sequence
	  EMBL_feature  CAAT_signal	Int Int Text #EMBL_info
			GC_signal	Int Int Text #EMBL_info
			TATA_signal	Int Int Text #EMBL_info
			allele_seq	Int Int Text #EMBL_info
			conflict	Int Int Text #EMBL_info
			mat_peptide	Int Int Text #EMBL_info
			misc_binding	Int Int Text #EMBL_info
			misc_feature	Int Int Text #EMBL_info
			misc_signal	Int Int Text #EMBL_info
			misc_recomb	Int Int Text #EMBL_info
			modified_base	Int Int Text #EMBL_info
			mutation	Int Int Text #EMBL_info
			old_sequence	Int Int Text #EMBL_info
			polyA_signal	Int Int Text #EMBL_info
			polyA_site	Int Int Text #EMBL_info
			prim_binding	Int Int Text #EMBL_info
			prim_transcript Int Int Text #EMBL_info
			promoter	Int Int Text #EMBL_info
			repeat_region	Int Int Text #EMBL_info
			repeat_unit	Int Int Text #EMBL_info
			satellite	Int Int Text #EMBL_info
			sig_peptide	Int Int Text #EMBL_info
			variation	Int Int Text #EMBL_info
			enhancer	Int Int Text #EMBL_info
			protein_bind	Int Int Text #EMBL_info
			stem_loop	Int Int Text #EMBL_info
			primer_bind	Int Int Text #EMBL_info
			transit_peptide Int Int Text #EMBL_info
			misc_structure  Int Int Text #EMBL_info
			precursor_RNA   Int Int Text #EMBL_info
                        feature_gene	Int Int Text #EMBL_info // GRL
                        feature_source  Int Int Text #EMBL_info // TPD
                        exon            Int Int Text #EMBL_info // TPD
                        intron          Int Int Text #EMBL_info // TPD
                        5'UTR           Int Int Text #EMBL_info // TPD
                        3'UTR           Int Int Text #EMBL_info // TPD
                        RBS             Int Int Text #EMBL_info // TPD
                        LTR             Int Int Text #EMBL_info // TPD
			terminator      Int Int Text #EMBL_info // GRL
                        misc_difference Int Int Text #EMBL_info // TPD
			misc_RNA	Int Int Text #EMBL_info // GRL
			rRNA		Int Int Text #EMBL_info // GRL
			tRNA		Int Int Text #EMBL_info // GRL
			STS		Int Int Text #EMBL_info // GRL
		// EMBL_features are for legitimate EMBL feature table entries only
	  Homol DNA_homol ?Sequence XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
		Pep_homol ?Protein XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
		Motif_homol ?Motif XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
			// We will generate a column for each distinct ?Method.  So for
			// distinct Worm_EST and Worm_genomic columns, use ?Method objects
			// Worm_EST_Blastn and Worm_genomic_Blastn.
	  Feature ?Method Int Int UNIQUE Float UNIQUE Text
		// Float is score
		// Text is shown on select, and same Text are neighbours
		// again, each method has a column
		// double-click shows the method
		// absorb TSL_site, TSL, Inverted, Tandem as features
		// and probably Assembly_tags (not yet)
	  In_alignment ?Alignment XREF Sequence Int UNIQUE Int
	  Pick_me_to_call Text Text	// GRL to call Genbank annotations

//4/94 Proposal:  Change to a #ConstructedType for situations where multiple
//	 types of sources are
//      valid, e.g.:
//?Source Colleague ?Colleague
//        Reference ?Reference
//        Collection ?Collection
//        General ?Text
?Source		Other_name ?Text // Full name
		Contents Text // Description of collection
		Remarks Text // other descriptions
		Contact ?Colleague
		Reference ?Reference
		Journal ?Journal
		Address Mail Text
                        Phone Text
                        E_mail Text
			Fax Text

//?Species 2/93 DEM, based on the PGD schema
//         3/6/93 KDK,DEM refined
// Object's id is full name, "Triticum turgidum L. group turgidum Bowden"
// 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.".
//v1.6:
//  Added Image
//  Feb 94: Haploid_chromosome_number not UNIQUE
//	    Synonym XREF from Correct_name to Synonym
//	    Species to Species_epithet
?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_epithet ?Text
	   Variety ?Text
           Authority ?Text
           Synonym ?Species XREF Synonym
           Common_name ?Text
           Sequence ?Sequence // TPD 
           Genome UNIQUE ?Text //E.g. "D", "ABD"
           Haploid_chromosome_number Int
	   Mapping_data ?Map_Data
           Linkage_data ?Linkage_Data
	   Disease ?Pathology XREF Host_species // diseases of this species
	   Causes ?Pathology XREF Causal_organism // diseases caused by it
	   Vector_of ?Pathology XREF Vector // diseases vectored by it
	   Reference ?Reference
	   Image ?Image XREF Species

//?Species 2/93 DEM, based on the PGD schema
//         3/6/93 KDK,DEM refined
// Object's id is full name, "Triticum turgidum L. group turgidum Bowden"
// 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.".
//v1.6:
//  Added Image
//  Feb 94: Haploid_chromosome_number not UNIQUE
//	    Synonym XREF from Correct_name to Synonym
//	    Species to Species_epithet
?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_epithet ?Text
	   Variety ?Text
           Authority ?Text
           Synonym ?Species XREF Synonym
           Common_name ?Text
           Sequence ?Sequence // TPD 
           Genome UNIQUE ?Text //E.g. "D", "ABD"
           Haploid_chromosome_number Int
	   Mapping_data ?Map_Data
           Linkage_data ?Linkage_Data
	   Disease ?Pathology XREF Host_species // diseases of this species
	   Causes ?Pathology XREF Causal_organism // diseases caused by it
	   Vector_of ?Pathology XREF Vector // diseases vectored by it
	   Reference ?Reference
	   Image ?Image XREF Species

?Splice_confirmation	cDNA
			EST
			Homology

?STS	Oligo1 UNIQUE ?Oligo
	Oligo2 UNIQUE ?Oligo
	Map ?Map #Map_position
	Grid_data ?Grid_data 

//?Trait:  A property of ?Germplasms, affected by ?Gene_Classes and ?QTLs, 
//    evaluated in ?Trait_Studies.
// DEM 9/93 Created
//	    ?Germplasms are not directly linked, only via ?Trait_Studies
// DEM 3/94 Affected_by caused ACEDB death, until database reinitialized.
?Trait  Description ?Text		//Brief explanation of the trait name
	See_also ?Trait XREF See_also
	Pathology ?Pathology XREF Trait //If trait is related to a disease
	Affected_by ?Gene_Class XREF Character_affected 
	QTL ?QTL XREF Trait_affected
	Evaluation ?Trait_Study XREF Trait //HUH?  For some reason, this isn't
		//creating the backreference.

//?Trait_scores:  Values measured for a particular trait in a particular
//    environment
// Scores = Value of trait for each member of mapping population, in the 
//   same order as listed for the molecular markers in ?Trait Mapping_data
// Germplasm_Mean_SD = Mean and SD for each germplasm (for a comparison
//   that is not a mapping study)
// Environment is not UNIQUE, to allow an averaged-over-evironments record.
// DEM 5/93
?Trait_scores Trait_study UNIQUE ?Trait_Study XREF Trait_scores
	      Environment ?Environment XREF Trait_scores
	      Comment Text
	//For QTLs:
	      Scores Text          //If only have means, list all on one line.
	      Score_Mean_SD Float Float	 //If (mean, SD) pairs, separate lines.
	//For trials of named germplasms:
	      Germplasm_Mean_SD ?Germplasm XREF Trait_scores Float Float
	      Germplasm_score Float ?Germplasm XREF Trait_scores 
			//If only have means, give number first for better
			//visual alignment.
	//For one-record-per-datum, e.g. ISWYN24:
	      Germplasm ?Germplasm XREF Trait_scores
	      Score Float
	      Standard_deviation Float
	      Replications Int
              Percent_of_local_check Float
	      Difference_from_local_check Float //When many values are Zero.
              Pathogen_race ?Isolate

//?Trait_Study:  Evaluation of a particular set of germplasms in a particular
//   experiment.  Other experiments measuring the "same" trait should have
//   different trait_study identifiers, e.g. "Yield, Smith93b"
//   Omit Species, Parents.  They're in Mapping_data if this is an evaluation
//   of a QTL mapping population, and not germane here if it's just a bunch of
//   random germplasms being compared.
//   For uniformity through database, always give R-squared as proportion 
//   (fraction of 1.00), rather than as percentage.
//   DEM 5/93
//   5/20: Added Type_I_error_rate_per_locus, Number_of_markers
//   6/8 : Changed Number_of_markers to Number_of_markers_tested
//   9/14: Changed name from ?Trait to ?Trait_Study
?Trait_Study Trait ?Trait XREF Evaluation
	     Pathology ?Pathology XREF Evaluation //If trait is disease-related
             Reference ?Reference XREF Trait_study
             Description Text       // JMW, 6-15-95; DEM is dubious.
             Protocol Text	//Description of the trait and how measured
	     Values ?Text // Description of possible scores, e.g. "1=Resistant"
	     Environment ?Environment XREF Trait_study
       	     Parental_description ?Germplasm XREF Trait_study ?Text
				        //Qualitative description
             Parental_Mean_SD ?Germplasm XREF Trait_study Float Float 
			//Value of mean and standard deviation for each parent
             Mapping_data ?Map_Data XREF Trait_study //Info about parents, loci
             Linkage_data ?Linkage_Data XREF Trait_study
             Population_size UNIQUE Int //Number of individuals in population
             Population_type Text	//Kind of mapping population, eg F5 RIs
             QTL_analysis_method ?Text  //Methods used, eg Single-factor ANOVA
             Statistics Text		//ANOVA table, etc. for this trait
             Heritability Float Text    //Value and basis, 
					// e.g. 0.84 "line mean basis"
             Type_I_error_rate_per_locus Float 	//Alpha, 
			// probability of calling locus significant by chance
             Number_of_markers_tested Int  //Number of loci in the Mapping_data
             QTLs_found UNIQUE Int	//How many QTLs were detected?
             Phenotypic_R2 Float Text   //Phenotypic variance explained by 
		// all QTLs.  Text is qualifier, for different values in 
		// different Environments or other conditions.
             Genetic_R2 Float Text
             R2_definition Text	   //Exact definition of "R-squared" used above
             Comment Text
             Image ?Image XREF Trait_study  //Photos of the rating scale, eg
             QTL ?QTL XREF Trait_study	//Location, significance, for each QTL
	     Germplasm_description ?Germplasm XREF Trait_description ?Text Text
	     Germplasm_score ?Germplasm Float ?Text  //NOTE:  No XREF.  Must
		//manually enter data for 
		//?Germplasm Trait_score ?Trait_Study Float ?Text
             Trait_scores ?Trait_scores XREF Trait_study 
					//For either a mapping population 
                                        //or individual named germplasms
	     Data_source ?Colleague ?Text // Text is date, yy.mm.dd
             Data_curated ?Colleague ?Text // Who converted source to .ace

// Future model for URL calling feature - now implemented:
?Url	Url UNIQUE Text // Simple, text of URL
	Template UNIQUE ?Url // use this object as a generic template
	Reference_tag UNIQUE Text // look for this tag in the reffing object for url
	Remove_prefix UNIQUE Text // prefix to remove to make url
	Remove_postfix UNIQUE Text // postfix to remove
	Prepend UNIQUE Text // then add these.
	Append UNIQUE Text

?View 	Type 	UNIQUE	Pepmap 	
			Fmap
		  	Gmap
			Grid  Grid_map Int #View_tags // Int is priority
			      Grid_edit_default UNIQUE Text UNIQUE Text 
			      Grid_edit_menu Text UNIQUE Text 
			Pmap  Pmap_probes Pmap_probe_query Text
					  Pmap_probe_height Int
			      Pmap_YAC  Pmap_YAC_query Text
					Pmap_YAC_bold_query Text
					Pmap_YAC_height Int
			      Pmap_cmid Pmap_cmid_query Text
					Pmap_cmid_bold_query Text
					Pmap_cmid_height Int
			      Pmap_locus Pmap_locus_query Text
					 Pmap_locus_height Int
			      Pmap_remark Pmap_remark_query Text
					  Pmap_remark_height Int
				// 1st text tag name, 2nd text optional "Negative"
	Display Submenus	// BOOL for submenus on item boxes
		Cambridge	// Cambridge v. Montpellier behaviour
		No_buttons      // suppress header buttons for WWW 
		Hide_header     // No headers and footers 
	Name 	UNIQUE 	Text
	Columns	Text UNIQUE Int #Column	// Int is BOOL for Hidden/Visible

?View_tags	Colour #Colour
		Surround_colour #Colour	// colour when surround
		Tag Text		// could be many tags
		 
// end of file