// ~/RDBMS/models.wrm.annotated, dem 18ja04, from: // /home/www/htdocs/ggmigration/models_030602_clean.wrm, ddh 27jun03, // "cleaned up Sequence tags based on Gerry's 030625 email" // Add descriptions of the tags to help convert to RDBMS tables/columns. // Tags that aren't actually used in GG, as per // /home/www/htdocs/ggmigration/maxtagcount, are marked "NOT USED". //// Allele is already done. ?Allele Reference ?Reference XREF Allele Correct_name UNIQUE ?Allele XREF Other_name Other_name ?Allele XREF Correct_name ?Reference XREF Allele Previous_name ?Allele ?Reference Current_name ?Allele ?Reference Synonym ?Allele XREF Synonym ?Reference Compound_allele ?Allele XREF Component_allele ?Reference Component_allele ?Allele XREF Compound_allele ?Reference Gene UNIQUE ?Gene 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 Origin ?Text ?Reference Germplasm ?Germplasm XREF Allele ?Reference Comment ?Text Mutagen UNIQUE ?Reagent Text Pathology ?Pathology XREF Resistant_allele Phenotype ?Text Properties 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 Probe ?Probe XREF Source_allele Mapping_data 3Point ?3_point_data Df_Dup ?Df_Dup_data Numbered_reference Int ?Reference XREF Allele Data_source ?Colleague ?Text Information_source ?Reference Data_curated ?Colleague ?Text Last_update ?Text ?Gene_Class Reference ?Reference XREF Gene_class // many/many URL Text Text // 1. For links to MASwheat. // First Text is the URL, second is optional description. Abbreviation Text // 1. See_also ?Gene_Class XREF See_also // many/1 Character_affected ?Trait XREF Affected_by // many/many Pathology ?Pathology XREF Gene_class // many G_C's / // 1 Pathology Orthologous_gene_set ?Gene_Set XREF Gene_class // 1 G_C / // many O_g_s's. // For the cross-species sets of corresponding genes. E.g. // Gli-1, Gli-2 and Gli-3 are three orthologous_gene_sets. Gene ?Gene XREF Gene_class // 1 G_C / many Genes QTL ?QTL XREF Gene_class // many/many Gene_product ?Gene_Product XREF Gene_class // NOT USED Locus ?Locus XREF Gene_class // many/many Clone ?Probe XREF Source_gene_class // 1 G_C / many Clones Sequence ?Sequence XREF Gene_Class // 1 G_C / many Sequences Comment ?Text Numbered_reference Int ?Reference XREF Gene_class //Int is a //numbered reference citation used in a Comment. // See ?Gene_Class Orthologous_gene_set. ?Gene_Set Reference ?Reference XREF Gene_Set // many/many Abbreviation ?Text // NOT USED Gene_class ?Gene_Class XREF Orthologous_gene_set // many G_S's / 1 Gene_class Character_affected ?Text // NOT USED Gene ?Gene XREF Orthologous_gene_set // 1 G_S / many Genes Comment ?Text Numbered_reference Int ?Reference XREF Gene_Set //Int is a //numbered reference citation used in a Comment. // Much of this is the same as for ?Allele. ?Gene Mapping_information Locus ?Locus XREF Associated_gene // 1 Gene / many Loci Candidate_locus ?Locus XREF Candidate_gene // 1 Gene / many Candidate_loci // Tag Locus vs. Candidate_locus: The former is used if // the gene was mapped by function, the latter if with a // probe. These can be merged to one column but an extra column // for How_mapped should be added. Full_name ?Text // 1. Reference ?Reference XREF Gene // many/many URL Text Text // 1 Gene / many URLs. // First Text is URL, second is optional description. Gene_class ?Gene_Class XREF Gene // many Genes / 1 Gene_class Orthologous_gene_set ?Gene_Set XREF Gene // many Genes / 1 O_g_s Other_name ?Gene XREF Correct_name ?Reference // (See ?Allele.) Correct_name ?Gene XREF Other_name ?Reference // " " Previous_name ?Gene ?Reference // ... Current_name ?Gene ?Reference 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 // 1 Gene / many QTLs Gene_product ?Gene_Product XREF Gene ?Reference // 1 Gene / many G_P's Chromosome ?Text ?Reference // 1 Gene / many Chromosomes Chromosome_arm ?Text ?Reference // 1 Gene / many Chromosome_arms 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 // Only used twice. Move to Comment. Reference_allele UNIQUE ?Allele XREF Gene ?Reference // NOT USED Reference_allele_and_background ?Allele XREF Gene ?Germplasm // 1. // Not in GG but is in Barley Genetic Stocks Database. Allele ?Allele XREF Gene ?Reference // 1 Gene / many Alleles Inheritance ?Text // Not in GG but is in BGS. Description ?Text // Not in GG but is in BGS. First_mutation ?Text // Not in GG but is in BGS. Comment ?Text Molecular_information Clone ?Probe XREF Source_gene // 1 Gene / many Clones Sequence ?Sequence XREF Gene // 1 Gene / many Sequences Pathology ?Pathology XREF Resistance_gene // many Genes / 1 Pathology Image ?Image XREF Gene // many/many BGS_photo Text // for links to images in Barley Genetic Stocks DB. // Omit this I guess. All have links via URL too. Mapping_data 2_point_data ?2_Point_Data XREF Gene // 1 Gene / many 2_p_d's 3Point ?3_point_data // NOT USED Df_Dup ?Df_Dup_data // NOT USED Related_genes ?Gene XREF Related_genes ?Text // NOT USED Numbered_reference Int ?Reference XREF Gene //Int is a numbered //reference citation used in a Comment. Data_source ?Colleague ?Text Information_source ?Reference Data_curated ?Colleague ?Text ?Rearrangement Name Correct_name ?Rearrangement XREF Other_name Other_name ?Rearrangement XREF Other_name Reference_germplasm ?Germplasm Text Remark ?Text Variant Text Molecular_Information Polymorphism Found ?Probe Absent ?Probe Mutagen ?Reagent Text Phenotype ?Text Dosage_effects Haplo_insufficiency Qualifier Text Location ?Colleague Author Text Date Text Type Deletion Uncovers Text Duplication Covers Text Translocation Compound Map ?Map XREF Rearrangement #map_position Proximal_breakpoint ?Breakpoint XREF Distal_rearrangement Distal_breakpoint ?Breakpoint XREF Proximal_rearrangement Positive Proximal_marker ?Locus Contains ?Locus XREF In_segment Negative Distal_marker ?Locus Does_not_contain ?Locus XREF Not_in_segment Mapping_data 2Point ?2_Point_Data 3Point ?3_point_data Df_Dup ?Df_Dup_data In_situ UNIQUE ?Map Float Float Germplasm ?Germplasm XREF Rearrangement Reference ?Reference XREF Rearrangement // Note, 22jan04: Halfway through marking ?Locus up, we decided to split up // GG's Locus records that are merged from all maps that use the same // name for the locus. In MySQL each Locus record will be unique, i.e. // it will be on only one map. // This change is so far only reflected in the tags from Linked_QTL on. ?Locus Type RFLP //controlled vocabulary CAPS //cleaved amplified polymorphic seqiemce RAPD APPCR //RAPD? arbitrarily primed PCR Microsatellite STS AFLP Gene QTL Translocation_break_point Centromere Telomere C_band Other_name ?Locus XREF Correct_name ?Reference //synonym w/type Correct_name ?Locus XREF Other_name ?Reference //synonym w/type Previous_name ?Locus ?Reference //synonym w/type Current_name ?Locus ?Reference //synonym w/type Synonym ?Locus XREF Synonym //synonym w/type Location Chromosome Text ?Species // many / many Chromosome_arm Text ?Species // many / many Map ?Map XREF Locus #map_position // many / many (for Cmap export) Main_Marker ?Map XREF Main_Marker // NOT USED Inside Chrom_Band ?Chrom_Band XREF Inside //NOT USED Interval ?Interval XREF Inside //NOT USED Bin ?Bin XREF Locus //NOT USED - using Breakpoint interval for EST records Bin_marker_for ?Bin XREF Bin_marker //NOT USED Positive In_QTL ?QTL XREF Significant_marker // many / many with type (positive vs. negetive) In_segment ?Rearrangement XREF Contains // many / many with type In_interval ?Breakpoint_interval XREF Contains // many / many with type b Negative Not_in_QTL ?QTL XREF Nonsignificant_marker Not_in_segment ?Rearrangement XREF Does_not_contain Not_in_interval ?Breakpoint_interval XREF Does_not_contain Data ?Map_Data XREF Locus #How_mapped // Change to "Map_Data"; many / many Background_marker ?Map_Data //axe Linkage_data ?Linkage_Data XREF Locus #How_mapped // Merging with Map_Data Mapping_data Well_ordered // not used 2_point ?2_Point_Data // many / many Species ?Species ?Reference // many / many Probe ?Probe XREF Locus ?Reference //many / 1 TABLE ?Text REPEAT // drop this for now, infor will come in with genotyping data Mapped_bands ?Restriction ?Text ?Germplasm ?Text // drop this for now, infor will come in with genotyping data Linked_QTL ?QTL XREF Nearest_marker // one locus / many QTL Associated_gene ?Gene XREF Locus // one to one Candidate_gene ?Gene XREF Candidate_locus // one to one Homology ?Protein Text Text // e value and title ; REMOVE and generate in report Gene_class ?Gene_Class XREF Locus // 1 gene class / many loci; generate in report Image ?Image XREF Locus // many / many Reference ?Reference XREF Locus // many / many Data_source ?Colleague Text // many / many Remarks Text // many / many Candidate_orthology_group ?Locus XREF Possible_orthologues // one group to many Possible_orthologues ?Locus XREF Candidate_orthology_group // many to one group Gale_orthology_group ?Locus XREF Gale_orthologues //REMOVE Gale_orthologues ?Locus XREF Gale_orthology_group //REMOVE ?Bin Locus ?Locus XREF Bin Bin_marker ?Locus XREF Bin_marker_for Data_source ?Colleague Text ?How_mapped Mapped_with_probe ?Probe Mapped_by_function ?Gene ?Germplasm Other_name ?Germplasm XREF Other_name // many / many Species ?Species // many / many Subspecies ?Species // many Germplasms / 1 Subspecies Donor_species ?Species // many Germplasms / 1 Species Type #Germplasm_type // many / many Collection_and_ID ?Collection ?Germplasm XREF Other_name // 1 Germplasm / // many Collection_and_ID pairs Cross_number ?Text // 1. Chromosome_configuration ?Text // 1. Deletion_distal_to ?Breakpoint XREF Distal_deletion_in // NOT USED. Contains_breakpoint ?Breakpoint XREF Germplasm // 1 Germplasm / many // Breakpoints. Abbreviation ?Germplasm XREF Full_name // Treat as Other_name. Full_name ?Germplasm XREF Abbreviation // Omit. Pairing_configuration ?Text // many. generic Text table. Chromosome_number ?Text // 1. Female_Parent ?Germplasm // Vickie will remove. Male_Parent ?Germplasm // Vickie will remove. Pedigree ?Text // many. generic Text table. Selection_history ?Germplasm XREF Other_name // 1. Market_Class ?Text // many. generic Text table. Characteristic ?Text // many. generic Text table. Pathology ?Pathology XREF Resistant_line // many / many Allele ?Allele XREF Germplasm // many / many (already handled) Gene ?Gene // many / many (already handled) Gene_product ?Gene_Product XREF Germplasm // omit. Use link via Allele. Rearrangement ?Rearrangement XREF Germplasm // many / many Sequence ?Sequence XREF Germplasm // NOT USED Derived_from ?Germplasm // 1. (Dave will make it so.) Chromosome_donor ?Text // 1. Cytoplasm ?Text // 1. (Dave will make it so.) Developed_by ?Text // many. generic Text table. Development_site ?Text // many. generic Text table. Collection_site ?Text // many. generic Text table. Date_collected ?Text // many. generic Text table. Primary_collection ?Collection // 1. Date_of_release ?Text // many (erroneously) Registration_No ?Text // 1. Remark ?Text // // many. generic Text table. Polymorphism ?Polymorphism #Presence // later. Trait_description ?Trait_Study XREF Germplasm_description ?Text ?Text // later. Trait_score ?Trait_Study Float ?Text // later. Reference ?Reference XREF Germplasm // many / many Data_source ?Colleague ?Text // as before Data_curated ?Colleague ?Text // as before Mapping_data ?Map_Data // many / many Linkage_data ?Linkage_Data // merge with Mapping_data 2_point_data ?2_Point_Data // many / many DNA_library ?Library XREF Germplasm // 1 Germplasm / many DNA libraries Trait_study ?Trait_Study // many / many Image ?Image XREF Germplasm // many / many Trait_scores ?Trait_scores // later (QTL studies.) Coefficient_of_parentage ?Germplasm Float // Omit. ?Germplasm_type Cultivar Elite_germplasm Germplasm Substitution Translocation Amphiploid Aneuploid Deletion Alien_addition Synthetic Recombinant_translocation_line Mutation Isogenic Marker Alloplasmic_line ?Presence Present ?Text REPEAT Absent ?Text REPEAT ?Map Type UNIQUE Genetic // as for other Type data Cytogenetic Physical Species ?Species // many / many Mapping_data ?Map_Data XREF Map // one mapping_data / many maps Linkage_data ?Linkage_Data XREF Map // (merge with mapping_data) Display Non_graphic // NOT USED Title UNIQUE ?Text // NOT USED Remark Text // Comments Flipped // Boolean Unit UNIQUE Text // 1 Centre UNIQUE Float UNIQUE Float // two unique floats Extent UNIQUE Float UNIQUE Float // NOT USED Default_view UNIQUE ?View // Ignore Minimal_view UNIQUE ?View // Ignore View ?View // Ignore Inherits From_map UNIQUE ?Map // NOT USED Author Text // NOT USED Date Text // NOT USED Main_Marker Main_Locus ?Locus // ignore Band ?Chrom_Band // ignore Contains Locus ?Locus XREF Map // 1 Map / many of each of these: Chrom_Band ?Chrom_Band XREF Map Rearrangement ?Rearrangement XREF Map Interval ?Interval XREF Map // NOT USED Breakpoint ?Breakpoint XREF Map Breakpoint_interval ?Breakpoint_interval XREF Map QTL ?QTL XREF Map Contig ?Contig // ignore till there's data ?map_position UNIQUE Position UNIQUE Float #map_error Ends Left UNIQUE Float #map_error Right UNIQUE Float #map_error Multi_Position Float #map_error // NOT USED Multi_Ends Float UNIQUE Float // NOT USED With UNIQUE With_locus UNIQUE ?Locus #Map_offset // NOT USED ?map_offset Offset UNIQUE Float ?map_error Error UNIQUE Float ?View Type UNIQUE Pepmap Fmap Gmap Grid Grid_map Int #View_tags 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 Display Submenus Cambridge No_buttons Hide_header Name UNIQUE Text Columns Text UNIQUE Int #Column ?Column UNIQUE Scale Scale_unit UNIQUE Float 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 Point_width UNIQUE Int Point_error_scale UNIQUE Float Point_segregate_ordered Point_show_marginal Point_pne #Colour Point_pe #Colour Point_nne #Colour Point_ne #Colour Point_symbol UNIQUE Text 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 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 ?View_tags Colour #Colour Surround_colour #Colour Tag Text ?Interval_col_conf Query UNIQUE Text Names_on No_neighbours Show_multiple Width UNIQUE Int Symbol UNIQUE Text Colours Text #Colour Pne #Colour Pe #Colour Nne #Colour Ne #Colour ?MultiMap Map ?Map Min Int Anchor UNIQUE Text UNIQUE Text UNIQUE Text ?Reagent Other_name ?Reagent XREF Other_name Description Text Remark Text Reference ?Reference Source ?Source Contact ?Colleague ?Library Type cDNA Genomic Species ?Species XREF DNA_library Germplasm ?Germplasm XREF DNA_library Developmental_stage ?Text Tissue ?Text Treatment ?Text Date ?Text Vector ?Text Cloning_site ?Text Sequencing_primers ?Text Source ?Colleague Reference ?Reference Remark ?Text Probe ?Probe XREF DNA_library Sequence ?Sequence XREF DNA_library ?Probe Locus ?Locus XREF Probe // 1 Probe / many Loci (Already done.) Other_name ?Probe XREF Please_see ?Reference // many / many Please_see ?Probe XREF Other_name // Reciprocal of Other_name, above. Synonym ?Probe XREF Synonym // NOT USED Related_probe ?Help ?Probe // For "Hybridization homologs", independent clones that probe the same locus. 1 to 1. Similar_probes ?Probe XREF Similar_probes // // Change. One "Probe-cluster" to many Probes. External_DB ?Text ?Text // Ignore. Go through Sequence instead. Reference ?Reference XREF Probe // many/many General_remark ?Text // many general_remarks / Probe (Sometimes // the remarks are repeated many times for different probes.) Type cDNA // as for other Type data. Genomic PCR SSR EST PCR_primers ?Text // many / many. Use {Primers + Size + // Amplification_conditions} vs. Type PCR,AFLP,SSR,Vector_PCR AFLP_primers ?Text STS_primers ?Text // Change STS to "PCR". STS_size ?Text SSR_size ?Text Amplification_conditions ?Text Specificity ?Text // Change to Comment, type Specifity. Sequence ?Sequence XREF Probe // 1 Probe / many Sequences Barley_rating Excellent // NOT USED. Good Fair Poor Copy_number Text // 1. Comment with Type Background ?Text // 1. Comment with Type Wheat_polymorphism ?Text ?Restriction ?Text // 1 probe / 1 W_p //Chromosome, Enzyme, Score. E.g. '2D EcoRI "15 (2/15)"' // Data used inconsistently in GG. Change to Comment "Polymorphism:" Barley_polymorphism ?Restriction ?Text // NOT USED Cross_hybridizes_to ?Species Text // Text is "good", "no", "fair". // many/many Polymorphism ?Polymorphism XREF Probe ?Text // 1 Probe / many // Polymorphisms. ?Text is the summary polymorphism score. Gel ?Gel XREF Probe // 1 Probe / 1 Gel Linkage_Group ?Text // Comment "Linkage_Group: " Origin DNA_library ?Library XREF Probe // many Probes / 1 Library Insert_enzyme ?Restriction ?Restriction // 1 pair / 1 Probe Source_gene_class ?Gene_Class XREF Clone // 1 S_g_c / many P's Source_gene ?Gene XREF Clone // 1 Source_gene / many Probes Source_allele ?Allele XREF Probe // 1 Source_allele / many P's Source_species ?Species // 1 Source_species / many Probes Source_germplasm ?Germplasm // 1 Source_germplasm / many P's Source_tissue ?Text // Comment "Source_tissue: " DNA_Origin ?Text // Comment "DNA_origin: " Insert Size Float ?Text // Float is size as excised by enzyme (KB) // Text is notes (Remove, move the 14 examples to // SSR_size.) Multivalued (!) PCR_size Float // If amplified from PCR_primers, as opposed // to Vector_PCR_primers. Multivalued (!) Clone Vector ?Text // Multivalued (!) Vector_enzyme ?Restriction // 1. Excision_enzyme ?Restriction ?Restriction // Up to 2. Vector_PCR_primers ?Text // Too many. Vector_amplification ?Text // 1. Conditions for amplifying // from vector primers. Bacterial_strain ?Text // 1. Antibiotic ?Text // 1. Subcloned_in ?Probe XREF Subclone_of // 1. Subclone_of ?Probe XREF Subcloned_in // Reciprocal Location ?Colleague // many/many Authority ?Colleague // many/many In_pool ?Pool XREF Probe // NOT USED Gridded ?Probe_Grid // Discard Position Hybridizes_to ?Probe_Grid ?Probe ?Text // NOT USED Positive_probe ?Probe // NOT USED Positive_pool_probe ?Pool // NOT USED Image ?Image XREF Probe // many/many Data_source ?Colleague ?Text Information_source ?Reference Note ?LongText // many/many ?Polymorphism Probe UNIQUE ?Probe XREF Polymorphism Enzyme UNIQUE ?Restriction TABLE ?Text REPEAT // Omit. Just a kludge for labeling. Size ?Gel Float ?Text ?Germplasm // Gel,Size,Intensity,Germplasm // Each subfield can be multivalued. // Example, Polymorphism "BCD1088 EcoRI" Value ?Species Text ?Germplasm // Species, Allele, Germplasm // Each subfield can be multivalued. // Example, Polymorphism "PSR100 5B DraI" Band_size ?Text // Unique. A column header for Pattern. Pattern Text ?Germplasm // Text is a string of 1's, 0's, ?'s etc. // Each subfield can be multivalued. // Example, Polymorphism "BCD1700 EcoRI" Germplasm ?Germplasm XREF Polymorphism // many-to-many Image ?Image XREF Polymorphism // many-to-many Remarks Text // many-to-many Reference ?Reference // many-to-many Data_source ?Colleague Text // currently only unique ?Gel Probe ?Probe XREF Gel // unique Date ?Text // NOT USED Run_by ?Colleague // NOT USED Conditions ?Text // NOT USED Polymorphism ?Polymorphism // many/many Germplasm ?Germplasm // NOT USED Image ?Image // NOT USED TABLE Text REPEAT // Omit. Just a kludge for formatting. Band ?Restriction Float UNIQUE Int UNIQUE Text // many/many // There may be multiple Float's per Restriction. // Example, Gel "PSR112 Gale" Data_source ?Colleague Text ?Probe_Grid Title ?Text Layout Columns Int Lines_at Int Int Space_at Int Int No_stagger A1_labelling Row Int ?Probe XREF Gridded REPEAT ?Contig bMap Length UNIQUE Int Position UNIQUE Int b2g UNIQUE Float Float gMap UNIQUE ?Map XREF Contig Float Float pMap UNIQUE Int Int ?2_Point_Data Point_1 UNIQUE Locus_1 UNIQUE ?Locus XREF 2_point Point_2 UNIQUE Locus_2 UNIQUE ?Locus XREF 2_point Gene ?Gene XREF 2_point_data Simple_distance Min Float Distance Float Max Float Error Float Distance_units Text Linkage Text Trait_marker QTL Location Chromosome Text Chromosome_arm Text Species ?Species Female_Parent ?Germplasm XREF 2_point_data Male_Parent ?Germplasm XREF 2_point_data Parent ?Germplasm XREF 2_point_data Population ?Text Generation ?Text Number_of_individuals Int Method ?Text Map_data ?Map_Data XREF 2_point Linkage_data ?Linkage_data XREF 2_point Contact ?Colleague Reference ?Reference XREF 2_point_data URL Text Text Remark ?Text Data_source ?Colleague ?Text // This class is completely empty in GG. //?Df_Dup_data Rearrangement ?Rearrangement XREF Df_Dup // This class is completely empty in GG. //?3_point_data Gene1 UNIQUE ?Gene XREF 3Point ?Allele XREF 3Point ?Colleague Position Text Profession Text Institution Address Mail ?Text Country ?Text Phone Text Fax Text E_mail Text Telex Text WWW_page Text Background Text Research_interest ?Text Image ?Image XREF Colleague Publishes_as ?Author XREF Full_name Remark Text Obtained_from ?Source Text Last_update UNIQUE ?Text ?Author Full_name ?Colleague XREF Publishes_as Paper ?Reference Image ?Image ?Journal Other_name ?Journal XREF Other_name Source_code ?Text ISSN_number Text URL Text Paper ?Reference XREF Journal ?Reference Reference Title UNIQUE ?Text Original_title Text Journal UNIQUE ?Journal XREF Paper Publisher UNIQUE Text Series ?Text Contained_in ?Reference XREF Contains Year Int Volume UNIQUE Int Text Page UNIQUE Int Int Remark Text URL Text Online Text Text Institution Text Author ?Author XREF Paper Editor ?Author XREF Paper Type UNIQUE Text Language Text 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 Probe ?Probe XREF Reference Sequence ?Sequence XREF Reference Germplasm ?Germplasm XREF Reference Mapping_data ?Map_Data XREF Reference Linkage_data ?Linkage_Data XREF Reference 2_point_data ?2_Point_Data Trait_study ?Trait_Study XREF Reference Isolate ?Isolate XREF Reference Keyword ?Keyword Agricola_code ?Text Gene_Catalogue_number Int Cited_in ?Reference Summary_of ?Reference XREF Summarized_in Summarized_in ?Reference XREF Summary_of ?Restriction Site UNIQUE Text Offset Text Cleavage Text Overhang Text Isoschizomers ?Restriction REPEAT Company ?Source Reference ?Reference Remark Text ?Sequence DNA UNIQUE ?DNA UNIQUE Int Peptide UNIQUE ?Peptide UNIQUE Int Contigset ?Contigset Contig_members ?Sequence XREF Contig Contig ?Sequence XREF Contig_members Singleton_in ?Contigset Tracefile Text Structure From Source UNIQUE ?Sequence Source_Exons Int UNIQUE Int Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int Sequence Text DB_info External_DB Text Text Database ?Database Text Text Blast_hits ?Database Text Text DB_remark Text EC_number UNIQUE Text Keyword Text Origin Germplasm UNIQUE ?Germplasm Species ?Species Cultivar Text Chromosome UNIQUE Text Clone_lib UNIQUE Text Tissue UNIQUE Text Dev_stage UNIQUE Text Sex UNIQUE Text Date UNIQUE Text Data_source ?Colleague Text Visible Title UNIQUE ?Text Other_name ?Text Corresponding_protein UNIQUE ?Protein XREF Corresponding_DNA Strain Text DNA_library UNIQUE ?Library XREF Sequence Clone Text Probe ?Probe XREF Sequence Gene UNIQUE ?Gene XREF Sequence Gene_class UNIQUE ?Gene_Class XREF Sequence Gene_product ?Gene_Product XREF Sequence Remark Text Reference ?Reference XREF Sequence Properties cDNA cDNA_EST UNIQUE Contig_Phrap UNIQUE Codon_start UNIQUE Int Allele ?Allele UNIQUE EMBL_feature CAAT_signal Int Int Text #EMBL_info GC_signal Int Int Text #EMBL_info TATA_signal 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 modified_base 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_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 exon Int Int Text #EMBL_info intron Int Int Text #EMBL_info 5_UTR Int Int Text #EMBL_info 3_UTR Int Int Text #EMBL_info RBS Int Int Text #EMBL_info LTR Int Int Text #EMBL_info terminator Int Int Text #EMBL_info misc_difference Int Int Text #EMBL_info misc_RNA Int Int Text #EMBL_info rRNA Int Int Text #EMBL_info tRNA Int Int Text #EMBL_info snRNA Int Int Text #EMBL_info scRNA Int Int Text #EMBL_info STS Int Int Text #EMBL_info m35_signal Int Int Text #EMBL_info m10_signal Int Int Text #EMBL_info unsure Int Int Text #EMBL_info Homol Best_DNA UNIQUE ?Sequence XREF DNA_homol Float Text Best_Pep UNIQUE ?Protein XREF DNA_homol Float Text 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 Alignment ?LongText ?EMBL_info Location UNIQUE Text Qualifier Note Text Product Text ?Splice_confirmation UNIQUE cDNA Homology ?Protein Title UNIQUE ?Text Peptide UNIQUE ?Peptide UNIQUE Int DB_info Database ?Database Text Text Origin From_Database ?Database UNIQUE Int Visible Corresponding_DNA ?Sequence XREF Corresponding_protein Homol DNA_homol ?Sequence XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int Pep_homol ?Protein XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int ?Contigset Author ?Author Date Text Description Text Species ?Species Software Text Parameters Text Procedure Text Contigs Int Singletons Int Remarks Text WWW_page Text ?Database Name Text Contents ?Text WWW Arg1_URL_prefix UNIQUE Text Arg1_URL_suffix UNIQUE Text Arg2_URL_prefix UNIQUE Text Arg2_URL_suffix UNIQUE Text ?Method Remark ?Text Display Colour #Colour Frame_sensitive Strand_sensitive Show_up_strand #Colour Score Score_by_offset Score_by_width Score_by_histogram UNIQUE Float Score_bounds UNIQUE Float UNIQUE Float Percent Overlap_mode UNIQUE Overlap Bumpable Cluster Width UNIQUE Float Symbol UNIQUE Text Right_priority UNIQUE Float Max_mag UNIQUE Float Min_mag UNIQUE Float Show_text Blastn Blixem Blixem_X Blixem_N Blixem_P Belvu ?Gene_Product Other_name ?Text Type ?Text ?Reference Text 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 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 Pathway ?Pathway #Components Substrate_specificity ?Text ?Reference ?Text pH_optimum Float ?Reference ?Text Temp_optimum 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 Purification Text Isoelectric_point Float Biochemistry Text Remarks Text Reference ?Reference Contact ?Colleague Sequence ?Sequence ?Regulators Activator ?Text Vmax Text Cooperativity Inhibitor ?Text Ki Text Developmental ?Reference Text Hormonal Text Environmental ?Reference Text Genetic ?Reference Text Inducer ?Text Repressor ?Text ?Mechanism Ping_Pong ?Components Reaction ?Reaction Reactant ?Text Km Text Product ?Text ?Source Other_name ?Text // 3 records, I'll delete. Omit. Contents Text // NOT USED Remarks Text // Unique Contact ?Colleague // Unique Reference ?Reference // Unique Journal ?Journal // Unique Address Mail Text // 3 records. Omit all Address tags. Phone Text E_mail Text Fax Text ?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 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 Trait_study ?Trait_Study XREF Image Caption ?Text Author ?Author XREF Image Reference ?Reference XREF Image Pick_me_to_call UNIQUE Text Text ?Pool Contains Probe ?Probe XREF In_pool Subpool ?Pool XREF In_pool In_pool ?Pool Map Hybridizes_to ?Probe_Grid ?Probe XREF Positive_pool_probe ?Text Chrom_Band ?Chrom_Band XREF Positive_pool_probe Location ?Colleague Reference ?Reference ?Chrom_Band Type Centromere p_Telomere q_Telomere Drawing Dark NOR Colour #Colour 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 Negative Does_not_contain_breakpoint ?Breakpoint XREF Not_in_chrom_band Locus Inside ?Locus XREF Chrom_Band Positive_pool_probe ?Pool XREF Chrom_Band Reference ?Reference ?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 ?Collection Curator ?Colleague Address Mail Text Country Text Phone Text Fax Text E_mail Text Cable Text Telex Text Description ?Text Please_see ?Collection Contained_in ?Collection XREF Contains Contains ?Collection XREF Contained_in IPGRI_code Text WWW_page Text Species ?Species Int Entries ?Germplasm XREF Collection_and_ID Update ?Source Text Data_source ?Source Text ?Pathology Other_name ?Pathology XREF Other_name 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 ?Isolate Synonym ?Isolate XREF Synonym Type Pathotype Strain Species ?Species Origin Collector ?Colleague ?Text Latitude ?Text Longitude ?Text Country ?Text Characteristic ?Text Avirulence ?Text Note ?Text Reference ?Reference XREF Isolate Data_source ?Colleague ?Text Reaction_to_host_genes ?Text ?Allele Reaction_to_host_germplasm ?Text ?Germplasm ?Species Correct_name UNIQUE ?Species Full_name UNIQUE ?Text Genus UNIQUE ?Text Species_epithet ?Text Variety ?Text Authority ?Text Synonym ?Species XREF Synonym Common_name ?Text Sequence ?Sequence Genome UNIQUE ?Text Haploid_chromosome_number Int Mapping_data ?Map_Data Linkage_data ?Linkage_Data Disease ?Pathology XREF Host_species Causes ?Pathology XREF Causal_organism Vector_of ?Pathology XREF Vector Reference ?Reference Image ?Image XREF Species DNA_library ?Library XREF Species ?Map_Data Map ?Map XREF Mapping_data // many Maps / 1 Map_data External_DB Text Text // multiple, to construct URL Species ?Species XREF Mapping_data // many / many Female_parent UNIQUE ?Germplasm XREF Mapping_data // 1 Male_parent UNIQUE ?Germplasm XREF Mapping_data // 1 Parent ?Germplasm XREF Mapping_data // many Type Genetic // Treat like other Types // add "Linkage_data" type Cytogenetic Chromosome_arm Physical Map_units Text // many. But combine into 1 Comments text. Reference ?Reference XREF Mapping_data // many / many URL Text Text // many. First text is // URL, second is optional description. Contact ?Colleague // many/many Remarks ?Text // multiple Data_curated ?Colleague Text // many/many // Text is date, e.g. 99.11 Image ?Image XREF Map // many/many Trait_study ?Trait_Study XREF Mapping_data // go via QTL QTL ?QTL XREF Mapping_data // already done in QTL tables 2_point ?2_Point_Data XREF Map_data // NOT USED Locus ?Locus XREF Data Text // Text is raw Mapmaker data Breakpoint ?Breakpoint XREF Map_data // Go via Map. Breakpoint_interval ?Breakpoint_interval XREF Map_data // Go via Map. // Merge with Map_Data. Add Type Linkage_Data, and column for Location. ?Linkage_Data Map ?Map XREF Linkage_data Species ?Species XREF Linkage_data Female_parent UNIQUE ?Germplasm XREF Linkage_data Male_parent UNIQUE ?Germplasm XREF Linkage_data Parent ?Germplasm XREF Linkage_data Type Genetic Cytogenetic Physical Map_units Text Location Chromosome Text //E.g. 3D Chromosome_arm Text //E.g. 3DS Reference ?Reference XREF Linkage_data Contact ?Colleague Remarks ?Text Image ?Image XREF Linkage_data Trait_study ?Trait_Study XREF Linkage_data QTL ?QTL XREF Linkage_data 2_point ?2_Point_Data XREF Linkage_data Locus ?Locus XREF Linkage_data Text Data_curated ?Colleague Text Breakpoint ?Breakpoint XREF Linkage_data Breakpoint_interval ?Breakpoint_interval XREF Linkage_data ?Trait Description ?Text See_also ?Trait XREF See_also Ontology ?Text Text Pathology ?Pathology XREF Trait Affected_by ?Gene_Class XREF Character_affected QTL ?QTL XREF Trait_affected Evaluation ?Trait_Study XREF Trait ?Trait_Study Trait ?Trait XREF Evaluation Pathology ?Pathology XREF Evaluation Reference ?Reference XREF Trait_study Description Text Protocol Text Ontology ?Text Text Values ?Text Environment ?Environment XREF Trait_study Parental_description ?Germplasm XREF Trait_study ?Text Parental_Mean_SD ?Germplasm XREF Trait_study Float Float Mapping_data ?Map_Data XREF Trait_study Linkage_data ?Linkage_Data XREF Trait_study Population_size UNIQUE Int Population_type Text QTL_analysis_method ?Text Statistics Text Heritability Float Text Type_I_error_rate_per_locus Float Number_of_markers_tested Int QTLs_found UNIQUE Int Phenotypic_R2 Float Text Genetic_R2 Float Text R2_definition Text Comment Text Image ?Image XREF Trait_study QTL ?QTL XREF Trait_study Germplasm_description ?Germplasm XREF Trait_description ?Text Text Germplasm_score ?Germplasm Float ?Text Trait_scores ?Trait_scores XREF Trait_study Data_source ?Colleague ?Text Data_curated ?Colleague ?Text // Need to split QTLs into equivalent unique ones of the same name, // as for Locus. ?QTL Trait_affected UNIQUE ?Trait XREF QTL // 1 trait / many QTLs Gene_class ?Gene_Class XREF QTL // many / many Trait_study ?Trait_Study XREF QTL // many / many Environment ?Environment XREF QTL // query via Trait_Study -> Environment Mapping_data UNIQUE ?Map_Data XREF QTL // many / many Linkage_data ?Linkage_Data XREF QTL // merge with Map_Data Chromosome_arm ?Text // unique (e.g. "half the genome") Associated_gene ?Gene XREF QTL // many/many Nearest_marker UNIQUE ?Locus XREF Linked_QTL // 1 Locus / 1 QTL Significance_level UNIQUE Float // 1 (Significance of marker. P < 0.what?) Positive Significant_marker ?Locus XREF In_QTL Text // many / many (ignore "Positive") // Text is significance level, e.g. "alpha < .01" Negative Nonsignificant_marker ?Locus XREF Not_in_QTL // NOT USED Position UNIQUE Map ?Map XREF QTL #map_position Map_label ?Text // Unique LOD_peak_location UNIQUE ?Locus XREF QTL // NOT USED LOD_peak_height Float // NOT USED Significant_LOD_interval gMap ?Map Float Float // NOT USED LOD_threshold Float // NOT USED Phenotypic_R2 UNIQUE Float // 1 Genetic_R2 UNIQUE Float // 1 Effect_of_allele_substitution UNIQUE Float Text //Magnitude of allelic // effect. Text is units. Additivity_Dominance_ratio UNIQUE Float // NOT USED Higher_scoring_allele_from ?Germplasm // 1 Germplasm / many QTLs Interactions Text // Comment text Significance_x_Environment Float ?Environment // many pairs of Float x Env. //QTL x Env. P < 0.what? Comment Text Image ?Image XREF QTL // many/many ?Trait_scores Trait_study UNIQUE ?Trait_Study XREF Trait_scores Environment ?Environment XREF Trait_scores Comment Text Scores Text Score_Mean_SD Float Float Germplasm_Mean_SD ?Germplasm XREF Trait_scores Float Float Germplasm_score Float ?Germplasm XREF Trait_scores Germplasm ?Germplasm XREF Trait_scores Score Float Standard_deviation Float Replications Int Percent_of_local_check Float Difference_from_local_check Float Pathogen_race ?Isolate ?Environment Year UNIQUE Text Location UNIQUE ?Text Latitude UNIQUE Text Longitude UNIQUE Text Elevation UNIQUE Text Experimental_design ?Text Replications UNIQUE Int Evaluator ?Colleague Institute ?Text Topography UNIQUE Text Drainage UNIQUE Text Soil_texture UNIQUE Text Irrigation Text Moisture Text Planting_date UNIQUE Text Harvest_date UNIQUE Text Testing_date Text N_applied Text P2O5_applied Text K2O_applied Text Remarks Text Trait_study ?Trait_Study XREF Environment Trait_scores ?Trait_scores XREF Environment QTL ?QTL XREF Environment ?Help Intro ?Text Overview ?Text Note ?Text Tip ?Text More ?LongText ?Breakpoint_interval Correct_name ?Breakpoint_interval XREF Other_name Other_name ?Breakpoint_interval XREF Other_name Map_data ?Map_Data XREF Breakpoint_interval Linkage_data ?Linkage_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 Phenotype ?Text Reference ?Reference Location ?Colleague Remark ?Text ?Breakpoint Correct_name ?Breakpoint XREF Other_name Other_name ?Breakpoint XREF Other_name Map_data ?Map_Data XREF Breakpoint Linkage_data ?Linkage_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