// 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 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