// %W% %G% // 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. // // Basic Map classes // ?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 // Include all objects in these maps (must be mapped and have extents) Includes ?Map Contains Locus ?Locus XREF Map Rearrangement ?Rearrangement 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 EMBL_chromosome UNIQUE Text ?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 and Columns // ?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 ?Column UNIQUE Scale Scale_unit UNIQUE Float // minimum increment Cursor Cursor_on Cursor_unit UNIQUE Float Scroller 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 // To be made redundant. 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 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 Int 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 ?View_tags Colour #Colour Surround_colour #Colour // colour when surround Tag Text // could be many tags ?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 ?Allele Name Other_name ?Text Qualifier Text // sd, sm, ts etc. Not systematic just now Rearrangement ?Rearrangement XREF Allele 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 Ochre Opal Missense Maternal Strictly_Maternal With_Maternal_Effect Paternal Remark ?Text Reference ?Paper XREF Allele // Mary Rescued_by_Transgene ?Transgene XREF Rescue ?Gene_Class Phenotype ?Text Designating_laboratory UNIQUE ?Laboratory XREF Gene_classes Allele ?Allele XREF Gene_class Loci ?Locus XREF Gene_Class Main_name ?Gene_Class XREF Other_name Other_name ?Gene_Class XREF Main_name ?Locus Name Other_name ?Text Gene_Class ?Gene_Class XREF Loci Old_name ?Locus XREF New_name New_name ?Locus XREF Old_name Description ?Text Type Gene Reference_Allele ?Allele Text Phenotype ?Text Complementation_data Text Controlled_phenotype ?Phenotype XREF Locus // added for Lincoln RNAi [001213 dl] Polymorphism RFLP Text Transposon_insertion Text Detection_method Text PCR_product Primers Text Length Int // bp Molecular_information Genomic_Sequence ?Sequence XREF Locus_genomic_seq // Split genomic and other XREFs Other_sequence ?Sequence XREF Locus_other_seq // dl 001128 Product ?Text Enzyme ?Enzyme XREF Locus Remark ?Text Map ?Map XREF Locus #Map_position Hide_under ?Locus XREF Representative_for Representative_for ?Locus XREF Hide_under Positive Inside_rearr ?Rearrangement XREF Locus_inside ?Author Positive_clone ?Clone XREF Positive_locus ?Author Negative Outside_rearr ?Rearrangement XREF Locus_outside ?Author 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 Reference ?Paper XREF Locus Expr_pattern ?Expr_pattern XREF Locus Contained_in ?Locus XREF Contains //sdm put in to accomodate HISTONE geneclusters Contains ?Locus XREF Contained_in Drives_Transgene ?Transgene XREF Driven_by_Locus Transgene_product ?Transgene XREF Worm_gene Rescued_by_Transgene ?Transgene XREF Rescue ?Balancer From_left_end To_right_end Locus ?Locus ?Rearrangement Name Other_name ?Text Allele ?Allele XREF Rearrangement Type Deletion Duplication Free_dup Translocation Compound Text Phenotype ?Text Balances ?Map #Balancer // possibility to refer to other Intervals to describe a complex rearrangement // for the worm this is not too necessary, but important for fly and mouse // or perhaps there should be another class Complex_Rear that refers to // several intervals. Reference_strain ?Strain Remark ?Text Isolation Author Text // should be ?Author Date DateType Mutagen UNIQUE Text UNIQUE Text // Text is dose Map ?Map XREF Rearrangement #Map_position Positive Locus_inside ?Locus XREF Inside_rearr ?Author Clone_inside ?Clone XREF Inside_rearr ?Author Rearr_inside ?Rearrangement Negative Locus_outside ?Locus XREF Outside_rearr ?Author Clone_outside ?Clone XREF Outside_rearr ?Author Rearr_outside ?Rearrangement Mapping_data Pos_neg_data ?Pos_neg_data 2_point ?2_point_data Multi_point ?Multi_pt_data Display Hide_under UNIQUE ?Rearrangement XREF Hides Hides ?Rearrangement // no XREF on purpose Location ?Laboratory #Lab_Location Strain ?Strain XREF Rearrangement Reference ?Paper XREF Rearrangement ?Strain Genotype Text Contains Gene ?Locus XREF Strain Allele ?Allele XREF Strain Rearrangement ?Rearrangement XREF Strain Clone ?Clone XREF In_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 Transgene ?Transgene XREF Strain ?Lab_Location Freezer Text LiquidN2 Text Minus70 Text Remark ?Text // //worm physical map classes // ?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_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 In_strain ?Strain XREF Clone 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 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 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 ?Paper XREF Clone cDNA_group Contains ?Clone XREF Contains Text Contained_in ?Clone XREF Contained_in Best_match UNIQUE ?Text Expr_pattern ?Expr_pattern XREF Clone Sequence_status Shotgun UNIQUE DateType Finished UNIQUE DateType Accession_number UNIQUE Text Type Cosmid // 000824 Lincoln's additions to segregate clones YAC cDNA Plasmid Transgene ?Transgene XREF Clone Derived_from ?Clone #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 ?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 ?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 ?Contig Map ?Map XREF Contig #Map_position pMap UNIQUE Int UNIQUE Int // extremities in pMap units Clone ?Clone XREF pMap ?Species Common_name ?Text Phylogeny Kingdom UNIQUE Text Phylum UNIQUE Text Subphylum UNIQUE Text Class UNIQUE Text Order UNIQUE Text Family UNIQUE Text Genus UNIQUE Text Protein ?Protein XREF Species // // Map data classes // ?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 Rearrangement_1 UNIQUE ?Rearrangement XREF 2_point Transgene_1 UNIQUE ?Transgene 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 Rearrangement_2 UNIQUE ?Rearrangement XREF 2_point Transgene_2 UNIQUE ?Transgene 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 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 ?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 Transgene_A UNIQUE ?Transgene XREF Multi_point B UNIQUE Locus_B UNIQUE ?Locus UNIQUE ?Allele XREF In_multi_point Allele_B UNIQUE ?Allele Rearrangement_B UNIQUE ?Rearrangement Transgene_B UNIQUE ?Transgene XREF Multi_point 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 Rearrangement UNIQUE ?Rearrangement 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 Clone UNIQUE ?Clone XREF Grid_data // tag 2 for probe - REQUIRED Default_negative // if set then all non-explicit elements on Grid score -ve // // Laboratory/Bibliography // ?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 ?Author XREF Laboratory ?Author Full_name Text EMBL_name Text Also_known_as Text Laboratory UNIQUE ?Laboratory XREF Staff Old_lab ?Laboratory Address Mail Text E_mail Text Phone Text Fax Text Paper ?Paper Sequence ?Sequence XREF From_author Keyword ?Keyword ?Journal Paper ?Paper XREF Journal ?Paper Reference Title UNIQUE ?Text Journal UNIQUE ?Journal XREF Paper Publisher UNIQUE Text Editor ?Text //used for books put in as whole objects Page UNIQUE Text UNIQUE Text Volume UNIQUE Text Text Year UNIQUE Int In_book #Paper Contained_in ?Paper XREF Contains // old form Medline_acc UNIQUE Int Author ?Author XREF Paper #Affiliation Affiliation Text // Authors' affiliation if available Brief_citation UNIQUE Text Abstract ?LongText Type UNIQUE Text //meaning review, article, chapter, monograph, news, book, meeting_abstract Contains ?Paper XREF Contained_in Refers_to Locus ?Locus XREF Reference Allele ?Allele XREF Reference Rearrangement ?Rearrangement XREF Reference Sequence ?Sequence XREF Reference Strain ?Strain XREF Reference Clone ?Clone XREF Reference Protein ?Protein XREF Reference Expr_pattern ?Expr_pattern XREF Reference Cell ?Cell XREF Reference Cell_group ?Cell_group XREF Reference Life_stage ?Life_stage XREF Reference RNAi ?RNAi XREF Reference // added for Lincoln RNAi [001213 dl] Transgene ?Transgene XREF Reference Keyword ?Keyword #Affiliation Affiliation_address UNIQUE Text //Affiliation Text // Authors' affiliation if available //usually comes with wbg abstracts and worm meeting abstracts //new ones used the hash structure, some old ones probably still use this // // Cell models // ?Cell Other_name Text 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 Sex_dimorphism Herm_origin ?Cell XREF Herm_fate // Added according to Sylvia 5/06/2000 Herm_fate ?Cell XREF Herm_origin Male_origin ?Cell XREF Male_fate Male_fate ?Cell XREF Male_origin Cell_group ?Cell_group XREF Cell Life_stage ?Life_stage XREF Cell Tree_Node ?TreeNode XREF Cell Reference ?Paper XREF Cell Data Expr_pattern ?Expr_pattern XREF Cell Reconstruction ?Reconstruction XREF Cell #ReconCellInfo Neurodata ?Cell #Neurodata Atlas ?Atlas XREF Cell Link_diagram Text // MODEL FOR WORMBASE ATLAS (VIRTUAL WORM) // 000824 added for Lincoln ?Atlas Cell ?Cell XREF Atlas Name UNIQUE Text Location UNIQUE Text Title UNIQUE Text Comments UNIQUE Text Banner UNIQUE Text Up_arrow UNIQUE Text Down_arrow UNIQUE Text Sx_arrow UNIQUE Text Dx_arrow UNIQUE Text X_position UNIQUE Text Y_position UNIQUE Text ?Neurodata Send Text UNIQUE Int // series count Send_joint Text UNIQUE Int // ditto for the rest Receive Text UNIQUE Int Receive_joint Text UNIQUE Int Gap_junction Text UNIQUE Int Contact Text UNIQUE Int ?Reconstruction Cell ?Cell Author ?Author Date UNIQUE DateType Remark ?Text Description ?LongText ?ReconCellInfo Birth UNIQUE Float Timepoint Float #Timepoint ?Timepoint XYZ UNIQUE Float UNIQUE Float UNIQUE Float // // Sequence models // ?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. SMap S_Parent Canonical_parent UNIQUE ?Sequence XREF Genomic_non_canonical S_Child Homol_data ?Homol_data XREF Sequence UNIQUE Int UNIQUE Int #SMap_info Feature_data ?Feature_data XREF Sequence UNIQUE Int UNIQUE Int #SMap_info Genomic_non_canonical ?Sequence XREF Canonical_parent UNIQUE Int UNIQUE Int #SMap_info RNAi ?RNAi XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // added for Lincoln RNAi [001213 dl] 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 Gap_right UNIQUE Int Text // 000909 dl added to track gap sizes Clone_left_end ?Clone XREF Clone_left_end UNIQUE Int Clone_right_end ?Clone XREF Clone_right_end UNIQUE Int Flipped DB_info Database ?Database Text ?Accession_number XREF Sequence UNIQUE Int // ID Accession_number & sequence version [dl 2000-07-27] AC_number Text Secondary_accession ?Accession_number XREF Sequence NI_number UNIQUE Text Protein_id ?Sequence UNIQUE Text UNIQUE Int // modified to deal with multiple protein_ids [dl 1999-12-22] DB_remark ?Text // EMBL/Genbank Keyword ?Keyword // EMBL/Genbank DB_annotation ?Database UNIQUE ?LongText EMBL_dump_info #EMBL_dump_info Annotation SwissProt_DE UNIQUE Text EC_number ?Url Pfam UNIQUE Text Origin From_Database UNIQUE ?Database UNIQUE Int // release number From_Author ?Author XREF Sequence From_Laboratory ?Laboratory Production_group Text Finishing_group Text Date DateType Text // Text for comments on operation Date_directory UNIQUE Text // date of this version for cosmids, changed sdm 000731 to text Species ?Species Map ?Map XREF Sequence #Map_position // use in particular for Genomic_canonical Interpolated_gMap ?Map UNIQUE Float Visible Title UNIQUE ?Text Other_name ?Text // for repeats Matching_Genomic ?Sequence XREF Matching_cDNA Matching_cDNA ?Sequence XREF Matching_Genomic Spliced_cDNA ?Sequence XREF Component_of Int UNIQUE Int UNIQUE Int UNIQUE Int Component_of ?Sequence XREF Spliced_cDNA Corresponding_protein UNIQUE ?Protein XREF Corresponding_DNA Clone ?Clone XREF Sequence Locus_genomic_seq ?Locus XREF Genomic_sequence // Split genomic and other Locus XREFs Locus_other_seq ?Locus XREF Other_sequence // dl 001128 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 RNAi_result ?RNAi XREF Predicted_gene // added for Lincoln RNAi [001213 dl] // 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 Briggsae_canonical Wormpep 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 Annotated 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. 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? Splices Confirmed_intron Int Int #Splice_confirmation Predicted_5 ?Method Int Int UNIQUE Float // (x, x+1) or (x, x-1) Predicted_3 ?Method Int Int UNIQUE Float // (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 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 // EMBL_features are for legitimate EMBL feature table entries only Analysis_details Analysis_history ?Method DateType Parent_model ?Sequence XREF Child_model DateType // parent/child relationship for history models [dl 000727] Child_model ?Sequence XREF Parent_model DateType // Homol DNA_homol ?Sequence XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Pep_homol ?Protein XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Motif_homol ?Motif XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Homol_homol ?Homol_data XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info // 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 // 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 Method UNIQUE ?Method Tree_Node ?TreeNode XREF Sequence // Phylogenetic trees Drives_Transgene ?Transgene XREF Driven_by_Sequence Transgene_product ?Transgene XREF Worm_sequence #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. #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 ?Paper CC_line Text source_organism UNIQUE Text gene_from_name #Splice_confirmation cDNA EST Homology UTR // Homol and Feature info #Homol_info Align Int UNIQUE Int UNIQUE Int // not needed if full alignment is ungapped // one row per ungapped alignment section // first int is position in query, second in target // third int is length - only necessary when gaps in both sequences align EMBL_dump UNIQUE EMBL_dump_YES EMBL_dump_NO // overrides for embl dump based on method EMBL_qualifier Text // additional to those in the method, includes '/' #Feature_info EMBL_dump UNIQUE EMBL_dump_YES EMBL_dump_NO // overrides for embl dump based on method EMBL_qualifier Text // additional to those in the method, includes '/' // Repeat_info - do we need this? #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 // SMap stuff #SMap_info Method ?Method // methods used in child (optional) Content Homol_only // useful for -nohomol gff option Feature_only // useful for -nofeature gff option Mapping Align Int UNIQUE Int UNIQUE Int // not needed if full alignment is ungapped // one row per ungapped alignment section // first int is position in parent, second in child // third int is length - only necessary when gaps in both sequences align Mismatch Int // Int give position(s) in parent of mismatches (technically in which they will // not create an error if they occur // if just the tag is set without values, then accept mismatches anywhere Display Max_mag UNIQUE Float // don't show if more bases per line Min_mag UNIQUE Float // don't show if fewer bases per line ?Homol_data SMap S_Parent Sequence ?Sequence Homol DNA_homol ?Sequence XREF Homol_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Pep_homol ?Protein XREF Homol_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Motif_homol ?Motif XREF Homol_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info // keep the standard model structure, so same code works ?Feature_data SMap S_Parent Sequence ?Sequence Feature ?Method Int Int UNIQUE Float UNIQUE Text #Feature_info Method ?Method // added for Lincoln RNAi [001213 dl] // keep the same model as in Sequence, so same code works ?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 // Protein class ?Protein Title UNIQUE ?Text Other_name ?Text // for repeats Peptide UNIQUE ?Peptide UNIQUE Int UNIQUE Int // Length + checksum Display View ?View Default_view UNIQUE ?View DB_info Database ?Database Text ?Accession_number XREF Protein // 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 Species ?Species //XREF Protein in geneace 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 Analysis_details Analysis_history ?Method DateType 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 Homol_homol ?Homol_data 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 Tree_Node ?TreeNode XREF Protein // Phylogenetic trees ?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 ?Accession_number XREF Motif // ID Accession_number DB_remark ?Text DB_text ?LongText Template ?Url //old way of making and clling URLs Web_location ?WWW_server Substrate UNIQUE DNA Peptide 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 Homol_homol ?Homol_data XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info ?Accession_number Entry Sequence ?Sequence Protein ?Protein Motif ?Motif Web_location ?Database // use for WWW display // The following is the model supported by wwwDisplay() in w4/display.c // UNIQUE URL UNIQUE Text // Web_location UNIQUE ? // class should have the Build_URL submodel // Build_URL Reference_tag Text Text // tag class(optional) // // use Text following tag if exists // // restricted to class if specified // Use_name Text // class(optional) // // applies only if no Reference_tag found // // restrict to class if specified // // one of Reference_tag or Use_name must succeed // Rewrite Text UNIQUE Text Text UNIQUE Text // // prefix_to_add postfix_to_add prefix_to_remove postfix_to_remove // // once (optional) prefix and postfix are removed, escape necessary chars // // then add specified prefix and postfix ?Database Name ?Text // Full name Contents ?Text // Description of material included WWW Reference_tag Text Text // tag class(optional) Use_name Text // class(optional) Rewrite Text UNIQUE Text Text UNIQUE Text // prefix_to_add postfix_to_add prefix_to_remove postfix_to_remove // Method ?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_info #EMBL_dump_info EMBL_dump EMBL_feature UNIQUE Text // require this EMBL_threshold UNIQUE Float // apply to score unless overridden EMBL_qualifier Text UNIQUE Text // 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 '/'. GFF GFF_source UNIQUE Text GFF_feature UNIQUE Text // // 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 ?RegulatorInfo Type UNIQUE Active_site Ki Text //for inhibitor Remark ?Text Reference ?Paper ?ReactantInfo Major_Role Minor_Role Cofactor N Int // etc. Km Text #Reference Vmax Text #Reference Substrate_specificity ?Text #Reference Remark ?Text Reference ?Paper ?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 ?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 ?Reference Reference ?Paper Remark ?Text Species ?Species Description ?Text //For trait information //NEW - one new tag added by Paul Sternberg and tag order reversed by SDM ?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 Localisation ?Text Subcellular_localization ?Text Type Reporter_gene ?Text In_situ ?Text Antibody ?Text Pattern ?Text Picture ?Picture XREF Expr_pattern Remark ?Text Experiment Laboratory ?Laboratory Author ?Author Date UNIQUE DateType Strain UNIQUE ?Strain Reference ?Paper XREF Expr_pattern Transgene ?Transgene XREF Expr_pattern ?Picture Description ?Text Pick_me_to_call Text Text Expr_pattern ?Expr_pattern XREF Picture ?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 Reference ?Paper XREF Cell_group Tree_Node ?TreeNode XREF Cell_group ?Life_stage Contains Cell ?Cell XREF Life_stage Cell_group ?Cell_group XREF Life_stage Sub_stage ?Life_stage XREF Contained_in Contained_in ?Life_stage XREF Contains Preceded_by ?Life_stage XREF Followed_by Followed_by ?Life_stage XREF Preceded_by Expr_pattern ?Expr_pattern XREF Life_stage Remark ?Text Reference ?Paper XREF Life_stage // // Alignment models // ?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 #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 #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 #Match_seg UNIQUE Int UNIQUE Int UNIQUE Int UNIQUE Int #Match_seg // Start, End of Aligment; Start, End of Subject // URL and WWW ?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 to make url Prepend UNIQUE Text // then add this to the beginning Append UNIQUE Text // then add this to the end Web_location UNIQUE ?WWW_server ?WWW_server Url UNIQUE Text // Simple, text of URL Use_name Text // (optional) Classname Rewrite Text UNIQUE Text Text UNIQUE Text Reference_tag UNIQUE Text // look for this tag in the reffing object for url /////////////////////////////////////////////////////////////////////////////// // // The Tree Classes from Richard Bruskiewich with a few fields commented out // species class not put in because we already have a different one in the worm database ?Tree Description UNIQUE ?Text // Used as graph display title if present Type UNIQUE Taxonomy // Controls semantics of tree display DNA Protein Cell_Lineage Root UNIQUE ?TreeNode Display No_Header // Suppresses display "header" Descriptive_Labels // Show descriptive labels Colour // Taxon_colouring if present Normalization UNIQUE Float // Normalization factor for display (defaults to 1.0) Bootstrap_Factor UNIQUE Float // Normalization factor for bootstrap values (defaults to 1.0) Hide_Bootstraps Alignment UNIQUE Top // How the dendrogram is to be drawn Middle Bottom Unrooted // Unrooted "star" tree Embedded_tree ?Tree ?TreeNode Label UNIQUE ?Text // Tree vertex label, e.g. sequence name or taxon Id UNIQUE Int // Node numbering... Description ?Text Type UNIQUE Root // Root ?TreeNode should be so designated! Interior Leaf Distance UNIQUE Float // "Evolutionary distance" or branch length Bootstrap UNIQUE Float // Node subtree "bootstrap" values Tree UNIQUE ?Tree Parent UNIQUE ?TreeNode XREF Child Child ?TreeNode XREF Parent Display Hide // Hide the subtree (children) of this node Colour UNIQUE #Colour // Fixes the colour of the subtree; // overridden by child node settings Hide_Bootstraps // Hide all bootstraps in subtree... Show_Bootstrap // ... except those with the "Show_Bootstrap" tag set Contains Sequence UNIQUE ?Sequence XREF Tree_Node Protein UNIQUE ?Protein XREF Tree_Node Cell UNIQUE ?Cell XREF Tree_Node Cell_group UNIQUE ?Cell_group XREF Tree_Node //URL UNIQUE ?Url XREF Tree_Node Pick_me_to_call UNIQUE Text Text Embedded_Tree ?Tree // Positive Has_Gene_Function ?Gene_Function XREF PosTreeNode // Family_Member ?Gene_Family XREF PosTreeNode // Negative Does_NOT_Have_Gene_Function ?Gene_Function XREF NegTreeNode // NOT_Family_Member ?Gene_Family XREF NegTreeNode // Map ?Map XREF Tree_Node #Map_Position // Leaf node ordinate // Jade model for Lincoln/Jean added by rd 000307 ?Jade Display Text Text Text UNIQUE Text StandAloneDisplay Text //transgene from Wen Chen 12/00 #Transgene Summary UNIQUE ?Text //Searchable description of the transgene Driven_by Driven_by_Sequence ?Sequence XREF Drives_Transgene Text //driving promoter Driven_by_Locus ?Locus XREF Drives_Transgene Reporter_product UNIQUE GFP LacZ Other_reporter ?Text Worm_gene ?Locus XREF Transgene_product Text Worm_sequence ?Sequence XREF Transgene_product Text Isolation Author ?Author Clone ?Clone XREF Transgene Text //injected clone conc. Fragment Text Text //injected DNA fragment conc. Injected_into_CGC_strain ?Strain Injected_into Text // for strains not available in CGC Integrated_by UNIQUE Gamma_ray X_ray Spontaneous UV Not_integrated Other_integration_method Text Location ?Laboratory #Lab_Location //Which Labs have the transgene. Strain ?Strain XREF Transgene //All strains in CGC with the transgene. Map ?Map #Map_position Mapping_data 2_point ?2_point_data Multi_point ?Multi_pt_data Phenotype ?Text //Phenotype should be described as "Unc. With other ..." Rescue ?Locus XREF Rescued_by_Transgene ?Allele XREF Rescued_by_Transgene Expr_pattern ?Expr_pattern XREF Transgene //Related Expr_pattern Remark ?Text //More comments on the transgene Reference ?Paper XREF Transgene //papers refered to the transgene. // RNAi from Lincoln Stein 001213 ?RNAi SMap S_Parent Sequence ?Sequence // canonical parent (reliable) Method ?Method Experiment Laboratory ?Laboratory Author ?Author Date UNIQUE DateType Strain UNIQUE ?Strain Inhibits Predicted_gene ?Sequence XREF RNAi_result // "gene" parent (unreliable) Reference ?Paper XREF RNAi Phenotype ?Phenotype XREF RNAi #Phenotype_info #Phenotype_info Remark ?Text // specific remarks about this instance Penetrance UNIQUE Int // estimated percent penetrance (0-100) Temperature_sensitive Int UNIQUE Int // temperature (degrees C), penetrance Quantity UNIQUE Int UNIQUE Int // for quantitative phenotypes low/high ?Phenotype Description ?Text Assay ?Phenotype_assay Remark ?Text Related_phenotypes Specialisation_of ?Phenotype XREF Generalisation_of Generalisation_of ?Phenotype XREF Specialisation_of Equivalent_to ?Phenotype XREF Equivalent_to Similar_to ?Phenotype XREF Similar_to Attribute_of RNAi ?RNAi XREF Phenotype Locus ?Locus XREF Controlled_phenotype ?Phenotype_Assay Description ?Text // end of file