// wheat:/mRNA/home/genbank/ggtest/wspec/models.xgraingenes, dem 18dec01,
// standard GG models with changes in ?Sequence to fit GenBankGG data:
// Cultivar ?Germplasm // 18dec01
// Chromosome Text // GRL
// Clone_lib Text // 18dec01
// Tissue Text // 18dec01
// Dev_stage Text // GRL
// DB_xref ?Sequence // GRL
// Codon_start Int // GRL
// Properties
// pseudo // GRL
// virion // GRL
// chloroplast // GRL
// mitochondrion // GRL
// germline // GRL
// macronuclear // GRL
// EMBL_feature
// feature_gene Int Int Text #EMBL_info // GRL
// misc_RNA Int Int Text #EMBL_info // GRL
// tRNA Int Int Text #EMBL_info // GRL
// STS Int Int Text #EMBL_info // GRL
// 5'UTR Int Int Text #EMBL_info // TPD
// DB_info
// Database ?Database Text Text // ID Accession_number //Score// GRL
// EC_number ?Enzyme // GRL
// (24dec01, second try)
// Keyword Text // instead of ?Keyword
// EC_number Text // oops, no ?Enzyme class installed yet
// (25dec01, third try)
// DB_remark ?Text -> Text
// Strain ?Text -> Text
// Clone ?Text -> Text
// Remark ?Text -> Text ("Feature: source:"? a bug?)
// Added Tags: 3'UTR, -35_signal, Sex, unsure
// Added/fixed Tags: uRNA, snRNA, scRNA, -10_signal
// 4jul02:
// Tags containing "'" and "-", e.g. 3'UTR, -35_signal, were illegal.
// 24jul02: Reordered some tags.
// Linkage_Data Map to top. (as in Map_Data)
// Gene Mapping_information to top. (Is this a bad idea?)
// master GrainGenes models.wrm, from:
// ~sbeer/AllWheat/Roeder/models.wrm 3feb99 SCB, ex:
// models.wrm 2.7, for GrainGenes 1.8, from GRL 18mar98, ex:
// models.wrm 2.2, enhanced 28 Aug 95 for ace4_1, ex:
// models.wrm v. 1.9, 28 Oct 1994, for GrainGenes 1.4. ex:...
// models.wrm for Soybase, from Lisa Lorenzen, 10 Sep 1992, based on:
// models.wrm - for AATDB, database release 1-6
// DEM 4/94 Removed some fossil tags and classes that weren't in use.
// Added ?Help
// DEM 10/94 Changed Comment Text to Comment ?Text in ?Gene, ?Gene_Class and
// and ?Gene_Set, thus squashing a big bad bug of long standing.
// Also changed ?Colleague Mail Text to ?Text, so Text Search's by
// city name etc. will work.
// v2.1, DEM 6/95: Patched errors reported by xace4_0b4 (mainly dangling XREFs)
// DEM 7/95 Added Orthologous_gene_set, Current_name, Alien_species to ?Gene
// and ?Allele
// JMW, 6-15-95: Added Candidate_orthology_group and Possible_orthologues
// tags from mapdb models.wrm to ?Locus
//
// JMW, 6-15-95: Added anchoring to ?MultiMap copying from mapdb models.wrm.
//
// JMW 6-15-95: Added tags to Trait_study and Trait_scores classes and an XREF
// to the Environment class (for R.Line stripe rust data).
//
// JMW 7/31/95: Added Gale_orthology_group and Gale_orthologues tags to ?Locus.
// JMW 8/01/95: Adding Translocation_break_point as a possible type to Type tag
// of Class ?Locus.
// JMW 8/04/95: Added Type STS to Locus data object model.
// DEM 3 Apr 95, version 2.4: Added Tom De Stein's ?Sequence modifications for
// Genbank data
// DEM 23feb01, changed ?Method as per Gerry Lazo's wEST database.
// DEM 5dec01, Revised invalid tags: C-bands, 5'UTR, 3'UTR, Temp_optimum(C)
// DEM 16dec01, Removed ?Sequence XREFs for Species and Germplasm.
// 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
//
//?Allele: DEM 5/93 Modified to load Cat. Gene Symb. for Wheat
//lines deleted or changed:
//?Allele Name Correct_name ?Allele XREF Other_name
// Other_name ?Allele XREF Other_name
// Reference_Germplasm ?Germplasm XREF Allele
// Origin ?Text
//10/93 Added link to ?Gene_Product
// Gary Hart, email of 11/16/93: v, tv, dv, al, and i stocks should be
// ?Germplasm; ad, s, su and tr should be ?Text
// Gary Hart, email of 1/5/94: For stocks OTHER than the reference stocks that
// are also known to bear a particular allele, use label "Other_stock".
?Allele Reference ?Reference XREF Allele
Correct_name UNIQUE ?Allele XREF Other_name
Other_name ?Allele XREF Correct_name ?Reference XREF Allele
Previous_name ?Allele ?Reference //DON'T XREF. For the case of two
//old names whose meanings are now swapped. XREF -> confusion!
Current_name ?Allele ?Reference //DON'T XREF.
Synonym ?Allele XREF Synonym ?Reference //For two valid names for same
//allele, e.g. wheat "Aco-H1a (Hordeum)" vs. barley "Aco-1a"
Compound_allele ?Allele XREF Component_allele ?Reference
Component_allele ?Allele XREF Compound_allele ?Reference
Gene UNIQUE ?Gene XREF Allele //Put the Reference in the ?Gene record
Gene_product ?Gene_Product XREF Allele ?Reference
Hexaploid_stock ?Germplasm XREF Allele ?Reference
Tetraploid_stock ?Germplasm XREF Allele ?Reference
Diploid_stock ?Germplasm XREF Allele ?Reference
Alien_species ?Germplasm XREF Allele ?Reference
Near_isogenic_stock ?Germplasm XREF Allele ?Reference
Unnamed_synthetic_stock ?Germplasm XREF Allele ?Reference
Homologous_chromosome_substitution_line ?Text ?Reference
Alien_chromosome_addition_line ?Text ?Reference
Alien_chromosome_substitution_line ?Text ?Reference
Translocation_line ?Text ?Reference
Origin ?Text ?Reference //for non-germplasms like "Ace*4/CS"
Germplasm ?Germplasm XREF Allele ?Reference //for germplasms in which
// the allele is present but which aren't the Stock for it
Comment ?Text
Mutagen UNIQUE ?Reagent Text //Text is dose, other conditions.
Pathology ?Pathology XREF Resistant_allele
Phenotype ?Text
//Some of these properties should be dropped or done another way.
Properties Recessive
Intragenic_revertant_of_dominant
Dominant
Semi_dominant
Codominant
Weak
Temperature_Sensitive Thermo_sensitive
Cryo_sensitive
Amber
Maternal Strictly_Maternal
Maternal_and_Zygotic
With_Maternal_effect
Paternal
Image ?Image XREF Allele
Interactions ?Text //Text says what kind of interaction.
Probe ?Probe XREF Source_allele
Mapping_data 3Point ?3_point_data
Df_Dup ?Df_Dup_data
Numbered_reference Int ?Reference XREF Allele //Int is a numbered reference
//citation used in a Comment.
Data_source ?Colleague ?Text //Text is date, eg 94.04.28
Information_source ?Reference // If source is a reference
Data_curated ?Colleague ?Text //Who validated and converted to .ace
Last_update ?Text //PGD wants this for all our data.
//To add:
//Clone_of_allele ?Clone //clones derived from this allele
//Molecular_phenotype ?Gel_pattern //MWs of bands for this allele
//External_DB_keys ?Text ?Text //links to external databases
//Dropped:
// Sequence ?Sequence //Use only for ?Probe or ?Clone
//?Gene_Class: DEM extended, 5/93
//see abbreviation list in Catalogue of Gene Symbols for Wheat, 1988, p.1295
//DEM 9/93 Added Trait_affected
//DEM 11/93 removed (should link to Allele instead, maybe Gene):
// Gene_product ?Gene_Product
// Should change Abbreviation from ?Text to Text. It's picking up values from
// the Germplasm Abbreviation ?Text, which are ALL CAPs. Or, change the
// name to 'Symbol'?
//DEM 2/94 Abbreviation ?Text -> Text (collided with Germplasm Abbreviation)
// Changed Character_affected from ?Text to ?Trait
//DEM 3/94 Appending "XREF Affected_by" to Character_affected caused ACEDB
// death, until database reinitialized.
//DEM 6/94 Gene <-> Gene_Class links are now routinely causing database death.
// There's some nonuniformity in Space vs. Tab alignment of tags
// in the model here; expanded to all Space's.
?Gene_Class Reference ?Reference XREF Gene_class
URL Text Text // First is URL, second is optional description.
Abbreviation Text //eg "Adh".
See_also ?Gene_Class XREF See_also
Character_affected ?Trait XREF Affected_by
Pathology ?Pathology XREF Gene_class
Orthologous_gene_set ?Gene_Set XREF Gene_class //e.g. Adh-1
Gene ?Gene XREF Gene_class //e.g. Adh-A1, Adh-B1...
QTL ?QTL XREF Gene_class
Gene_product ?Gene_Product XREF Gene_class // GRL
Locus ?Locus XREF Gene_class
Clone ?Probe XREF Source_gene_class //DEM 3/94
Sequence ?Sequence XREF Gene_Class // GRL
Comment ?Text
Numbered_reference Int ?Reference XREF Gene_class //Int is a
//numbered reference citation used in a Comment.
//DEM 11/93 created. E.g. Aadh-1 is a homologous gene set in the Gene_Class
//Aadh. The set includes the individuals on homoeologous chromosomes of wheat
//or other species: Aadh-A1 (Triticum), Aadh-B1 (Triticum), Adh-R1 (Secale),
//etc.
?Gene_Set Reference ?Reference XREF Gene_Set
Abbreviation ?Text //eg "Adh-1"
Gene_class ?Gene_Class XREF Orthologous_gene_set
Character_affected ?Text
Gene ?Gene XREF Orthologous_gene_set
Comment ?Text
Numbered_reference Int ?Reference XREF Gene_Set //Int is a
//numbered reference citation used in a Comment.
//?Gene: DEM May 93 Modified to load the Catalogue of Gene Symbols for Wheat
//lines removed or changed:
//?Gene Name Gene_class UNIQUE ?Gene_Class XREF Gene
// Correct_name ?Gene XREF Other_name
// Other_name ?Gene XREF Other_name
// Reference_Allele ?Allele XREF Gene Text
// Allele ?Allele XREF Gene
// Origin ?Text
// New:
// Hexaploid_stock ?Germplasm XREF Gene ?Reference, etc.
//10/93 Added link to ?Gene_Product. Moved Reference to top of model.
// Gary Hart, email of 11/16/93: v, tv, dv, al, and i stocks should be
// ?Germplasm; ad, s, su and tr should be ?Text.
// Gary Hart, email of 1/14/94: Add Previous_name and Synonym for the special
// usages indicated below.
// 6/94: Expanded Tab's to Space's in this model.
// aug00, added for Barley Genetic Stocks: Inheritance, Description,
// First_mutation, Reference_allele_and_background
?Gene Mapping_information Locus ?Locus XREF Associated_gene
Candidate_locus ?Locus XREF Candidate_gene
Full_name ?Text //Barley uses full names a lot.
Reference ?Reference XREF Gene //The standard reference for this gene
URL Text Text // First is URL, second is optional description.
Gene_class ?Gene_Class XREF Gene
Orthologous_gene_set ?Gene_Set XREF Gene
Other_name ?Gene XREF Correct_name ?Reference
Correct_name ?Gene XREF Other_name ?Reference
Previous_name ?Gene ?Reference //DON'T XREF. For the case of two
//old names whose meanings are now swapped. XREF -> confusion!
Current_name ?Gene ?Reference //DON'T XREF.
Synonym ?Gene XREF Synonym ?Reference //For two valid names for same
//gene, e.g. wheat and barley names Aco-H1(Hordeum) vs. Aco-1
//Use instead of Other_name<->Correct_name for ALL barley genes
Compound_gene ?Gene XREF Component_gene ?Reference
Component_gene ?Gene XREF Compound_gene ?Reference
QTL ?QTL XREF Associated_gene
Gene_product ?Gene_Product XREF Gene ?Reference
Chromosome ?Text ?Reference
Chromosome_arm ?Text ?Reference
Hexaploid_stock ?Germplasm XREF Gene ?Reference
Tetraploid_stock ?Germplasm XREF Gene ?Reference
Diploid_stock ?Germplasm XREF Gene ?Reference
Alien_species ?Germplasm XREF Gene ?Reference
Near_isogenic_stock ?Germplasm XREF Gene ?Reference
Unnamed_synthetic_stock ?Germplasm XREF Gene ?Reference
Homologous_chromosome_substitution_line ?Text ?Reference
Alien_chromosome_addition_line ?Text ?Reference
Alien_chromosome_substitution_line ?Text ?Reference
Translocation_line ?Text ?Reference
Origin ?Text ?Reference //for non-germplasms like "Ace*4/CS"
Reference_allele UNIQUE ?Allele XREF Gene ?Reference
Reference_allele_and_background ?Allele XREF Gene ?Germplasm
Allele ?Allele XREF Gene ?Reference
Inheritance ?Text
Description ?Text
First_mutation ?Text
Comment ?Text
Molecular_information Clone ?Probe XREF Source_gene //3/94
Sequence ?Sequence XREF Gene
Pathology ?Pathology XREF Resistance_gene //DEM
Image ?Image XREF Gene
BGS_photo Text // for links to Barley Genetic Stocks DB
Mapping_data 2_point_data ?2_Point_Data XREF Gene
3Point ?3_point_data
Df_Dup ?Df_Dup_data
Related_genes ?Gene XREF Related_genes ?Text //4/94: Text describes
//kind of relationship.
Numbered_reference Int ?Reference XREF Gene //Int is a numbered
//reference citation used in a Comment.
Data_source ?Colleague ?Text //Text is date, eg 94.04.28
Information_source ?Reference // If source is a reference.
Data_curated ?Colleague ?Text //Who validated and converted to .ace
?Rearrangement Name Correct_name ?Rearrangement XREF Other_name
Other_name ?Rearrangement XREF Other_name
Reference_germplasm ?Germplasm XREF Rearrangement Text
Remark ?Text
Variant Text
Molecular_Information Polymorphism Found ?Probe
Absent ?Probe
Mutagen ?Reagent Text // Text is dose
Phenotype ?Text
Dosage_effects Haplo_insufficiency
Qualifier Text
Location ?Colleague
Author Text
Date Text
Type Deletion Uncovers Text
Duplication Covers Text
Translocation
Compound // More types needed?
Map ?Map XREF Rearrangement #map_position
Proximal_breakpoint ?Breakpoint XREF Distal_rearrangement // 3feb99
Distal_breakpoint ?Breakpoint XREF Proximal_rearrangement // 3feb99
Positive Proximal_marker ?Locus
Contains ?Locus XREF In_segment
Negative Distal_marker ?Locus
Does_not_contain ?Locus XREF Not_in_segment
Mapping_data 2Point ?2_Point_Data
3Point ?3_point_data
Df_Dup ?Df_Dup_data
In_situ UNIQUE ?Map Float Float
Germplasm ?Germplasm XREF Rearrangement //approx=line 122
Reference ?Reference XREF Rearrangement
//?Locus
//DEM 5 Oct 92:
// New "Type" values: RAPD, Gene
// Removed:
// Mapped_bands Map ?Map_Data //Lisa
// Enzyme ?Restriction //Lisa
// A81-356022 float //Lisa
// PI468.916 float //Lisa
//v1.5, Feb 93:
// "Mapping_information" -> "Map"
// Data ?F2_data -> Data ?Map_Data
// S.Tanksley 3/93 says Locus_type's should include: RFLP RAPD PCR VNTR
// Microsatellite Isozyme Gene (Gene includes Morph, Resistance, etc.)
//v1.6: Added: QTL, Linked_QTL, Image
// Removed:
// Not_used ?Restriction REPEAT
// Polymorphic_for ?Restriction REPEAT //Lisa
// Not_polymorphic_for ?Restriction REPEAT
//4/94: Drop the Wheat_name, Published_name, GrainGenes_name business,
// and switch to listing only under published name and Homoeology_
// name?
// Wheat_name ?Locus XREF GrainGenes_name//Name that follows Wheat rules
// Published_name ?Locus XREF GrainGenes_name //Name published as
// GrainGenes_name ?Locus //Put gMap values only in this object
//Feb 95: Added Candidate_gene, for Gary Hart
//JMW, 6-15-95: Added Candidate_orthology_group and Possible_orthologues
// tags from mapdb models.wrm
//JMW, 7-31-95: Added Gale_orthology_group, Gale_orthologues.
//JMW, 8-04-95: Added Type STS.
//DEM, 6 Dec 95: Removed: (old version of Candidate_orthology_group
// Homoeology_name ?Locus //Common name for homoeologs on all maps.
?Locus Type RFLP
CAPS //DEM added apr03
RAPD
APPCR //DEM added 10/95
Microsatellite
STS
AFLP
Gene
QTL
Translocation_break_point
Centromere
Telomere
C_band
//7/95: Add Other_name, Previous_name, for Wheat Gene Catalog
Other_name ?Locus XREF Correct_name ?Reference
Correct_name ?Locus XREF Other_name ?Reference
Previous_name ?Locus ?Reference //DON'T XREF. For the case of two
//old names whose meanings are now swapped. XREF -> confusion!
Current_name ?Locus ?Reference //DON'T XREF.
Synonym ?Locus XREF Synonym //When neither name is preferred.
Location Chromosome Text ?Species //E.g. 3D
Chromosome_arm Text ?Species //E.g. 3DS, short arm of 3D
Map ?Map XREF Locus #map_position
Main_Marker ?Map XREF Main_Marker
Inside Chrom_Band ?Chrom_Band XREF Inside
Interval ?Interval XREF Inside
Bin ?Bin XREF Locus // for Kleinhofs' bins
Bin_marker_for ?Bin XREF Bin_marker
Positive In_QTL ?QTL XREF Significant_marker // to draw GMAP colors
In_segment ?Rearrangement XREF Contains
In_interval ?Breakpoint_interval XREF Contains // 3fe99
Negative Not_in_QTL ?QTL XREF Nonsignificant_marker
Not_in_segment ?Rearrangement XREF Does_not_contain
Not_in_interval ?Breakpoint_interval XREF Does_not_contain // 3feb99
Data ?Map_Data XREF Locus #How_mapped
Background_marker ?Map_Data //If used specially in Composite Interval
// Mapping
Linkage_data ?Linkage_Data XREF Locus #How_mapped
Mapping_data Well_ordered // DEM 6/95 for ace4
2_point ?2_Point_Data
Species ?Species ?Reference // Species in which location was determined
Probe ?Probe XREF Locus ?Reference
//Float is size(s) of restriction bands that were mapped at this locus:
TABLE ?Text REPEAT //Column headings for Mapped_bands table, e.g.
// Enzyme "Size (kb)" Germplasm Chromosome
Mapped_bands ?Restriction ?Text ?Germplasm ?Text
//First ?Text is size in kb. Second is chromosome name, e.g. 6D
Linked_QTL ?QTL XREF Nearest_marker
Associated_gene ?Gene XREF Locus //If locus mapped by gene function.
Candidate_gene ?Gene XREF Candidate_locus //If mapped by probe.
Homology ?Protein Text Text // dem mar02: Data from Probe -> Sequence
// -> Best_pep. Texts are E-value, Title.
Gene_class ?Gene_Class XREF Locus
Image ?Image XREF Locus
BGS_photo Text // for links to Barley Genetic Stocks DB
Reference ?Reference XREF Locus
Data_source ?Colleague Text // Text is date, eg 95.11.10
Remarks Text
Candidate_orthology_group ?Locus XREF Possible_orthologues
Possible_orthologues ?Locus XREF Candidate_orthology_group
Gale_orthology_group ?Locus XREF Gale_orthologues
Gale_orthologues ?Locus XREF Gale_orthology_group
//Dropped:
// Sequence ?Sequence XREF Locus //Use only for ?Probe or ?Clone
//10/97, for Kleinhofs' bins
?Bin Locus ?Locus XREF Bin
Bin_marker ?Locus XREF Bin_marker_for
Data_source ?Colleague Text // Text is date, eg 97.09.23
//4/94 Proposed:
//List of all loci that are homoeologous, i.e. homologous in function and/or
//DNA sequence, and not-non-syntenic in location. Includes loci that are
//variant names for the same probe used by different authors.
//?Homoeology_group
// Homoeologues ?Locus XREF Homoeology_name
// Constructed type used in ?Locus Data ?Map_Data #How_mapped
?How_mapped Mapped_with_probe ?Probe
Mapped_by_function ?Gene
//?Germplasm
//DEM 25 Feb 93 Removed the dumb "Pedigree" indentation pseudotag, but no
// effect on data display even after "Read models",quit,restart; must
// rebuild database.
// Added tags for describing genetic stocks.
// Removed the XREF from Collection_and_ID ?Collection
// Added XREF for Other_name
// Changed Summary_pedigree to Pedigree, and made UNIQUE
// Made Species ?Species instead of ?Text
//v1.6: Added Image, Trait, Trait_scores
//DEM 13 Aug 94 Removed UNIQUE from Species, Pedigree, etc. Data should be
// loaded and then tested for COUNT > 1 to test for inconsistencies.
?Germplasm Other_name ?Germplasm XREF Other_name // Put data in only one.
Species ?Species //Required. Even if Subspecies also given.
Subspecies ?Species //e.g. "Triticum turgidum ssp. durum"
Donor_species ?Species //For addition chromosomes
Type #Germplasm_type
Collection_and_ID ?Collection ?Germplasm XREF Other_name
Cross_number ?Text //Identifier used by CIMMYT
Chromosome_configuration ?Text
Deletion_distal_to ?Breakpoint XREF Distal_deletion_in // 3feb99
Contains_breakpoint ?Breakpoint XREF Germplasm // 3feb99
Abbreviation ?Germplasm XREF Full_name //DEM 3/94
Full_name ?Germplasm XREF Abbreviation // " "
Pairing_configuration ?Text
Chromosome_number ?Text //Not Int. "42tt" = ditelosomic substn.
Female_Parent ?Germplasm
Male_Parent ?Germplasm
Pedigree ?Text
Selection_history ?Germplasm XREF Other_name
Market_Class ?Text
Characteristic ?Text //e.g. "Awn-color: blue-black"
Pathology ?Pathology XREF Resistant_line
Allele ?Allele XREF Germplasm
Gene ?Gene //No XREF, load only from Gene side
Gene_product ?Gene_Product XREF Germplasm //To add Reference,
//load from other side.
Rearrangement ?Rearrangement XREF Germplasm
Sequence ?Sequence XREF Germplasm
Derived_from ?Germplasm //DEM: should XREF?
Chromosome_donor ?Text //for additions, substitutions. May be
// a Germplasm or Species (or any text)
Cytoplasm ?Text
Developed_by ?Text //changed from ?Colleague for KDK, 2/94
Development_site ?Text //e.g. Alabama-USA
Collection_site ?Text //e.g. "By the road, near Tel Aviv"
Date_collected ?Text //e.g. 72.08.09
Primary_collection ?Collection
Date_of_release ?Text
Registration_No ?Text //lisa
Remark ?Text
Polymorphism ?Polymorphism #Presence //list of band sizes
Trait_description ?Trait_Study XREF Germplasm_description ?Text ?Text
// First Text is coded score, second is rough
// translation.
Trait_score ?Trait_Study Float ?Text
// Float is score, Text is units. NOTE: No XREF.
// Must manually add data to
///?Trait_Study Germplasm_score ?Germplasm Float ?Text
Reference ?Reference XREF Germplasm
Data_source ?Colleague ?Text //Text is date, e.g. 93.08.27
Data_curated ?Colleague ?Text // Who converted source to .ace
Mapping_data ?Map_Data
Linkage_data ?Linkage_Data
2_point_data ?2_Point_Data
DNA_library ?Library XREF Germplasm
Trait_study ?Trait_Study
Image ?Image XREF Germplasm
Trait_scores ?Trait_scores //Should be near end of model,
//could be a long list.
Coefficient_of_parentage ?Germplasm Float //Must be at end of
//model; this could be a Long list. Should XREF, or
//let folks query for the other matrix direction?
//DEM 5/93: Old tags expunged:
// Traits ?Trait #Trait_Information
// 9/93: Changed 'Remark General_remark' to 'Remark'
//DEM 4/94: Old tags expunged:
// Generation_derived UNIQUE Text
// Selection_method ?Text
// Maturity_group ?Text
// Phenotype UNIQUE ?Text //DEM: Delete?
// Genotype Text //3/94: not used yet
// Growth_Req UNIQUE Text
// Mutagen UNIQUE ?Reagent
// Location ?Colleague #Lab_Location
// Source ?Text
//?Germplasm_type, DEM 2/93
// Controlled vocabulary for ?Germplasm Type tag.
?Germplasm_type Cultivar
Elite_germplasm
Germplasm
Substitution
Translocation
Amphiploid
Aneuploid
Deletion
Duplication
Alien_addition
Synthetic
Recombinant_translocation_line
Mutation
Isogenic
Marker
Alloplasmic_line
// ?Presence, DEM 1/95
// List of band sizes present or absent for a polymorphism in a ?Germplasm.
// Used in
// ?Germplasm
// Polymorphism ?Polymorphism #Presence
?Presence Present ?Text REPEAT // e.g. 14.5 6.6 4.4
Absent ?Text REPEAT
// 5/94 DEM updated for acedb 3.0
// 8/95 DEM partly updated for ace4_1
?Map Type UNIQUE Genetic // this flag can be used to define subclasses
Cytogenetic //Chromosome could be Map, filtered Cytogenetic
Physical
Species ?Species // GRL to assist queries
Mapping_data ?Map_Data XREF Map
Linkage_data ?Linkage_Data XREF Map
Display Non_graphic // Prevents a graphic display
Title UNIQUE ?Text
Remark Text // Will appear in top right corner
Flipped // Then coordinates go upwards
Unit UNIQUE Text // i.e. kb, centiMorgan, MegaParsec
Centre UNIQUE Float UNIQUE Float // centre, width - else 0, 10
Extent UNIQUE Float UNIQUE Float // min, max
Default_view UNIQUE ?View
Minimal_view UNIQUE ?View // use this when >1 map displayed
View ?View // Columns to display
Inherits From_map UNIQUE ?Map // To locally edit
Author Text // login name of who edited it
Date Text
Main_Marker Main_Locus ?Locus // Items shown left of locator
Band ?Chrom_Band
Contains Locus ?Locus XREF Map
Chrom_Band ?Chrom_Band XREF Map
Rearrangement ?Rearrangement XREF Map
Interval ?Interval XREF Map
Breakpoint ?Breakpoint XREF Map // 3feb99
Breakpoint_interval ?Breakpoint_interval XREF Map // 3feb99
QTL ?QTL XREF Map
Contig ?Contig
?map_position UNIQUE Position UNIQUE Float #map_error
Ends Left UNIQUE Float #map_error
Right UNIQUE Float #map_error
Multi_Position Float #map_error //2 places on same Map
Multi_Ends Float UNIQUE Float
With UNIQUE With_locus UNIQUE ?Locus #Map_offset
// see probe.nalusda.gov:/acedocs/magic/map.html
// used for ?map_position With
?map_offset Offset UNIQUE Float
?map_error Error UNIQUE Float
?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
Locator Magnification UNIQUE Float
Projection_lines_on
Marker_points
Marker_intervals
Contigs
Reversed_physical
Physical_genes
Two_point
Multi_point
Likelihood
Points Point_query UNIQUE Text
Point_yellow UNIQUE Text
Point_colour Text #Colour // to replace above
Point_width UNIQUE Int // max width if not at RHS
Point_error_scale UNIQUE Float
Point_segregate_ordered
Point_show_marginal
Point_pne #Colour // positive, no error
Point_pe #Colour // positive, error
Point_nne #Colour // negative, no error
Point_ne #Colour // negative, error
Point_symbol UNIQUE Text // can now have more than one of these
Interval_JTM #Interval_col_conf
Interval_RD #Interval_col_conf
Interval_SRK #Interval_col_conf
Derived_tags DT_query UNIQUE Text
DT_width UNIQUE Int
DT_no_duplicates
DT_neighbours
DT_parents
DT_follow_parent
DT_symbol_query
DT_tag Text
DT_hide
Spacer Spacer_colour #Colour
Spacer_width Float
RH_data RH_query UNIQUE Text
RH_spacing UNIQUE Float
RH_show_all
RH_positive #Colour
RH_negative #Colour
RH_contradictory #Colour
pepSequence PS_Highlight_residue // il all needed for colomn display of peptides
PS_Residues_per_wrap Int
PS_Colours Text #Colour
Hydrophobicity HP_Show_Zero_bar
HP_Fixed_Scaling
HP_Calculation_window Int
HP_Display_width Int
Homol HOM_bump
pepFeature FEA_bump
FEA_Query Text
Homol_Name HOM_NAME_bump
HOM_NAME_width Int
pepActiveZone
?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
//JMW 6-15-95: Added everything below ?MultiMap Map ?Map from mapdb
// models.wrm to allow anchoring.
?MultiMap Map ?Map
Min Int // keep loci appearing on at least min maps. Default = 2
Anchor UNIQUE Text UNIQUE Text UNIQUE Text // Class tag1 tag2
// i.e Locus Homeology_group Homelogs
// class members on different maps with the
// same Anchor tag will be chained
?Reagent Other_name ?Reagent XREF Other_name
Description Text
Remark Text
Reference ?Reference
Source ?Source
Contact ?Colleague
//?Library
//Created DEM 15mar01
//For DNA clone libraries, especially ones for EST sequencing and RFLP probes
?Library Type cDNA
Genomic
Species ?Species XREF DNA_library
Germplasm ?Germplasm XREF DNA_library
Developmental_stage ?Text
Tissue ?Text
Treatment ?Text
Date ?Text
Vector ?Text
Cloning_site ?Text
Sequencing_primers ?Text
Source ?Colleague
Reference ?Reference
Remark ?Text
Probe ?Probe XREF DNA_library
Sequence ?Sequence XREF DNA_library
//?Probe
//DEM 8/27/93: Added Data_source, changed Derived_from to Source_germplasm
//DEM 12/16/93: Removed the following unused and undesired tags:
// Type #Probe_Type //Replaced with local booleans under Origin
// Y_Remark Text
// PCR_Remark ?Text
// Hybridizes_to_YAC ?Probe XREF Positive_probe REPEAT//obselete
// Vaxmap UNIQUE Float
// Insert_sequence ?Sequence //Lisa
// Length Seq_length UNIQUE Int
// Gel_length Float Float // Kb
// HindIII_sites UNIQUE Int
// Map ?Map_Data
// FingerPrint Gel_number UNIQUE Int
// Approximate_match_to UNIQUE ?Probe XREF Canonical_for
// Exact_match_to UNIQUE ?Probe XREF Canonical_for
// Funny_match_to UNIQUE ?Probe XREF Canonical_for
// Canonical_for ?Probe
// Bands UNIQUE Int Int
// Flag UNIQUE Int
// Calcul Session Int
// Neighbours ?Probe UNIQUE Float
// Cor Int
// Common_bands FREE
//DEM 10/94: Added the Other_name <-> Please_see aliasing.
?Probe Locus ?Locus XREF Probe
Other_name ?Probe XREF Please_see ?Reference //Please_see is the
// accepted name,
Please_see ?Probe XREF Other_name // Other_name is for alternates.
Synonym ?Probe XREF Synonym // Nov97, added for Katrien.
Related_probe ?Help ?Probe // ?Help is a word for the
// relationship, explained in the ?Help object.
Similar_probes ?Probe XREF Similar_probes // Probe _clusters_, based
// on sequence homology.
External_DB ?Text ?Text //e.g. "Sequence L43928", for GenBank link
Reference ?Reference XREF Probe //DEM Added
General_remark ?Text
Type cDNA //booleans
Genomic
PCR
SSR
EST
PCR_primers ?Text // mar00, currently being used for STSs, RAPDs,
// SSRs. Need to separate these out.
AFLP_primers ?Text // E.g. "E37 5' GACTGCGTACCAATTCACG"
STS_primers ?Text // Both primers in one text field.
STS_size ?Text
SSR_size ?Text
Amplification_conditions ?Text
Specificity ?Text // What genes or alleles are known to be recognized
// or distinguished, or not.
Sequence ?Sequence XREF Probe
Barley_rating Excellent
Good
Fair
Poor
Copy_number Text
Background ?Text //Lowest is clearest. Show scale, e.g. "3/5".
//Chromosome, Enzyme, Score. E.g. '7A EcorI "33 (3/13)"'
Wheat_polymorphism ?Text ?Restriction ?Text
//Chromosome, Enzyme, Score. E.g. '2D EcoRI "15 (2/15)"'
Barley_polymorphism ?Restriction ?Text
// Band sizes for this probe, a different ?Polymorphism for each
// restriction enzyme. Each one contains data for all germplasms.
// ?Text is "Polymorphic", "Not", "Maybe", "Mapped"
Cross_hybridizes_to ?Species Text
Polymorphism ?Polymorphism XREF Probe ?Text
Gel ?Gel XREF Probe //Electrophoretogram, autoradiogram...
Linkage_Group ?Text
//DEM: Insert_enzyme is the enzyme used to cut the insert DNA before
// inserting into the vector. Is there a better name? "Cloning_
// enzyme"? "DNA_enzyme"?
Origin DNA_library ?Library XREF Probe
Insert_enzyme ?Restriction ?Restriction
Source_gene_class ?Gene_Class XREF Clone //if Gene not known
Source_gene ?Gene XREF Clone //3/94
Source_allele ?Allele XREF Probe
Source_species ?Species
Source_germplasm ?Germplasm
Source_tissue ?Text
DNA_Origin ?Text //eg Hydroxylapatite-PERT-genomic (Bad label)
Insert Size Float ?Text // Text: additional bands, notes
PCR_size Float //size using Vector_PCR_primers
//Change to Insert_PCR_size?
Clone Vector ?Text
Vector_enzyme ?Restriction //enzyme used to open the vector
Excision_enzyme ?Restriction ?Restriction // enzyme(s) used
// to remove insert from the vector
Vector_PCR_primers ?Text
Vector_amplification ?Text
Bacterial_strain ?Text
Antibiotic ?Text
Subcloned_in ?Probe XREF Subclone_of
Subclone_of ?Probe XREF Subcloned_in
Location ?Colleague
Authority ?Colleague
In_pool ?Pool XREF Probe
Gridded ?Probe_Grid
Position Hybridizes_to ?Probe_Grid ?Probe XREF Positive_probe ?Text
Positive_probe ?Probe
Positive_pool_probe ?Pool
Image ?Image XREF Probe //Lisa
Data_source ?Colleague ?Text //Text is date, e.g. 93.08.27
Information_source ?Reference //If source is a Reference, other than
// the primary reference.
Note ?LongText
//4/94 Old tags expunged:
// Position In_situ UNIQUE Int Int
// Chrom_Band ?Chrom_Band XREF Probe
// pMap UNIQUE ?Contig XREF Probe Int Int // bands pMap units
// bMap UNIQUE Int Int // base units
// Autopos
//DEM 8/93 Restructured
//Information describing an electophoretic polymorphism: RFLP, PCR, isozyme,
//seed proteins, etc.
//DEM 11/93 removed old version of table:
// TABLE ?Text //Column headings for the Size table, e.g.
// //" Germplasm Gel Number Size (kb) Intensity"
// // Float is in Kb, ?Text is "Faint", "Medium", "Dark":
// Size ?Germplasm XREF Polymorphism ?Gel XREF Polymorphism Float ?Text
//DEM 1/95 Added Band_sizes, Pattern (based on RiceGenes)
//DEM 10/95 Removed:
// Locus_mapped ?Locus // no XREF; load ?Locus Mapped_bands
?Polymorphism Probe UNIQUE ?Probe XREF Polymorphism
Enzyme UNIQUE ?Restriction // For RFLPs; omit for PCR probes.
//
TABLE ?Text REPEAT //Column headings for the Size table, e.g.
// " Gel Number Size (kb) Intensity Germplasm"
// or the Value table, e.g.
// "Species " "Allele" "Germplasm"
// Float is in Kb, ?Text is "Faint", "Medium", "Dark":
Size ?Gel XREF Polymorphism Float ?Text ?Germplasm XREF Polymorphism
// Gale-style table. Text is Allele letter.:
Value ?Species Text ?Germplasm
//
Band_size ?Text //Column headings for the Pattern table, e.g.
//"14.5 12.3 4.4"
Pattern Text ?Germplasm // Don't just XREF, say Present/Absent
//
Germplasm ?Germplasm XREF Polymorphism //Use when there are no
//size measurements, just an image.
Image ?Image XREF Polymorphism // Autoradiogram, gel photo
Remarks Text
Reference ?Reference
Data_source ?Colleague Text // Text is date, eg 95.11.10
//DEM 8/93 New
//Information about a gel electrophoretogram or autoradiogram (DNA, protein...)
//A blot or film is also a ?Gel.
//Better name for this class? "Phoretogram"?
?Gel Probe ?Probe XREF Gel
Date ?Text // Date of gel or blot or autorad, then what procedure
// E.g. "93.08.05 DNA extraction"
// Standard date format: "93.08.05" (5 Aug 93)
Run_by ?Colleague // Who did the lab work
Conditions ?Text // Stringency, exposure time,...
Polymorphism ?Polymorphism //LOAD AS ?POLYMORPHISM XREF, NOT DIRECTLY
Germplasm ?Germplasm // Source of sample.
Image ?Image
TABLE Text REPEAT // Column headings for Band table.
Band ?Restriction Float UNIQUE Int UNIQUE Text // Kb, Intensity, Chrom
Data_source ?Colleague Text // Text is date, e.g. 97.11
?Probe_Grid Title ?Text
Layout Columns Int
Lines_at Int Int // x, y spacing
Space_at Int Int // x, y spacing
No_stagger // default is with alternate lines staggered
A1_labelling // label spaced blocks a-h down LHS, 1-12 across top
Row Int ?Probe XREF Gridded REPEAT
//4/94: Unused, possibly unusable in acedb3.0
?Contig bMap Length UNIQUE Int // in base units
Position UNIQUE Int // left extremity in bases
b2g UNIQUE Float Float // gMap = ax + b
gMap UNIQUE ?Map XREF Contig Float Float // extremities on gMap
pMap UNIQUE Int Int // extremities in pMap units
// Probe ?Probe XREF Contig
// Locus ?Locus XREF bMap
//DEM 11/94 First use. Based on current SolGenes + old Soybase
// 11/95 'Results' -> 'Simple_distance', to allow 'Gmap data' display
// Removed 'Standard_error'.
?2_Point_Data Point_1 UNIQUE Locus_1 UNIQUE ?Locus XREF 2_point
//? Edie appends "UNIQUE Int".
Point_2 UNIQUE Locus_2 UNIQUE ?Locus XREF 2_point
Gene ?Gene XREF 2_point_data // A convenience link for querying
// from the Gene side. ?Locus values are still required.
Simple_distance Min Float
Distance Float
Max Float
Error Float
Distance_units Text
Linkage Text
Trait_marker //== Locus_1 is a gene or qtl and Locus_2 is
// a molecular marker for it.
QTL
Location Chromosome Text //E.g. 3D
Chromosome_arm Text //E.g. 3DS
Species ?Species // Give this even if parents also given.
Female_Parent ?Germplasm XREF 2_point_data
Male_Parent ?Germplasm XREF 2_point_data
Parent ?Germplasm XREF 2_point_data // If cross was reciprocal,
// or unknown
Population ?Text // If parents not known
Generation ?Text // e.g. "BC1F2"
Number_of_individuals Int
Method ?Text
// for raw segregation data:
Map_data ?Map_Data XREF 2_point
Linkage_data ?Linkage_data XREF 2_point
//Mapped_by ?Colleague // DEFUNCT, EXPUNGED 2/96
Contact ?Colleague // Replaces Mapped_by, for Penner & Sorrells
Reference ?Reference XREF 2_point_data
URL Text Text // First is URL, second is optional description.
Remark ?Text
Data_source ?Colleague ?Text // Text is date, 94.11.30 e.g.
?Df_Dup_data Rearrangement ?Rearrangement XREF Df_Dup
Allele1 Text // when the def is also known as allele
Gene UNIQUE ?Gene XREF Df_Dup
Allele UNIQUE ?Allele XREF Df_Dup
Linkage_Group ?Map
Temperature UNIQUE Text
Date UNIQUE Text
Mapper ?Author
Genotype UNIQUE Text
Results UNIQUE Text
CGC Flag Text
Laboratory UNIQUE ?Colleague
Linkage Text
AATDB Note UNIQUE Text
Total UNIQUE Int
A_deletes_B UNIQUE Text Text
A_does_not_delete_B UNIQUE Text Text
A_includes_B UNIQUE Text Text
A_does_not_include_B UNIQUE Text Text
?3_point_data Gene1 UNIQUE ?Gene XREF 3Point ?Allele XREF 3Point
Allele1 UNIQUE ?Allele XREF 3point
Gene2 UNIQUE ?Gene XREF 3Point ?Allele XREF 3Point
Allele2 UNIQUE ?Allele XREF 3point
Gene3 UNIQUE ?Gene XREF 3Point ?Allele XREF 3Point
Allele3 UNIQUE ?Allele XREF 3point
Linker ?3_point_data XREF Linker
Linkage_group ?Map
Temperature UNIQUE Text
Date UNIQUE Text
Mapper ?Author
Genotype Text
Results Text
Result_type ABC
AB_C
A_BC
Recombinant_1 Text
Recombinant_2 Text
Recombinant_3 Text
Counts UNIQUE Int Text Int Text Int Text Int Text
CGC Laboratory UNIQUE ?Colleague
//?Colleague
// New version from Edie Paul, 3/93
// DEM 10/93 Added Image
?Colleague Position Text
Profession Text
Institution // Boolean, = "not_person"
Address Mail ?Text
Country ?Text
Phone Text
Fax Text
E_mail Text
Telex Text
WWW_page Text
Background Text // Training, experience, degrees
Research_interest ?Text
Image ?Image XREF Colleague
Publishes_as ?Author XREF Full_name
Remark Text // Note uncertainties, possible other_names etc.
Obtained_from ?Source Text // Text is date, e.g. 95.10.27
Last_update UNIQUE ?Text // For info direct from source, yy.mm
//?Author
//DEM: On R.Durbin's advice, 11 Mar 93 (~/Mail/acedb), removed the
// "XREF Author" after "Paper ?Reference". To avoid scrambled Author orders
// in papers loaded from dump files.
?Author Full_name ?Colleague XREF Publishes_as
Paper ?Reference
Image ?Image
?Journal Other_name ?Journal XREF Other_name
Source_code ?Text
ISSN_number Text
URL Text
Paper ?Reference XREF Journal
//?Reference
//DEM Jan 94 Added Agricola_code, Gene_Catalogue_number, Cited_in.
// Feb 94 Added Series
?Reference Reference Title UNIQUE ?Text
Original_title Text
Journal UNIQUE ?Journal XREF Paper
Publisher UNIQUE Text
Series ?Text // for named series of named volumes
Contained_in ?Reference XREF Contains
Year Int // Pers.Comm.s might have more than one.
Volume UNIQUE Int Text //Text when Int isn't complete
Page UNIQUE Int Int
Remark Text //e.g. when page numbers aren't Int's
URL Text //for WWW hrefs
Online Text Text //e.g. "PubMed" "10417723", Text1 is
//database, Text2 is accession.
Institution Text
Author ?Author XREF Paper
Editor ?Author XREF Paper
Type UNIQUE Text //Article, Book, Proceedings, Abstract,
//Dissertation, Bulletin, or Report
Language Text //English, Spanish, ...
Image ?Image XREF Reference
Abstract Text
Contains ?Reference XREF Contained_in
Refers_to Gene_class ?Gene_Class XREF Reference
Gene_set ?Gene_Set XREF Reference
Gene ?Gene XREF Reference
Allele ?Allele XREF Reference
Locus ?Locus XREF Reference
Rearrangement ?Rearrangement XREF Reference
Breakpoint ?Breakpoint XREF Reference // 3fe99
Probe ?Probe XREF Reference
Sequence ?Sequence XREF Reference
Germplasm ?Germplasm XREF Reference
Mapping_data ?Map_Data XREF Reference
Linkage_data ?Linkage_Data XREF Reference
2_point_data ?2_Point_Data //Lisa
Trait_study ?Trait_Study XREF Reference
Isolate ?Isolate XREF Reference
QTL ?QTL XREF Reference
Keyword ?Keyword
Agricola_code ?Text
Gene_Catalogue_number Int //Ref number in 1993 Wheat Gene Catalog
Cited_in ?Reference //4/94 DEM changed from ?Text
Summary_of ?Reference XREF Summarized_in //e.g. Plant Breeding
//Abstracts
Summarized_in ?Reference XREF Summary_of
?Restriction Site UNIQUE Text
Offset Text
Cleavage Text
Overhang Text
Isoschizomers ?Restriction REPEAT
Company ?Source
Reference ?Reference
Remark Text
// DEM 4/95 Added External_DB_key, like RiceGenes's
// 4/96: This version replaced by the TPD (Tom De Stein) revision below.
// ?Sequence Title UNIQUE ?Text
// Other_name ?Text // for repeats
// External_DB ?Text ?Text //e.g. "Sequence" "X63202". "Sequence" makes // link to EMBL, Genobase etc. via WWW
// Sequence Text // To show sequence in this Tree window instead of fMap
// Type UNIQUE DNA UNIQUE ?DNA UNIQUE Int // Int is the length
// Peptide UNIQUE ?AA
// RNA // if this tag is set display AUGC
// Length UNIQUE Int
// Library ?Source Text Text // ID Accession_number
// Subsequence_of Source UNIQUE ?Sequence
// Source_Exons Int Int // sequence of positions in genomic
// General cDNA
// Probe ?Probe XREF Sequence
// Gene ?Gene XREF Sequence
// Gene_product ?Gene_Product XREF Sequence
// Related_Sequence ?Sequence XREF Related_Sequence
// Keyword ?Keyword
// Remark ?Text
// DB_remark ?Text
// Reference ?Reference XREF Sequence
// DB_searched ?Source Int // number of homologues found
// Data_source ?Colleague ?Text // ?Text is date.
// Properties Pseudogene Text
// Transposon
// Coding CDS UNIQUE Int Int
// Precursor
// Transcript End_not_found
// Start_not_found Int // Int is frame of base 1
// mRNA Processed_mRNA
// Unprocessed_mRNA
// tRNA Text
// rRNA Text
// snRNA Text
// Contains Has_CDS ?Sequence XREF Source Int Int
// Has_Transcript ?Sequence XREF Source Int Int
// Has_Pseudogene ?Sequence XREF Source Int Int
// Has_Structural_RNA ?Sequence XREF Source Int Int
// Has_Transposon ?Sequence XREF Source Int Int
// Has_Subsequence ?Sequence XREF Source Int Int
// Has_Other_Subsequence ?Sequence XREF Source Int Int
// Features polyA_signal Int Int // putative
// promoter Int Int ?Text
// polyA_site Int Int Text
// misc_signal Int Int ?Text
// misc_feature Int Int ?Text
// repeat_region Int Int Text
// repeat_unit Int Int Text
// mutation Int Int ?Text
// sig_peptide Int Int Text
// mat_peptide Int Int Text
// old_sequence Int Int Text
// protein_bind Int Int Text
// modified_base Int Int Text
// Start copy from SAMPLEDB
?Sequence DNA UNIQUE ?DNA UNIQUE Int // Int is the length
Peptide UNIQUE ?Peptide UNIQUE Int // GRL
// if you want to register a length without a DNA sequence, then use
// a dummy sequence object, say "-". This ensures that when a real
// sequence appears, its length dominates.
Contigset ?Contigset // dem 1mar02, for EST contig sets
Contig_members ?Sequence XREF Contig
Contig ?Sequence XREF Contig_members
Singleton_in ?Contigset
Tracefile Text
Structure From Source UNIQUE ?Sequence
Source_Exons Int UNIQUE Int // start at 1
Subsequence ?Sequence XREF Source UNIQUE Int UNIQUE Int
Sequence Text // TPD
Overlap_right UNIQUE ?Sequence XREF Overlap_left UNIQUE Int
// potentially use Overlap_right integer for auto-linking
Overlap_left UNIQUE ?Sequence XREF Overlap_right
// Clone_left_end ?Clone XREF Clone_left_end UNIQUE Int // TPD
// Clone_right_end ?Clone XREF Clone_right_end UNIQUE Int // TPD
// DB_info Database ?Database Text Text // ID Accession_number // TPD
DB_info External_DB Text Text // TPD
Database ?Database Text Text // ID Accession_number //Score// GRL
DB_xref ?Sequence // GRL
Blast_hits ?Database Text Text // GRL database-geneid-accession
DB_remark Text // EMBL/Genbank
// EC_number ?Enzyme // GRL
EC_number Text // dem 24dec01 temporary
Keyword Text // EMBL/Genbank
Origin Germplasm ?Germplasm
Species ?Species
Cultivar Text // 25dec01
Chromosome Text // 18dec01
Clone_lib Text // 18dec01
Tissue Text // 18dec01
Dev_stage Text // 18dec01
Sex Text // GRL
Length Int // TPD
Date Text // TPD
// TPD Date DateType Text // Text for comments on operation
Data_source ?Colleague Text // TPD Text is date from Genbank
Map ?Map // TPD XREF Sequence #Map_position // use in particular for Genomic_canonical
Visible Title UNIQUE Text
Other_name ?Text // for repeats
Matching_Genomic ?Sequence XREF Matching_cDNA
Matching_cDNA ?Sequence XREF Matching_Genomic
Corresponding_protein UNIQUE ?Protein XREF Corresponding_DNA // GRL
Strain Text // GRL
DNA_library ?Library XREF Sequence // DEM
Clone Text // GRL
Probe ?Probe XREF Sequence // TPD
Locus ?Locus // TPD XREF Sequence
Enzyme ?Enzyme // TPD XREF DNA
Gene ?Gene XREF Sequence
Related_DNA ?Sequence XREF Related_DNA Text // Text gives relationship.
// TPD Related_protein ?Protein XREF Related_DNA
Gene_class ?Gene_Class XREF Sequence
Gene_product ?Gene_Product XREF Sequence
Remark Text
Confidential_remark ?Text
Brief_identification UNIQUE ?Text
Reference ?Reference XREF Sequence
// tag2 system: names of all objects following next tag are shown in the
// general annotation display column as "tag:objname"
Contains Has_CDS ?Sequence XREF Source Int Int // TPD
Has_Transcript ?Sequence XREF Source Int Int // TPD
Has_Pseudogene ?Sequence XREF Source Int Int // TPD
Has_Structural_RNA ?Sequence XREF Source Int Int // TPD
Has_Transposon ?Sequence XREF Source Int Int // TPD
Has_Subsequence ?Sequence XREF Source Int Int // TPD
Has_Other_Subsequence ?Sequence XREF Source Int Int // TPD
Properties 5prime_EST // DEM
3prime_EST
Pseudogene Text // explanation
pseudo // GRL
virion // GRL
chloroplast // GRL
mitochondrion // GRL
germline // GRL
macronuclear // GRL
Transposon Text // transposon type
Genomic_canonical
cDNA cDNA_EST
Contig_Phrap
RNA // if set then use U in place of T
Coding CDS UNIQUE Int UNIQUE Int
// TPD CDS_predicted_by ?Method Float // score of method
Precursor
End_not_found
Start_not_found
Codon_start Int // GRL
Transcript UNIQUE mRNA UNIQUE Processed_mRNA
Unprocessed_mRNA
// tRNA UNIQUE Text
// rRNA UNIQUE Text // GRL commented out
// snRNA UNIQUE Text
// scRNA UNIQUE Text
uRNA UNIQUE Text // GRL
// misc_RNA UNIQUE Text // GRL commented out
Status Received UNIQUE DateType
Library_construction UNIQUE DateType
Shotgun UNIQUE DateType
Shotgun_complete UNIQUE DateType
Contiguous UNIQUE DateType
Finished UNIQUE DateType
Submitted UNIQUE DateType
Archived UNIQUE DateType UNIQUE Text // Date Disk
Match_type UNIQUE Match_with_function
Match_without_function
// These are designed specifically for measuring
// statistics. What you match should be listed in
// Brief_id, Remark etc. The aim now is to use Brief_id
// exactly for what you would like a half-line summary to
// contain, for making tables etc.
// TPD ABI Clipping UNIQUE Int UNIQUE Int
// TPD SCF_File UNIQUE Text
Assembly Total_contig_length Int
Nbr_gel_readings Int
Nbr_contigs Int // total number
Nbr_large_contigs Int // number > 750bp
Large_contig_length Int // lengths > 750bp
Pads_in_large_contigs Int
Ns_in_large_contigs Int
Double_strand Int // amount of sequence left to double strand
// Should most of these be UNIQUE, giving the current status, or is
// the idea that they will show the time progression?
// TPD Splices Confirmed_intron Int Int #Splice_confirmation
// TPD Predicted_5 ?Method Float Int Int // (x, x+1) or (x, x-1)
// TPD Predicted_3 ?Method Float Int Int // (x, x+1) or (x, x-1)
// TPD Oligo ?Oligo XREF In_sequence Int UNIQUE Int // for human mapping mostly
Assembly_tags Text Int Int Text // type, start, stop, comment
Allele ?Allele // TPD XREF Sequence UNIQUE Int UNIQUE Int UNIQUE Text
// start, stop, replacement sequence
// if an insertion point Text is transposon name (distinguished
// by containing non ACTG letters), and (n, n+1) = T A, so indicates
// direction (if known).
// if a deletion, put '-' as the replacement sequence
EMBL_feature CAAT_signal Int Int Text #EMBL_info
GC_signal Int Int Text #EMBL_info
TATA_signal Int Int Text #EMBL_info
allele_seq Int Int Text #EMBL_info
conflict Int Int Text #EMBL_info
mat_peptide Int Int Text #EMBL_info
misc_binding Int Int Text #EMBL_info
misc_feature Int Int Text #EMBL_info
misc_signal Int Int Text #EMBL_info
misc_recomb Int Int Text #EMBL_info
modified_base Int Int Text #EMBL_info
mutation Int Int Text #EMBL_info
old_sequence Int Int Text #EMBL_info
polyA_signal Int Int Text #EMBL_info
polyA_site Int Int Text #EMBL_info
prim_binding Int Int Text #EMBL_info
prim_transcript Int Int Text #EMBL_info
promoter Int Int Text #EMBL_info
repeat_region Int Int Text #EMBL_info
repeat_unit Int Int Text #EMBL_info
satellite Int Int Text #EMBL_info
sig_peptide Int Int Text #EMBL_info
variation Int Int Text #EMBL_info
enhancer Int Int Text #EMBL_info
protein_bind Int Int Text #EMBL_info
stem_loop Int Int Text #EMBL_info
primer_bind Int Int Text #EMBL_info
transit_peptide Int Int Text #EMBL_info
misc_structure Int Int Text #EMBL_info
precursor_RNA Int Int Text #EMBL_info
feature_source Int Int Text #EMBL_info // TPD
feature_gene Int Int Text #EMBL_info // GRL
exon Int Int Text #EMBL_info // TPD
intron Int Int Text #EMBL_info // TPD
//illegal 5'UTR Int Int Text #EMBL_info // TPD
//illegal 3'UTR Int Int Text #EMBL_info // TPD
5_UTR Int Int Text #EMBL_info // TPD
3_UTR Int Int Text #EMBL_info // TPD
RBS Int Int Text #EMBL_info // TPD
LTR Int Int Text #EMBL_info // TPD
terminator Int Int Text #EMBL_info // GRL
misc_difference Int Int Text #EMBL_info // TPD
misc_RNA Int Int Text #EMBL_info // GRL
rRNA Int Int Text #EMBL_info // GRL
tRNA Int Int Text #EMBL_info // GRL
snRNA Int Int Text #EMBL_info // GRL
scRNA Int Int Text #EMBL_info // GRL
STS Int Int Text #EMBL_info // GRL
//illegal -35_signal Int Int Text #EMBL_info // GRL
//illegal -10_signal Int Int Text #EMBL_info // GRL
m35_signal Int Int Text #EMBL_info // dem
m10_signal Int Int Text #EMBL_info // dem
unsure Int Int Text #EMBL_info // GRL
// EMBL_features are for legitimate EMBL feature table entries only
Homol Best_DNA ?Sequence XREF DNA_homol Float Text
Best_Pep ?Protein XREF DNA_homol Float Text
DNA_homol ?Sequence XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
Pep_homol ?Protein XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
// TPD Motif_homol ?Motif XREF DNA_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
// TPD Feature ?Method Int Int UNIQUE Float UNIQUE Text
// Float is score
// Text is shown on select, and same Text are neighbours
// again, each method has a column
// double-click shows the method
// absorb TSL_site, TSL, Inverted, Tandem as features
// and probably Assembly_tags (not yet)
Method UNIQUE ?Method // DEM
// 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.
Pick_me_to_call Text Text // GRL to call Genbank annotations
Alignment ?LongText // dem mar01, for CAP3 output
// Future model for URL calling feature:
// ?Url Url UNIQUE Text // Simple, text of URL
// Template UNIQUE ?Url // use this object as a generic template
// Reference_tag UNIQUE Text // look for this tag in the reffing object for url
// Remove_prefix UNIQUE Text // prefix to remove to make url
// Remove_postfix UNIQUE Text // postfix to remove to make url
// Prepend UNIQUE Text // then add this to the beginning
// Append UNIQUE Text // then add this to the end
?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.
?Splice_confirmation UNIQUE cDNA
Homology
// TPD?Repeat_info Percent_Identity UNIQUE Int
// TPD Score ?Method UNIQUE Float
// TPD N_gaps UNIQUE Int
// TPD Loop UNIQUE Int UNIQUE Int // rel start, stop
// TPD Unit_Length UNIQUE Int
?Protein Title UNIQUE ?Text // GRL
// TPD Other_name ?Text // for repeats
Peptide UNIQUE ?Peptide UNIQUE Int // Length, GRL ?Peptide replaced
DB_info Database ?Database Text Text // ID Accession_number
// TPD DB_remark ?Text // Swissprot CC entries
// TPD Keyword ?Keyword // Swissprot
// TPD DB_searched ?Database Int // Int = version - should this be here?
Origin From_Database ?Database UNIQUE Int // release number
// TPD Date DateType Text // Text for comments on operation
// TPD Species ?Species
// TPD Wormpep Replaces ?Protein XREF Replaced_by
// TPD Inactive Replaced_by ?Protein XREF Replaces
// TPD // inactive wormpep entries won't be output in standard wormpep dumps
Visible Corresponding_DNA ?Sequence XREF Corresponding_protein // GRL
// TPD Related_DNA ?Sequence XREF Related_protein
// TPD Related_protein ?Protein XREF Related_protein
// TPD Enzyme ?Enzyme // TPD XREF Protein
// TPD Reference ?Reference // TPD XREF Protein
// TPD // tag2 system. For now I have not populated this column. For C. elegans
// TPD // wormpep we want to get the information from the ?Corresponding_DNA
// TPD // object. Because those objects have long term continuity, while wormpep
// TPD // objects are one per protein sequence. At least that is the current
// TPD // plan.
// TPD Swiss_feature Text Int Int Text // feature name, start, stop, note
Homol DNA_homol ?Sequence XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
Pep_homol ?Protein XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
// TPD Motif_homol ?Motif XREF Pep_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
// TPD Feature ?Method Int Int UNIQUE Float // display according to method
// double-click shows the method
// TPD?Motif Match_sequence UNIQUE Text // Text is the DNA or protein sequence
// TPD Num_mismatch UNIQUE Int // Allowed number of mismatches when matching
// TPD // (default 0)
// TPD Restriction Isoschizomer ?Motif XREF Isoschizomer
// TPD Offset UNIQUE Int
// TPD Cleavage UNIQUE Text // will show the cleavage points ex: G_ACGT'C
// TPD Overhang UNIQUE Int
// TPD Company UNIQUE Text
// TPD Remark ?Text
// TPD Title ?Text
// TPD DB_info Database ?Database Text Text // ID Accession_number
// TPD DB_remark ?Text
// TPD DB_text ?LongText
// TPD Substrate UNIQUE DNA
// TPD Peptide
// TPD Homol DNA_homol ?Sequence XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
// TPD Pep_homol ?Protein XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
// TPDD Motif_homol ?Motif XREF Motif_homol ?Method Float Int UNIQUE Int Int UNIQUE Int
// dem 1mar02, created
?Contigset Author ?Author
Date Text
Description Text
Species ?Species
Software Text
Parameters Text
Procedure Text
Contigs Int
Singletons Int
Remarks Text
WWW_page Text
// DEM 8may00 Found this was commented out, though it's actually being used.
?Database Name Text // Full name
Contents ?Text // Description of material included
WWW Arg1_URL_prefix UNIQUE Text
Arg1_URL_suffix UNIQUE Text
Arg2_URL_prefix UNIQUE Text
Arg2_URL_suffix UNIQUE Text
?Method Remark ?Text
// the Display information controls how the column looks.
Display Colour #Colour
Frame_sensitive
Strand_sensitive Show_up_strand #Colour
Score Score_by_offset // has priority over width, for Jean
Score_by_width
Score_by_histogram UNIQUE Float // baseline value
Score_bounds UNIQUE Float UNIQUE Float
// limits for squashing
Percent // '%' in text, + default bounds 25, 100
Overlap_mode UNIQUE Overlap // draw on top - default
Bumpable // bump to avoid overlap
Cluster // one column per homol target
Width UNIQUE Float
Symbol UNIQUE Text // first char only is used
Right_priority UNIQUE Float // the greater the more right
Max_mag UNIQUE Float // don't show if more bases per line
Min_mag UNIQUE Float // don't show if fewer bases per line
Show_text // only put text in right-hand column if set
Blastn // can calculate percent from score if blastn
Blixem Blixem_X
Blixem_N
Blixem_P
Belvu
// ?Oligo Sequence UNIQUE ?Sequence // verbatim sequence - useful
// In_sequence ?Sequence XREF Oligo
// STS STS1 UNIQUE ?STS XREF Oligo1
// STS2 UNIQUE ?STS XREF Oligo2
//?STS Oligo1 UNIQUE ?Oligo
// Oligo2 UNIQUE ?Oligo
// Map ?Map #Map_position
// End copy from SAMPLEDB
?Gene_Product Other_name ?Text
Type ?Text ?Reference Text //Enzyme, Protein, etc
Function ?Text
RNA_type
IUB_number UNIQUE ?Text ?Reference
EC_number UNIQUE ?Text
Gene ?Gene XREF Gene_product
Gene_class ?Gene_Class XREF Gene_product // GRL
Allele ?Allele XREF Gene_product
Source Species ?Species ?Reference
Germplasm ?Germplasm XREF Gene_product ?Reference ?Text
Tissue ?Text ?Reference ?Text
Organelle ?Text ?Reference ?Text
Membrane_Associated ?Reference //boolian +ref.
Pathway ?Pathway #Components
Substrate_specificity ?Text ?Reference ?Text
pH_optimum Float ?Reference ?Text
Temp_optimum Text ?Reference ?Text
Regulation #Regulators
Ancillary_enzyme ?Gene_Product
Catalytic_mechanism #Mechanism
Prosthetic_group ?Text
Isozymes ?Gene_Product
Structure Native_Mr Float
3D_structure Text //boolian with comment
Purification Text
Isoelectric_point Float
Biochemistry Text //
Remarks Text //
Reference ?Reference //
Contact ?Colleague //
Sequence ?Sequence //
?Regulators Activator ?Text
Vmax Text
Cooperativity //boolian
Inhibitor ?Text
Ki Text
Developmental ?Reference Text
Hormonal Text
Environmental ?Reference Text
Genetic ?Reference Text
Inducer ?Text
Repressor ?Text
?Mechanism Ping_Pong
?Components Reaction ?Reaction
Reactant ?Text
Km Text
Product ?Text
//4/94 Proposal: Change to a #ConstructedType for situations where multiple
// types of sources are
// valid, e.g.:
//?Source Colleague ?Colleague
// Reference ?Reference
// Collection ?Collection
// General ?Text
?Source Other_name ?Text // Full name
Contents Text // Description of collection
Remarks Text // other descriptions
Contact ?Colleague
Reference ?Reference
Journal ?Journal
Address Mail Text
Phone Text
E_mail Text
Fax Text
// DEM v1.5: Added Pathology, Probe, Caption
// v1.6: Added Germplasm, Species, Map, Trait; changed Paper to Reference
// Added Locus, QTL
?Image Continued_from ?Image XREF Continued_in
Continued_in ?Image XREF Continued_from
Gene ?Gene XREF Image
Locus ?Locus XREF Image
Allele ?Allele XREF Image
Pathology ?Pathology XREF Image
Probe ?Probe XREF Image
Polymorphism ?Polymorphism XREF Image
//A QTL link is for an image of a particular QTL, e.g. an autorad of
//bulked segregant analysis of the linked marker. See also Trait.
QTL ?QTL XREF Image
Germplasm ?Germplasm XREF Image
Species ?Species XREF Image
Map ?Map_Data XREF Image
Linkage_data ?Linkage_Data XREF Image
Colleague ?Colleague XREF Image //For pix of people. cf Author, below.
Trait_study ?Trait_Study XREF Image
Caption ?Text //DEM
Author ?Author XREF Image
Reference ?Reference XREF Image
Pick_me_to_call UNIQUE Text Text //Program name followed by file name
// Secret Text // If set prevents display except by owner (uid == Text). DEM deactivated.
?Pool Contains Probe ?Probe XREF In_pool
Subpool ?Pool XREF In_pool
In_pool ?Pool
Map Hybridizes_to ?Probe_Grid ?Probe XREF Positive_pool_probe ?Text
Chrom_Band ?Chrom_Band XREF Positive_pool_probe
Location ?Colleague
Reference ?Reference
// 5/94, modified for acedb 3.0
?Chrom_Band Type Centromere
p_Telomere // Left end of chromosome
q_Telomere // Right end of chromosome
Drawing Dark
NOR
Colour #Colour
Position UNIQUE Map ?Map XREF Chrom_Band #map_position
Contains ?Chrom_Band XREF Contained_in
Contained_in UNIQUE ?Chrom_Band XREF Contains
Positive Contains_breakpoint ?Breakpoint XREF In_chrom_band // 3feb99
Negative Does_not_contain_breakpoint ?Breakpoint XREF Not_in_chrom_band // 3feb99
Locus Inside ?Locus XREF Chrom_Band
Positive_pool_probe ?Pool XREF Chrom_Band
Reference ?Reference
// DEM 98apr. For miscellaneous map intervals.
?Interval Position UNIQUE Map ?Map XREF Interval #map_position
Contains ?Interval XREF Contained_in
Contained_in UNIQUE ?Interval XREF Contains
Locus Inside ?Locus XREF Interval
Remark Text
//?Collection lisa added the Collection class
// DEM removed the "Collection_and_ID ?Collection XREF Entries" from
// ?Germplasm, so ?Collection no longer contains an automatic list of
// all its entries.
// DEM 1/96 added new fields for IPGRI database of collections. Previous
// records should have their addresses moved from Description to Mail
?Collection Curator ?Colleague
Address Mail Text
Country Text
Phone Text
Fax Text
E_mail Text
Cable Text
Telex Text
Description ?Text
Please_see ?Collection // For the GrainGenes name_of_record.
Contained_in ?Collection XREF Contains
Contains ?Collection XREF Contained_in
IPGRI_code Text
WWW_page Text
Species ?Species Int // Int is number of entries.
Entries ?Germplasm XREF Collection_and_ID
Update ?Source Text // When our source was last updated, e.g.
// IPGRI 94.11.07
Data_source ?Source Text // Text is date.
//?Pathology Lisa added the pathology class
// 2/93 Dave extended
// 11/93 Added fields for Ken Kephart
?Pathology Other_name ?Pathology XREF Other_name //Choose one,
//put the data in that.
Type Fungus
Bacterium
Virus
Nematode
Insect
Abiotic
Mycoplasma
Parasitic_plant
Mollusk
Host_species ?Species XREF Disease
Causal_organism ?Species XREF Causes
Vector ?Species XREF Vector_of
Trait ?Trait XREF Pathology
Evaluation ?Trait_Study XREF Pathology
Gene_class ?Gene_Class XREF Pathology
Resistance_gene ?Gene XREF Pathology
Resistant_allele ?Allele XREF Pathology
Resistant_line ?Germplasm XREF Pathology
Symptoms Text
Image ?Image XREF Pathology
Reference ?Reference
//?Isolate 5/97 DEM, based on PathoGenes
// For all kinds of pathogen and pest "germplasm"s.
?Isolate Synonym ?Isolate XREF Synonym
Type Pathotype
Strain
Species ?Species
Origin Collector ?Colleague ?Text
Latitude ?Text
Longitude ?Text
Country ?Text
Characteristic ?Text //eg "Mating type: +" "1 mM Ethirimol: Resistant"
Avirulence ?Text //for formulae
Note ?Text
Reference ?Reference XREF Isolate
Data_source ?Colleague ?Text // Text is date, eg. 95.03.07
Reaction_to_host_genes ?Text ?Allele //e.g. "2-3", "A", "V"
Reaction_to_host_germplasm ?Text ?Germplasm
//?Species 2/93 DEM, based on the PGD schema
// 3/6/93 KDK,DEM refined
// Object's id is full name, "Triticum turgidum L. group turgidum Bowden"
// Correct_name is not XREF'd as Synonym. This allows two classes of wrong
// names: dumb ones like "A. squarrosa" that aren't even listed as Synonyms,
// and valid (common or historical) ones like "Ae. squarrosa L.".
//v1.6:
// Added Image
// Feb 94: Haploid_chromosome_number not UNIQUE
// Synonym XREF from Correct_name to Synonym
// Species to Species_epithet
?Species Correct_name UNIQUE ?Species //If object is a Synonym, say only this
Full_name UNIQUE ?Text //Genus not abbreviated, with Authority
Genus UNIQUE ?Text
Species_epithet ?Text
Variety ?Text
Authority ?Text
Synonym ?Species XREF Synonym
Common_name ?Text
Sequence ?Sequence // TPD
Genome UNIQUE ?Text //E.g. "D", "ABD"
Haploid_chromosome_number Int
Mapping_data ?Map_Data
Linkage_data ?Linkage_Data
Disease ?Pathology XREF Host_species // diseases of this species
Causes ?Pathology XREF Causal_organism // diseases caused by it
Vector_of ?Pathology XREF Vector // diseases vectored by it
Reference ?Reference
Image ?Image XREF Species
DNA_library ?Library XREF Species
//?Map_Data: A result of a particular mapping study, or perhaps a summary map.
// Added by Lisa, extended by Dave Matthews
// v1.5: Now contains what used to be ?F2_data
// v1.6: Added Image, Trait, QTL
?Map_Data Map ?Map XREF Mapping_data
External_DB Text Text // for Gramene, NCBI
Species ?Species XREF Mapping_data //If interspecies cross, give both
Female_parent UNIQUE ?Germplasm XREF Mapping_data
Male_parent UNIQUE ?Germplasm XREF Mapping_data
Parent ?Germplasm XREF Mapping_data //for reciprocal, multiparental
Type Genetic
Cytogenetic
Chromosome_arm
Physical
Map_units Text // e.g. centiMorgans, microns, KB
Reference ?Reference XREF Mapping_data
URL Text Text // First is URL, second is optional description.
Contact ?Colleague
Remarks ?Text //Number of progeny, markers; kind of mapping populat'n
Data_curated ?Colleague Text // Text is date, e.g. 99.11
Image ?Image XREF Map
Trait_study ?Trait_Study XREF Mapping_data //Trait analyzed for QTLs
//with this map
QTL ?QTL XREF Mapping_data //Each QTL found
2_point ?2_Point_Data XREF Map_data
Locus ?Locus XREF Data Text //Text is raw Mapmaker data
Breakpoint ?Breakpoint XREF Map_data // 3feb99
Breakpoint_interval ?Breakpoint_interval XREF Map_data // 3feb99
//?Linkage_Data: A subchromosomal region resulting from a particular mapping
// study (population). Bigger than 2 or 3 markers (see ?2_Point_Data), and/or
// with the raw population segregation data given.
// Added by Dave Matthews, 3/96, based on ?Map_Data.
// Removed Type Chromosome_arm
?Linkage_Data Map ?Map XREF Linkage_data
Species ?Species XREF Linkage_data //If interspecies cross,
// give both parental species.
Female_parent UNIQUE ?Germplasm XREF Linkage_data
Male_parent UNIQUE ?Germplasm XREF Linkage_data
Parent ?Germplasm XREF Linkage_data //for reciprocal etc.
Type Genetic
Cytogenetic
Physical
Map_units Text // e.g. centiMorgans, microns, KB
Location Chromosome Text //E.g. 3D
Chromosome_arm Text //E.g. 3DS
Reference ?Reference XREF Linkage_data
Contact ?Colleague
Remarks ?Text //Number of progeny, kind of mapping populat'n
Image ?Image XREF Linkage_data
Trait_study ?Trait_Study XREF Linkage_data //Trait analyzed for
// QTLs with this map
QTL ?QTL XREF Linkage_data //Each QTL found
2_point ?2_Point_Data XREF Linkage_data
Locus ?Locus XREF Linkage_data Text //Text is raw Mapmaker data
Data_curated ?Colleague Text // Text is date, e.g. 99.11
Breakpoint ?Breakpoint XREF Linkage_data // 11mar03
Breakpoint_interval ?Breakpoint_interval XREF Linkage_data
//?Trait: A property of ?Germplasms, affected by ?Gene_Classes and ?QTLs,
// evaluated in ?Trait_Studies.
// DEM 9/93 Created
// ?Germplasms are not directly linked, only via ?Trait_Studies
// DEM 3/94 Affected_by caused ACEDB death, until database reinitialized.
?Trait Description ?Text //Brief explanation of the trait name
See_also ?Trait XREF See_also
Ontology ?Text Text // First Text is T.O. ID#, second is its name
Pathology ?Pathology XREF Trait //If trait is related to a disease
Affected_by ?Gene_Class XREF Character_affected
QTL ?QTL XREF Trait_affected
Evaluation ?Trait_Study XREF Trait //HUH? For some reason, this isn't
//creating the backreference.
//?Trait_Study: Evaluation of a particular set of germplasms in a particular
// experiment. Other experiments measuring the "same" trait should have
// different trait_study identifiers, e.g. "Yield, Smith93b"
// Omit Species, Parents. They're in Mapping_data if this is an evaluation
// of a QTL mapping population, and not germane here if it's just a bunch of
// random germplasms being compared.
// For uniformity through database, always give R-squared as proportion
// (fraction of 1.00), rather than as percentage.
// DEM 5/93
// 5/20: Added Type_I_error_rate_per_locus, Number_of_markers
// 6/8 : Changed Number_of_markers to Number_of_markers_tested
// 9/14: Changed name from ?Trait to ?Trait_Study
?Trait_Study Trait ?Trait XREF Evaluation
Pathology ?Pathology XREF Evaluation //If trait is disease-related
Reference ?Reference XREF Trait_study
Description Text // JMW, 6-15-95; DEM is dubious.
Protocol Text //Description of the trait and how measured
Ontology ?Text Text // First Text is T.O. ID#, second is its name
Values ?Text // Description of possible scores, e.g. "1=Resistant"
Environment ?Environment XREF Trait_study
Parental_description ?Germplasm XREF Trait_study ?Text
//Qualitative description
Parental_Mean_SD ?Germplasm XREF Trait_study Float Float
//Value of mean and standard deviation for each parent
Mapping_data ?Map_Data XREF Trait_study //Info about parents, loci
Linkage_data ?Linkage_Data XREF Trait_study
Population_size UNIQUE Int //Number of individuals in population
Population_type Text //Kind of mapping population, eg F5 RIs
QTL_analysis_method ?Text //Methods used, eg Single-factor ANOVA
Statistics Text //ANOVA table, etc. for this trait
Heritability Float Text //Value and basis,
// e.g. 0.84 "line mean basis"
Type_I_error_rate_per_locus Float //Alpha,
// probability of calling locus significant by chance
Number_of_markers_tested Int //Number of loci in the Mapping_data
QTLs_found UNIQUE Int //How many QTLs were detected?
Phenotypic_R2 Float Text //Phenotypic variance explained by
// all QTLs. Text is qualifier, for different values in
// different Environments or other conditions.
Genetic_R2 Float Text
R2_definition Text //Exact definition of "R-squared" used above
Comment Text
Image ?Image XREF Trait_study //Photos of the rating scale, eg
QTL ?QTL XREF Trait_study //Location, significance, for each QTL
Germplasm_description ?Germplasm XREF Trait_description ?Text Text
Germplasm_score ?Germplasm Float ?Text //NOTE: No XREF. Must
//manually enter data for
//?Germplasm Trait_score ?Trait_Study Float ?Text
Trait_scores ?Trait_scores XREF Trait_study
//For either a mapping population
//or individual named germplasms
Data_source ?Colleague ?Text // Text is date, yy.mm.dd
Data_curated ?Colleague ?Text // Who converted source to .ace
//?QTL: An individual Quantitative Trait Locus for a particular trait.
// DEM 5/93
// 5/20: Changed Type_I_error_per_locus to Significance_level
// Effect_on_score to Size_of_allelic_effect
// Positive_allele_from to Higher_scoring_allele_from
// Type_I_error_x_Environment to Significance_x_Environment
// 6/8: Changed Size_of_allelic_effect to Effect_of_allele_substitution
// 6/24: Added Image
?QTL Trait_affected UNIQUE ?Trait XREF QTL
Gene_class ?Gene_Class XREF QTL
Trait_study ?Trait_Study XREF QTL
Environment ?Environment XREF QTL
Mapping_data UNIQUE ?Map_Data XREF QTL //Molecular markers used to map it
Linkage_data ?Linkage_Data XREF QTL
Chromosome_arm ?Text //eg 3BL, long arm of chromosome 3B
Associated_gene ?Gene XREF QTL
Nearest_marker UNIQUE ?Locus XREF Linked_QTL
Significance_level UNIQUE Float //Significance of marker. P < 0.what?
Positive Significant_marker ?Locus XREF In_QTL Text // Text is
// significance level, e.g. "alpha < .01"
Negative Nonsignificant_marker ?Locus XREF Not_in_QTL
Position UNIQUE Map ?Map XREF QTL #map_position // to draw a bar on Map
Map_label ?Text // label for the bar
LOD_peak_location UNIQUE ?Locus XREF QTL //? Or gMap position?
LOD_peak_height Float //LOD value at this position
Significant_LOD_interval gMap ?Map Float Float //Endpoints of
//region (eg in cM) where LOD exceeds value of LOD_threshold.
LOD_threshold Float //Threshold value for Significant_LOD_interval
Phenotypic_R2 UNIQUE Float //Phenotypic variance explained by this QTL
Genetic_R2 UNIQUE Float //Genetic " " " " "
Effect_of_allele_substitution UNIQUE Float Text//Magnitude of allelic
// effect. Text is units.
Additivity_Dominance_ratio UNIQUE Float
Higher_scoring_allele_from ?Germplasm //Which parent's allele gives higher
//scores
Interactions Text //Epistasis, interaction with environment
Significance_x_Environment Float ?Environment //QTL x Env. P < 0.what?
Comment Text //Eg R-squared of nearby markers
Image ?Image XREF QTL //Eg for blot of bulk segregant analysis.
Reference ?Reference XREF QTL
//?Trait_scores: Values measured for a particular trait in a particular
// environment
// Scores = Value of trait for each member of mapping population, in the
// same order as listed for the molecular markers in ?Trait Mapping_data
// Germplasm_Mean_SD = Mean and SD for each germplasm (for a comparison
// that is not a mapping study)
// Environment is not UNIQUE, to allow an averaged-over-evironments record.
// DEM 5/93
?Trait_scores Trait_study UNIQUE ?Trait_Study XREF Trait_scores
Environment ?Environment XREF Trait_scores
Comment Text
//For QTLs:
Scores Text //If only have means, list all on one line.
Score_Mean_SD Float Float //If (mean, SD) pairs, separate lines.
//For trials of named germplasms:
Germplasm_Mean_SD ?Germplasm XREF Trait_scores Float Float
Germplasm_score Float ?Germplasm XREF Trait_scores
//If only have means, give number first for better
//visual alignment.
//For one-record-per-datum, e.g. ISWYN24:
Germplasm ?Germplasm XREF Trait_scores
Score Float
Standard_deviation Float
Replications Int
Percent_of_local_check Float
Difference_from_local_check Float //When many values are Zero.
Pathogen_race ?Isolate
//?Environment: Location and experimental conditions for a (field) test of
// a trait.
// DEM 5/93, built on Lisa's version
?Environment Year UNIQUE Text //eg 1993-4
Location UNIQUE ?Text //eg "Ketola Farm, Ithaca, NY, USA"
Latitude UNIQUE Text
Longitude UNIQUE Text
Elevation UNIQUE Text
Experimental_design ?Text //eg "Randomized Complete Block"
Replications UNIQUE Int //How many replications here?
Evaluator ?Colleague
Institute ?Text
Topography UNIQUE Text
Drainage UNIQUE Text
Soil_texture UNIQUE Text
Irrigation Text //Type, number of days, total amount
Moisture Text //Amount, units; eg 455 mm
Planting_date UNIQUE Text //Format: 88.04.16
Harvest_date UNIQUE Text
Testing_date Text
N_applied Text //Nitrogen fertilizer used, units
P2O5_applied Text //Phosphorus, in units of P2O5
K2O_applied Text //Potassium, in units of K2O
Remarks Text //Special conditions or events here
Trait_study ?Trait_Study XREF Environment //What study(ies) were
//performed at this Environment. (Usually only one.)
Trait_scores ?Trait_scores XREF Environment //Scores obtained here
QTL ?QTL XREF Environment
//?Help. Added by DEM 4/94
?Help Intro ?Text
Overview ?Text
Note ?Text
Tip ?Text
More ?LongText
// ?Breakpoint_interval added 3feb99
?Breakpoint_interval Correct_name ?Breakpoint_interval XREF Other_name
Other_name ?Breakpoint_interval XREF Other_name
Map_data ?Map_Data XREF Breakpoint_interval
Linkage_data ?Linkage_Data XREF Breakpoint_interval
Map ?Map XREF Breakpoint_interval #map_position
Proximal_breakpoint ?Breakpoint XREF Distal_interval
Distal_breakpoint ?Breakpoint XREF Proximal_interval
Positive Contains ?Locus XREF In_interval
Negative Does_not_contain ?Locus XREF Not_in_interval
Reference_stocks ?Germplasm ?Germplasm //15feb99
Phenotype ?Text
Reference ?Reference
Location ?Colleague
Remark ?Text
// ?Breakpoint added 3feb99
?Breakpoint Correct_name ?Breakpoint XREF Other_name
Other_name ?Breakpoint XREF Other_name
Map_data ?Map_Data XREF Breakpoint
Linkage_data ?Linkage_Data XREF Breakpoint
Map ?Map XREF Breakpoint #map_position
Positive In_chrom_band ?Chrom_Band XREF Contains_breakpoint
Negative Not_in_chrom_band ?Chrom_Band XREF Does_not_contain_breakpoint
Fraction_length UNIQUE Float UNIQUE ?Reference
Germplasm ?Germplasm XREF Contains_breakpoint
Distal_deletion_in ?Germplasm XREF Deletion_distal_to
Distal_interval ?Breakpoint_interval XREF Proximal_breakpoint
Proximal_interval ?Breakpoint_interval XREF Distal_breakpoint
Distal_rearrangement ?Rearrangement XREF Proximal_breakpoint
Proximal_rearrangement ?Rearrangement XREF Distal_breakpoint
Reference ?Reference XREF Breakpoint
Remark ?Text
.