WormBase Model:Variation
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Curator Comments/Description
Model
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//
//Variation class
//
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?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
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, <WSversion> ?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 Text #Evidence // wild type and mutant sequence
Insertion UNIQUE Text #Evidence
Deletion UNIQUE Text #Evidence
Inversion
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 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
Laboratory ?Laboratory
Author ?Author // use Person when known, else use Author
Person ?Person //
Analysis ?Analysis
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 //added before WS242?
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
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 XREF Derivative
Derivative ?Variation XREF Derived_from
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
Nonsense UNIQUE Amber_UAG Text #Evidence
Ochre_UAA Text #Evidence
Opal_UGA Text #Evidence
Missense Text #Evidence // text fields stored details of codon change
Silent Text #Evidence
Splice_site Donor Text #Evidence
Acceptor Text #Evidence
Frameshift Text #Evidence // added sdm
Readthrough Text #Evidence // klh WS228
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 Missense Int Text #Evidence
Silent Text #Evidence
Nonsense UNIQUE Amber_UAG Text #Evidence
Ochre_UAA Text #Evidence
Opal_UGA Text #Evidence
Ochre_UAA_or_Opal_UGA Text #Evidence
Amber_UAG_or_Ochre_UAA Text #Evidence
Amber_UAG_or_Opal_UGA Text #Evidence
Splice_site UNIQUE Donor Text #Evidence
Acceptor Text #Evidence
Frameshift Text #Evidence
Readthrough Text #Evidence //klh WS228
Intron #Evidence
Coding_exon #Evidence
Noncoding_exon #Evidence
Promoter #Evidence
UTR_3 #Evidence
UTR_5 #Evidence
Regulatory_feature #Evidence
Genomic_neighbourhood #Evidence
Proposed Changes
Approved Changes
WS231
Mating_efficiency Male UNIQUE ME0_Mating_not_successful
ME1_Mating_rarely_successful
ME2_Mating_usually_successful
ME3_Mating_always_successful
Hermaphrodite UNIQUE
HE0_Mating_not_successful
HE1_Mating_rarely_successful
HE2_Mating_usually_successful
HE3_Mating_always_successful
Unused tags
Inversion
Nature_of_variation (new)
Polymorphic
Synthetic
Linked_to
Rescued_by_transgene
Phenotype_remark
Haplo_insufficient
Hypermorph
Nonsense
Amber_UAG
Ochre_UAA
Opal_UGA
Missense
Silent
Paternal
Supporting_data
Movie
Picture
