/// // models.wrm - main file defining tree class structures for the WormBase database // This file is read only when starting a new database or when you select // "Read Models" or "Add Update File" from the main menus. // // Explanation about class/object count limits // ----------------------------------------------------------------------------- // Every single object specified in this file is represented in acedb by a key, // this key is an unsigned int (32 bits), the top 8 bits are the class and the // next 24 bits are the object. // In other words you can have 2^8 classes (= 256) and 2^24 objects in each of // those classes (= 16,777,216) // ----------------------------------------------------------------------------- // // ALL WormBase groups should be in sync with this set of models // // // Additional things to consider. If classes are added or new data in the ?Gene class // Then we should consider the elegans_config (and possibly others) so the data makes // it into the build! // // // Notes: // // Add a Build tag line at the end of the file when the models are fully prepared for a // WB build to start, this allows for one final commit and message. // // Tags that shouldn't be used: // ----------------------------------------------------------------------------- // "Name" this should always be implemented as Public_name or Similar // //////////////////////// // 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 ?Gene // 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 Gene ?Gene XREF Map Rearrangement ?Rearrangement XREF Map Contig ?Contig XREF Map Clone ?Clone XREF Map Sequence ?Sequence XREF Map Variation ?Variation XREF Map Map_shown ?Map XREF Map Transgene ?Transgene //sdm added to display gmaps //removed XREF ky 2011 // 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 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 ///////////////////////// CLASSICAL GENETICS /////////////////////////////// // // ?Locus class, ?Allele class, ?Gene_class class // /////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////// // // ?Gene_class class // Used for grouping genes into families // /////////////////////////////////////// ?Gene_class Evidence #Evidence Phenotype ?Text Description UNIQUE ?Text // [krb 020614] Designating_laboratory UNIQUE ?Laboratory XREF Gene_classes Former_designating_laboratory DateType UNIQUE ?Laboratory XREF Former_gene_classes //This is a one way XREF to track responsibility for a class. Variation ?Variation XREF Gene_class Genes ?Gene XREF Gene_class Old_member ?Gene_name XREF Former_member_of Other_name ?Gene_class XREF Other_name_for Other_name_for ?Gene_class XREF Other_name Remark ?Text #Evidence /////////////////////////////////////////////////////////////////////////////////// // // ?Locus class - krb Feb 2004 // slimmed down Locus class will initially just store Polymorphisms and gene clusters. // /////////////////////////////////////////////////////////////////////////////////// ?Locus Evidence #Evidence Name Other_name ?Gene_name #Evidence // unidirectional link Species UNIQUE ?Species // added by krb 15/02/02 Type Polymorphism SNP Text // Todd [171001 krb] Status Text SNP_assay ?PCR_product XREF SNP_locus ?Text RFLP Text Transposon_insertion Text Detection_method Text Map UNIQUE ?Map XREF Locus #Map_position Positive Inside_rearr ?Rearrangement XREF Locus_inside ?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 Laboratory ?Laboratory Remark ?Text #Evidence //////////////////////////////////////////////////////////////////////////////////////// // // ?Gene class - krb // //////////////////////////////////////////////////////////////////////////////////////// ?Gene Evidence #Evidence SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Gene_child Identity Version UNIQUE Int Name CGC_name UNIQUE ?Gene_name XREF CGC_name_for #Evidence Sequence_name UNIQUE ?Gene_name XREF Sequence_name_for // captures main CDS name without isoforms Molecular_name ?Gene_name XREF Molecular_name_for // for linking to full CDS names, wormpep etc. Other_name ?Gene_name XREF Other_name_for #Evidence // other unapproved CGC-style gene names Public_name UNIQUE ?Gene_name XREF Public_name_for // the one name that should be used DB_info Database ?Database ?Database_field ?Text Species UNIQUE ?Species History Version_change Int UNIQUE DateType UNIQUE ?Person #Gene_history_action Merged_into UNIQUE ?Gene XREF Acquires_merge Acquires_merge ?Gene XREF Merged_into Split_from UNIQUE ?Gene XREF Split_into Split_into ?Gene XREF Split_from Transposon_in_origin // for genes that are identified as having CDSs/Proteins that are Transposon in origin Status UNIQUE Live #Evidence Suppressed #Evidence Dead #Evidence Gene_info Biotype UNIQUE ?SO_term Gene_class UNIQUE ?Gene_class XREF Genes Laboratory ?Laboratory Cloned_by #Evidence // mt3 acreditation of person who cloned gene [060829 ar2] Reference_allele ?Variation #Evidence Allele ?Variation XREF Gene #Evidence Possibly_affected_by ?Variation XREF Possibly_affects #Evidence Legacy_information Text #Evidence Complementation_data Text Strain ?Strain XREF Gene Component_of_genotype ?Genotype XREF Gene In_cluster ?Gene_cluster XREF Contains_gene // linking to Clusters in locus class RNASeq_FPKM ?Life_stage Float #Evidence GO_term ?GO_term XREF Gene ?GO_code #Evidence GO_annotation ?GO_annotation XREF Gene Contained_in_operon ?Operon XREF Contains_gene Ortholog ?Gene XREF Ortholog ?Species #Evidence Paralog ?Gene XREF Paralog ?Species #Evidence Structured_description Provisional_description ?Text #Evidence // Erich [020322 krb] Detailed_description ?Text #Evidence // Erich [020322 krb] Concise_description ?Text #Evidence // Erich [020523 krb] Other_description ?Text #Evidence // Carol [050202 dl] Automated_description ?Text #Evidence // Ranjana [140917 pad] Sequence_features ?Text #Evidence // Carol [050202 dl] Functional_pathway ?Text #Evidence // Carol [050202 dl] Functional_physical_interaction ?Text #Evidence // Carol [050202 dl] Biological_process ?Text #Evidence // Carol [050202 dl] Molecular_function ?Text #Evidence // Carol [050202 dl] Expression ?Text #Evidence // Carol [050202 dl] Disease_info Experimental_model ?DO_term XREF Gene_by_biology ?Species #Evidence Potential_model ?DO_term XREF Gene_by_orthology ?Species #Evidence Disease_relevance ?Text ?Species #Evidence Modifies_disease ?DO_term XREF Disease_modifier_gene //New tag WS278 Models_disease_in_annotation ?Disease_model_annotation XREF Disease_relevant_gene //New tag WS278 Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_gene //New tag WS278 Models_disease_asserted ?Disease_model_annotation XREF Asserted_gene // Indicates the gene the disease affects // new tag request for WS287 Models_disease_inferred ?Disease_model_annotation XREF Inferred_gene // Indicates the gene the disease affects // new tag request for WS287 Molecular_info Corresponding_CDS ?CDS XREF Gene #Evidence // to link to live CDSs Corresponding_CDS_history ?CDS XREF Gene_history // to link to history CDSs Corresponding_transcript ?Transcript XREF Gene #Evidence Corresponding_transcript_history ?Transcript XREF Gene_history Corresponding_pseudogene ?Pseudogene XREF Gene #Evidence Corresponding_pseudogene_history ?Pseudogene XREF Gene_history Corresponding_transposon ?Transposon XREF Gene #Evidence Other_sequence ?Sequence XREF Gene #Evidence // for linking to mRNAs etc. that correspond to a gene Associated_feature ?Feature XREF Associated_with_gene #Evidence Associated_transcription_factor ?Transcription_factor XREF Associated_with_gene #Evidence Gene_product_binds ?Feature XREF Bound_by_product_of Transcription_factor ?Transcription_factor XREF Product_of Experimental_info RNAi_result ?RNAi XREF Gene #Evidence Expr_pattern ?Expr_pattern XREF Gene Drives_construct ?Construct XREF Driven_by_gene #Evidence Construct_product ?Construct XREF Gene #Evidence Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_gene // Wen WS228 Antibody ?Antibody XREF Gene Microarray_results ?Microarray_results XREF Gene Expression_cluster ?Expression_cluster XREF Gene #Evidence //Igor: create clusters of Genes from microarray exps SAGE_tag ?SAGE_tag XREF Gene #SAGE_mapping_info 3d_data ?3d_data XREF Gene // for NESGC structure information Interaction ?Interaction Anatomy_function ?Anatomy_function XREF Gene Product_binds_matrix ?Position_Matrix XREF Bound_by_gene_product #Evidence WBProcess ?WBProcess XREF Gene #Evidence Map_info Map UNIQUE ?Map XREF Gene #Map_position Well_ordered // "on the line" Hide_under ?Gene XREF Representative_for Representative_for ?Gene XREF Hide_under Positive Inside_rearr ?Rearrangement XREF Gene_inside #Evidence Positive_clone ?Clone XREF Positive_gene #Evidence Negative Outside_rearr ?Rearrangement XREF Gene_outside #Evidence Negative_clone ?Clone XREF Negative_gene #Evidence Mapping_data 2_point ?2_point_data Multi_point ?Multi_pt_data Pos_neg_data ?Pos_neg_data Interpolated_map_position UNIQUE ?Map UNIQUE Float // for loci with CDSs but no real Map position Landmark_gene // for those genes that will appear in genetic map of Genome Browser Pseudo_map_position // should be added to flag those genes which have Map position tags that // were 'promoted' from Interpolated_map_position tags Reference ?Paper XREF Gene #Evidence Picture ?Picture XREF Gene Remark ?Text #Evidence Method UNIQUE ?Method //////////////////////////// // // ?Gene_cluster class // //////////////////////////// ?Gene_cluster Title UNIQUE ?Text // Information on the Gene cluster Description ?Text Contains_gene ?Gene XREF In_cluster Contains_non_WB_gene DB_info Database ?Database ?Database_field ?Text //for genes from non WB species Attribute_of Analysis ?Analysis XREF Gene_cluster Associated_with WBProcess ?WBProcess XREF Gene_cluster Reference ?Paper XREF Gene_cluster //////////////////////////////////////////////////////////////////////////////// // // hash to track details of what actually happened for each change to a gene // //////////////////////////////////////////////////////////////////////////////// #Gene_history_action Event Created Killed Suppressed Resurrected Merged_into UNIQUE ?Gene Acquires_merge UNIQUE ?Gene Split_from UNIQUE ?Gene Split_into UNIQUE ?Gene Imported Text // for the first set of Gene IDs created Changed_class Text Text // added to capture CDS->Pseudogene changes, two text fields should list old and new classes Transposon_in_origin // for CDSs that become Transposon CDSs Name_change CGC_name UNIQUE Text Sequence_name UNIQUE Text Other_name UNIQUE Text // Text field to store 'Other_name' of Gene //////////////////////////////////////////////////////////////////////////////// // // ?Gene_name class to allow easier indexing of gene names and other names // [krb 030124] // //////////////////////////////////////////////////////////////////////////////// ?Gene_name CGC_name_for ?Gene XREF CGC_name Sequence_name_for ?Gene XREF Sequence_name Molecular_name_for ?Gene XREF Molecular_name // captures CDS names, Wormpep names etc. Other_name_for ?Gene XREF Other_name // main reason for this class Former_member_of ?Gene_class XREF Old_member // track old members of a class Public_name_for ?Gene XREF Public_name // the main name for a gene ////////////////////////////////////////////////////////////////////////////////////// // // ?Interaction class Proposal, 1-30-2012 // See: http://wiki.wormbase.org/index.php/WormBase_Model:Interaction for details // This unifies Physical and genetic interactions into a single class. // Chris Grove & Kimberly Van Auken // ////////////////////////////////////////////////////////////////////////////////////// ?Interaction Interaction_type Physical UNIQUE ProteinProtein ProteinDNA ProteinRNA Predicted Regulatory Change_of_localization Change_of_expression_level Genetic Genetic_interaction Neutral_genetic Synthetic Enhancement Unilateral_enhancement Mutual_enhancement Positive_genetic Suppression Complete_suppression Partial_suppression Unilateral_suppression Complete_unilateral_suppression Partial_unilateral_suppression Mutual_suppression Complete_mutual_suppression Partial_mutual_suppression Suppression_enhancement Asynthetic Negative_genetic Oversuppression Unilateral_oversuppression Mutual_oversuppression Oversuppression_enhancement Phenotype_bias No_interaction // Negative data; no interaction was observed after testing Epistasis Positive_epistasis Maximal_epistasis Minimal_epistasis Neutral_epistasis Qualitative_epistasis Opposing_epistasis Quantitative_epistasis GI_module_one A_phenotypic Mono_phenotypic Cis_phenotypic Iso_phenotypic Trans_phenotypic GI_module_two Enhancing Suppressing All_suppressing Super_suppressing Sub_suppressing Inter_suppressing Semi_suppressing Co_suppressing Masking GI_module_three Neutral Non_neutral Positive Negative Converging Diverging Interactor PCR_interactor ?PCR_product XREF Interaction #Interactor_info // PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments Sequence_interactor ?Sequence XREF Interaction #Interactor_info // Sequence of the interacting gene or protein Interactor_overlapping_CDS ?CDS XREF Interaction #Interactor_info // CDS of the interacting gene or protein (or related sequence) Interactor_overlapping_gene ?Gene XREF Interaction #Interactor_info // Gene (or portion of gene) involved in the interaction Interactor_overlapping_protein ?Protein XREF Interaction #Interactor_info // Protein (or portion of protein) involved in the interaction Molecule_interactor ?Molecule XREF Interaction #Interactor_info // Molecule that regulates a gene or protein (ported from Gene_regulation Class) Modified Chris WS244 Other_interactor ?Text #Interactor_info Rearrangement ?Rearrangement XREF Interactor #Interactor_info Feature_interactor ?Feature XREF Associated_with_Interaction #Interactor_info Variation_interactor ?Variation XREF Interactor #Interactor_info Interaction_summary ?Text #Evidence Detection_method Affinity_capture_luminescence // A physical interaction detection technique Affinity_capture_MS // A physical interaction detection technique Affinity_capture_RNA // A physical interaction detection technique Affinity_capture_Western // A physical interaction detection technique Chromatin_immunoprecipitation // Chris WS244 Cofractionation // A physical interaction detection technique Colocalization // A physical interaction detection technique Construct Copurification // A physical interaction detection technique DNase_I_footprinting // Fluorescence_resonance_energy_transfer // A physical interaction detection technique Protein_fragment_complementation_assay // A physical interaction detection technique Yeast_two_hybrid // A physical interaction detection technique (Protein-protein) Biochemical_activity // A physical interaction detection technique Cocrystal_structure // A physical interaction detection technique Far_western // A physical interaction detection technique Protein_peptide // A physical interaction detection technique Protein_RNA // A physical interaction detection technique Reconstituted_complex // A physical interaction detection technique Electrophoretic_mobility_shift_assay // A physical interaction detection technique Yeast_one_hybrid // A physical interaction detection technique (Protein-DNA) Directed_yeast_one_hybrid // A physical interaction detection technique (Protein-DNA) Antibody // A regulatory interaction detection technique; Antibody name and details captured in Interactor_info hash Reporter_gene ?Text // A regulatory interaction detection technique Transgene // A regulatory interaction detection technique; Trasnsgene name and details captured in Interactor_info hash In_situ Text // A regulatory interaction detection technique Northern Text // A regulatory interaction detection technique Western Text // A regulatory interaction detection technique RT_PCR Text // A regulatory interaction detection technique Other_method ?Text // A regulatory interaction detection technique Library_info Library_screened Text INT // In the context of Y2H or YH screens, for example, the library may have been cDNA library or a pool of clones Origin From_laboratory UNIQUE ?Laboratory // A library generated at an academic laboratory From_company UNIQUE ?Text // A library generated at a company Regulation_level Transcriptional // Regulation occurs at the transcriptional level Post_transcriptional // Regulation occurs at the post-transcriptional level Post_translational // Regulation occurs at the post-translational level Regulation_result Positive_regulate #GR_condition Negative_regulate #GR_condition Does_not_regulate #GR_condition // added to capture negative data [040220 krb] Confidence Description Text // Free text description of the confidence, e.g. "Core" vs "Noncore" (Vidal Interactome terms) P_value UNIQUE Float // P-value confidence of interaction, if given Log_likelihood_score UNIQUE Float // Only used for Predicted interactions Throughput UNIQUE High_throughput // See BioGRID curation criteria for discussion Low_throughput Interaction_RNAi ?RNAi XREF Interaction // RNAi experiment associated with the interaction Interaction_phenotype ?Phenotype XREF Interaction // Phenotype associated with a genetic interaction Unaffiliated_variation ?Variation Unaffiliated_transgene ?Transgene Unaffiliated_antibody ?Antibody Unaffiliated_expr_pattern ?Expr_pattern Unaffiliated_construct ?Construct WBProcess ?WBProcess XREF Interaction // WormBase biological process associated with the interaction DB_info Database ?Database ?Database_field ?Text // Any database reference to the interaction outside of WormBase, e.g. BioGRID, Interactome Paper ?Paper XREF Interaction Antibody_remark ?Text Historical_gene ?Gene Text Remark ?Text #Evidence #Interactor_info Interactor_type Non_directional // An interactor that has no inherent directionality Bait // The interactor of interest or focus; the focus/starting point of an interaction screen Target // The discovered interactor; interactors found as a result of an interaction screen Effector // In a genetic interaction, the perturbation that affects the phenotype of the other perturbation Affected // In a genetic interaction, the perturbation whose phenotype is affected by the other perturbation Trans_regulator // A trans-acting regulator, e.g. a transcription factor Cis_regulator // A cis-acting regulator, e.g. an enhancer element Trans_regulated // A gene regulated in trans, e.g. by a transcription factor Cis_regulated // A gene regulated in cis, e.g. by an enhancer element Expr_pattern ?Expr_pattern // An expression pattern altered to indicate Transgene ?Transgene XREF Interactor // Transgene XREF Interactor that carries an interacting gene //removed XREF from proposal Construct ?Construct XREF Interactor Antibody ?Antibody XREF Interactor // Free text description of the antibody used to detect a regulation event //removed XREF from proposal Inferred_automatically Text // a script has updated this connection /////////////////////////////////// // // ?Balancer class // /////////////////////////////////// ?Balancer From_left_end To_right_end Locus ?Locus Gene ?Gene //////////////////////////////////////////////////////////////////////////////// // // ?Rearrangement class // //////////////////////////////////////////////////////////////////////////////// ?Rearrangement Evidence #Evidence Name Other_name ?Text Variation ?Variation XREF Rearrangement Type Deletion Duplication Free_dup Translocation Inversion Compound Text Introgression Phenotype ?Phenotype XREF Rearrangement #Phenotype_info Phenotype_not_observed ?Phenotype XREF Not_in_Rearrangement #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes Balances ?Map #Balancer Interactor ?Interaction XREF Rearrangement Marked By_variation ?Variation XREF Marked_rearrangement By_transgene ?Transgene XREF Marked_rearrangement By_other ?Text Component_of_genotype ?Genotype XREF Rearrangement // 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 Species UNIQUE ?Species Remark ?Text #Evidence Isolation Author ?Author // use Person where possible, else use Author Person ?Person Date UNIQUE DateType Mutagen UNIQUE Text UNIQUE Text // Text is dose Source_rearrangement UNIQUE ?Rearrangement XREF Derived_rearrangement Derived_rearrangement ?Rearrangement XREF Source_rearrangement Map ?Map XREF Rearrangement #Map_position Positive Gene_inside ?Gene XREF Inside_rearr #Evidence Locus_inside ?Locus XREF Inside_rearr ?Author Clone_inside ?Clone XREF Inside_rearr ?Author Rearr_inside ?Rearrangement Negative Gene_outside ?Gene XREF Outside_rearr #Evidence 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 URL Text Strain ?Strain XREF Rearrangement Reference ?Paper XREF Rearrangement //////////////////////////////////////////////////////////////////////////////// // // ?Strain class // //////////////////////////////////////////////////////////////////////////////// ?Strain Evidence #Evidence Status UNIQUE Live #Evidence Dead #Evidence Genotype UNIQUE Text Public_name UNIQUE ?Text Other_name ?Text #Evidence Contains Gene ?Gene XREF Strain Variation ?Variation XREF Strain Rearrangement ?Rearrangement XREF Strain Clone ?Clone XREF In_strain Transgene ?Transgene XREF Strain Disease_info Models_disease ?DO_term XREF Disease_model_strain Modifies_disease ?DO_term XREF Disease_modifier_strain //New tag Models_disease_in_annotation ?Disease_model_annotation XREF Strain //New tag Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_strain //New tag Database ?Database ?Database_field ?Text Properties Inbreeding_state UNIQUE Selfed Text Isofemale Text Multifemale Text Inbred Text Outcrossed UNIQUE Text Mutagen Text Strain_history Text Date_first_frozen UNIQUE DateType CGC_received DateType Phenotype ?Phenotype XREF Strain #Phenotype_info Phenotype_not_observed ?Phenotype XREF Not_in_Strain #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes Location ?Laboratory #Lab_Location Made_by ?Person //updated from ?text Contact ?Person Remark ?Text #Evidence Reference ?Paper XREF Strain Species UNIQUE ?Species // added by krb [021021] NCBITaxonomyID UNIQUE Int // Allows for finer grade attachment of NCBItaxon IDs Wild_isolate // to identify wild isolates - since genotype is free text Isolation GPS UNIQUE Float UNIQUE Float #Position_confidence // Latitude +/-DD.DDDDD Longitude +/-DD.DDDDD Elevation UNIQUE Float #Position_confidence // Elevation above sea level. Place UNIQUE ?Text Landscape UNIQUE Urban_garden Forest Wild_grassland Agricultural_land Oasis Rural_garden Botanical_garden_zoo Wet_shrubland Dry_shrubland Substrate UNIQUE ?Text // e.g. snail, soil, apple, rotting fruit Associated_organisms ?Text Life_stage ?Life_stage Log_size_of_population UNIQUE Float Sampled_by Text // the person who found the worms Isolated_by ?Person // the person who isolated the worms from the sample Date UNIQUE DateType Picture ?Picture //Used to define a metric to the elevation and GPS positions in the Strain Class #Position_confidence UNIQUE Exact Approximate UNIQUE Float Inferred_from_GPS //////////////////////////////////////////////////////////////////////////////// // // ?Genotype class // //////////////////////////////////////////////////////////////////////////////// ?Genotype Genotype_name UNIQUE ?Text // e.g. “unc-1(e103);unc-2(e234)”; eventually to be automatically generated Genotype_synonym ?Text // To capture literal representations in the literature Genotype_component Gene ?Gene XREF Component_of_genotype #Evidence Variation ?Variation XREF Component_of_genotype Rearrangement ?Rearrangement XREF Component_of_genotype Transgene ?Transgene XREF Component_of_genotype Other_component UNIQUE ?Text // Free text components including RNAi Disease_info Models_disease ?DO_term XREF Disease_model_genotype Modifies_disease ?DO_term XREF Disease_modifier_genotype Models_disease_in_annotation ?Disease_model_annotation XREF Genotype Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_genotype Species UNIQUE ?Species Remark ?Text Reference ?Paper XREF Genotype //////////////////////////////////////////////////////////////////////////////// // // ?Lab_Location class // //////////////////////////////////////////////////////////////////////////////// ?Lab_Location Freezer Text LiquidN2 Text Minus70 Text Remark ?Text #Evidence //////////////////////////////////////////////////////////////////////////////// // // worm physical map classes // //////////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////////// // // ?Clone class // Class extended to incorporate AddGene data for WS244 // //////////////////////////////////////////////////////////////////////////////// ?Clone Evidence #Evidence Species UNIQUE ?Species Reference ?Paper XREF Clone Produced_by Person ?Person // Paul D. WS244 Author ?Author // Paul D. WS244 Sequences Sequence ?Sequence XREF Clone End_sequence ?Sequence XREF Clone_end_seq_read // New Tag for distinguishing between the full sequence and the end reads 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 Positive_gene ?Gene XREF Positive_clone Positive_variation ?Variation XREF Positive_clone ?Author Inside_rearr ?Rearrangement XREF Clone_inside ?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_gene ?Gene XREF Negative_clone 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 Mutation ?Text // Paul D. WS244 PCR_product ?PCR_product XREF Clone Primer1 ?Text // Paul D. WS244 Primer2 ?Text // Paul D. WS244 Resistance_marker ?Text // Paul D. WS244 Length Seq_length UNIQUE Int // bp Gel_length UNIQUE Float // Kb Insert UNIQUE Int // bp Paul D. WS244 Backbone UNIQUE Int // bp Paul D. WS244 Location ?Laboratory #Lab_Location URL Text // to link to MRC_geneservice website ar2 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 Construct ?Construct 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 Used_in_RNAi ?RNAi XREF Clone // Chris WS244 Sequence_status Shotgun UNIQUE DateType Finished UNIQUE DateType Accession_number UNIQUE ?Text DB_info Database ?Database ?Database_field ?Text // added [031120 krb] Type UNIQUE Cosmid // 000824 Lincoln's additions to segregate clones Fosmid // added 06/12/01 by krb for dl YAC cDNA Plasmid Other Text // added to catch all clones 011017 dl Vector_type ?Text Derived_from ?Clone XREF Parent_of Parent_of ?Clone XREF Derived_from Ligation ?Text #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 class // //////////////// ?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_data class // //////////////////// ?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 //////////////////// // // ?Grid_row class // //////////////////// ?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 class // /////////////////////////////// ?Species Evidence #Evidence Short_name UNIQUE Text // e.g. 'C. elegans' Other_name Text // sp. 7 etc. G_species UNIQUE Text // e.g. 'c_elegans' - used internally for file generation Reference ?Paper XREF Species Remark ?Text #Evidence NCBITaxonomyID UNIQUE Int In_analysis ?Analysis XREF Species_in_analysis Assembly ?Sequence_collection //used for linking to the species assemblies /////////////////////////////// // // Map data classes // /////////////////////////////// //////////////////// // // ?2_point_data class // //////////////////// ?2_point_data Evidence #Evidence Genotype UNIQUE Text Results UNIQUE Text Experiment Mapper ?Author Laboratory ?Laboratory Date UNIQUE DateType Temperature UNIQUE Text Point_1 UNIQUE Gene_1 UNIQUE ?Gene XREF 2_point UNIQUE ?Variation XREF In_2_point Locus_1 UNIQUE ?Locus XREF 2_point UNIQUE ?Variation XREF In_2_point Allele_1 UNIQUE ?Variation XREF 2_point Rearrangement_1 UNIQUE ?Rearrangement XREF 2_point Point_2 UNIQUE Gene_2 UNIQUE ?Gene XREF 2_point UNIQUE ?Variation XREF In_2_point Locus_2 UNIQUE ?Locus XREF 2_point UNIQUE ?Variation XREF In_2_point Allele_2 UNIQUE ?Variation XREF 2_point Rearrangement_2 UNIQUE ?Rearrangement 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 #Evidence // 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 class // //////////////////// ?Pos_neg_data Evidence #Evidence Genotype UNIQUE Text Results UNIQUE Text Experiment Mapper ?Author Laboratory ?Laboratory Date UNIQUE DateType Item_1 UNIQUE Gene_1 UNIQUE ?Gene XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data Locus_1 UNIQUE ?Locus XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data Rearrangement_1 UNIQUE ?Rearrangement XREF Pos_neg_data Allele_1 UNIQUE ?Variation XREF Pos_neg_data Clone_1 UNIQUE ?Clone XREF Pos_neg_data Item_2 UNIQUE Gene_2 UNIQUE ?Gene XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data Locus_2 UNIQUE ?Locus XREF Pos_neg_data UNIQUE ?Variation XREF In_pos_neg_data Rearrangement_2 UNIQUE ?Rearrangement XREF Pos_neg_data Allele_2 UNIQUE ?Variation XREF Pos_neg_data Clone_2 UNIQUE ?Clone XREF Pos_neg_data Calculation UNIQUE Positive Negative Remark ?Text #Evidence // code uses Item_1, Item_2, Positive and Negative //////////////////////// // // ?Multi_pt_data class // //////////////////////// ?Multi_pt_data Evidence #Evidence Genotype UNIQUE Text Experiment Mapper ?Author Laboratory ?Laboratory Date UNIQUE DateType Selected A UNIQUE Gene_A UNIQUE ?Gene UNIQUE ?Variation XREF In_multi_point Locus_A UNIQUE ?Locus UNIQUE ?Variation XREF In_multi_point Allele_A UNIQUE ?Variation Rearrangement_A UNIQUE ?Rearrangement B UNIQUE Gene_B UNIQUE ?Gene UNIQUE ?Variation XREF In_multi_point Locus_B UNIQUE ?Locus UNIQUE ?Variation XREF In_multi_point Allele_B UNIQUE ?Variation Rearrangement_B UNIQUE ?Rearrangement Gene ?Gene UNIQUE ?Variation XREF In_multi_point // Connect to ?Gene model Locus ?Locus UNIQUE ?Variation XREF In_multi_point // Pair up alleles Results A_non_B #Multi_counts B_non_A #Multi_counts Combined #Multi_counts Old_CGC_results Text Remark ?Text #Evidence // code uses all the Results subtags, and the #Multi_counts structure // There is acedb magic associated with the #?Multi_counts usage. //////////////////////// // // ?Multi_counts class // //////////////////////// ?Multi_counts UNIQUE Gene UNIQUE ?Gene XREF Multi_point UNIQUE Int #Multi_counts Locus UNIQUE ?Locus XREF Multi_point UNIQUE Int #Multi_counts Allele UNIQUE ?Variation XREF Multi_point UNIQUE Int #Multi_counts Rearrangement UNIQUE ?Rearrangement XREF Multi_point UNIQUE Int #Multi_counts Transgene UNIQUE ?Transgene XREF Multi_point UNIQUE Int #Multi_counts //////////////////////////////////////////////////////////////////////////////// // Evidence hash //////////////////////////////////////////////////////////////////////////////// #Evidence Paper_evidence ?Paper // Data from a Paper Published_as ?Text // .. track other names for the same data Person_evidence ?Person // Data communicated to wormbase from a Person (pre-publication/unpublished) Author_evidence ?Author UNIQUE Text // Data from an Author Accession_evidence ?Database ?Text // Data from a database (NDB/UNIPROT etc) Protein_id_evidence ?Text // Reference a protein_ID GO_term_evidence ?GO_term // Reference a GO_term Expr_pattern_evidence ?Expr_pattern // Reference a Expression pattern Microarray_results_evidence ?Microarray_results // Reference a Microarray result RNAi_evidence ?RNAi // Reference a RNAi knockdown CGC_data_submission // bless the data as comning from CGC Curator_confirmed ?Person // bless the data manually Inferred_automatically Text // bless the data via a script Date_last_updated UNIQUE DateType // Stores last update timestamp Feature_evidence ?Feature // Reference a Feature - eg for creation of isoform based on TEC-RED SL2 Laboratory_evidence ?Laboratory // Reference a Lab From_analysis ?Analysis // Reference an analysis Variation_evidence ?Variation // Explicitly record variation from which IMP manual GO annotations are made Mass_spec_evidence ?Mass_spec_peptide Sequence_evidence ?Sequence // for sequence data that hasn't been submitted to a public resource Remark ?Text ////////////////////////////////////////// // // ?Disease_model_annotation class WS260 // ////////////////////////////////////////// ?Disease_model_annotation Disease_term UNIQUE ?DO_term XREF Disease_model_annotation Disease_of_species ?Species Modeled_by Strain UNIQUE ?Strain XREF Models_disease_in_annotation ?Text // WS278 XREF tag modified Variation UNIQUE ?Variation XREF Models_disease_in_annotation ?Text // WS278 XREF tag modified Transgene UNIQUE ?Transgene XREF Models_disease_in_annotation ?Text // WS278 XREF tag modified Disease_relevant_gene UNIQUE ?Gene XREF Models_disease_in_annotation ?Text // WS278 XREF tag modified Genotype UNIQUE ?Genotype XREF Models_disease_in_annotation //to associate genotypes Modeled_by_remark UNIQUE ?Text Asserted_gene ?Gene XREF Models_disease_asserted // Indicates asserted gene in Variation or Strain // new tag request for WS287 Asserted_human_gene ?Text //for capturing the human gene via HGNC ID for transgenic models of disease Inferred_gene ?Gene XREF Models_disease_inferred // Indicates the // new tag request for WS287 Asserted_variation ?Variation XREF Modifies_disease_asserted_variation // request for WS287 Association_type UNIQUE is_model_of // Describe relationship between genetic entity and disease (condition) is_implicated_in is_marker_for is_ameliorated_model_of // new tag for WS285 is_exacerbated_model_of // new tag for WS285 Evidence_code GO_code ?GO_code // will use ECO later on ECO_term ?ECO_term Qualifier_not // to indicate that a disease is NOT modeled by X change tag WS262 Experimental_condition Inducing_chemical ?Molecule XREF Disease_model_inducer //to indicate the disease-inducing agent Inducing_agent ?Text //e.g. diet, radiation,etc not in Molecule class Modifier_info Modifier_transgene ?Transgene XREF Modifies_disease_in_annotation Modifier_variation ?Variation XREF Modifies_disease_in_annotation Modifier_strain ?Strain XREF Modifies_disease_in_annotation Modifier_gene ?Gene XREF Modifies_disease_in_annotation Modifier_molecule ?Molecule XREF Disease_model_modifier // to indicate chemical modifiers of the disease Modifier_genotype ?Genotype XREF Modifies_disease_in_annotation //to annotate genotype modifiers of disease Other_modifier ?Text //to indicate other modifiers of the disease eg. diet,radiation, surgery etc Modifier_association_type UNIQUE condition_ameliorated_by //to indicate the association type between modifiers and disease condition_exacerbated_by Modifier_qualifier_not //new tag for WS262 Genetic_sex UNIQUE hermaphrodite //indicates genetic sex of the disease model male female Disease_phenotype_info Disease_phenotype ?Phenotype //Phenotypes similar to human disease Ameliorated_phenotype ?Phenotype // Phenotypes ameliorated by modifier Exacerbated_phenotype ?Phenotype // Phenotypes exacerbated by modifier Phenotype_comment ?Text // To describe non-WPO phenotypes Paper_evidence UNIQUE ?Paper Disease_model_description ?Text DB_info Database ?Database ?Database_field ?Text //To indicate the OMIM gene/disease Curator_confirmed ?Person Date_last_updated UNIQUE DateType //////////////////////////////////////////////////////// // // ?GO_annotation class // /////////////////////////////////////////////////////// ?GO_annotation Gene UNIQUE ?Gene XREF GO_annotation ECO_term UNIQUE ?ECO_term GO_term UNIQUE ?GO_term XREF GO_annotation GO_code UNIQUE ?GO_code Noctua_model_id ?Text Annotation_relation UNIQUE ?RO_term XREF GO_annotation Annotation_relation_not UNIQUE ?RO_term XREF Not_GO_annotation Annotation_made_with Interacting_gene ?Gene Inferred_from_GO_term ?GO_term Motif ?Motif RNAi_result ?RNAi Variation ?Variation Phenotype ?Phenotype Database ?Database ?Database_field ?Text Annotation_extension Life_stage_relation ?Text UNIQUE ?Life_stage Gene_relation ?Text UNIQUE ?Gene Molecule_relation ?Text UNIQUE ?Molecule Anatomy_relation ?Text UNIQUE ?Anatomy_term GO_term_relation ?Text UNIQUE ?GO_term Annotation_isoform ?Text ?Protein Interacting_species ?Species ?Strain Reference UNIQUE ?Paper XREF GO_annotation GO_reference UNIQUE ?Database ?Database_field ?Text Contributed_by UNIQUE ?Analysis Date_last_updated UNIQUE DateType //////////////////////////////////////////////////////// // // ?GO_term class modified 19/09/01 dl // /////////////////////////////////////////////////////// ?GO_term Name ?Text Definition ?Text Alt_id ?Text Synonym Broad ?Text Exact ?Text Narrow ?Text Related ?Text Status UNIQUE Valid Obsolete Type UNIQUE Biological_process Cellular_component Molecular_function Child Instance ?GO_term XREF Instance_of Component ?GO_term XREF Component_of Parent Instance_of ?GO_term XREF Instance Component_of ?GO_term XREF Component Attributes_of Cell ?Cell XREF GO_term Motif ?Motif XREF GO_term Gene ?Gene XREF GO_term // will this replace CDS? [040203 krb] CDS ?CDS XREF GO_term Sequence ?Sequence XREF GO_term // Erich, [011210 krb] Transcript ?Transcript XREF GO_term // [030411 krb] Phenotype ?Phenotype XREF GO_term // Erich, [020128 dl] Index Ancestor ?GO_term XREF Descendant // Lincoln [020709 [krb] Descendant ?GO_term XREF Ancestor Anatomy_term ?Anatomy_term XREF GO_term // added [031107 krb] Homology_group ?Homology_group XREF GO_term // added [031120 krb] Expr_pattern ?Expr_pattern XREF GO_term Picture ?Picture XREF Cellular_component GO_annotation ?GO_annotation XREF GO_term Version UNIQUE Text /////////////////////////////////////////////////////////////// // // ?GO_code class - 030224 krb // /////////////////////////////////////////////////////////////// ?GO_code Description ?Text Remark ?Text #Evidence /////////////////////////////////////////////////////////////// // // ?ECO_term class - kimberly WS278 // //////////////////////////////////////////////////////////////// ?ECO_term Name UNIQUE ?Text Status UNIQUE Valid Obsolete Alt_id ?Text Definition UNIQUE ?Text Synonym Broad ?Text Exact ?Text Narrow ?Text Related ?Text Child ?ECO_term XREF Parent Parent ?ECO_term XREF Child Version UNIQUE Text /////////////////////////////////////////////////////////////// // // ?SO_term class - krb 30062004 // - klh 2011-04 //////////////////////////////////////////////////////////////// ?SO_term SO_name UNIQUE ?Text SO_definition UNIQUE ?Text SO_synonym ?Text SO_version ?Text Located_sequence_feature UNIQUE Junction Region Sequence_alteration Sequence_comparison Parent Is_a ?SO_term XREF Is Part_of ?SO_term XREF Part Derived_from ?SO_term XREF Derives Member_of ?SO_term XREF Member Child Is ?SO_term XREF Is_a Part ?SO_term XREF Part_of Derives ?SO_term XREF Derived_from Member ?SO_term XREF Member_of Ancestor ?SO_term XREF Descendant Descendant ?SO_term XREF Ancestor /////////////////////////////////////////////////////////////// // ?Ace2SO class: gives a mapping from Acedb objects to their SO terms. // // SO_subpart_tags - Tag pointing to subpart of this object, e.g. "Source_exon". // SO_parent_obj_tag - Tag pointing to semantic parent of this object, e.g. "Gene" // SO_children - this object has child objects which refer to it. /////////////////////////////////////////////////////////////// ?Ace2SO Description UNIQUE Text SO_subparts Exons UNIQUE ?SO_Term Introns UNIQUE ?SO_term Coding_region UNIQUE ?SO_term No_span SO_parent_obj_tag UNIQUE Text SO_children /////////////////////////////////////////////////////////////// // // ?DO_term class - Ranjana WS236 // //////////////////////////////////////////////////////////////// ?DO_term Name UNIQUE ?Text Status UNIQUE Valid Obsolete Alternate_id ?Text Definition UNIQUE ?Text Worm_disease_model ?Text ?Species #Evidence // Textual description of the worm disease model Comment Text Synonym Broad ?Text Exact ?Text Narrow ?Text Related ?Text Parent Is_a ?DO_term XREF Is Child Is ?DO_term XREF Is_a DB_info Database ?Database ?Database_field ?Text Disease_model_annotation ?Disease_model_annotation XREF Disease_term //to hold all the details of a disease model Type GOLD Gram_negative_bacterial_infectious_disease Gram_positive_bacterial_infectious_disease Sexually_transmitted_infectious_disease Tick_borne_infectious_disease Zoonotic_infectious_disease Attribute_of Gene_by_biology ?Gene XREF Experimental_model Gene_by_orthology ?Gene XREF Potential_model Phenotype ?Phenotype XREF DO_term WBProcess ?WBProcess XREF DO_term Reference ?Paper XREF DO_term Disease_modifier_gene ?Gene XREF Modifies_disease // Tag missing from original proposal WS268 Disease_model_variation ?Variation XREF Models_disease //To associate Variations to a disease Disease_modifier_variation ?Variation XREF Modifies_disease //New tag Disease_model_strain ?Strain XREF Models_disease //To associate Strains to a disease Disease_modifier_strain ?Strain XREF Modifies_disease //New tag Disease_model_transgene ?Transgene XREF Models_disease //To associate Transgenes to disease Disease_modifier_transgene ?Transgene XREF Modifies_disease //New tag Disease_model_genotype ?Genotype XREF Models_disease Disease_modifier_genotype ?Genotype XREF Modifies_disease Chemical_inducer ?Molecule XREF Induces_disease //To associate inducing chemicals to a disease Other_inducer ?Text //New tag Molecule_modifier ?Molecule XREF Modifies_disease //To associate modifying chemicals to a disease Reagent_info Associated_construct ?Construct XREF Construct_for_disease Associated_transgene ?Transgene XREF Transgene_for_disease Version UNIQUE Text /////////////////////////////////////////////////////////////// // // ?RO_term class - Kimberly WS267 // //////////////////////////////////////////////////////////////// ?RO_term Name UNIQUE ?Text Status UNIQUE Valid Obsolete Alt_id ?Text Definition UNIQUE ?Text Synonym Broad ?Text Exact ?Text Narrow ?Text Related ?Text Child Instance ?RO_term XREF Instance_of Parent Instance_of ?RO_term XREF Instance Index Ancestor ?RO_term XREF Descendant Descendant ?RO_term XREF Ancestor Attribute_of GO_annotation ?GO_annotation XREF Annotation_relation Not_GO_annotation ?GO_annotation XREF Annotation_relation_not Version UNIQUE Text /////////////////////////////////////////////////////////////// // // ?PATO_term class - Chris WS251 // //////////////////////////////////////////////////////////////// ?PATO_term Name ?Text Definition ?Text Alt_id ?Text Synonym ?Text Status UNIQUE Valid Obsolete Child ?PATO_term Parent ?PATO_term Version UNIQUE Text ////////////////////////////////////////////////////////// // ?AO_code class - Raymond Lee 040203 // Evidence codes only relevant to the Anatomy_term Class ////////////////////////////////////////////////////////// ?AO_code Description ?Text Remark ?Text #Evidence Attribute_of Anatomy_function ?Anatomy_function XREF Assay //addition ////////////////////////////////////////////////////////// // ?Atlas class - Lincoln 000824 // WORMBASE ATLAS (VIRTUAL WORM) ////////////////////////////////////////////////////////// ?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 class /////////////////// ?Neurodata Send Text UNIQUE Int #Neuro_location // Text=series,Int=count Send_joint Text UNIQUE Int #Neuro_location // "joint" indicates polyadic synapse Receive Text UNIQUE Int #Neuro_location Receive_joint Text UNIQUE Int #Neuro_location Gap_junction Text UNIQUE Int #Neuro_location Evidence #Evidence //////////////////////////// // ?Neurodata_location class //////////////////////////// ?Neuro_location Section Int Int Text //Int1=first EM section where the connection was //found,Int2=last section,Text=remark //////////////////////////// // ?Reconstruction class //////////////////////////// ?Reconstruction Cell ?Cell Anatomy_term ?Anatomy_term //[2006-04-21 ar2] Raymond Author ?Author Date UNIQUE DateType Remark ?Text #Evidence Description ?LongText /////////////////////// // ?ReconCellInfo class /////////////////////// ?ReconCellInfo Birth UNIQUE Float Timepoint Float #Timepoint ////////////////// // ?Timepoint class ////////////////// ?Timepoint XYZ UNIQUE Float UNIQUE Float UNIQUE Float //////////////////////////////////////////////////////////////////////////////////////////////////////////// // // // S E Q U E N C E A N D S - M A P P E D G E N E C L A S S E S // // ?Sequence, ?CDS, ?Transcript, ?Pseudogene, ?Transposon // // //////////////////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////// // // ?Sequence class // // Stores: genomic DNA objects (chromosomes, superlinks, and clones) // cDNAs (ESTs, OSTs, mRNAs) // sequences from other species (e.g. targets of BLAT_NEMATODE) // /////////////////////////////////////////////////////////////////////// ?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, e.g. "-" // This ensures that when a real sequence appears, its length dominates. SMap S_parent UNIQUE Canonical_parent UNIQUE ?Sequence XREF Genomic_non_canonical Genomic_parent UNIQUE ?Sequence XREF Nongenomic AGP_parent UNIQUE ?Sequence XREF AGP_fragment // added to hold briggsae data [krb 020726] S_child Gene_child ?Gene XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // maximal extent of Gene objects CDS_child ?CDS XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // For ?CDS [031104 krb] Transcript ?Transcript XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // for ?Transcript [021126 krb] Pseudogene ?Pseudogene XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // For ?Pseudogene [030801 krb] Transposon ?Transposon XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // for transposons [020128 dl] Genomic_non_canonical ?Sequence XREF Canonical_parent UNIQUE Int UNIQUE Int #SMap_info Nongenomic ?Sequence XREF Genomic_parent UNIQUE Int UNIQUE Int #SMap_info // for Lincoln RNAi [010226 dl] PCR_product ?PCR_product XREF Canonical_parent UNIQUE Int UNIQUE Int #SMap_info // for Lincoln RNAi [010226 dl] Operon ?Operon XREF Canonical_parent UNIQUE Int UNIQUE Int #SMap_info // for Operon data [dl] AGP_fragment ?Sequence XREF AGP_parent Int UNIQUE Int #SMap_info // for Briggsae data [020726 krb] Allele ?Variation XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // SMapped Allele [021217 krb] Oligo_set ?Oligo_set XREF Canonical_parent UNIQUE Int UNIQUE Int #SMap_info //added for Oligo_set Feature_object ?Feature XREF Sequence UNIQUE Int UNIQUE Int #SMap_info // dl feature play Feature_data ?Feature_data XREF Sequence UNIQUE Int UNIQUE Int #SMap_info Homol_data ?Homol_data XREF Sequence UNIQUE Int UNIQUE Int #SMap_info Structure From Source UNIQUE ?Sequence XREF Subsequence Source_exons Int UNIQUE Int // start at 1 // WARNING: is this still needed when ?CDS Class is present??? 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 ?Database_field ?Text Protein_id ?Sequence UNIQUE Text UNIQUE Int // DB_info tag added [011030 krb] Secondary_accession ?Text DB_remark ?Text #Evidence // EMBL/Genbank Keyword ?Keyword // EMBL/Genbank DB_annotation ?Database UNIQUE ?LongText EMBL_dump_info #EMBL_dump_info Origin From_database UNIQUE ?Database UNIQUE Int // release number From_author ?Author XREF Sequence From_laboratory UNIQUE ?Laboratory Genetic_code UNIQUE ?Genetic_code // krb 030506 Date DateType Text // Text for comments on operation Date_directory UNIQUE Text // date of this version for cosmids, changed sdm 000731 to text Life_stage UNIQUE ?Life_stage // to capture details of ESTs that are from different libraries Species UNIQUE ?Species Library UNIQUE ?Library Strain UNIQUE ?Strain Anatomy_term ?Anatomy_term // life-stage and tissues that the sequence comes from Analysis UNIQUE ?Analysis // analysis or project that produced this set of data Read_coverage UNIQUE Float // average read-coverage in a short-read cluster sequence Visible Title UNIQUE ?Text Matching_CDS ?CDS XREF Matching_cDNA #Evidence // to link ESTs/mRNAs to CDS Matching_transcript ?Transcript XREF Matching_cDNA #Evidence // to link ESTs/mRNAs to RNA genes Matching_pseudogene ?Pseudogene XREF Matching_cDNA #Evidence // to link ESTs/mRNAs to Pseudogenes Clone ?Clone XREF Sequence //This should be the link used if this is the complete seq of a clone. Clone_end_seq_read ?Clone XREF End_sequence //Addition to help distinguish type of sequence GO_term ?GO_term XREF Sequence ?GO_code #Evidence Gene ?Gene XREF Other_sequence // for where mRNAs etc. correspond to a gene Paired_read ?Sequence XREF Paired_read // dl 020110 Reference ?Paper XREF Sequence Expr_pattern ?Expr_pattern XREF Sequence Interaction ?Interaction RNAi ?RNAi XREF Sequence Confidential_remark ?Text Remark ?Text #Evidence // tag2 system: names of all objects following next tag are shown in the // general annotation display column as "tag:objname" Properties Genomic_canonical Gene_count UNIQUE Int // added tag for dot name tracking [020128 dl] Briggsae_canonical Genomic // added tag to define genomic sequences not from the consortium Checksum MD5 UNIQUE Text //checksums should only be created for an upper-cased sequence. CRC64 UNIQUE Text //checksums should only be created for an upper-cased sequence. cDNA cDNA_EST EST_5 // Indicate whether this is a 5' or 3' read [010423 dl] EST_3 Capped_5 // Indicates capped 5' end - for Lincoln [06/12/01 krb] TSL_tag // Indicates a short RT-PCR product for TSL detection [030220 dl] EST_consensus // Designates this object as a consensus // if RNA tag, acedb outputs U in place of T in sequence output RNA UNIQUE mRNA UNIQUE Processed_mRNA // Whole section needs retiring///////////////////////// Unprocessed_mRNA tRNA Type UNIQUE Text // ck1 [030926] krb Anticodon UNIQUE Text // rRNA UNIQUE Text snRNA UNIQUE Text snoRNA UNIQUE Text // [030102 krb] scRNA UNIQUE Text miRNA UNIQUE Text // [020306 kj] ncRNA UNIQUE Text // true non-coding RNA molecules Ignore #Evidence // tag to flag problem Sequence objects to avoid certain analysis [031120 krb] Show_in_reverse_orientation // Draw 3' reads in reverse orientation [010423 dl] 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. Link // Enable gene curation of link genes [020805 krb] 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) Cluster_information Contains_reads ?Sequence XREF Contained_in_cluster // Links cluster contig and Contained_in_cluster ?Sequence XREF Contains_reads // individual reads Map ?Map XREF Sequence #Map_position // use in particular for Genomic_canonical Interpolated_map_position UNIQUE ?Map UNIQUE Float // For updated CDS-based interpolated map positions [krb 030502] Oligo ?Oligo XREF In_sequence Int UNIQUE Int ?Method Defines_feature ?Feature XREF Defined_by_sequence #Evidence // Feature data model [dl 030304] Assembly_tags Text Int Int Text // type, start, stop, comment 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. Method UNIQUE ?Method ///////////////////////////////////////////// // // hashes relating to ?Sequence class // ///////////////////////////////////////////// #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 ?Sequence // ?Sequence link to flag which cDNA is confirming EST ?Sequence // or falsifying the intron in question, added [031121 krb] OST ?Sequence RST ?Sequence RNASeq ?Analysis Int Mass_spec ?Mass_spec_peptide mRNA ?Sequence Homology ?Text UTR ?Sequence False ?Sequence Inconsistent ?Sequence // 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 AlignDNAPep Int UNIQUE Int UNIQUE Int AlignPepDNA Int UNIQUE Int UNIQUE Int Match_string UNIQUE RefFwd_HitFwd UNIQUE Text RefFwd_HitRev UNIQUE Text RefRev_HitFwd UNIQUE Text RefRev_HitRev UNIQUE Text Align_id Text Target_species UNIQUE ?Species 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 UNIQUE ?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 /////////////////////////////////////////////////////////////////////////// // // ?Sequence_collection class // holds a collection of sequences and some descriptions // /////////////////////////////////////////////////////////////////////////// ?Sequence_collection Origin Evidence #Evidence Name ?Text // name that the author gave this collection Species UNIQUE ?Species Strain ?Strain Laboratory ?Laboratory DB_info Database ?Database ?Database_field ?Text History First_WS_release Int // first WormBase release this assembly was used Latest_WS_release Int // latest release where it was used Supercedes UNIQUE ?Sequence_collection XREF Superceded_by Superceded_by UNIQUE ?Sequence_collection XREF Supercedes Remark ?Text Status UNIQUE Live #Evidence Suppressed #Evidence Dead #Evidence Sequences ?Sequence ///////////////////////////////////////////////////////////////////////////////////////////////// // // ?CDS class - To store all coding genes // ///////////////////////////////////////////////////////////////////////////////////////////////// ?CDS Evidence #Evidence SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF CDS_child Transposon UNIQUE ?Transposon XREF CDS_child Structure Source_exons Int UNIQUE Int DB_info Database ?Database ?Database_field UNIQUE ?Text Protein_id ?Sequence UNIQUE Text UNIQUE Int // DB_info tag added [011030 krb] DB_remark ?Text #Evidence Origin From_laboratory UNIQUE ?Laboratory Species UNIQUE ?Species Genetic_code UNIQUE ?Genetic_code // needed for one gene with selenocysteine! Properties Coding CDS UNIQUE Int UNIQUE Int CDS_predicted_by ?Method Float // score of method Prediction_status UNIQUE Predicted // all CDSs must be one of these three things Partially_confirmed Confirmed Isoform #Evidence Artificial_intron UNIQUE Ribosomal_slippage Low_quality_sequence Start_not_found UNIQUE Int //UNIQUE added by MH6 WS228 End_not_found Visible Gene UNIQUE ?Gene XREF Corresponding_CDS // when live Gene_history UNIQUE ?Gene XREF Corresponding_CDS_history // when dead Corresponding_transcript ?Transcript XREF Corresponding_CDS #Evidence // links CDS' to new-style ?Transcript objects, 1-to-1 relationship Corresponding_protein UNIQUE ?Protein XREF Corresponding_CDS #Evidence Corresponding_PCR_product ?PCR_product XREF Overlaps_CDS // added for PCR mappings [010419 dl] Corresponding_oligo_set ?Oligo_set XREF Overlaps_CDS Corresponding_transposon UNIQUE ?Transposon XREF Corresponding_CDS Matching_cDNA ?Sequence XREF Matching_CDS #Evidence Interaction ?Interaction Expr_pattern ?Expr_pattern XREF CDS RNAi_result ?RNAi XREF Predicted_gene // Lincoln RNAi [001213 dl] GO_term ?GO_term XREF CDS ?GO_code #Evidence Variation ?Variation XREF Predicted_CDS // replaces Has_allele tag in ?Sequence Microarray_results ?Microarray_results XREF CDS //added for Microarray_results Reference ?Paper XREF CDS // added [011030 krb] Provisional_description ?Text #Evidence Detailed_description ?Text #Evidence Concise_description ?Text #Evidence Brief_identification UNIQUE ?Text #Evidence Confidential_remark ?Text SAGE_tag ?SAGE_tag XREF Predicted_CDS #SAGE_mapping_info 3d_data ?3d_data XREF CDS //Structure_data ?Structure_data XREF Corresponding_CDS #Evidence RNASeq_FPKM ?Life_stage Float #Evidence Last_reviewed UNIQUE DateType UNIQUE ?Person Remark ?Text #Evidence Associated_feature ?Feature XREF Associated_with_CDS #Evidence Method UNIQUE ?Method /////////////////////////////////////////////////////////////////// // // ?Transcript class - krb 021126 // /////////////////////////////////////////////////////////////////// ?Transcript Evidence #Evidence SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Transcript Structure Source_exons Int UNIQUE Int DB_info DB_remark ?Text #Evidence // was missing from first draft of Transcript Class krb Database ?Database ?Database_field UNIQUE ?Text Origin From_laboratory UNIQUE ?Laboratory // [020306 kj] Species UNIQUE ?Species // [020306 kj] Visible Gene UNIQUE ?Gene XREF Corresponding_transcript // for live transcripts Gene_history UNIQUE ?Gene XREF Corresponding_transcript_history // when Transcript is dead Variation ?Variation XREF Transcript // added to fit two alleles of RNA genes [021127 krb] Matching_cDNA ?Sequence XREF Matching_transcript #Evidence // to attach non-coding RNA genes to matching ESTs Corresponding_CDS UNIQUE ?CDS XREF Corresponding_transcript #Evidence // 1-2-1 relationships with coding genes Corresponding_PCR_product ?PCR_product XREF Overlaps_transcript Corresponding_oligo_set ?Oligo_set XREF Overlaps_transcript Reference ?Paper XREF Transcript // [020306 kj] RNAi_result ?RNAi XREF Transcript //was missing from model [021126 krb] GO_term ?GO_term XREF Transcript ?GO_code #Evidence // [030411 krb] Microarray_results ?Microarray_results XREF Transcript //added for Microarray_results Provisional_description ?Text #Evidence Detailed_description ?Text #Evidence Concise_description ?Text #Evidence Brief_identification UNIQUE ?Text Confidential_remark ?Text SAGE_tag ?SAGE_tag XREF Transcript #SAGE_mapping_info RNASeq_FPKM ?Life_stage Float #Evidence Last_reviewed UNIQUE DateType UNIQUE ?Person Remark ?Text #Evidence Properties Transcript UNIQUE asRNA UNIQUE Text // antisense long ncRNAs lincRNA UNIQUE Text // long intergenic/intervening ncRNAs mRNA UNIQUE Processed_mRNA Unprocessed_mRNA miRNA UNIQUE Text // microRNAs ncRNA UNIQUE Text // true non-coding RNAs piRNA UNIQUE Text // 21U-RNA/piwi-interacting RNA/piRNA Gary W. WS228 rRNA UNIQUE Text // Ribosomal RNAs scRNA UNIQUE Text // Small Cytoplasmic RNAs snoRNA UNIQUE Text // Small Nucleolar RNAs snRNA UNIQUE Text // Samll nuclear RNAs snlRNA UNIQUE Text // small nuclear like tRNA Type UNIQUE Text // transfer RNAs Anticodon UNIQUE Text // The anticodon of the tRNA Isoform #Evidence // Set if this is a RNA isoform Ignore #Evidence // Set for putative NMD targets which we do not want to see in wormrna Start_not_found // [020306 kj] End_not_found // [020306 kj] Associated_feature ?Feature XREF Associated_with_transcript #Evidence Method UNIQUE ?Method /////////////////////////////////////////////////////////////////// // // ?Pseudogene class - krb 030801 // /////////////////////////////////////////////////////////////////// ?Pseudogene Evidence #Evidence SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Pseudogene Transposon UNIQUE ?Transposon XREF Pseudogene_child Structure Source_exons Int UNIQUE Int DB_info DB_remark ?Text #Evidence Database ?Database ?Database_field UNIQUE ?Text Origin From_laboratory UNIQUE ?Laboratory Species UNIQUE ?Species Type UNIQUE Coding_pseudogene #Evidence //Pseudogene of a once coding loci RNA_pseudogene #Evidence //Pseudogene of a ncRNA loci Transposon_pseudogene #Evidence //Pseudogene of Transposon origins Attributes Transcribed #Evidence Fragment #Evidence SubType UNIQUE processed_pseudogene #Evidence unprocessed_pseudogene #Evidence Truncated_5 #Evidence Truncated_3 #Evidence Frameshifts UNIQUE Int Properties Isoform #Evidence Visible Gene UNIQUE ?Gene XREF Corresponding_pseudogene // when Pseudogene is live Gene_history UNIQUE ?Gene XREF Corresponding_pseudogene_history // when Pseudogene is dead Matching_cDNA ?Sequence XREF Matching_pseudogene #Evidence Brief_identification UNIQUE ?Text #Evidence Corresponding_PCR_product ?PCR_product XREF Overlaps_pseudogene Corresponding_oligo_set ?Oligo_set XREF Overlaps_pseudogene Corresponding_transposon UNIQUE ?Transposon XREF Corresponding_pseudogene RNAi_result ?RNAi XREF Pseudogene Variation ?Variation XREF Pseudogene // for completeness of variation connecting to all gene types Provisional_description ?Text #Evidence Detailed_description ?Text #Evidence Concise_description ?Text #Evidence SAGE_tag ?SAGE_tag XREF Pseudogene #SAGE_mapping_info Microarray_results ?Microarray_results XREF Pseudogene //added for Microarray_results RNASeq_FPKM ?Life_stage Float #Evidence Last_reviewed UNIQUE DateType UNIQUE ?Person Remark ?Text #Evidence Associated_feature ?Feature XREF Associated_with_pseudogene #Evidence Confidential_remark ?Text Method UNIQUE ?Method /////////////////////////////////////////////////////////////////////////// // // ?Transposon class [020128 dl] // /////////////////////////////////////////////////////////////////////////// ?Transposon Evidence #Evidence Name Public_name UNIQUE ?Text Other_name ?Text SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Transposon Structure S_child CDS_child ?CDS XREF Transposon UNIQUE Int UNIQUE Int #SMap_info // Transposon_CDSs will now link to parent Transposons ar2 02-DEC-05 Pseudogene_child ?Pseudogene XREF Transposon UNIQUE Int UNIQUE Int #SMap_info LTR_region Int UNIQUE Int Origin Species UNIQUE ?Species From_laboratory UNIQUE ?Laboratory Member_of ?Transposon_family XREF Family_members Old_Name ?Text #Evidence //to store old Transposon name Copy_status UNIQUE Full #Evidence //track if the transposon is essentially complete or a fragment. Partial #Evidence Molecular_info Corresponding_CDS ?CDS XREF Corresponding_transposon #Evidence Corresponding_pseudogene ?Pseudogene XREF Corresponding_transposon #Evidence Gene ?Gene XREF Corresponding_transposon #Evidence Visible Remark ?Text #Evidence Associated_feature ?Feature XREF Associated_with_transposon #Evidence Method UNIQUE ?Method ////////////////////////////////////////////////////////////////////////////////// // // ?Transposon_family class - used for grouping Transposons and adding meta data. // ////////////////////////////////////////////////////////////////////////////////// ?Transposon_family Evidence #Evidence Title UNIQUE ?Text // Information on the Transposon family Description ?Text Remark Text #Evidence DB_annotation ?Database UNIQUE ?LongText Family_members ?Transposon XREF Member_of // Connects to Transposon object In_variation ?Variation XREF Transposon_insertion Associated_motif ?Motif XREF Associated_transposon_family // to connect Transposon famillies to Repeat motifs ar2 /////////////////////////////////////////////////////////////////////////// // // ?Library class [040723 dl1] // // To represent libraries used for sequencing of nematode ESTs // Information to come from Mark Blaxters group in Edinburgh // /////////////////////////////////////////////////////////////////////////// ?Library DB_info Database ?Database ?Database_field UNIQUE ?Text Origin Species UNIQUE ?Species Strain UNIQUE ?Strain Life_stage UNIQUE ?Life_stage Tissue ?Text Description ?Text // Description lifted from NEMBASE Vector ?Sequence // Should we store vector sequences in the database? ///////////////////////////////////////////////////////////////////////////////// // // ?Homology_group class - krb 031120 // Class to handle clusters of orthologus genes (COG) and other related data // ///////////////////////////////////////////////////////////////////////////////// ?Homology_group Evidence #Evidence Title ?Text DB_info Database ?Database ?Database_field ?Text Group_type UNIQUE COG COG_type #Homology_type COG_code #COG_codes eggNOG eggNOG_type #Homology_type eggNOG_code #COG_codes InParanoid_group OrthoMCL_group //erich Nov06 GO_term ?GO_term XREF Homology_group Protein ?Protein XREF Homology_group Remark ?Text #Evidence #COG_codes Code_J // Translation, ribosomal structure and biogenesis Code_A // RNA processing and modification Code_K // Transcription Code_L // Replication, recombination and repair Code_B // Chromatin structure and dynamics Code_D // Cell cycle control, cell division, chromosome partitioning Code_Y // Nuclear structure Code_V // Defense mechanisms Code_T // Signal transduction mechanisms Code_M // Cell wall/membrane/envelope biogenesis Code_N // Cell motility Code_Z // Cytoskeleton Code_W // Extracellular structures Code_U // Intracellular trafficking, secretion, and vesicular transport Code_O // Posttranslational modification, protein turnover, chaperones Code_C // Energy production and conversion Code_G // Carbohydrate transport and metabolism Code_E // Amino acid transport and metabolism Code_F // Nucleotide transport and metabolism Code_H // Coenzyme transport and metabolism Code_I // Lipid transport and metabolism Code_P // Inorganic ion transport and metabolism Code_Q // Secondary metabolites biosynthesis, transport and catabolism Code_R // General function prediction only Code_S // Function unknown // J, A, K, L, B == Information storage and processing // D, Y, V, T, M, N, Z, W, U, O == Cellular processes and signalling // C, G, E, F, H, I, P, Q == Metabolism // R, S == Poorly characterized #Homology_type KOG TWOG FOG LSE NOG //eggNOG - standard cluster euNOG //eggNOG - eukaryote cluster meNOG //eggNOG - metazoan cluster COG //eggNOG - COG cluster // MH6 WS228 nemNOG //eggNOG - nematode clusters ?Homol_data SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Homol_data 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 Homol_homol ?Homol_data XREF Homol_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info RNAi_homol ?RNAi XREF Homol_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //added for RNAi mapping Oligo_set_homol ?Oligo_set XREF Homol_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Structure_homol ?Structure_data XREF Homol_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //ar2_struct Expr_homol ?Expr_pattern XREF Homol_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //added for Expr_pattern mapping [ar2 27-APR-2006] MSPeptide_homol ?Mass_spec_peptide XREF Homol_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //[ar2 07-JUN-2006] SAGE_homol ?SAGE_tag XREF Homol_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info /////////////////////////////////////////////////////////////////////////// // // ?Feature class // /////////////////////////////////////////////////////////////////////////// ?Feature SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Feature_object Name Public_name UNIQUE ?Text Other_name ?Text Status UNIQUE Live #Evidence Suppressed #Evidence Dead #Evidence Sequence_details Flanking_sequences UNIQUE Text UNIQUE Text Mapping_target UNIQUE ?Sequence Source_location UNIQUE Int UNIQUE ?Sequence UNIQUE Int UNIQUE Int UNIQUE #Evidence //source data, ?Sequence pos1 pos2 Evidence(Paper/person etc. remarks) DNA_text UNIQUE ?Text // for storing the sequence of the feature...can use IUPAC codes to be able // store consensus sequences, e.g. binding site consensus sequence Origin Species UNIQUE ?Species //added by pad, as we are moving towards multi species readyness. Strain UNIQUE ?Strain//added by pad, as we are moving towards multi strain readyness. History Merged_into UNIQUE ?Feature XREF Acquires_merge #Evidence Acquires_merge ?Feature XREF Merged_into #Evidence Deprecated Text #Evidence Visible Description ?Text SO_term ?SO_term Defined_by Defined_by_sequence ?Sequence XREF Defines_feature #Evidence Defined_by_paper ?Paper XREF Feature #Evidence Defined_by_person ?Person Defined_by_analysis ?Analysis Int Score Float Text #Evidence // this would be a log score as indicated by the analysis used in gff dump Associations Associated_with_gene ?Gene XREF Associated_feature #Evidence // richard Associated_with_CDS ?CDS XREF Associated_feature #Evidence // richard Associated_with_transcript ?Transcript XREF Associated_feature #Evidence // richard Associated_with_pseudogene ?Pseudogene XREF Associated_feature #Evidence // richard Associated_with_transposon ?Transposon XREF Associated_feature #Evidence //richard Associated_with_variation ?Variation XREF Feature #Evidence Associated_with_Position_Matrix ?Position_Matrix XREF Associated_feature #Evidence Associated_with_operon ?Operon XREF Associated_feature #Evidence Associated_with_Interaction ?Interaction XREF Feature_interactor Associated_with_expression_pattern ?Expr_pattern XREF Associated_feature #Evidence Associated_with_Feature ?Feature XREF Associated_with_Feature #Evidence Associated_with_construct ?Construct XREF Sequence_feature Associated_with_transcription_factor ?Transcription_factor XREF Associated_feature #Evidence Bound_by_product_of ?Gene XREF Gene_product_binds #Evidence //pad added this to show what gene it binds Confidential_remark ?Text //pad Remark ?Text #Evidence Method UNIQUE ?Method /////////////////////////////////////////////////////////////////////////// // // ?Feature_data class // /////////////////////////////////////////////////////////////////////////// ?Feature_data Species UNIQUE ?Species Strain UNIQUE ?Strain SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Feature_data Feature ?Method Int Int UNIQUE Float UNIQUE Text #Feature_info 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) // keep the same model as in Sequence, so same code works Method UNIQUE ?Method // Lincoln RNAi [001213 dl] ////////////////////////////////////////////////////////////////////////////////////////// // // ?Transcription_factor class This describes a type of transcription factor (and Pol II) // Gary W. 14/10/2010 // ////////////////////////////////////////////////////////////////////////////////////////// ?Transcription_factor Name UNIQUE Text Species UNIQUE ?Species Position_matrix ?Position_Matrix XREF Transcription_factor #Evidence Product_of ?Gene XREF Transcription_factor Associated_with_gene ?Gene XREF Associated_transcription_factor #Evidence Type Text #Evidence Remark Text #Evidence Associated_feature ?Feature XREF Associated_with_transcription_factor #Evidence //////////////////////////////////////////////////////////////////////////////////////////// // // ?Position_Matrix class // General data model for known or inferred binding sites of transcription factors to DNA, // accomodating either a straight position-frequency matrix (PFM), or a position-specific // weight matrix // //////////////////////////////////////////////////////////////////////////////////////////// ?Position_Matrix Description ?Text #Evidence Brief_id UNIQUE ?Text // Addition Xiaodong Type UNIQUE Frequency Weight Background_model Text UNIQUE Float Site_values Text UNIQUE Float REPEAT Threshold Float Consensus Text #Evidence Associated_feature ?Feature XREF Associated_with_Position_Matrix #Evidence Sites_used UNIQUE Int Derived_from_matrix ?Position_Matrix Bound_by_gene_product ?Gene XREF Product_binds_matrix #Evidence Transcription_factor ?Transcription_factor XREF Position_matrix #Evidence //gw3 Remark ?Text #Evidence //////////////////////////////////////////////////////////////////////////////////////////// // // ?Oligo class // //////////////////////////////////////////////////////////////////////////////////////////// ?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 PCR_product ?PCR_product XREF Oligo //added 15/02/2002 krb /////////////////////////////////////////////////////////////////// // // ?Genetic_code class - krb 030506 // Support alternative genetic codes for translation of mitochondrial genes etc. // //////////////////////////////////////////////////////////////////// ?Genetic_code Other_name ?Text NCBI_id UNIQUE Int Translation UNIQUE Text Start UNIQUE Text Stop UNIQUE Text Base1 UNIQUE Text Base2 UNIQUE Text Base3 UNIQUE Text Remark ?Text ////////////////// // // ?Protein class // ////////////////// ?Protein Peptide UNIQUE ?Peptide UNIQUE Int UNIQUE Int // Length + checksum Display View ?View Default_view UNIQUE ?View DB_info Database ?Database ?Database_field ?Text Gene_name ?Text Description UNIQUE ?Text Molecular_weight Float #Evidence Origin Species UNIQUE ?Species Wormpep // for C. elegans or C. briggsae proteins, used by subclass definitions Brigpep // History Int Text ?Text //history logging [020801 krb] Live // replace use of 'Inactive' krb 06/12/01 Visible Corresponding_CDS ?CDS XREF Corresponding_protein Homology_group ?Homology_group XREF Protein // added [031120 krb] 3d_data ?3d_data XREF Protein Interaction ?Interaction XREF Interactor_overlapping_protein // Structure_data ?Structure_data XREF Corresponding_protein #Evidence 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 Structure_homol ?Structure_data 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 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 Contains_peptide ?Mass_spec_peptide Remark ?Text #Evidence // ?Database_field - A tiny class to support ?Protein. // The Remark should explain a bit more about what the Database_field object // refers to - could be culled if class numbers get close to the max allowed. ?Database_field Remark Text //////////////// // ?Motif class //////////////// ?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 #Evidence Title ?Text DB_info Database ?Database ?Database_field ?Text // ID Accession_number DB_remark ?Text #Evidence DB_text ?LongText 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 GO_term ?GO_term XREF Motif ?GO_code #Evidence Associated_transposon_family ?Transposon_family XREF Associated_motif // to connect Transposon famillies to Repeat motifs ar2 02-DEC-05 //////////////////////////////////////////////////////////////////////////////////////////////////// // ?Database class. This is to be used in the construction of cgi URLs // an RNAi object would have a Database connection . . // Database Phenobank GeneID 512754 // RNAID 3004316 // The Phenobank Database object would have a URL_constructor // eg "http://worm.mpi-cbg.de/phenobank2/cgi-bin/GenePage.py?GeneID=&RNAID=" // // Combining the two would give a URL of // http://worm.mpi-cbg.de/phenobank2/cgi-bin/GenePage.py?GeneID=512754&RNAID=3004316 //////////////////////////////////////////////////////////////////////////////////////////////////// ?Database Name UNIQUE ?Text // name of the database Description UNIQUE Text // description of database contacts URL UNIQUE Text // Link to database home page Email Text // Contact email URL_constructor UNIQUE Text // rule to build URL to specific database entry page Database_type Text // Type or category of database WS287 /////////////////////////////////////////////////////////////////////////////////////////// // // ?Method class // // Used a lot by acedb code for displaying data (on the FMap) and dumping data (via GFF) // /////////////////////////////////////////////////////////////////////////////////////////// ?Method Remark ?Text #Evidence // the Display information controls how the column looks. Display No_display // column is not displayed at all. Colour #Colour CDS_colour #Colour // CDS outlined in this 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 // Score will be displayed as a '%' in fmap reportline + bounds default to 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 Join_blocks // link up all blocks of a single feature with lines Display_gaps // draw sequences or homols with gaps Gapped // draw sequences or homols with gaps //leaving this is preserved backwards compatibility // Alignment options (default is map only with no misaligns or clipping and do not map gaps). Align_mapping Allow_misalign // Homol reference/match coords do not have to align exactly, ref coords override. Allow_clipping // Map gaps even if they need to be clipped. Map_gaps // Map gaps for gapped aligns. Blastn // can calculate percent from score if blastn Blixem Blixem_X Blixem_N Blixem_P Belvu 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 '/'. 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 GFF GFF_source UNIQUE Text GFF_feature UNIQUE Text GFF_SO UNIQUE ?SO_term UNIQUE ?Ace2SO EMBL_dump_info #EMBL_dump_info // when used for controlling dump ?Reference Reference ?Paper Remark ?Text #Evidence Species ?Species Description ?Text //For trait information /////////////////////////////////// // // ?Expr_pattern class // /////////////////////////////////// ?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence Reflects_endogenous_expression_of ?Gene CDS ?CDS XREF Expr_pattern // for coding genes Sequence ?Sequence XREF Expr_pattern // for clones??? Clone ?Clone XREF Expr_pattern Homol Homol_homol ?Homol_data XREF Expr_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info //Expr_pattern mapping [060427 ar2] Expression_data Life_stage ?Life_stage XREF Expr_pattern #Qualifier Anatomy_term ?Anatomy_term XREF Expr_pattern #Qualifier GO_term ?GO_term XREF Expr_pattern #GR_condition Not_in_Life_stage ?Life_stage #Qualifier Not_in_Anatomy_term ?Anatomy_term #Qualifier Not_in_GO_term ?GO_term #GR_condition Subcellular_localization ?Text Type Antibody ?Text Cis_regulatory_element Text EPIC ?Text Genome_editing ?Text In_situ Text Localizome ?Text Microarray ?Microarray_experiment Northern Text Reporter_gene ?Text RNASeq ?Analysis RT_PCR Text Tiling_array ?Analysis Western Text Expression_cluster ?Expression_cluster XREF Expr_pattern //added for localizome Microarray_results ?Microarray_results XREF Expr_Pattern Pattern ?Text Picture ?Picture XREF Expr_pattern Movie ?Movie XREF Expr_pattern //Added by Wen to curate Expr_pattern video Species UNIQUE ?Species Remark ?Text #Evidence DB_info ?Database ?Database_field Text Experiment Strain UNIQUE ?Strain Reference ?Paper XREF Expr_pattern Person UNIQUE ?Person Transgene ?Transgene XREF Expr_pattern Variation ?Variation XREF Expr_pattern Construct ?Construct XREF Expression_pattern Associated_feature ?Feature XREF Associated_with_expression_pattern #Evidence Antibody_info ?Antibody XREF Expr_pattern // This applies to both Western & Antibody staining // added [031120 krb] Curated_by UNIQUE Text // Hinxton (HX) or Caltech (CIT) Sylvia [010927 krb] Historical_gene ?Gene Text //Qualifer hash will be used for Expr_pattern curation to specify the reliability of data. #Qualifier Certain Uncertain //For faint or variable expression Partial //For expression of unidentified cell in a cell group Anatomy_term ?Anatomy_term //combines life stage with anatomy term in expr pattern annotation Life_stage ?Life_stage //combines life stage with anatomy term in expr pattern annotation Remark Text //New tag to take the optional text from the Certain/Uncertain/Partial nested tags above. // ?Expr_profile class // ?SK_map class added at request of Raymond [010912 krb] // more tweaks added [010927 krb] ?Expr_profile SMap S_parent UNIQUE PCR_product UNIQUE ?PCR_product XREF Expr_profile Expr_map ?SK_map XREF Expr_profile Reference ?Paper XREF Expr_profile RNAi_result ?RNAi XREF Expr_profile // Connection made by script during build [030106 krb] Species UNIQUE ?Species Remark ?Text #Evidence Method UNIQUE ?Method ?SK_map X_coord UNIQUE Float Y_coord UNIQUE Float Mountain UNIQUE Int Date UNIQUE DateType Attribute_of Expr_profile ?Expr_profile XREF Expr_map Remark ?Text #Evidence ///////////////////////////////////////////////////////////////////////////////////////////// // // ?Antibody class model // // Summary records the whole description extracted from paper // Other_name holds the antibody's name appeared in the paper, such as MH27 // XREF from ?Antibody to ?CDS Class will be added after ?CDS is integrated // into models.wrm and gets stable. // // added by krb 031120 // // Well defined antibodies will be full populated with Isolation data. Ambigous anibodies // will be connected to what it is believed to be by the Possible_pseudonym(_of) pair of tags // No connection to CDS is required - just Gene is fine // ///////////////////////////////////////////////////////////////////////////////////////////// ?Antibody Summary UNIQUE ?Text #Evidence Public_name Text Other_name Text Gene ?Gene XREF Antibody #Evidence Isolation Original_publication UNIQUE ?Paper No_original_reference Text //proposed by Wen Location ?Laboratory Clonality UNIQUE Polyclonal UNIQUE Text Monoclonal UNIQUE Text Antigen UNIQUE Peptide UNIQUE Text Protein UNIQUE Text Other_antigen UNIQUE Text Animal UNIQUE Rabbit Mouse Rat Guinea_pig Chicken Goat Historical_gene ?Gene Text Expr_pattern ?Expr_pattern XREF Antibody_info Interactor ?Interaction Reference ?Paper XREF Antibody Remark ?Text #Evidence ///////////////////////////////////////////////////// // // ?Picture class - substantially modified by Daniela // ///////////////////////////////////////////////////// ?Picture Evidence #Evidence Description ?Text Name UNIQUE Text Species UNIQUE ?Species Crop Crop_picture ?Picture XREF Cropped_from Cropped_from ?Picture XREF Crop_picture Pick_me_to_call Text Text Remark ?Text #Evidence Type Expr_graph ?Text // #161 added by Wen for HTP expression graphs Depict Expr_pattern ?Expr_pattern XREF Picture Microarray ?Microarray_experiment // #161 added by Wen for HTP expression graphs RNASeq ?Analysis // #161 added by Wen for HTP expression graphs Tiling_array ?Analysis // #161 added by Wen for HTP expression graphs Anatomy ?Anatomy_term XREF Picture Cellular_component ?GO_term XREF Picture WBProcess ?WBProcess XREF Picture Gene ?Gene XREF Picture Microarray_results ?Microarray_results // #161 added by Wen for HTP expression graphs Life_stage ?Life_stage XREF Picture Acknowledgment Template UNIQUE Text Publication_year UNIQUE Text Article_URL UNIQUE ?Database UNIQUE ?Database_field UNIQUE ?Text Journal_URL UNIQUE ?Database Publisher_URL UNIQUE ?Database Person_name UNIQUE Text Reference ?Paper XREF Picture Contact ?Person ////////////////////////////////////////////////////////////////////////////////////////////// // // // ?Cell class // ?Cell_group class // // ////////////////////////////////////////////////////////////////////////////////////////////// ?Cell Main_name ?Anatomy_name XREF Name_for_cell #Evidence Other_name ?Anatomy_name XREF Synonym_for_cell #Evidence Brief_id ?Text //put in for Raymond and Paul, equivalent to old Remark but shorter Fate Cell_type ?Text // e.g. muscle, neuron,hypodermis, gland Program ?Text //division, differentiation, death, and differs between sexes Syncitial_cell ?Cell_group XREF Nucleus //see Cell_group, Summary UNIQUE ?Text #Evidence // the whole of old remark plus more to be added by Raymond Embryo_division_time Text Remark ?Text #Evidence 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 Anatomy_term ?Anatomy_term XREF Cell Tree_Node ?TreeNode XREF Cell Reference ?Paper XREF Cell GO_term ?GO_term XREF Cell ?GO_code #Evidence Data Reconstruction ?Reconstruction XREF Cell #ReconCellInfo Neurodata ?Cell #Neurodata Atlas ?Atlas XREF Cell Link_diagram Text ?Cell_group Main_name ?Anatomy_name XREF Name_for_cell_group #Evidence Other_name ?Anatomy_name XREF Synonym_for_cell_group #Evidence Fate ?Text Remark ?Text #Evidence Contains Cell ?Cell XREF Cell_group Nucleus ?Cell XREF Syncitial_cell // for syncitia like hyp7 Sub_group ?Cell_group XREF Contained_in Contained_in ?Cell_group XREF Sub_group Type UNIQUE Tissue Organ Region Lineage //put in for Lilncoln some time ago Life_stage ?Life_stage XREF Cell_group Anatomy_term ?Anatomy_term XREF Cell_group Reference ?Paper XREF Cell_group Tree_Node ?TreeNode XREF Cell_group Group_derivation Expression_experiment //groups made by experimenters in their reports Top_down_modelling // sylvia's anatomy modelling shown on dendrograms starting with whole animal and working downwards Bottom_up_modelling // for Raymond in the future for cell upwards approach /////////////////////////////////////////////////////////////////////// // // ?Anatomy_name - Raymond, krb [030916] // /////////////////////////////////////////////////////////////////////// ?Anatomy_name Primary Name_for_cell ?Cell XREF Main_name Name_for_cell_group ?Cell_group XREF Main_name Name_for_anatomy_term ?Anatomy_term XREF Term Secondary Synonym_for_cell ?Cell XREF Other_name Synonym_for_cell_group ?Cell_group XREF Other_name Synonym_for_anatomy_term ?Anatomy_term XREF Synonym /////////////////////////////////////////////////////////////////////// // // ?Anatomy_term class // // a model to store cell and anatomy ontology terms and relationships // ?Anatomy_term object names should be in the form of WBca:1234567 // //////////////////////////////////////////////////////////////////////// ?Anatomy_term Evidence #Evidence Version UNIQUE Int UNIQUE Int Definition UNIQUE ?Text #Evidence Term UNIQUE ?Anatomy_name XREF Name_for_anatomy_term #Evidence Synonym ?Anatomy_name XREF Synonym_for_anatomy_term #Evidence Legacy Cell ?Cell XREF Anatomy_term Embryo_division_time Text Fate Cell_type ?Text // e.g. muscle, neuron,hypodermis, gland Program ?Text //division, differentiation, death, and differs between sexes Syncitial_cell ?Anatomy_term XREF Nucleus //see Cell_group, Lineage Parent_term UNIQUE ?Anatomy_term XREF Daughter_term Daughter_term ?Anatomy_term XREF Parent_term Lineage_name Text Equivalence_fate ?Anatomy_term XREF Equivalence_origin Equivalence_origin ?Anatomy_term XREF Equivalence_fate Sex_dimorphism Herm_origin ?Anatomy_term XREF Herm_fate // Added according to Sylvia 5/06/2000 Herm_fate ?Anatomy_term XREF Herm_origin Male_origin ?Anatomy_term XREF Male_fate Male_fate ?Anatomy_term XREF Male_origin Life_stage ?Life_stage XREF Anatomy_term Tree_Node ?TreeNode XREF Anatomy_term Cell_group ?Cell_group XREF Anatomy_term Contains Cell_term ?Anatomy_term XREF Sub_group Nucleus ?Anatomy_term XREF Syncitial_cell //for syncitia like hyp7 Sub_group ?Anatomy_term XREF Contained_in Contained_in ?Anatomy_term XREF Sub_group Reconstruction ?Reconstruction XREF Anatomy_term #ReconCellInfo Neurodata ?Anatomy_term #Neurodata Link_diagram Text DB_info Database ?Database ?Database_field ?Text URL Text // for storing static URLs, such as WormAtlas, WormBook Child PART_OF_c ?Anatomy_term XREF PART_OF_p IS_A_c ?Anatomy_term XREF IS_A_p DESCENDENT_OF_c ?Anatomy_term XREF DESCENDENT_OF_p DESC_IN_HERM_c ?Anatomy_term XREF DESC_IN_HERM_p DESC_IN_MALE_c ?Anatomy_term XREF DESC_IN_MALE_p DEVELOPS_FROM_c ?Anatomy_term XREF DEVELOPS_FROM_p CELL_c ?Anatomy_term XREF CELL_p XUNION_OF_c ?Anatomy_term XREF XUNION_OF_p Parent PART_OF_p ?Anatomy_term XREF PART_OF_c IS_A_p ?Anatomy_term XREF IS_A_c DESCENDENT_OF_p ?Anatomy_term XREF DESCENDENT_OF_c DESC_IN_HERM_p ?Anatomy_term XREF DESC_IN_HERM_c DESC_IN_MALE_p ?Anatomy_term XREF DESC_IN_MALE_c DEVELOPS_FROM_p ?Anatomy_term XREF DEVELOPS_FROM_c CELL_p ?Anatomy_term XREF CELL_c XUNION_OF_p ?Anatomy_term XREF XUNION_OF_c Attribute_of Expr_pattern ?Expr_pattern XREF Anatomy_term Expression_cluster ?Expression_cluster XREF Anatomy_term #Evidence GO_term ?GO_term XREF Anatomy_term ?AO_code #Evidence Reference ?Paper XREF Anatomy_term Function Anatomy_function ?Anatomy_function XREF Involved Anatomy_function_not ?Anatomy_function XREF Not_involved Attribute_index Expr_ancestor ?Expr_pattern //attribute assigned to broader terms Expr_descendent ?Expr_pattern GO_ancestor ?GO_term //attribute assigned to narrower terms GO_descendent ?GO_term Index Ancestor ?Anatomy_term XREF Descendant //store ancestors of relationship IS_A and PART_OF Descendant ?Anatomy_term XREF Ancestor //store descendents of relationship IS_A and PART_OF Remark ?Text #Evidence Picture ?Picture XREF Anatomy WBProcess ?WBProcess XREF Anatomy_term // ?Anatomy_function class for Raymond // allow the connection between ?Anatomy_term, ?Phenotype (proxy of biological function), and // ?Gene and still give some information about the experiment itself. //name shall be "WBbtf0001" ?Anatomy_function Assay ?AO_code XREF Anatomy_function ?Condition Phenotype UNIQUE ?Phenotype XREF Anatomy_function #Anatomy_function_info Gene UNIQUE ?Gene XREF Anatomy_function #Evidence //use Published_as tag Body_part Involved ?Anatomy_term XREF Anatomy_function #Anatomy_function_info Not_involved ?Anatomy_term XREF Anatomy_function_not #Anatomy_function_info Remark Text #Evidence Reference UNIQUE ?Paper XREF Anatomy_function #Anatomy_function_info Autonomous Nonautonomous Autonomous_remark UNIQUE Text // Applies to both of the above tags Sufficient Insufficient Sufficient_remark UNIQUE Text // Applies to both of the above tags Necessary Unnecessary Necessary_remark UNIQUE Text // Applies to both of the above tags Remark Text /////////////////// // // ?Life_stage class // /////////////////// ?Life_stage Contains Cell ?Cell XREF Life_stage Cell_group ?Cell_group XREF Life_stage Anatomy_term ?Anatomy_term XREF Life_stage Sub_stage ?Life_stage XREF Contained_in Contained_in ?Life_stage XREF Sub_stage Preceded_by ?Life_stage XREF Followed_by Followed_by ?Life_stage XREF Preceded_by Expr_pattern ?Expr_pattern XREF Life_stage WBProcess ?WBProcess XREF Life_stage Picture ?Picture XREF Life_stage Remark ?Text #Evidence Definition UNIQUE ?Text #Evidence Public_name UNIQUE ?Text Other_name ?Text Reference ?Paper XREF Life_stage Curated_by UNIQUE Text /////////////////////////////////////////////////////////////////////////////// // // ?Tree class 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 // ?TreeNode class // /////////////////////////////////////////////////////////////////////////////// ?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 Taxon // UNIQUE ?Taxon XREF Tree_Node Cell UNIQUE ?Cell XREF Tree_Node Cell_group UNIQUE ?Cell_group XREF Tree_Node Anatomy_term UNIQUE ?Anatomy_term XREF Tree_Node // [2006-04-21 ar2] Raymond Pick_me_to_call UNIQUE Text Text Embedded_Tree ?Tree /////////////////////////////////////////////////////////////////////////////// // ?Jade class - model for Lincoln/Jean added by rd 000307 /////////////////////////////////////////////////////////////////////////////// ?Jade Display Text Text Text UNIQUE Text StandAloneDisplay Text /////////////////////////////////////////////////////////////////////////////// // // ?Transgene class from Wen Chen 12/00 // Reorganised by Karen/Wen May 2011 // /////////////////////////////////////////////////////////////////////////////// ?Transgene Evidence #Evidence Public_name UNIQUE ?Text Summary UNIQUE ?Text #Evidence Synonym ?Text Corresponding_variation UNIQUE ?Variation XREF Corresponding_transgene //put in to unambiguously associate the allele/transgene Construction Construct ?Construct XREF Transgene_construct Coinjection ?Construct XREF Transgene_coinjection Coinjection_other ?Text //for coinjection markers that are not specified as a construct Integration_method UNIQUE ?Text Integrated_from ?Transgene XREF Transgene_derivation Laboratory ?Laboratory #Lab_Location Author ?Author Construction_summary ?Text Genetic_information Extrachromosomal Integrated Map ?Map #Map_position //needed for transgenes with no granular mapping, e.g., just mapped to a LG Map_evidence #Evidence Mapping_data Multi_point ?Multi_pt_data Phenotype ?Phenotype XREF Transgene #Phenotype_info Phenotype_not_observed ?Phenotype XREF Not_in_Transgene #Phenotype_info Used_for Transgene_derivation ?Transgene XREF Integrated_from Expr_pattern ?Expr_pattern XREF Transgene Marker_for ?Text #Evidence Interactor ?Interaction Associated_with Marked_rearrangement ?Rearrangement XREF By_transgene Strain ?Strain XREF Transgene Component_of_genotype ?Genotype XREF Transgene Transgene_for_disease ?DO_term XREF Associated_transgene #Evidence Disease_info Models_disease ?DO_term XREF Disease_model_transgene Modifies_disease ?DO_term XREF Disease_modifier_transgene //New tag Models_disease_in_annotation ?Disease_model_annotation XREF Transgene //New tag Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_transgene //New tag Reference ?Paper XREF Transgene Species UNIQUE ?Species Remark ?Text #Evidence ////////////////////////////////////////////////////////////////// // // ?Construct class // any single contiguous stretch of engineered DNA sequence // // Introduced by Karen Y. WS245 July 2014 // ////////////////////////////////////////////////////////////////// ?Construct Evidence #Evidence Public_name ?Text Other_name ?Text Summary UNIQUE ?Text #Evidence //genotype like [Pmyo-2::GFP] Database ?Database ?Database_field ?Text Sequence_feature ?Feature XREF Associated_with_construct Driven_by_gene ?Gene XREF Drives_construct #Evidence Gene ?Gene XREF Construct_product #Evidence UTR_3 ?Gene #Evidence Fusion_reporter ?Text // Fluorescent proteins GFP, RFP, mCherry, etc. Other_reporter ?Text // to add reporters, tags that arent included in model Purification_tag ?Text // FLAG, HA, Myc, TAP, etc. Recombination_site ?Text // LoxP, FRT Type_of_construct ?Text // A controlled value list of terms is used during curation Selection_marker ?Text // Construction_summary ?Text // Backbone vector, mol bio DNA_text Text // for mapping, can include entire construct sequence Clone ?Clone XREF Construct Used_for Transgene_construct ?Transgene XREF Construct Transgene_coinjection ?Transgene XREF Coinjection Engineered_variation ?Variation XREF Derived_from_construct Topic_output_indicator ?WBProcess XREF Marker_construct Expression_pattern ?Expr_pattern XREF Construct Interactor ?Interaction Construct_for_disease ?DO_term XREF Associated_construct #Evidence Reference ?Paper Person ?Person Laboratory ?Laboratory #Lab_Location Historical_gene ?Gene Text Remark ?Text #Evidence ////////////////////////////////////////////////////////////////// // // ?RNAi class // Initially from Lincoln Stein December, 2000 // Heavily modified by Igor November, 2004 // ////////////////////////////////////////////////////////////////// ?RNAi Evidence #Evidence History_name UNIQUE ?Text Homol Homol_homol ?Homol_data XREF RNAi_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Sequence_info DNA_text Text UNIQUE Text //stores actual probe sequence for automated mapping // 1st Text is DNA, 2nd is probe name Sequence ?Sequence XREF RNAi //links to a real Sequence object used in the experiment // such as yk clone; not UNIQUE anymore Clone ?Clone XREF Used_in_RNAi // Chris WS244 PCR_product ?PCR_product XREF RNAi // links to a PCR_product object used in // the experiment; not UNIQUE anymore Uniquely_mapped //boolean; if present, signifies that ?RNAi object has a unique sequence // which maps to a single place in the genome Experiment Laboratory ?Laboratory Date UNIQUE DateType Strain UNIQUE ?Strain Genotype UNIQUE ?Text //used when no Strain object exists Treatment UNIQUE ?Text Life_stage UNIQUE ?Life_stage Temperature UNIQUE Int Delivered_by UNIQUE Bacterial_feeding //RL [010327] Injection //RL [010327] Soaking //RL [010327] Transgene_expression //RL [010327] Inhibits Predicted_gene ?CDS XREF RNAi_result #Evidence // "gene" parent (unreliable) Gene ?Gene XREF RNAi_result #Evidence //RL [010327] Transcript ?Transcript XREF RNAi_result #Evidence // [021126 krb] Pseudogene ?Pseudogene XREF RNAi_result #Evidence // [030801 krb] Supporting_data Movie ?Movie XREF RNAi // Lincoln, krb [010807] DB_info Database ?Database ?Database_field ?Text //to link out to Phenobank ar2 02-DEC-05 //removed UNIQUE as reqs multiple connections Species UNIQUE ?Species Interaction ?Interaction XREF Interaction_RNAi Reference UNIQUE ?Paper XREF RNAi //[070215 ar2] made reference unique so Paper sort of equates to a Study class for Will S Phenotype ?Phenotype XREF RNAi #Phenotype_info Phenotype_not_observed ?Phenotype XREF Not_in_RNAi #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes Expr_profile ?Expr_profile XREF RNAi_result // connection added during build [030106 krb] Remark ?Text #Evidence Method UNIQUE ?Method //////////////////////////////////////////// // // ?Phenotype_info Class // //////////////////////////////////////////// #Phenotype_info Paper_evidence ?Paper Person_evidence ?Person Curator_confirmed ?Person Remark ?Text #Evidence // specific remarks about the phenotype Quantity_description ?Text #Evidence //Remark to describe what quantity describes, below Quantity UNIQUE Int UNIQUE Int #Evidence Not #Evidence //This is being phased out but is needed for the next phase [06/08/10]. Image ?Picture #Evidence Penetrance Incomplete Text #Evidence Low Text #Evidence High Text #Evidence Complete Text #Evidence Range UNIQUE Int UNIQUE Int #Evidence // Range of penetrance Recessive #Evidence Semi_dominant #Evidence Dominant #Evidence Haplo_insufficient #Evidence Caused_by_gene ?Gene #Evidence Caused_by_other ?Text #Evidence Rescued_by_transgene ?Transgene Variation_effect Gain_of_function_undetermined_type #Evidence Antimorph_gain_of_function #Evidence Dominant_negative_gain_of_function #Evidence Hypermorph_gain_of_function #Evidence Neomorph_gain_of_function #Evidence Loss_of_function_undetermined_extent #Evidence Null #Evidence Predicted_null_via_sequence #Evidence Probable_null_via_phenotype #Evidence Hypomorph_reduction_of_function #Evidence Predicted_hypomorph_via_sequence #Evidence Probable_hypomorph_via_phenotype #Evidence Wild_allele #Evidence Affected_by Molecule ?Molecule #Evidence // ?Molecule model Karen Yook Pathogen ?Species #Evidence EQ_annotations Anatomy_term ?Anatomy_term ?PATO_term #Evidence Life_stage ?Life_stage ?PATO_term #Evidence GO_term ?GO_term ?PATO_term #Evidence Molecule_affected ?Molecule ?PATO_term #Evidence Temperature_sensitive Heat_sensitive Text #Evidence Cold_sensitive Text #Evidence Maternal UNIQUE Strictly_maternal #Evidence With_maternal_effect #Evidence Paternal #Evidence Phenotype_assay Strain ?Strain #Evidence Control_strain ?Strain #Evidence Treatment ?Text #Evidence Temperature ?Text #Evidence Genotype ?Text #Evidence Ease_of_scoring UNIQUE ES0_Impossible_to_score #Evidence ES1_Very_hard_to_score #Evidence ES2_Difficult_to_score #Evidence ES3_Easy_to_score #Evidence /////////////////////////////////////////////////////////////////////////////// // ?PCR_product class - Lincoln [010226] /////////////////////////////////////////////////////////////////////////////// ?PCR_product SMap S_parent UNIQUE Canonical_parent UNIQUE ?Sequence XREF PCR_product S_child Expr_profile ?Expr_profile XREF PCR_product UNIQUE Int UNIQUE Int #SMap_info // added for Expr_profile Class [010912 krb] Mapping_primers Left_mapping_primer UNIQUE Text Right_mapping_primer UNIQUE Text Species UNIQUE ?Species Overlaps_CDS ?CDS XREF Corresponding_PCR_product // Dan PCR mappings [010419 dl] Overlaps_transcript ?Transcript XREF Corresponding_PCR_product Overlaps_pseudogene ?Pseudogene XREF Corresponding_PCR_product // [030801 krb] Oligo ?Oligo XREF PCR_product UNIQUE Int UNIQUE Int Assay_conditions ?LongText From_laboratory UNIQUE ?Laboratory // Lincoln Orfeome attribution [020304 dl] Amplified Int SNP_locus ?Locus XREF SNP_assay // Todd [171001 krb] Variation ?Variation XREF PCR_product // For KO allele data [krb 021217]// ar2 PCR_products used in RFLPs etc Microarray_results ?Microarray_results XREF PCR_product //added for Microarray_results Class Clone ?Clone XREF PCR_product // added [krb 031126] Interaction ?Interaction RNAi ?RNAi XREF PCR_product Remark ?Text #Evidence Method UNIQUE ?Method /////////////////////////////////////////////// // ?Phenotype class // ?Phenotype_name class // ?Phenotype_Assay class /////////////////////////////////////////////// ?Phenotype Description UNIQUE ?Text #Evidence Name Primary_name UNIQUE ?Phenotype_name XREF Primary_name_for #Evidence Synonym ?Phenotype_name XREF Synonym_for #Evidence Short_name ?Phenotype_name XREF Short_name_for #Evidence Assay UNIQUE ?Text #Evidence Remark ?Text #Evidence Related_phenotypes Replaced_by ?Phenotype XREF Replaces Replaces ?Phenotype XREF Replaced_by Specialisation_of ?Phenotype XREF Generalisation_of Generalisation_of ?Phenotype XREF Specialisation_of Dead Alternate_phenotype ?Phenotype Attribute_of RNAi ?RNAi XREF Phenotype Variation ?Variation XREF Phenotype Transgene ?Transgene XREF Phenotype // Added by Carol Anatomy_function ?Anatomy_function XREF Phenotype Interaction ?Interaction XREF Interaction_phenotype Rearrangement ?Rearrangement XREF Phenotype Strain ?Strain XREF Phenotype Not_in_RNAi ?RNAi XREF Phenotype_not_observed //added by Wen for Not observed phenotypes Not_in_Variation ?Variation XREF Phenotype_not_observed //added by Wen for Not observed phenotypes Not_in_Strain ?Strain XREF Phenotype_not_observed //added by Wen for Not observed phenotypes Not_in_Transgene ?Transgene XREF Phenotype_not_observed //added by Wen for Not observed phenotypes Not_in_Rearrangement ?Rearrangement XREF Phenotype_not_observed //added by Wen for Not observed phenotypes Associated_with GO_term ?GO_term ECO_term ?ECO_term // Tag changes from GO to ECO for WS278 WBProcess ?WBProcess XREF Phenotype DO_term ?DO_term #Evidence ?Phenotype_name Primary_name_for UNIQUE ?Phenotype XREF Primary_name #Evidence Synonym_for ?Phenotype XREF Synonym #Evidence Short_name_for ?Phenotype XREF Short_name #Evidence ?Phenotype_Assay Description ?Text ////////////////////////////////////////////// // // ?Operon class - [010928 dl] // ////////////////////////////////////////////// ?Operon Public_name UNIQUE ?Text //Used for storing a publically accepted name for an Operon, not populated by default. SMap S_parent UNIQUE Canonical_parent UNIQUE ?Sequence XREF Operon Species UNIQUE ?Species Contains_gene ?Gene XREF Contained_in_operon #Trans_splice_leader Associated_feature ?Feature XREF Associated_with_operon #Evidence Reference ?Paper XREF Operon Description UNIQUE ?Text #Evidence Method UNIQUE ?Method History Merged_into UNIQUE ?Operon XREF Acquires_merge #Evidence Acquires_merge ?Operon XREF Merged_into #Evidence Split_from UNIQUE ?Operon XREF Split_into #Evidence Split_into ?Operon XREF Split_from #Evidence Deprecated Text #Evidence //pad - for operons no longer believed. Remark Text #Evidence #Trans_splice_leader SL1 #Evidence SL2 #Evidence Microarray #Evidence // Handles Blumenthal microarray assignments Inferred #Evidence ///////////////////////////////////////////////////////////////////// // ?Movie class - Lincoln ///////////////////////////////////////////////////////////////////// ?Movie Description ?Text Public_name UNIQUE Text Reference ?Paper XREF Movie DB_info ?Database ?Database_field Text Pick_me_to_call Text Text RNAi ?RNAi XREF Movie Variation ?Variation XREF Movie //[2006-04-21 ar2] Carol Expr_pattern ?Expr_pattern XREF Movie //Added by Wen to curate Expr_pattern video Remark ?Text #Evidence ///////////////////////////////////////////////////////////////////// // // Classes for microarray data // ////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////// // // ?Microarray class - Igor [030815 krb] // ///////////////////////////////////////////////////////////////////// ?Microarray Chip_type UNIQUE ?Text //SMD, Affymetrix, etc. Chip_info ?Text //Describes batch number of the chip, etc. Reference ?Paper //Describes design of the chip URL Text //to link to manufacturers site. Remark ?Text #Evidence Microarray_experiment ?Microarray_experiment XREF Microarray ///////////////////////////////////////////////////////////////////// // // ?Microarray_results class // Contains multiple results for one microarray spot. Used for both SMD and Affymetrix chips as well as for generic chips. // ///////////////////////////////////////////////////////////////////// ?Microarray_results Species UNIQUE ?Species Sequence_info UNIQUE PCR_product UNIQUE ?PCR_product XREF Microarray_results Oligo_set UNIQUE ?Oligo_set XREF Microarray_results Gene ?Gene XREF Microarray_results #Evidence // should be mapped during the build CDS ?CDS XREF Microarray_results #Evidence // should be mapped during the build Transcript ?Transcript XREF Microarray_results #Evidence // should be mapped during the build Pseudogene ?Pseudogene XREF Microarray_results #Evidence // should be mapped during the build Microarray ?Microarray Results ?Microarray_experiment UNIQUE #Microarray_data Expr_Pattern ?Expr_pattern XREF Microarray_results Range Min UNIQUE Float UNIQUE ?Microarray_experiment // mix observed ratio or frequency in all experiments and corresponding experiment Max UNIQUE Float UNIQUE ?Microarray_experiment // max observed ratio or frequency in all experiments and corresponding experiment Remark ?Text #Evidence //////////////////////////////// // // #Microarray_data // Used by ?Microarray_results. // //////////////////////////////// #Microarray_data Result A_vs_B_log_ratio UNIQUE Float // relative abundance A_vs_B_SD UNIQUE Float // standard deviation over a set of experiments Frequency UNIQUE Float // absolute abundance in ppm - [14-Mar-06 ar2] Igor wants a float (absolute?) Number_of_experiments UNIQUE Int Range_within_paper UNIQUE Float UNIQUE Float // min and max observed ratio or frequency in all experiments from a paper Confidence Confidence_level UNIQUE Float // Igor [031020 P_value UNIQUE Float Presence UNIQUE PA // present always PS // present sometimes - marginal call NP // never present Expression_cluster ?Expression_cluster XREF Microarray_results // one way XREF used to populate Cluster Class (prev ?Cluster) Remark Text #Evidence //////////////////////////////// // // ?Microarray_experiment // Used by ?Microarray_results. // //////////////////////////////// ?Microarray_experiment Microarray ?Microarray XREF Microarray_experiment Expression_cluster ?Expression_cluster XREF Microarray_experiment // Wen WS228 Species UNIQUE ?Species Sample Sample_A UNIQUE ?Condition //for PCR product-base (SMD-type) chips Sample_B UNIQUE ?Condition //for PCR product-base (SMD-type) chips Microarray_sample UNIQUE ?Condition //for oligo-based (Affymetrix-type) chips Reference ?Paper XREF Microarray_experiment Remark Text #Evidence //Will eventually replace Microarray_aff Class. //Used for Affymetrix and other oligo-based arrays. //////////////////////////////// // // ?Oligo_set class // //////////////////////////////// ?Oligo_set Species UNIQUE ?Species SMap S_parent UNIQUE Canonical_parent UNIQUE ?Sequence XREF Oligo_set Structure Target_exons Int UNIQUE Int Homol Homol_homol ?Homol_data XREF Oligo_set_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Microarray_results ?Microarray_results XREF Oligo_set Oligo ?Oligo //used in case oligos are specified Overlaps_CDS ?CDS XREF Corresponding_oligo_set #Evidence Overlaps_transcript ?Transcript XREF Corresponding_oligo_set #Evidence Overlaps_pseudogene ?Pseudogene XREF Corresponding_oligo_set #Evidence Remark Text #Evidence Type Affymetrix_microarray_probe WashU_GSC_microarray_probe Agilent_microarray_probe Affymetrix_tiling_array_probe Method UNIQUE ?Method ////////////////////////////////// // // ?Expression_cluster class // For microarray data clustering results. // ////////////////////////////////// ?Expression_cluster Description ?Text // refers to Biological meaning of this cluster group Species UNIQUE ?Species Algorithm Text // refers to the algorithm that was used to get this clustering result. Reference ?Paper XREF Expression_cluster Based_on_WB_Release Int // Wen - if authors did not provide probe information. Microarray_results ?Microarray_results Text #Evidence // refers to all experimental results included in the cluster. SAGE_tag ?SAGE_tag Text #Evidence Gene ?Gene XREF Expression_cluster Text #Evidence // Igor - populated during build based on Microarray_results mapping Attribute_of Microarray_experiment ?Microarray_experiment XREF Expression_cluster // Wen Mass_spectrometry ?Mass_spec_experiment XREF Expression_cluster // Wen WS244 RNAseq ?Analysis XREF Expression_cluster_RNAseq Single_Cell_RNASeq ?Analysis XREF Expression_cluster_scRNASeq //Wen WS285 for CenGen data Tiling_array ?Analysis XREF Expression_cluster_tiling_array qPCR ?Analysis XREF Expression_cluster_qPCR //added by Wen for qPCR curation Expr_pattern ?Expr_pattern XREF Expression_cluster #Evidence // Wen originally for Localizome Regulation Regulated_by_gene ?Gene XREF Regulate_expr_cluster // Wen WS228 Regulated_by_treatment Text // Wen WS228 Regulated_by_molecule ?Molecule XREF Regulate_expr_cluster // Wen WS228 Associated_with Life_stage ?Life_stage // Wen WS228 GO_term ?GO_term // Wen WS228 Anatomy_term ?Anatomy_term XREF Expression_cluster #Expression_cluster_info //Describes microarray experiments involving expression profiling in a particular tissue or cell WBProcess ?WBProcess XREF Expression_cluster #Evidence Remark ?Text #Evidence #Expression_cluster_info Expressed Depleted Enriched Dissection mRNA_tagging FACS ////////////////////////////////////////////////////////////////// // ?SAGE_tag class // contains sequence and mapping information for a tag ////////////////////////////////////////////////////////////////// ?SAGE_tag Evidence #Evidence Homol Homol_homol ?Homol_data XREF SAGE_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Tag_sequence UNIQUE Text // tag sequence including the restriction site Anchoring_enzyme UNIQUE ?Motif // NlaIII most commonly Tag_length UNIQUE Int // 14 most commonly Most_three_prime // added for tags which are the most 3' in a transcript Unambiguously_mapped // boolean; describes whether tag is unambiguously mapped to one SAGE transcript or to splice isoforms of the same gene at the same genomic location Corresponds_to Predicted_CDS ?CDS XREF SAGE_tag #SAGE_mapping_info Gene ?Gene XREF SAGE_tag #SAGE_mapping_info Transcript ?Transcript XREF SAGE_tag #SAGE_mapping_info Pseudogene ?Pseudogene XREF SAGE_tag #SAGE_mapping_info Results ?SAGE_experiment UNIQUE #SAGE_data //contains SAGE data for all experiments using the tag Remark ?Text #Evidence Method UNIQUE ?Method #SAGE_mapping_info Transcript_source UNIQUE ?Text //Coding RNA, Mitochondrial, Other... Position UNIQUE Int //the number of the SAGE anchoring enzyme restriction site from the 3' end of the cDNA molecule Strand UNIQUE Sense //sense/antisense Antisense Most_three_prime Unambiguously_mapped #SAGE_data Result Frequency UNIQUE Int // tag count Total_tag_count UNIQUE Int // sum of all tag counts in the experiment Relative_abundance UNIQUE Float // Frequency/Total_tag_count Significance UNIQUE Float Confidence_level UNIQUE Float Standard_deviation UNIQUE Float Number_of_experiments UNIQUE Int Expression_cluster ?Expression_cluster XREF SAGE_tag //Replaces ?Cluster connection Sequence_quality UNIQUE Float //most commonly cumulative phred scores associated with the tag // sequences; not in ?SAGE_tag since it will vary from experiment to experiment /////////////////////////////////////////////////////// // ?SAGE_experiment model // connects to condition and paper objects /////////////////////////////////////////////////////// ?SAGE_experiment Sample UNIQUE ?Condition XREF SAGE_experiment Species UNIQUE ?Species Reference ?Paper XREF SAGE_experiment Remark ?Text #Evidence ///////////////////////////////////////////////////////////////// // // ?Y2H - 14-04-2004 // ?YH class - retired Feb 2013 (WS237 models) // stores yeast two-hybrid data, initially for Interactome data // ///////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////// // // ?3d_data class - 14042004 // A protein structure class which will store data from the NESGC // /////////////////////////////////////////////////////////////////////////////////////// ?3d_data Evidence #Evidence DB_info Database ?Database ?Database_field ?Text CDS ?CDS XREF 3d_data Protein ?Protein XREF 3d_data Gene ?Gene XREF 3d_data Status Selected Cloned Expressed Soluble Purified Crystallized Diffraction_quality_crystals //Diffraction-quality Crystals Diffraction NMR_assigned //NMR assigned HSQC Crystal_structure //Crystal Structure NMR_structure //NMR Structure In_PDB //In PDB Work_stopped //Work Stopped Test_target //Test Target Other Origin Location UNIQUE NESGC //3d data sources can be added as new sub-tags to the model in the future First_imported UNIQUE DateType Last_updated UNIQUE DateType Remark ?Text #Evidence ///////////////////////// PEOPLE, PLACES AND PAPERS ////////////////////////////// // // ?Person, #Address, ?Person_name, ?Author, ?Paper, ?Journal, and ?Laboratory // /////////////////////////////////////////////////////////////////////////////////// /////////////////// // ?Person class // /////////////////// ?Person PostgreSQL_id UNIQUE Text // for linking to internal RDB // Text instead of Int so it says WBperson#### DB_info Database ?Database ?Database_field ?Text //used for storing ORCID IDs etc. Name First_name UNIQUE Text // prefered first name Middle_name Text // middle name(s) Last_name UNIQUE ?Person_name XREF Last_name_of // prefered last name Standard_name UNIQUE ?Person_name XREF Standard_name_of // name to be used for displays // default is "First_name Last_name" Full_name UNIQUE ?Person_name XREF Full_name_of // field for storing long name [030321 krb] Also_known_as ?Person_name XREF Other_name_of // new XREF added [030310 krb] Principal_investigator // Tag used to identify a person who has a lab (used when CGC lab or not.) CGC_representative_for ?Laboratory XREF Representative Laboratory ?Laboratory XREF Registered_lab_members Affiliation Text // used for storing institute affiliations that aren't in their Address Conducted ?Analysis XREF Conducted_by Address #Address Tracking Old_laboratory ?Laboratory XREF Past_lab_members // Lab(s) the person previously worked in Last_verified UNIQUE DateType // Last time the name/contact information in this record was actively verified Last_attempt_to_contact UNIQUE DateType UNIQUE Text // Text is method of attempt to contact Old_address DateType #Address // for history Left_the_field Text History Merged_into UNIQUE ?Person XREF Acquires_merge Acquires_merge ?Person XREF Merged_into Status Valid Invalid Comment Text Community_curation Author_first_pass_curation ?Paper XREF Author_first_pass Phenotype_curator_for ?Paper XREF Phenotype_curation_by Lineage Supervised ?Person XREF Supervised_by #Role Supervised_by ?Person XREF Supervised #Role Worked_with ?Person XREF Worked_with #Role Publication Paper ?Paper XREF Person #Evidence Not_paper ?Paper XREF Not_person #Evidence Publishes_as ?Author // confirmed author names (curated) can't XREF because of paper model Possibly_publishes_as ?Author XREF Possible_person // curated for Author->Paper->Person // connection but not yet verified by // the Person #Address Street_address Text // multiple lines including town, state, zip/postcode, whatever Country UNIQUE Text Institution Text // Removed the unique from this to allow multiple affiliations. Email Text // multiple emails allowed Main_phone Text // phone number for the institution, I presume Lab_phone Text Office_phone Text Other_phone Text UNIQUE Text // second text can be used to indicate type Fax Text Web_page Text // web page is part of the address info I think /////////////////////////////////////////////////////////////////////////////////////// // // #Role hash - Juancarlos October 2003 // works with the Person Class for Person lineage only. // The two DateType fields allow you to specify a start year and optionally an 'end' year. // If the second field is not specified, it is taken to mean that they are currently active at that particular role // /////////////////////////////////////////////////////////////////////////////////////// #Role Assistant_professor DateType UNIQUE DateType Phd DateType UNIQUE DateType Postdoc DateType UNIQUE DateType Masters DateType UNIQUE DateType Undergrad DateType UNIQUE DateType Highschool DateType UNIQUE DateType Sabbatical DateType UNIQUE DateType Lab_visitor DateType UNIQUE DateType Collaborated DateType UNIQUE DateType Research_staff DateType UNIQUE DateType Coauthor DateType UNIQUE DateType Unknown DateType UNIQUE DateType /////////////////////// // // ?Person_name class - krb 030210 // Simple way of searching for peoples full name (using Standard_name field of ?Person Class) or just surname. // /////////////////////// ?Person_name Name Full_name_of ?Person XREF Full_name Standard_name_of ?Person XREF Standard_name // added [030321 krb] Last_name_of ?Person XREF Last_name Other_name_of ?Person XREF Also_known_as // added [030310 krb] /////////////////// // ?Author class // /////////////////// ?Author Full_name Text Also_known_as Text // Need to keep Laboratory connected to Author since People haven't been connected to Labs yet Old_lab ?Laboratory Possible_person ?Person XREF Possibly_publishes_as Address Mail Text // this address section for Authors not yet connected to Person E_mail Text Phone Text Fax Text Paper ?Paper Sequence ?Sequence XREF From_author Keyword ?Keyword /////////////////////////////////////////////////////////////////////////////////////////////////////// // // ?Paper class - krb 040223 // ID-based system (WBPaperXXXXXXXX) to allow paper tracking and an associated ?Paper_name Class // //////////////////////////////////////////////////////////////////////////////////////////////////////// ?Paper Original_timestamp Datetype // temporary tag in transition period [krb 040223] Name ?Text //used for storing legacy names, like cgc5654 or wm95p426 DB_info Database ?Database ?Database_field ?Text //used for storing PubMed or other database identifiers, for PubMed, Database_field would be PMID History Merged_into UNIQUE ?Paper XREF Acquires_merge Acquires_merge ?Paper XREF Merged_into Status Valid Invalid Erratum_in ?Paper XREF Erratum_for Erratum_for ?Paper XREF Erratum_in Retraction_in ?Paper XREF Retraction_of Retraction_of ?Paper XREF Retraction_in Reference Title UNIQUE ?Text Journal UNIQUE ?Text //we are cleaning up Journal names and considering retiring the class Publisher UNIQUE Text Editor ?Text //used for books put in as objects Page UNIQUE Text Volume UNIQUE Text Publication_date UNIQUE ?Text //YYYY-MM-DD or YYYY-MM, replaces DateType which led to erroneous pub dates Contained_in ?Paper XREF Contains // old form Contains ?Paper XREF Contained_in Author ?Author XREF Paper #Affiliation Person ?Person XREF Paper #Evidence Describes_analysis ?Analysis XREF Reference Not_person ?Person XREF Not_Paper #Evidence Affiliation Text // Authors' affiliation if available Brief_citation UNIQUE Text Abstract ?LongText URL Text //will be used for Worm Breeder's Gazette articles and other citations available online but not through PubMed Type Journal_article #Evidence Review #Evidence Comment #Evidence News #Evidence Letter #Evidence Editorial #Evidence Congresses #Evidence Historical_article #Evidence Biography #Evidence Interview #Evidence Lectures #Evidence Interactive_tutorial #Evidence Retraction_of_publication #Evidence Retracted_publication #Evidence Technical_report #Evidence Directory #Evidence Monograph #Evidence Published_erratum #Evidence Meeting_abstract #Evidence Gazette_article #Evidence Book_chapter #Evidence Book #Evidence Email #Evidence WormBook #Evidence Other #Evidence Micropublication #Evidence Method #Evidence Refers_to Gene ?Gene XREF Reference #Evidence Allele ?Variation XREF Reference #Evidence Rearrangement ?Rearrangement XREF Reference #Evidence Sequence ?Sequence XREF Reference #Evidence CDS ?CDS XREF Reference #Evidence Transcript ?Transcript XREF Reference #Evidence Species ?Species XREF Reference #Evidence Strain ?Strain XREF Reference #Evidence Genotype ?Genotype XREF Reference Clone ?Clone XREF Reference #Evidence Expr_pattern ?Expr_pattern XREF Reference #Evidence Expr_profile ?Expr_profile XREF Reference #Evidence Cell ?Cell XREF Reference #Evidence Cell_group ?Cell_group XREF Reference #Evidence Life_stage ?Life_stage XREF Reference #Evidence RNAi ?RNAi XREF Reference #Evidence Transgene ?Transgene XREF Reference #Evidence Operon ?Operon XREF Reference #Evidence Expression_cluster ?Expression_cluster XREF Reference #Evidence Gene_cluster ?Gene_cluster XREF Reference #Evidence Feature ?Feature XREF Defined_by_paper // added [030424 dl] Microarray_experiment ?Microarray_experiment XREF Reference //added for Microarray_experiment model Anatomy_term ?Anatomy_term XREF Reference #Evidence Anatomy_function ?Anatomy_function XREF Reference Antibody ?Antibody XREF Reference #Evidence // added [031120 krb] SAGE_experiment ?SAGE_experiment XREF Reference Interaction ?Interaction XREF Paper Mass_spec_experiment ?Mass_spec_experiment XREF Reference Molecule ?Molecule XREF Reference WBProcess ?WBProcess XREF Reference Picture ?Picture XREF Reference Movie ?Movie XREF Reference DO_term ?DO_term #Evidence GO_annotation ?GO_annotation XREF Reference GO_term ?GO_term Community_curation Phenotype_curation_by ?Person XREF Phenotype_curator_for Author_first_pass ?Person XREF Author_first_pass_curation Curation_pipeline Phenotype2GO Keyword ?Keyword Remark ?Text #Evidence #Affiliation Affiliation_address UNIQUE Text Person ?Person //////////////////////// // ?Laboratory class // //////////////////////// ?Laboratory Address Mail Text Phone Text E_mail Text Fax Text URL Text //to link to lab homepage ar2 02-DEC-05 Clean_address #Address // Put back Address instead of #Address because citace doesn't have // control of Laboratory data, so anything parsed here won't be read. // If Keith or someone with control of Laboratory data wants to parse // it into #Address, please do so CGC Representative ?Person XREF CGC_representative_for Strain_designation UNIQUE Text Allele_designation UNIQUE Text Alleles ?Variation Gene_classes ?Gene_class XREF Designating_laboratory Former_gene_classes ?Gene_class Staff Registered_lab_members ?Person XREF Laboratory // for people with WormBase Person IDs Past_lab_members ?Person XREF Old_laboratory // for anyone who has left the field, or the circle of life Remark ?Text #Evidence ////////////////////////////////////////////////////////////////////////////////////////////// // // ?Gene_regulation model - Wen 05082003// // ?Gene_regulation model - retired Feb 2013 (WS237 models) // ////////////////////////////////////////////////////////////////////////////////////////////// // #GR_condition provides information on when(Life_stage) and where(Cell, Cell_group, Subcellular) certain kinds of // regulation happen. #GR_condition Life_stage ?Life_stage Cell ?Cell Cell_group ?Cell_group Anatomy_term ?Anatomy_term //Added by wen 02132006 Subcellular_localization ?Text ////////////////////////////////////////////////////////////////////////////////////////////// // // ?Variation class // ////////////////////////////////////////////////////////////////////////////////////////////// ?Variation Evidence #Evidence Name Public_name UNIQUE ?Variation_name XREF Public_name_for Other_name ?Variation_name XREF Other_name_for #Evidence Rearrangement ?Rearrangement XREF Variation // some alleles are really rearrangements HGVSg UNIQUE Text #Evidence Sequence_details SMap S_parent UNIQUE Sequence UNIQUE ?Sequence XREF Allele Flanking_sequences UNIQUE Text UNIQUE Text Mapping_target UNIQUE ?Sequence Source_location UNIQUE Int UNIQUE ?Sequence UNIQUE Int UNIQUE Int UNIQUE #Evidence //source data, ?Sequence pos1 pos2 Evidence(Paper/person etc. remarks) CGH_deleted_probes UNIQUE Text UNIQUE Text CGH_flanking_probes UNIQUE Text UNIQUE Text Type_of_mutation Substitution UNIQUE Text UNIQUE Text #Evidence // wild type and mutant sequence Insertion UNIQUE Text #Evidence Deletion UNIQUE Text #Evidence Tandem_duplication #Evidence PCR_product ?PCR_product XREF Variation SeqStatus UNIQUE Not_sequenced //[2006-02-17 ar2] to differentiate between mutations which have been sequenced and those which have not. Sequenced Pending_curation Deletion_verification Text #Evidence //[14-Mar-06 ar2] Mark Edgely of KO_alleles has developed test to confirm deletion (mt3) Variation_type Engineered_allele //construct model addition Allele SNP // replaces the old 'Status Text' part of ?Locus model Confirmed_SNP Predicted_SNP RFLP Reference_strain_digest Text Text Text // storing site, enzyme, and band size Polymorphic_strain_digest Text Text Text Transposon_insertion ?Transposon_family XREF In_variation Natural_variant Origin Species UNIQUE ?Species Strain ?Strain XREF Variation #Evidence Component_of_genotype ?Genotype XREF Variation Laboratory ?Laboratory Author ?Author // use Person when known, else use Author Person ?Person // Analysis ?Analysis Corresponding_transgene UNIQUE ?Transgene XREF Corresponding_variation Production_method CRISPR_Cas9 Homologous_recombination //Homologous_recombination MosSci MosDEL NHEJ //Non-homologous DNA end-joining, imprecise DNA repair TALENs ZFNNHEJ_repair //Zinc-finger nuclease ZFNHR_repair Expr_pattern ?Expr_pattern XREF Variation #Evidence DB_info Database ?Database ?Database_field UNIQUE ?Text //to link out to KO pages ar2 02-DEC-05 KO_consortium_allele // North American knockout consortium NBP_allele // Japanese knockout consortium NemaGENETAG_consortium_allele //NemaGENETAG consortium allele - Nektarios et al Detection_method Text Positive_clone ?Clone XREF Positive_variation #Evidence Nature_of_variation UNIQUE Polymorphic Synthetic History Merged_into UNIQUE ?Variation XREF Acquires_merge Acquires_merge ?Variation XREF Merged_into Split_from UNIQUE ?Variation XREF Split_into Split_into ?Variation XREF Split_from Status UNIQUE Live #Evidence Suppressed #Evidence Dead #Evidence Linked_to ?Variation XREF Linked_to // for being able to specify paired substitutions which are part of the same allele Affects Gene ?Gene XREF Allele #Molecular_change //#Molecular_change mh6 define precise changes [060217 ar2] Predicted_CDS ?CDS XREF Variation #Molecular_change Transcript ?Transcript XREF Variation #Molecular_change Pseudogene ?Pseudogene XREF Variation #Molecular_change Feature ?Feature XREF Associated_with_variation Interactor ?Interaction XREF Variation_interactor Possibly_affects ?Gene XREF Possibly_affected_by #Evidence Isolation Date DateType Mutagen UNIQUE Text #Evidence Forward_genetics Text #Evidence // Capture the basis of the experiment that isolated Reverse_genetics Text #Evidence // the allele. [040206 krb] Transposon_excision ?Transposon_family Derived_from_variation ?Variation XREF Derivative Derivative ?Variation XREF Derived_from_variation Derived_from_construct ?Construct XREF Engineered_variation Genetics Gene_class ?Gene_class XREF Variation Mating_efficiency Male UNIQUE ME0_Mating_not_successful #Evidence ME1_Mating_rarely_successful #Evidence ME2_Mating_usually_successful #Evidence ME3_Mating_always_successful #Evidence Hermaphrodite UNIQUE HME0_Mating_not_successful #Evidence HME1_Mating_rarely_successful #Evidence HME2_Mating_usually_successful #Evidence HME3_Mating_always_successful #Evidence Map ?Map XREF Variation #Map_position Interpolated_map_position UNIQUE ?Map UNIQUE Float 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 Marked_rearrangement ?Rearrangement XREF By_variation Description Phenotype ?Phenotype XREF Variation #Phenotype_info Phenotype_remark ?Text #Evidence Phenotype_not_observed ?Phenotype XREF Not_in_Variation #Phenotype_info //added by Wen to separate Not phenotype from real phenotypes Disease_info Models_disease ?DO_term XREF Disease_model_variation Modifies_disease ?DO_term XREF Disease_modifier_variation //New tag Models_disease_in_annotation ?Disease_model_annotation XREF Variation //New tag Modifies_disease_in_annotation ?Disease_model_annotation XREF Modifier_variation //New tag Modifies_disease_asserted_variation ?Disease_model_annotation XREF Asserted_variation // request for WS287 Reference ?Paper XREF Allele Remark ?Text #Evidence Method UNIQUE ?Method Supporting_data Movie ?Movie XREF Variation #Evidence //Carol [060421 ar2] ?Variation_name Other_name_for ?Variation XREF Other_name // main reason for this class Public_name_for ?Variation XREF Public_name // the main name for a gene // hash to contain detailed changes caused by mutations [2006-02-17 ar2] #Molecular_change VEP_consequence Text // proposed addition as well as mapping to the WB tags. VEP_impact Text #Evidence SIFT Float Text #Evidence PolyPhen Float Text #Evidence HGVSc Text #Evidence HGVSp Text #Evidence cDNA_position Text #Evidence CDS_position Text #Evidence Protein_position Text #Evidence Intron_number Text #Evidence Exon_number Text #Evidence Codon_change Text #Evidence Amino_acid_change Text #Evidence /////////////////////////////////// // ?Structure_data class for Payan /////////////////////////////////// ?Structure_data Evidence #Evidence //Contains Date_last_updated DB_info Database ?Database ?Database_field ?Text Sequence Protein UNIQUE ?Protein // Protein sequence as included in the source data Homol Pep_homol ?Protein XREF Structure_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Homol_homol ?Homol_data XREF Structure_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Status Selected UNIQUE DateType Cloned UNIQUE DateType Expressed UNIQUE DateType Soluble UNIQUE DateType Purified UNIQUE DateType Crystallized UNIQUE DateType Diffraction_quality_crystals UNIQUE DateType Diffraction UNIQUE DateType Native_diffraction_data UNIQUE DateType Phasing_diffraction_data UNIQUE DateType Nmr_assigned UNIQUE DateType Hsqc UNIQUE DateType Crystal_structure UNIQUE DateType Nmr_structure UNIQUE DateType In_pdb UNIQUE DateType In_bmrb UNIQUE DateType Work_stopped UNIQUE DateType Test_target UNIQUE DateType Other UNIQUE DateType Status_updated UNIQUE DateType // Date when status was updated as reported by the source data Wormpep_release UNIQUE Int// The Wormpep release that was used for mapping Remark ?Text #Evidence ////////////////////////////////////////////////// // // ?Mass_spec_experiment class // ////////////////////////////////////////////////// ?Mass_spec_experiment Reference ?Paper XREF Mass_spec_experiment // Describes the experiment Remark Text #Evidence Laboratory ?Laboratory // use when a CGC-derived laboratory code is available, else ignore Contact Person ?Person // use Person where possible, else use Author Author ?Author Origin Species UNIQUE ?Species Strain UNIQUE ?Strain Genotype ?Text // in many cases the proper strain name is not available, use this instead Life_stage ?Life_stage Anatomy_term ?Anatomy_term Cell_type ?Cell Sub_cellular_localization Text Digestion UNIQUE Trypsin Red_ALK Ionisation_source UNIQUE MALDI ESI Instrumentation UNIQUE IonTrap FT QTOF Database Text // database used to search for matches Program Text // program used to match MS data against databases Minimum_ion_proportion UNIQUE Float Multiple_ambiguous_IDs_allowed Minimum_peptide_length UNIQUE Int False_discovery_rate UNIQUE Float // percentage Mass_spec_peptide ?Mass_spec_peptide XREF Mass_spec_experiments // the resulting peptide data Expression_cluster ?Expression_cluster XREF Mass_spectrometry // Wen WS244 ////////////////////////////// // // ?Mass_spec_peptide class // ////////////////////////////// ?Mass_spec_peptide Peptide UNIQUE Text // the deduced peptide sequence Protein_seq UNIQUE ?Protein // the protein object of this Mass_spec_peptide Petide_is_natural // the peptide is known to occur naturally, e.g. a neuro-peptide Homol Homol_homol ?Homol_data XREF MSPeptide_homol ?Method Float Int UNIQUE Int Int UNIQUE Int #Homol_info Mass_spec_experiments ?Mass_spec_experiment XREF Mass_spec_peptide #Mass_spec_data // // The data from an experiment describing the peptide // #Mass_spec_data XCorr UNIQUE Float // SEQUEST score DeltaCN UNIQUE Float // SEQUEST score Charge_state UNIQUE Int // SEQUEST score Sp_rank UNIQUE Int // SEQUEST score Sp_score UNIQUE Float // SEQUEST score Protein_probability UNIQUE Float // from Prophet or a corresponding program Peptide_probability UNIQUE Float // from Prophet or a corresponding program Matches_database_uniquely Matches Protein ?Protein XREF Contains_peptide // matched protein ////////////////////////////////////////////////// // // ?Analysis class - used for adding meta data from large scale experiments // ////////////////////////////////////////////////// ?Analysis DB_info Database ?Database ?Database_field ?Text Title Text Based_on_WB_Release Int Based_on_DB_Release Text Group Project ?Analysis XREF Subproject Subproject ?Analysis XREF Project Description ?Text Category ?Text //Dataset Category search in AGR Sample ?Condition XREF Analysis Independent_variable Life_stage Sex Food Exposure_time Species Strain Preparation Temperature Genotype Tissue Treatment Concentration ?Text Expression_cluster_RNAseq ?Expression_cluster XREF RNAseq Expression_cluster_tiling_array ?Expression_cluster XREF Tiling_array Expression_cluster_scRNASeq ?Expression_cluster XREF Single_Cell_RNASeq //Wen WS285 for CenGen data Expression_cluster_qPCR ?Expression_cluster XREF qPCR //added by Wen for qPCR curation Microarray_experiment ?Microarray_experiment // To create Microarray Datasets in AGR Gene_cluster ?Gene_cluster XREF Analysis Molecule ?Molecule XREF Analysis Species_in_analysis ?Species XREF In_analysis Reference ?Paper XREF Describes_analysis Conducted_by ?Person XREF Conducted // not always the same as the author of the paper - eg Erich running OrthoMCL URL Text // eg www.treefam.org (or would this be covered by Source_database?) ////////////////////////////////// // // ?Condition class // ////////////////////////////////// ?Condition Life_stage ?Life_stage Sex UNIQUE Hermaphrodite Male Female //not all worms are elegans! Unknown Food Text Exposure_time Text Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid Species UNIQUE ?Species Strain ?Strain // added for Microarry_result [030127 krb] Preparation ?Text // added for Microarray_result [030127 krb] Temperature Float // Int -> Float WS236 Genotype ?Text Other ?Text Relationship Contains ?Condition XREF Contained_in Contained_in ?Condition XREF Contains Precedes ?Condition XREF Follows Follows ?Condition XREF Precedes Reference ?Paper //Defines the condition. Tissue ?Anatomy_term // added for Experiment (Microarray_results) Treatment ?Text // added for Experiment (Microarray_results) SAGE_experiment ?SAGE_experiment XREF Sample Analysis ?Analysis XREF Sample Remark ?Text #Evidence ////////////////////////////////////////////////// // // ?Molecule class Model // ////////////////////////////////////////////////// ?Molecule Name ?Text //WBMoleculeID Public_name ?Text Formula ?Text //imported from ChEBI Monoisotopic_mass Float //need to set up automated calculation based on formula IUPAC ?Text //imported from ChEBI SMILES ?Text //imported from ChEBI InChi ?Text //imported from ChEBI InChiKey ?Text //imported from ChEBI Synonym ?Text //mainly from CTD, but also from papers and ChEBI DB_info Database ?Database ?Database_field ?Text //links molecule to ChEBI, CTD, KEGG, etc Status Detected #Evidence Predicted #Evidence Detection_method ?Text #Evidence //NMR, MALDI-MS, HPLC-UV, shotgun lipidomics Extraction_method ?Text #Evidence //MeOH, exometabolome, MeOH/Chloroform, 5% trichloroacetic acid Analysis ?Analysis XREF Molecule Nonspecies_source ?Text Chemical_synthesis #Evidence Endogenous_in ?Species #Evidence Biofunction_role Metabolite #Evidence Regulator #Evidence Structural_component #Evidence Cofactor #Evidence Activator #Evidence Inhibitor #Evidence Product #Evidence Substrate #Evidence Ligand #Evidence Receptor #Evidence Essential_for ?Species #Evidence WBProcess ?WBProcess XREF Molecule Regulate_expr_cluster ?Expression_cluster XREF Regulated_by_molecule Affects_phenotype_of Variation ?Variation ?Phenotype #Evidence Strain ?Strain ?Phenotype #Evidence Transgene ?Transgene ?Phenotype #Evidence RNAi ?RNAi ?Phenotype #Evidence Rearrangement ?Rearrangement ?Phenotype #Evidence Disease_info Induces_disease ?DO_term XREF Chemical_inducer Modifies_disease ?DO_term XREF Molecule_modifier Disease_model_inducer ?Disease_model_annotation XREF Inducing_chemical Disease_model_modifier ?Disease_model_annotation XREF Modifier_molecule Interaction ?Interaction XREF Molecule_interactor Molecule_use ?Text #Evidence Reference ?Paper XREF Molecule Remark ?Text #Evidence ////////////////////////////////////////////////// // // ?WBProcess class Model - Proposed by Karen Yook WS225 // Connects to: ?Gene // ?Expression_cluster // ?Interaction // ?Anatomy_term // ?Life_stage // ?Molecule // ?Phenotype // ////////////////////////////////////////////////// ?WBProcess Public_name UNIQUE ?Text Summary UNIQUE ?Text #Evidence Other_name ?Text Related_topic Specialisation_of ?WBProcess XREF Generalisation_of Generalisation_of ?WBProcess XREF Specialisation_of Taxon NCBITaxonomyID ?Text Involved_entity Gene ?Gene XREF WBProcess #Evidence Expression_cluster ?Expression_cluster XREF WBProcess #Evidence Interaction ?Interaction XREF WBProcess #Evidence Anatomy_term ?Anatomy_term XREF WBProcess #Evidence Life_stage ?Life_stage XREF WBProcess #Evidence Molecule ?Molecule XREF WBProcess #Evidence Gene_cluster ?Gene_cluster XREF WBProcess #Evidence Associated_with Phenotype ?Phenotype XREF WBProcess #Evidence GO_term ?GO_term #Evidence DO_term ?DO_term #Evidence Picture ?Picture XREF WBProcess #Evidence Marker_construct ?Construct XREF Topic_output_indicator Movie ?Movie #Evidence Pathway DB_info Database ?Database ?Database_field ?Text //Can be used for any pathway db with unique accessionIDs Remark ?Text #Evidence Historical_gene ?Gene Text Reference ?Paper XREF WBProcess //////////////////////// // END OF FILE // //////////////////////// // CVS tagging lines // Add a line for the WS release the models file is going to be CVS tagged for // This give you a final shot at creating a nicely formatted CVS commit message // // WS292