// // Structure of classes for the malaria database, MalDB // /////////////////////////////////////////////////////////////////////////// // Genetic map ?Map No_cache // Don't cache segs for this map. Display Non_graphic // Prevents a graphic display! Title UNIQUE ?Text Flipped // Then coordinates go upwards Unit UNIQUE Text // e.g. kb, centiMorgan, MegaParsec Centre UNIQUE Float UNIQUE Float // default centre, width - else 0, 10 Extent UNIQUE Float UNIQUE Float // min, max - else min, max gene/locus 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 created it Main_Marker Main_Locus ?Locus // XREF Main_Marker removed to // allow tag2 system // tag2 system for items shown left of locator Map ?Map XREF Map_shown #Map_position Contains Locus ?Locus XREF Map Contig ?Contig XREF Map Clone ?Clone XREF Map Sequence ?Sequence XREF Map Allele ?Allele XREF Map Map_shown ?Map XREF Map // tag2 system for items shown in main region Reference ?Paper XREF Map Organism ?Organism XREF Map // the following can occur in any class, to make it display on a map // Map ?Map #Map_position // Positive // // object will highlight appropriately when parent does // Negative // // object will highlight appropriately when parent does // Mapping_data 2_point ?2_point_data // Multi_point ?Multi_pt_data // Pos_neg_data ?Pos_neg_data // // these three refer to mapping data objects that can // // be displayed and take part in likelihood calculations // // the position to draw the object, and whether it is a point or a line, // are determined by the #structure in the object to the right of the // specific map. ?Map_position UNIQUE Position UNIQUE Float #Map_error Ends Left UNIQUE Float #Map_error Right UNIQUE Float #Map_error Multi_Position Float #Map_error Multi_Ends Float UNIQUE Float With UNIQUE With_locus UNIQUE ?Locus #Map_offset With_clone UNIQUE ?Clone #Map_offset // tag2 system for "burying" ?Map_error Error UNIQUE Float ?Map_offset Relative #Map_position ?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 ?ManyMap Map ?Map UNIQUE ?View //////////////////////////////////////////////////////////////////////////// // Views - control Map and Grid displays // Almost everything in these is meaningful. The data is best set for // Map displays by the interactive view editor. ?View Type UNIQUE 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 structure used for Grid tag->colour specification ?View_tags Colour #Colour Surround_colour #Colour // colour when surround Tag Text // could be many tags // the column structure is a list of different column types, with // any parameters ?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_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 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_tag Text Int 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 ?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 //////////////////////////////////////////////////////////////////////////// // Physical map - PMAP display - will be subsumed in Map ?Contig Map ?Map XREF Contig #Map_position pMap UNIQUE Int UNIQUE Int // extremities in pMap units Clone ?Clone XREF pMap ?Clone Remark General_remark ?Text Type YAC COSMID PHAGE PLASMID FREE_DNA OTHER 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 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 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 Isolate ?Text 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 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 Reference ?Paper XREF Clone cDNA_group Contains ?Clone XREF Contains Text Contained_in ?Clone XREF Contained_in Best_match UNIQUE ?Text Antigen ?Antigen XREF Clone Expr_pattern ?Expr_pattern XREF Clone Organism ?Organism /////////////////////////////////////////////////////////////////////////// /// // grids of objects, traditionally clones gridded for filter hybridisation ?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 A1_labelling Location ?Text View ?View Row Int #Grid_row Virtual_row Int UNIQUE ?Grid XREF In_grid REPEAT In_grid ?Grid ?Grid_row UNIQUE Clone UNIQUE ?Clone XREF Gridded REPEAT Mixed #Mixed_grid_row ?Mixed_grid_row UNIQUE Clone UNIQUE ?Clone XREF Gridded #Mixed_grid_row ?Pool Contains Clone ?Clone XREF In_pool Subpool ?Pool XREF In_pool // etc. Contains is tag2 In_pool ?Pool XREF Subpool /////////////////////////////////////////////////////////////////////////////// // sequence stuff ?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 Remark ?Text Title ?Text DB_info Database ?Database Text Text // ID Accession_number DB_remark ?Text DB_text ?LongText Substrate UNIQUE DNA Peptide Homol DNA_homol ?Sequence XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int Pep_homol ?Protein XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int Motif_homol ?Motif XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int Organism ?Organism ?Protein Title UNIQUE ?Text Other_name ?Text // for repeats Peptide UNIQUE ?Peptide UNIQUE Int // Length DB_info Database ?Database Text Text // ID Accession_number DB_remark ?Text // Swissprot CC entries Keyword ?Keyword // Swissprot DB_searched ?Database Int // Int = version - should this be here? Origin From_Database ?Database UNIQUE Int // release number Date DateType Text // Text for comments on operation 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 ?Paper XREF Protein Expr_pattern ?Expr_pattern 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 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 Motif_homol ?Motif XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int Feature ?Method Int Int UNIQUE Float // display according to method // double-click shows the method Organism ?Organism ?Sequence DNA UNIQUE ?DNA UNIQUE Int // Int is the length // 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 XREF Subsequence Source_Exons Int UNIQUE Int // start at 1 Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int Overlap_right UNIQUE ?Sequence XREF Overlap_left UNIQUE Int // 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 Clone_right_end ?Clone XREF Clone_right_end UNIQUE Int DB_info Database ?Database Text Text // ID Accession_number DB_remark ?Text // EMBL/Genbank Keyword ?Keyword // EMBL/Genbank DB_annotation ?Database UNIQUE ?LongText Origin From_Database UNIQUE ?Database UNIQUE Int // release number From_Author ?Author XREF Sequence From_Laboratory ?Laboratory Production_group Text Finishing_group Text Contact ?Contact Entry_date DateType Text // Text for comments on operation Modification_date DateType Date_directory UNIQUE Int // date of this version for cosmids Map ?Map XREF Sequence #Map_position // use in particular for Genomic_canonical EC_number ?Text Visible Title UNIQUE ?Text Other_name ?Text // for repeats Matching_Genomic ?Sequence XREF Matching_cDNA Matching_cDNA ?Sequence XREF Matching_Genomic Gene_product ?Text Corresponding_protein UNIQUE ?Protein XREF Corresponding_DNA Clone ?Clone XREF Sequence Locus ?Locus XREF Sequence Enzyme ?Enzyme XREF DNA Related_DNA ?Sequence XREF Related_DNA Related_protein ?Protein XREF Related_DNA Remark ?Text Confidential_remark ?Text Brief_identification UNIQUE ?Text Reference ?Paper XREF Sequence Expression_construct ?Clone // archaic Expr_pattern ?Expr_pattern XREF Sequence Antigen ?Antigen XREF Sequence Organism ?Organism XREF Sequence Strain ?Strain XREF Sequence // tag2 system: names of all objects following next tag are shown in the // general annotation display column as "tag:objname" Properties Pseudogene Text // explanation Transposon Text // transposon type Genomic_canonical cDNA cDNA_EST RNA // if set then use U in place of T Coding CDS UNIQUE Int UNIQUE Int CDS_predicted_by ?Method Float // score of method Precursor End_not_found Start_not_found Transcript UNIQUE mRNA UNIQUE Processed_mRNA Unprocessed_mRNA tRNA UNIQUE Text rRNA UNIQUE Text snRNA UNIQUE Text scRNA UNIQUE Text misc_RNA UNIQUE Text 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. Splices Confirmed_intron Int Int #Splice_confirmation Predicted_5 ?Method Float Int Int // (x, x+1) or (x, x-1) Predicted_3 ?Method Float Int Int // (x, x+1) or (x, x-1) Oligo ?Oligo XREF In_sequence Int UNIQUE Int // for human mapping mostly Assembly_tags Text Int Int Text // type, start, stop, comment Allele ?Allele 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 LTR Int Int Text #EMBL_info terminator Int Int Text #EMBL_info intron Int Int Text #EMBL_info exon Int Int Text #EMBL_info // 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 #Feature_info // Method determines column and display style // Ints are start, end of feature // 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) ?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. ?Feature_info EMBL_dump UNIQUE EMBL_dump_YES EMBL_dump_NO // overrides for embl dump based on method ?Splice_confirmation UNIQUE cDNA Homology ?Oligo Sequence UNIQUE Text // verbatim sequence - useful In_sequence ?Sequence XREF Oligo STS UNIQUE ?STS ?STS Oligo1 UNIQUE ?Oligo Oligo2 UNIQUE ?Oligo Map ?Map #Map_position Grid_data ?Grid_data ?Expr_pattern Experiment Laboratory ?Laboratory Author ?Author Date UNIQUE DateType Strain UNIQUE ?Strain Reference ?Paper XREF Expr_pattern Expression_of Sequence ?Sequence XREF Expr_pattern Clone ?Clone XREF Expr_pattern Locus ?Locus XREF Expr_pattern Protein ?Protein XREF Expr_pattern Expressed_in Cell ?Cell XREF Expr_pattern Cell_group ?Cell_group XREF Expr_pattern Life_stage ?Life_stage XREF Expr_pattern Type Reporter_gene ?Text In_situ ?Text Antibody ?Antibody XREF Expr_pattern Pattern ?Text Remark ?Text Organism ?Organism ?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_bounds UNIQUE Float UNIQUE Float // limits for squashing Percent // '%' in text, + default bounds 25, 100 Bumpable Width UNIQUE Float Symbol UNIQUE Text // first char only is used Right_priority UNIQUE Float // the greater the more right Blastn // can calculate percent from score if blastn Blixem Blixem_X Blixem_N 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 // very ambitious - 1st Text is an sprintf format, remaining ones are // names of tags. If "Score" or "Note" get from these fields of Feature. // otherwise bsPushObj() after note, and bsGetData(tag). /////////////////////////////////////////////////////////////////////////////// // bibliographic stuff ?Lab_location Building Text Room_number Text Biological Freezer Text LiquidN2 Text Minus70 Text Digital Computer Text Directory Text Filename Text Remark ?Text ?Laboratory Address Mail Text Phone Text E_mail Text Fax Text CGC Representative UNIQUE ?Author XREF Laboratory Strain_designation Text Allele_designation Text Gene_classes ?Gene_class XREF Designating_laboratory Staff ?Contact XREF Member_of_lab ?Contact Position Text Publishes_as ?Author XREF Full_name Member_of_lab ?Laboratory XREF Staff Old_lab ?Laboratory Address Mail Text Institution Text Address1 Text Address2 Text Address3 Text Address4 Text Address5 Text City Text State Text Region Text PostalCode Text Country Text Phone Text E_mail Text Fax Text Telex Text Profession Text Research_interest ?Text Keyword ?Keyword Associate ?Contact XREF Associate Last_update Text Obtained_from ?database Hint ?LongText ?Journal Paper ?Paper XREF Journal ?Paper Reference Title UNIQUE ?Text Original_title UNIQUE ?Text Journal UNIQUE ?Journal XREF Paper Publisher UNIQUE Text Source UNIQUE Text Page UNIQUE Text UNIQUE Text Volume UNIQUE Text Text Number UNIQUE Int Text Year UNIQUE Int In_book #Paper Contained_in ?Paper XREF Contains // old form Medline_ID UNIQUE Int Agricola_ID UNIQUE Int Author ?Author XREF Paper Adviser ?Author XREF Paper Editor ?Author XREF Paper Affiliation Text // Authors' affiliation if available Institution Text Language Text Abstract ?LongText Type UNIQUE Text Contains ?Paper XREF Contained_in Refers_to Allele ?Allele XREF Reference Clone ?Clone XREF Reference Gene_class ?Gene_class XREF Reference Locus ?Locus XREF Reference Map ?Map XREF Reference Protein ?Protein XREF Reference Expr_pattern ?Expr_pattern XREF Reference Sequence ?Sequence XREF Reference Strain ?Strain XREF Reference Antibody ?Antibody XREF Reference Antigen ?Antigen XREF Reference Keyword ?Keyword ?Author Full_name ?Contact XREF Publishes_as Address Mail Text E_mail Text Phone Text Fax Text Paper ?Paper Laboratory ?Laboratory XREF Representative Sequence ?Sequence XREF From_Author ?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 /////////////////////////////////////////////////////////////////////////////// // Map data -- all the following fields are used by the genetic map data // calculation package ?2_point_data Genotype UNIQUE Text Results UNIQUE Text Experiment Mapper ?Author Laboratory ?Laboratory Date UNIQUE DateType Temperature UNIQUE Text Point_1 UNIQUE Locus_1 UNIQUE ?Locus XREF 2_point UNIQUE ?Allele XREF In_2_point Allele_1 UNIQUE ?Allele XREF 2_point Point_2 UNIQUE Locus_2 UNIQUE ?Locus XREF 2_point UNIQUE ?Allele XREF In_2_point Allele_2 UNIQUE ?Allele XREF 2_point // 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 Recs_all UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int // X Y ALL One_let 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 Back_one UNIQUE Int UNIQUE Int // WT X Sex_full UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int // WT X Y XY Sex_one UNIQUE Int UNIQUE Int // WT X Sex_cis UNIQUE Int UNIQUE Int // X ALL Dom_one UNIQUE Int UNIQUE Int // WT nonWT Dom_selected UNIQUE Int UNIQUE Int // WT X Dom_semi UNIQUE Int UNIQUE Int // XD ALL Dom_let UNIQUE Int UNIQUE Int // WT 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 Max UNIQUE Float Error UNIQUE Float Linkage UNIQUE Text // some of these are used for drawing in the absence of Calculation data Remark ?Text // code uses Point_1, Point_2, Calculation and all its subtags, all the Calc subtags, // and most of the Simple_distance subtags. ?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 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 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 ?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 B UNIQUE Locus_B UNIQUE ?Locus UNIQUE ?Allele XREF In_multi_point Allele_B UNIQUE ?Allele 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 ?Multi_counts UNIQUE Locus UNIQUE ?Locus XREF Multi_point UNIQUE Int #Multi_counts Allele UNIQUE ?Allele XREF Multi_point UNIQUE Int #Multi_counts ?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 ///////////////////////////////////////////////////////////// // // Locus ?Locus Name Other_name ?Text Description ?Text Entry_date Datetype Modification_date Datetype Type Gene Reference_Allele ?Allele Text Phenotype ?Text Complementation_data Text Polymorphism RFLP Text Transposon_insertion Text Detection_method Text PCR_product Primer1 Text Primer2 Text Length Int // bp React_cond Text Clone_as_locus UNIQUE ?Clone XREF Clone_as_locus Molecular_information Sequence ?Sequence XREF Locus Product ?Text Enzyme ?Enzyme XREF Locus Remark ?Text Display_map ?Map // Only display these map(s) when drawing Map ?Map XREF Locus #Map_position Positive Positive_clone ?Clone XREF Positive_locus ?Author Negative Negative_clone ?Clone XREF Negative_locus ?Author Mapping_data Well_ordered // "on the line" 2_point ?2_point_data Multi_point ?Multi_pt_data Pos_neg_data ?Pos_neg_data Allele ?Allele XREF Gene Strain ?Strain XREF Gene Laboratory ?Laboratory Status ?Text Provisional ?Text Reference ?Paper XREF Locus Expr_pattern ?Expr_pattern XREF Locus Antigen ?Antigen XREF Locus Subsequence Text Int Int Organism ?Organism XREF Locus ////////////////////////////////////////////////////////////////////////////// // General microbiological classes ?Organism Common_name Text Contig ?Contig Strain ?Strain XREF Organism Locus ?Locus XREF Organism Map ?Map XREF Organism Sequence ?Sequence XREF Organism ?Allele Name Other_name ?Text Qualifier Text // sd, sm, ts etc. Not systematic just now Source UNIQUE Gene ?Locus XREF Allele Gene_class ?Gene_class XREF Allele Sequence ?Sequence XREF Allele Reference_Allele Isolation Author Text // Isolator - should be ?Author Date DateType Mutagen UNIQUE Text UNIQUE Text 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 Strain ?Strain XREF Allele Genetics Map ?Map #Map_position Mapping_data 2_point ?2_point_data Multi_point ?Multi_pt_data Pos_neg_data ?Pos_neg_data // above three are for mapping on its own behalf 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 Description Phenotype ?Text Recessive Dominant Semi_dominant Weak Temperature_sensitive Heat_sensitive Cold_sensitive Amber Maternal Strictly_Maternal With_Maternal_Effect Paternal Muscle Remark ?Text Reference ?Paper XREF Allele // Mary Organism ?Organism ?Gene_class Phenotype ?Text Designating_laboratory UNIQUE ?Laboratory XREF Gene_classes Allele ?Allele XREF Gene_class Reference ?Paper XREF Gene_class Organism ?Organism ?Strain Genotype Text Contains Gene ?Locus XREF Strain Allele ?Allele XREF Strain Antigen ?Antigen XREF Strain Properties Males Text Reference_strain Text Outcrossed Mutagen Text CGC_received DateType Location ?Laboratory #Lab_Location Made_by Text Remark ?Text Reference ?Paper XREF Strain Sequence ?Sequence XREF Strain Organism ?Organism XREF Strain ?Antibody Code UNIQUE ?Text //from CDC bank Other_name ?Antibody XREF Other_name Antigen ?Antigen XREF Antibody Type Monoclonal Polyclonal Serum Tcell_clone Other_type ?Text Reactivity Recognized ?Strain // probably should be XREFed Not_recognized ?Strain Expr_pattern ?Expr_pattern XREF Antibody Origin Mouse Human Other_origin ?Text Location ?Contact #Lab_Location Contact ?Contact // probably should be XREFed Source ?Database Reference ?Paper XREF Antibody Remark ?Text Organism ?Organism ?Antigen Code UNIQUE ?Text //from the IMMLEP/IMMTUB paper Other_name ?Antigen XREF Other_name Strain ?Strain XREF Antigen Size Float //subunit size in kDa on SDS gel -- maybe should have a Text describing the the conditions Antibody ?Antibody XREF Antigen Molecular_information Clone ?Clone XREF Antigen Locus ?Locus XREF Antigen //@"Sequence" would remove the need for the next line Sequence ?Sequence XREF Antigen Epitope Text Related_antigen ?Antigen XREF Related_antigen Reference ?Paper XREF Antigen Location ?Contact #Lab_Location Remark ?Text Function ?Text Immunology ?Text Organism ?Organism /////////////////////////////////////////////////////////////////////////////////// // // // 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 Text 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 Text Activator ?Metabolite XREF Activates #RegulatorInfo Inhibitor ?Metabolite XREF Inhibits #RegulatorInfo Remark ?Text ?RegulatorInfo Type UNIQUE Active_site Ki Text //for inhibitor Remark ?Text Reference ?Paper ?ReactantInfo Major_Role Minor_Role Cofactor N Int // etc. Km Text Vmax Text Substrate_specificity ?Text Remark ?Text Reference ?Paper ?Enzyme Other_name ?Text EC_Number ?Text // probably should be under reaction Corresponds_to Locus ?Locus XREF Enzyme DNA ?Sequence XREF Enzyme Protein ?Protein XREF Enzyme Catalyzes ?Pathway Remark ?Text Reference ?Paper ?Metabolite Consumed_by ?Pathway Produced_by ?Pathway Activates ?Pathway Inhibits ?Pathway XREF Inhibitor 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 ?Cell_group Fate ?Text Remark ?Text Contains Cell ?Cell XREF Cell_group Sub_group ?Cell_group XREF Contained_in Contained_in ?Cell_group XREF Sub_group Type UNIQUE Tissue Organ Region Expr_pattern ?Expr_pattern XREF Cell_group Life_stage ?Life_stage XREF Cell_group Organism ?Organism ?Life_stage Contains Cell ?Cell XREF Life_stage Cell_group ?Cell_group XREF Life_stage Expr_pattern ?Expr_pattern XREF Life_stage Remark ?Text Organism ?Organism ?Cell Fate ?Text Embryo_division_time Text Remark ?Text Lineage Parent UNIQUE ?Cell XREF Daughter Daughter ?Cell XREF Parent Lineage_name Text Equivalence_fate ?Cell XREF Equivalence_origin Equivalence_origin ?Cell XREF Equivalence_fate Group In_group ?Cell XREF Group_member // archaic Group_member ?Cell XREF In_group // archaic Cell_group ?Cell_group XREF Cell Life_stage ?Life_stage XREF Cell Data Expr_pattern ?Expr_pattern XREF Cell Organism ?Organism