// models.wrm - main file defining tree class structures // This file is read only when starting a new database or when you select // "Read Models" or "Add Update File" from the main menu. // // all tags must appear in tags.wrm or systags.wrm //=================================================================== // SAMPLE DATABASE VERSION Jan. 20, 2004 //=================================================================== //=================================================================== // The following are visible classes listed in the order in which // they appear in options.wrm, and hence, in the ACEDB Main Menu. //------------------------------------------------------------------ ?Author Full_name Text Image ?Image Laboratory ?Laboratory Mail Text Phone Text Fax Text E_mail Text WWW ?LongText Paper ?Paper //------------------------------------------------------------------ ?Journal Paper ?Paper XREF Journal //------------------------------------------------------------------ ?Paper Reference Title UNIQUE ?Text Journal UNIQUE ?Journal XREF Paper Publisher UNIQUE Text Pages UNIQUE Text Volume UNIQUE Text Text Year UNIQUE Int In_book #Paper Contained_in ?Paper XREF Contains // old form Medline_acc UNIQUE Int Author ?Author XREF Paper Affiliation Text // Authors' affiliation if available Abstract ?LongText Type UNIQUE Text Contains ?Paper XREF Contained_in Refers_to Species ?Species XREF Paper Vector ?Vector XREF Paper Plasmid ?Plasmid XREF Paper Library ?Library XREF Paper Accession Text EST ?EST XREF Paper Keyword ?Keyword //------------------------------------------------------------------ ?Experiment Title Text Author ?Author Blot ?Blot XREF Experiment DNA_Sample ?DNA_Sample XREF Experiment Linear_DNA ?Linear_DNA Plasmid ?Plasmid XREF Experiment EST ?EST XREF Experiment Vector ?Vector XREF Experiment Library ?Library XREF Experiment Cell_Stock ?Cell_Stock XREF Experiment Phage_Stock ?Phage_Stock XREF Experiment Transgenic_Line ?Transgenic_Line XREF Experiment Line ?Line XREF Experiment Isolate ?Isolate XREF Experiment Comment ?LongText //------------------------------------------------------------------ ?Oligo Name Text DNA UNIQUE ?DNA Int // Int is the length Molar_Extinction_Coefficient Float Specificity ?Gene XREF Oligo DNA_Sample ?DNA_Sample XREF Oligo Comment ?LongText //------------------------------------------------------------------ ?GenBank Locus Text Accession Text Gene ?Gene XREF GenBank EST ?EST XREF GenBank Pick_me_to_call Text Text //------------------------------------------------------------------ ?Gene_Family Common_Name Text Description ?LongText Gene ?Gene XREF Gene_Family EST ?EST XREF Gene_Family Paper ?Paper //------------------------------------------------------------------ ?Gene Name Text Description ?LongText Species ?Species XREF Gene Gene_Family ?Gene_Family XREF Gene GenBank ?GenBank XREF Gene Plasmid ?Plasmid XREF Gene Vector ?Vector XREF Gene Transgenic_Line ?Transgenic_Line XREF Transgene Line ?Line XREF Transgene Linear_DNA ?Linear_DNA XREF Gene Oligo ?Oligo XREF Specificity Paper ?Paper //------------------------------------------------------------------ #Similarity Name ?LongText Species ?Species GenBank ?GenBank ?EST Experiment ?Experiment XREF EST Species ?Species XREF EST Gene_Family ?Gene_Family XREF EST GenBank ?GenBank XREF EST Plasmid ?Plasmid XREF EST Library ?Library XREF EST Paper ?Paper XREF EST Similar_to #Similarity //------------------------------------------------------------------ ?Vector Name Text Description ?LongText Gene ?Gene XREF Vector Map ?Image Accession Text Pick_me_to_call UNIQUE Text Text DNA_Sample ?DNA_Sample XREF Vector REPEAT Plasmid ?Plasmid Derived_from UNIQUE Vector ?Vector Experiment ?Experiment XREF Vector Paper ?Paper XREF Vector //------------------------------------------------------------------ ?Library Description ?Text // Description of material included Laboratory ?Laboratory Author ?Author Paper ?Paper XREF Library Experiment ?Experiment XREF Library REPEAT Donor_Species #SPST Library_Type UNIQUE cDNA Genomic UNIQUE sheared Restriction_Enzyme Text Restriction_Site Text Text Vector ?Vector Host_Strain #SPST Plasmid ?Plasmid XREF Library REPEAT EST ?EST XREF Library Phage_Stock ?Phage_Stock //------------------------------------------------------------------ ?Cell_Stock Species ?Species Strain Text Genotype Text Isolate ?Isolate XREF Cell_Stock Paper ?Paper Vector ?Vector Plasmid ?Plasmid XREF Cell_Stock Experiment ?Experiment XREF Cell_Stock Freezer Text Box Text Comment Text //------------------------------------------------------------------ ?Phage_Stock Name Text Library ?Library XREF Phage_Stock Host ?Species Strain Text Genotype Text Paper ?Paper Vector ?Vector Experiment ?Experiment XREF Phage_Stock Titer_PFU_per_ul Float Freezer Text Box Text Comment Text //------------------------------------------------------------------ #SPST Species ?Species Strain Text //------------------------------------------------------------------ ?DNA_Sample Name Text Experiment ?Experiment XREF DNA_Sample Image ?Image Accession Text DNA_Type UNIQUE Plasmid ?Plasmid XREF DNA_Sample Vector ?Vector XREF DNA_Sample Genomic #SPST Linear_DNA ?Linear_DNA XREF DNA_Sample Oligo ?Oligo XREF DNA_Sample Concentration UNIQUE ug_per_ul Float umol_per_L Float Freezer Text Box Text Comments Text //------------------------------------------------------------------ ?Plasmid Name Text Description ?LongText Image ?Image Accession Text GenBank ?GenBank Vector ?Vector XREF Plasmid Gene ?Gene XREF Plasmid Author ?Author Experiment ?Experiment REPEAT Derived_from UNIQUE Library ?Library XREF Plasmid Plasmid ?Plasmid DNA_Sample ?DNA_Sample XREF Plasmid REPEAT EST ?EST XREF Plasmid Cell_Stock ?Cell_Stock XREF Plasmid REPEAT Paper ?Paper XREF Plasmid //------------------------------------------------------------------ ?Linear_DNA Experiment ?Experiment XREF Linear_DNA Strandedness UNIQUE dsDNA ssDNA Ends 5prime Text 3prime Text Feature_Expression Text DNA ?DNA DNA_Sample ?DNA_Sample Gene ?Gene XREF Linear_DNA //------------------------------------------------------------------ ?Motif Site UNIQUE Text // AA or DNA or some more elaborate descriptor Oligo Restriction_Enzyme Isoschizomers ?Motif XREF Isoschizomers REPEAT Offset Int Cleavage Text // will show the cleavage points ex: G_ACGT'C Overhang Text // was Int Company Text Paper Text Remark Text //------------------------------------------------------------------ ?Species Common_Name Text Genome Haploid_Genome_bp Float Map ?Image Paper ?Paper Gene ?Gene XREF Species EST ?EST XREF Species Transgenic_Line ?Transgenic_Line XREF Host Line ?Line XREF Species Host ?Species XREF Symbiont Symbiont ?Species XREF Host Isolate ?Isolate XREF Species //------------------------------------------------------------------ ?Transgenic_Line Name Text Experiment ?Experiment XREF Transgenic_Line Author ?Author Construct UNIQUE Plasmid ?Plasmid Vector ?Vector Transgene ?Gene XREF Transgenic_Line Copy_Num Int Host ?Species XREF Transgenic_Line Cultivar Text Ploidy UNIQUE Diploid DoubledHaploid Reference ?Paper //------------------------------------------------------------------ ?Line Name Text Experiment ?Experiment XREF Line Author ?Author Construct UNIQUE Plasmid ?Plasmid Vector ?Vector Transgene ?Gene XREF Line Copy_Num Int Species ?Species XREF Line Cultivar Text Ploidy UNIQUE Diploid DoubledHaploid Genotype ?Gene REPEAT Reference ?Paper //------------------------------------------------------------------ ?Isolate Description Long_Text Experiment ?Experiment XREF Isolate Author ?Author Species ?Species XREF Isolate Host ?Species XREF Isolate Cultivar Text Pathotype Text Genotype ?Gene REPEAT Cell_Stock ?Cell_Stock XREF Isolate Reference ?Paper //------------------------------------------------------------------ ?Blot Experiment ?Experiment XREF Blot Lane Int Text // Paper ?Paper XREF Blot //=================================================================== // These don't appear in the Main Menu, but we still use them. //------------------------------------------------------------------ //------------------------------------------------------------------ ?Source Name ?Text Address Text //------------------------------------------------------------------ ?Image Pick_me_to_call UNIQUE Text Text // A program name followed by a file name Author ?Author XREF Image Paper ?Paper //------------------------------------------------------------------ ?Laboratory Contact ?Author /=================================================================== //===================================================================== // These objects are defined in the original ACEDB release, but // we don't need them. They have been relegated to Hidden // display in options.wrm.