Difference between revisions of "WormBase Model:Variation"
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?Variation Evidence #Evidence | ?Variation Evidence #Evidence | ||
− | + | Name Public_name UNIQUE ?Variation_name XREF Public_name_for | |
− | + | Other_name ?Variation_name XREF Other_name_for #Evidence | |
− | Rearrangement | + | 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 | |
− | Variation_type Allele | + | 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 // | 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 | KO_consortium_allele // North American knockout consortium | ||
NBP_allele // Japanese 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 | |
− | Status UNIQUE Live #Evidence | + | 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 | Suppressed #Evidence | ||
Dead #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 | Isolation Date DateType | ||
Mutagen UNIQUE Text #Evidence | Mutagen UNIQUE Text #Evidence | ||
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Transposon_excision ?Transposon_family | Transposon_excision ?Transposon_family | ||
Derived_from ?Variation XREF Derivative | Derived_from ?Variation XREF Derivative | ||
− | + | Derivative ?Variation XREF Derived_from | |
Genetics Gene_class ?Gene_class XREF 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 | Mapping_data 2_point ?2_point_data | ||
Multi_point ?Multi_pt_data | Multi_point ?Multi_pt_data | ||
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In_pos_neg_data ?Pos_neg_data | In_pos_neg_data ?Pos_neg_data | ||
// these are for when the locus is mapped | // 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_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 | Nonsense UNIQUE Amber_UAG Text #Evidence | ||
Ochre_UAA Text #Evidence | Ochre_UAA Text #Evidence | ||
Opal_UGA Text #Evidence | Opal_UGA Text #Evidence | ||
− | Missense Text #Evidence | + | Missense Text #Evidence // text fields stored details of codon change |
Silent Text #Evidence | Silent Text #Evidence | ||
Splice_site Donor Text #Evidence | Splice_site Donor Text #Evidence | ||
Acceptor Text #Evidence | Acceptor Text #Evidence | ||
Frameshift Text #Evidence // added sdm | Frameshift Text #Evidence // added sdm | ||
+ | Readthrough Text #Evidence // klh WS228 | ||
Reference ?Paper XREF Allele | Reference ?Paper XREF Allele | ||
Remark ?Text #Evidence | Remark ?Text #Evidence | ||
− | + | Method UNIQUE ?Method | |
Supporting_data Movie ?Movie XREF Variation #Evidence //Carol [060421 ar2] | Supporting_data Movie ?Movie XREF Variation #Evidence //Carol [060421 ar2] | ||
− | |||
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Ochre_UAA Text #Evidence | Ochre_UAA Text #Evidence | ||
Opal_UGA 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 | Splice_site UNIQUE Donor Text #Evidence | ||
Acceptor Text #Evidence | Acceptor Text #Evidence | ||
Frameshift Text #Evidence | Frameshift Text #Evidence | ||
+ | Readthrough Text #Evidence //klh WS228 | ||
Intron #Evidence | Intron #Evidence | ||
Coding_exon #Evidence | Coding_exon #Evidence | ||
Noncoding_exon #Evidence | Noncoding_exon #Evidence | ||
− | + | Promoter #Evidence | |
− | + | UTR_3 #Evidence | |
− | + | UTR_5 #Evidence | |
− | + | Regulatory_feature #Evidence | |
− | + | Genomic_neighbourhood #Evidence | |
</pre> | </pre> | ||
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== Proposed Changes == | == Proposed Changes == | ||
− | Unused tags | + | |
+ | == Approved Changes == | ||
+ | ===WS231=== | ||
+ | <pre> | ||
+ | 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 | ||
+ | </pre> | ||
+ | |||
+ | == Unused tags == | ||
Inversion | Inversion |
Latest revision as of 23:50, 16 April 2014
Contents
Curator Comments/Description
Model
////////////////////////////////////////////////////////////////////////////////////////////// // //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 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