// 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

?Allele Name    Other_name ?Text
                Qualifier Text      // sd, sm, ts etc.  Not systematic just now
                Rearrangement ?Interval XREF Allele
        Source  UNIQUE Gene ?Locus XREF Allele
                       Gene_class ?Gene_Class XREF Allele
        Reference_Allele
        Isolation       Author  Text            // should be ?Author
                        Date    Text
                        Mutagen UNIQUE ?Mutagen  UNIQUE Text    // Text is dose
                        Procedure Text
        Location ?Laboratory #Lab_Location
        Strain ?Strain XREF Allele
        Genetics        Map ?Map   // define a Locus if you want to appear on map 
                        Mapping_data    2_point ?2_point_data
                                        Multi_point ?Multi_pt_data
                                        Df_Dup ?Df_Dup_data
                        Covers Text // from MRC allele list
        Description     Phenotype       ?Text
                        Recessive
                        Dominant
                        Semi_dominant
                        Intragenic_revertant_of_dominant        // used twice
                        Weak
                        Temperature_sensitive   Heat_sensitive
                                                Cold_sensitive
                        Amber
        Remark  ?Text
        Reference ?Paper XREF Allele               // Mary

?Annotation     Summary ?Text
                Paper ?Paper XREF Annotation
                Note ?Text
                Hint ?LongText

?Gene_Class     Description ?Text
                Designating_laboratory UNIQUE ?Colleague XREF Gene_classes
                Allele ?Allele  XREF Gene_class
                Other_name ?Gene_Class XREF Other_name
                Conflict   Text
                Contact    ?Colleague
                Note       ?Text
                Locus      ?Locus XREF Gene_class
                Hint       ?LongText

?Locus  Name    Other_name ?Locus XREF Other_name
                Description ?Text
                Gene_class UNIQUE ?Gene_Class XREF Locus
                Gene_product ?Text
	        Gene_info ?Gene_Info XREF Locus
		Protein_info ?Protein_Info XREF Locus
                Phenotype ?Text
                Contact    ?Colleague
	Not_Standard_Name
        Type    Gene    Reference_Allele ?Allele 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
		Mitochondrial Text
        Molecular_information   Positive_clone ?Clone XREF Positive_locus ?Paper XREF Positive_clone
                                Negative_clone ?Clone XREF Negative_locus
                                Sequence ?Sequence XREF Locus
                                Product ?Text
        Remark ?Text
        Position  UNIQUE Map    ?Map XREF Locus UNIQUE Float UNIQUE Float ?Paper XREF Map_data REPEAT
	                 Maps_with UNIQUE ?Locus XREF Canonical_for
        Allele  ?Allele XREF Gene
        Strain  ?Strain XREF Gene
        Laboratory ?Laboratory
        Reference ?Paper XREF Locus
        Mortimer Int ?Text
        Note ?Text
        Mapping_data    Well_ordered            // "on the line"
                        Canonical_for ?Locus XREF Maps_with
                        2_point ?2_point_data
                        Multi_point ?Multi_pt_data
                        Df_Dup ?Df_Dup_data
                        Inside ?Interval XREF Inside
                        Outside ?Interval XREF Outside

?Interval       Name    Other_name ?Text
                        Allele ?Allele XREF Rearrangement
                Type    Rearrangement   Deletion
                                        Duplication     Free_dup
                                        Translocation
                                        Compound        Text
                                        Phenotype ?Text             // Mary
                                        Balances ?Map #Balancer
//      possibility to refer to other Intervals to describe a complex rearrangement
//      for the worm this is not too necessary, but important for fly and mouse
//      or perhaps there should be another class Complex_Rear that refers to
//      several intervals.
                        Hybrid_cell_line
//                              ?add Chrom_Band here, or reciprocal pointers
                Reference_strain ?Strain
                Remark ?Text
                Isolation       Author Text             // should be ?Author
                                Date Text
                                Mutagen UNIQUE ?Mutagen UNIQUE Text // Text is dose
                Map     ?Map XREF Interval #Interval_ends
                Mapping_data    Df_Dup ?Df_Dup_data
                                Inside ?Locus XREF Inside
                                Outside ?Locus XREF Outside
                Molecular_information   Clone_inside  ?Clone XREF Inside
                                        Clone_outside ?Clone XREF Outside
                Location ?Laboratory #Lab_Location
                Strain   ?Strain XREF Rearrangement
                Reference ?Paper XREF Rearrangement

?Interval_ends  Left UNIQUE Float UNIQUE Float
                Right UNIQUE Float UNIQUE Float
      
?Strain  Genotype Text
         Males Text
         Gene    ?Locus XREF Strain
         Allele    ?Allele XREF Strain 
         Rearrangement   ?Interval XREF Strain
         Reference_strain Text
         Location ?Laboratory XREF Strain #Lab_Location
         Remark ?Text

?Map    Display Non_graphic  // Prevents a graphic display of f, A etc
                Centre UNIQUE Float UNIQUE Float  // centre, width - else 0, 10
                Extent UNIQUE Float UNIQUE Float  // min, max - else min, max gene/locus
                Error_scale UNIQUE Float  // factor for horizontal positioning
        Inherits  From_map ?Map           // To locally edit 
                  Author Text             // login name of who edited it
        Marker_locus ?Locus
        Locus ?Locus 
        Interval ?Interval
        Contig ?Contig

?MultiMap Map ?Map

?Mutagen Protocol Text

?Clone  Remark  General_remark ?Text
                Y_remark ?Text
                PCR_remark ?Text
        ATCC ?Clone XREF WashU 
        WashU ?Clone XREF ATCC
        Olson_Map Text Text Text        // Olson_Map Units are base pairs
        Olson_Rest_Data  ?Olson_Rest_Data
	Mitochondrial Text
        Position  pMap UNIQUE  ?Contig XREF Clone  UNIQUE Int UNIQUE Int 
                                        // pMap units are fingerprint bands
                  Clone_as_locus ?Locus XREF Clone_as_locus
                  Hybridizes_to ?Clone_Grid ?Clone XREF Positive_probe ?Text
                  Does_not_hybridize_to ?Clone_Grid ?Clone XREF Negative_probe
                  Positive_probe ?Clone
                  Negative_probe ?Clone
                  Positive_pool_probe ?Pool
                  Positive_locus ?Locus XREF Positive_clone ?Paper XREF Clone
                  Negative_locus ?Locus XREF Negative_clone
                  Inside ?Interval XREF Clone_inside
                  Outside ?Interval XREF Clone_outside
        Sequence        ?Sequence XREF Clone
        Length          Seq_length UNIQUE Int                   // bp
                        Gel_length UNIQUE Float                 // Kb
        Location ?Laboratory #Lab_Location
        In_pool ?Pool XREF Clone
        Gridded ?Clone_Grid
        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
        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

?Clone_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 UNIQUE ?Clone XREF Gridded REPEAT

?Contig Map     ?Map XREF Contig UNIQUE Float UNIQUE Float      // extremities on gMap
        pMap    UNIQUE Int UNIQUE Int         // extremities in pMap units
        Clone   ?Clone XREF Contig

?2_point_data   Genotype  UNIQUE Text
                Remark ?Text
                Locus_1 ?Locus XREF 2_point UNIQUE ?Allele XREF 2_point
                Locus_2 ?Locus XREF 2_point UNIQUE ?Allele XREF 2_point
                Experiment      Mapper ?Author
                                Colleague ?Colleague
                                Paper ?Paper XREF 2_point
                                Date  UNIQUE Text
                                Temperature UNIQUE Text
                Results	Min      UNIQUE Float 
                        Distance UNIQUE Float
                        Rec_percent Float
                        Max      UNIQUE Float
                        Error    UNIQUE Float
                        Standard_error Float
                        LOD      Float
                        Linkage  UNIQUE Text

                Calculation UNIQUE Tetrad UNIQUE Int UNIQUE Int UNIQUE Int // PD NPD TT
                                   Centromere_segregation UNIQUE Int UNIQUE Int // FD SD
                Calc    Calc_distance UNIQUE Float
                        Calc_lower_conf UNIQUE Float
                        Calc_upper_conf UNIQUE Float
                        Segregation First_Division Int
                                    Second_Division Int
                        Ascus_type  Parental_Ditype Int
                                    Non-Parental_Ditype Int
                                    Tetratype Int
                        Interference Float
                        Interference_Std_Err Float

?Df_Dup_data    Genotype  UNIQUE Text
                Experiment      Mapper ?Author
                                Laboratory ?Laboratory
                                Date  UNIQUE Text
                Results  UNIQUE Text
                Type UNIQUE Type_1 Locus        UNIQUE ?Locus XREF Df_Dup UNIQUE ?Allele XREF Df_Dup
                                   Rearrangement UNIQUE ?Interval XREF Df_Dup
                                   Calculation_1 UNIQUE Inside
                                                        Outside
                            Type_2 Rearrangement_1 ?Interval XREF Df_Dup
                                   Rearrangement_2 ?Interval XREF Df_Dup
                                   Calculation_2 UNIQUE Overlap
                                                        No_overlap
                                                        1_includes_2
                                                        1_does_not_include_2
                Remark ?Text

?Multi_pt_data  Genotype  UNIQUE Text
                Selected_loci   Locus_A UNIQUE ?Locus UNIQUE ?Allele XREF Multi_point
                                Locus_B UNIQUE ?Locus UNIQUE ?Allele XREF Multi_point
                Locus ?Locus UNIQUE ?Allele XREF Multi_point
                Experiment      Mapper ?Author
                                Laboratory ?Laboratory
                                Date  UNIQUE Text
                Results A_non_B #Multi_counts
                        B_non_A #Multi_counts
                        Combined #Multi_counts
                Old_CGC_results Text
                Remark ?Text

?Multi_counts   UNIQUE ?Locus XREF Multi_point UNIQUE Int #Multi_counts

?Author Full_name ?Colleague XREF Publishes_as
        Colleague ?Laboratory XREF Staff
        Paper ?Paper

?Journal Paper ?Paper XREF Journal

?Paper  Reference       Title UNIQUE ?Text 
			Citation UNIQUE Text
                        Journal UNIQUE ?Journal XREF Paper
                        Publisher UNIQUE Text
                        Contained_in ?Paper XREF Contains
                        Year UNIQUE Int
                        Volume UNIQUE Text Text
                        Page  UNIQUE  Text UNIQUE Text
                        Agricola UNIQUE Text
                        Medline UNIQUE Text
                        WWW_URL Text
        Author ?Author XREF Paper
        Adviser ?Author XREF Paper
        Editor ?Author XREF Paper
        Institution     Text
        Type UNIQUE Text
        Language Text
        Abstract ?LongText
        Contains ?Paper XREF Contained_in
        Refers_to       Locus ?Locus XREF Reference
			Positive_locus ?Locus XREF Positive_clone
			Mapping_data ?Locus XREF Map
                        Allele ?Allele XREF Reference
                        2_Point ?2_point_data XREF Paper
                        Rearrangement ?Interval XREF Reference
                        Sequence ?Sequence XREF Reference
                        Annotation ?Annotation XREF Paper
                        Gene_info ?Gene_Info XREF Paper
			Protein_info ?Protein_Info XREF Paper
			Clone ?Clone XREF Paper
        Keyword ?Keyword
        Note ?Text
        Hint ?LongText

?Restriction    Site UNIQUE Text
                Isoschizomers ?Restriction XREF Isoschizomers REPEAT
                Offset Int   
                Cleavage Text  // will show the cleavage points ex: G_ACGT'C
                Overhang  Int
                Company  Text
                Remark Text

?Sequence Title UNIQUE ?Text
          Other_name ?Text      // for repeats
          Type UNIQUE DNA UNIQUE ?DNA UNIQUE Int        // Int is the length
                      Peptide UNIQUE ?Peptide UNIQUE Int // Length
          RNA                   // if this tag is set display AUGC
          DB_remark Text Text
          Remark ?Text
          Structure  Length UNIQUE Int
                     From       Source UNIQUE ?Sequence
                                Source_Exons Int UNIQUE Int // start at 1
                     Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int
                     Overlap_right UNIQUE ?Sequence XREF Overlap_left UNIQUE Int
                     Overlap_left UNIQUE ?Sequence XREF Overlap_right
          Library       ?Library Text Text // ID  Accession_number
          Genomic_Canonical UNIQUE Float // from the project: order
          Is_Chromosome
          Origin  From_Library ?Library
                  From_Author ?Author
                  From_Laboratory ?Laboratory
                  Date Text
                  Species ?Species XREF Sequence
		  Mitochondrial Text
          General       cDNA 
                        Matching_Genomic ?Sequence XREF Matching_cDNA
                        Matching_cDNA ?Sequence XREF Matching_Genomic
                        Corresponding_DNA ?Sequence XREF Corresponding_peptide
                        Corresponding_peptide ?Sequence XREF Corresponding_DNA
                        Clone ?Clone XREF Sequence 
                        Locus ?Locus XREF Sequence
                        Related_Sequence ?Sequence XREF Related_Sequence
                        Keyword ?Keyword
                        Brief_identification ?Text
                        Reference ?Paper XREF Sequence
                        Foreign_Reference ?Text
                        DB_searched ?Library Int // version
          Protein       Prosite ?Text Int Int   // ?Prosite start, stop
                        Similar_PDB ?Text // should be ?PDB
                        Transmembrane Int
                        Evolutionary_match      Eukaryotic_match
                                                Bacterial_match
                                                Yeast_match ?Text
                                                Non_yeast_match ?Text
                        CAI Float
                        FOP Float
                        ENC Float
          Properties    Pseudogene Text
                        Transposon Text
                        Coding  CDS UNIQUE Int UNIQUE Int
                                Precursor
                        Transcript      End_not_found
                                        Start_not_found Int // Int is frame of base 1
                                        mRNA    Processed_mRNA
                                                Unprocessed_mRNA
                                        tRNA Text
                                        tRNA_codon ?Text
                                        tRNA_AA ?Text
                                        rRNA Text
                                        snRNA Text
                        Status UNIQUE   Shotgun Text
                                        Contiguous Text
                                        Finished Text
          Repeats       Inverted        Int UNIQUE Int #Match
                        Tandem          Int UNIQUE Int #Match
                        Direct          Int UNIQUE Int #Match
          Assembly_tags Comment Int Int Text
                        Compression Int Int Text
                        Stop Int Int Text
                        Assembly_repeat Int Int Text
                        Cosmid_vector Int Int Text
                        Alu_segment Int Int Text
                        Sequencing_vector Int Int Text
                        Cloning_vector Int Int Text
                        Oligo Int Int Text
                        A_Repeat Int Int Text
          Features      TSL_site Int UNIQUE Int Text // Trans-spliced leader
                        TSL Int UNIQUE Int Text
                        Possible_exon Int UNIQUE Int UNIQUE Int ?Method UNIQUE Float // 3rd Int is frame
                        promoter Int UNIQUE Int ?Text
                        polyA_site Int UNIQUE Int Text
                        polyA_signal Int UNIQUE Int Text  // AATAA
                        misc_signal Int UNIQUE Int ?Text
                        misc_feature Int UNIQUE Int ?Text
                        repeat_region Int UNIQUE Int Text
                        repeat_unit Int UNIQUE Int Text
                        mutation Int UNIQUE Int ?Text
                        sig_peptide Int UNIQUE Int Text
                        mat_peptide Int UNIQUE Int Text
                        old_sequence Int UNIQUE Int Text
                        unsure Int UNIQUE Int Text
                        modified_base Int UNIQUE Int Text
                        TATA_signal Int UNIQUE Int Text
          Similarity    Homol ?Sequence XREF Homol ?Method Float Int UNIQUE Int Int UNIQUE Int
			Reported_homol ?Sequence
          Consensus     Calc_Consensus
                        Contains ?Sequence XREF Contained_in
                        Contained_in ?Sequence XREF Contains


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

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

//Library is -R Source in options.wrm
?Source         Other_name ?Source XREF Other_name // Full name
                Contents Text // Description of collection
                Remark Text // other descriptions
                Paper ?Paper
                Contact ?Colleague
                Address Mail Text
                        Phone Text
                        E_mail Text
                        Fax Text
                See_also ?Source XREF See_also

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

?Lab_Location   Freezer         Text
                LiquidN2        Text
                Minus70         Text
                Remark          ?Text

?Colleague      Position Text
                Profession Text
                E_mail Text
                       Bitnet Text
                       Internet Text
                Address Mail Text
                        Institution     Text
                        Address1 Text
                        Address2 Text
                        Address3 Text
                        Address4 Text
                        Address5 Text
                        City    Text
                        State   Text
                        Region  Text
                        PostalCode Text
                        Country Text
                        Phone Text
                        Fax Text
                        Telex Text
                Research_interest ?Text
                Keyword ?Keyword
                Publishes_as ?Author XREF Full_name
                Associate ?Colleague XREF Associate
                Last_update Text
                Obtained_from ?Source
                Hint ?LongText

?Gene_Info      Other_name ?Text
                Colleague ?Colleague
                Source ?Source
                Locus ?Locus XREF Gene_info
                Paper ?Paper XREF Gene_info
                Sequence ?Sequence
                Remark Text
                EC_number ?Text
                Biochemistry Text
                Protein_product ?Annotation
                Phase_Involved ?Annotation
                Essential_Dispensable ?Annotation
                Mutants_Constructs ?Annotation
                Suppressors ?Annotation
                Transcription ?Annotation
                Physical_Properties ?Annotation
                Sequence_Motif ?Annotation
                Mechanism_of_Action ?Annotation
                Protein_Modification ?Annotation
                Other_Interactions ?Annotation
                Related_Genes ?Annotation
                Homologs ?Annotation
                Protein_Family ?Annotation
                Cloning_Mapping ?Annotation
                Sequences ?Annotation
                Protein_Isolation ?Annotation
                General_Info ?Annotation
                Interesting_Features ?Annotation

?Olson_Rest_Data        Frags_Calc_from_Sequence
                        Frag_info Text Text Text Text Text Text

?Protein_Info	Locus ?Locus XREF Protein_info
		Description ?Text
		Identical_seqs Int
		Related_seqs Int
		Systematic_seq
		pI_plus-one-charge Float
		pI Float
		pI_minus-one-charge Float
		MW Int
		Codon_Bias Float
		Contains_Intron
		Knockout Text
		GenBank_Acc Text
		SwissProt_Acc Text
		PIR_Acc Text
		YEPD_Acc Text
		Major_Localization Text
		Minor_Localization Text
		Molecular_Environ Text
		Function_Group Text
		N-term_modification Text
		C-term_modification Text
		Phosphorylated
		Glycosylation Text
		Precursor_addition Int
		Length Int
		AA_composition-a Int
		AA_composition-c Int
		AA_composition-d Int
		AA_composition-e Int
		AA_composition-f Int
		AA_composition-g Int
		AA_composition-h Int
		AA_composition-i Int
		AA_composition-k Int
		AA_composition-l Int
		AA_composition-m Int
		AA_composition-n Int
		AA_composition-p Int
		AA_composition-q Int
		AA_composition-r Int
		AA_composition-s Int
		AA_composition-t Int
		AA_composition-v Int
		AA_composition-w Int
		AA_composition-y Int
		AA_composition-N-m Int
		CDC28_motif Int
		CKII_motif Int
		PKA_motif Int
		N-glc_motif Int
		TM_motif Int
		N-term_seq Text
		N-term-proc_seq Text
		C-term-proc_seq Text
		Paper ?Paper XREF Protein_info
		Note ?Text