Difference between revisions of "WormBase Model:Variation"
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== Model == | == Model == | ||
<pre> | <pre> | ||
+ | ////////////////////////////////////////////////////////////////////////////////////////////// | ||
+ | // | ||
+ | //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 | ||
+ | CGH_deleted_probes UNIQUE Text UNIQUE Text | ||
+ | FivePrimeGap UNIQUE Int | ||
+ | ThreePrimeGap UNIQUE Int | ||
+ | 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 | ||
+ | Laboratory ?Laboratory XREF Alleles | ||
+ | Author ?Author // use Person when known, else use Author | ||
+ | Person ?Person // | ||
+ | DB_info Database ?Database ?Database_field UNIQUE ?Accession_number //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 | ||
+ | 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 | ||
+ | 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 | ||
+ | Rescued_by_transgene ?Transgene | ||
+ | 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 | ||
+ | Reference ?Paper XREF Allele | ||
+ | Remark ?Text #Evidence | ||
+ | Method UNIQUE ?Method | ||
+ | Supporting_data Movie ?Movie XREF Variation #Evidence //Carol [060421 ar2] | ||
+ | Picture ?Picture XREF Variation #Evidence | ||
+ | |||
+ | |||
+ | ?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 | ||
+ | Intron #Evidence | ||
+ | Coding_exon #Evidence | ||
+ | Noncoding_exon #Evidence | ||
+ | Promoter #Evidence | ||
+ | UTR_3 #Evidence | ||
+ | UTR_5 #Evidence | ||
+ | Regulatory_feature #Evidence | ||
+ | Genomic_neighbourhood #Evidence | ||
</pre> | </pre> | ||
== Proposed Changes == | == Proposed Changes == |
Revision as of 09:26, 10 August 2010
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 CGH_deleted_probes UNIQUE Text UNIQUE Text FivePrimeGap UNIQUE Int ThreePrimeGap UNIQUE Int 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 Laboratory ?Laboratory XREF Alleles Author ?Author // use Person when known, else use Author Person ?Person // DB_info Database ?Database ?Database_field UNIQUE ?Accession_number //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 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 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 Rescued_by_transgene ?Transgene 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 Reference ?Paper XREF Allele Remark ?Text #Evidence Method UNIQUE ?Method Supporting_data Movie ?Movie XREF Variation #Evidence //Carol [060421 ar2] Picture ?Picture XREF Variation #Evidence ?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 Intron #Evidence Coding_exon #Evidence Noncoding_exon #Evidence Promoter #Evidence UTR_3 #Evidence UTR_5 #Evidence Regulatory_feature #Evidence Genomic_neighbourhood #Evidence