// Protobuf file for representing the types from the ClinVar VCV XSD file. syntax = "proto3"; package annonars.clinvar_data.clinvar_public; import "google/protobuf/timestamp.proto"; // Enumeration describing connection between genes and variants. // // Corresponds to XSD type "GeneVariantRelationship". enum GeneVariantRelationship { // unspecified gene variant GENE_VARIANT_RELATIONSHIP_UNSPECIFIED = 0; // corresponds to "variant within gene" GENE_VARIANT_RELATIONSHIP_VARIANT_WITHIN_GENE = 1; // corresponds to "gene overlapped by variant" and // (legacy:) "genes overlapped by variant" GENE_VARIANT_RELATIONSHIP_GENE_OVERLAPPED_BY_VARIANT = 2; // corresponds to "variant near gene, upstream" and // (legacy:) "near gene, upstream" GENE_VARIANT_RELATIONSHIP_NEAR_GENE_UPSTREAM = 3; // corresponds to "variant near gene, downstream" and // (legacy:) "near gene, downstream" GENE_VARIANT_RELATIONSHIP_NEAR_GENE_DOWNSTREAM = 4; // corresponds to "asserted, but not computed" GENE_VARIANT_RELATIONSHIP_ASSERTED_BUT_NOT_COMPUTED = 5; // corresponds to "within multiple genes by overlap" GENE_VARIANT_RELATIONSHIP_WITHIN_MULTIPLE_GENES_BY_OVERLAP = 6; // corresponds to "within single gene" GENE_VARIANT_RELATIONSHIP_WITHIN_SINGLE_GENE = 7; } // Enumeration describing severity. // // Corresponds to XSD type "typeSeverity" enum Severity { // unspecified severity SEVERITY_UNSPECIFIED = 0; // corresponds to "mild" SEVERITY_MILD = 1; // corresponds to "moderate" SEVERITY_MODERATE = 2; // corresponds to "sever" SEVERITY_SEVERE = 3; } // Enumeration describing status. // // Corresponds to `typeStatus` in XSD. enum Status { // unspecified status STATUS_UNSPECIFIED = 0; // corresponds to "current" STATUS_CURRENT = 1; // corresponds to "completed and retired" STATUS_COMPLETED_AND_RETIRED = 2; // corresponds to "delete" STATUS_DELETE = 3; // corresponds to "in development" STATUS_IN_DEVELOPMENT = 4; // corresponds to "reclassified" STATUS_RECLASSIFIED = 5; // corresponds to "reject" STATUS_REJECT = 6; // corresponds to "secondary" STATUS_SECONDARY = 7; // corresponds to "suppressed" STATUS_SUPPRESSED = 8; // corresponds to "under review" STATUS_UNDER_REVIEW = 9; } // Enumeration describing submitter review status. // // Corresponds to `typeSubmitterReviewStatusValue` in XSD. enum SubmitterReviewStatus { // unspecified status SUBMITTER_REVIEW_STATUS_UNSPECIFIED = 0; // corresponds to "no classification provided" SUBMITTER_REVIEW_STATUS_NO_CLASSIFICATION_PROVIDED = 1; // corresponds to "no assertion criteria provided" SUBMITTER_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED = 2; // corresponds to "criteria provided, single submitter" SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER = 3; // corresponds to "reviewed by expert panel" SUBMITTER_REVIEW_STATUS_REVIEWED_BY_EXPERT_PANEL = 4; // corresponds to "practice guideline" SUBMITTER_REVIEW_STATUS_PRACTICE_GUIDELINE = 5; // corresponds to "flagged submission" SUBMITTER_REVIEW_STATUS_FLAGGED_SUBMISSION = 6; // corresponds to "criteria provided, multiple submitters, no conflicts" SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS = 7; // corresponds to "criteria provided, conflicting classifications" SUBMITTER_REVIEW_STATUS_CRITERIA_PROVIDED_CONFLICTING_CLASSIFICATIONS = 8; // corresponds to "classified by single submitter" SUBMITTER_REVIEW_STATUS_CLASSIFIED_BY_SINGLE_SUBMITTER = 9; // corresponds to "reviewed by professional society" SUBMITTER_REVIEW_STATUS_REVIEWED_BY_PROFESSIONAL_SOCIETY = 10; // corresponds to "not classified by submitter" SUBMITTER_REVIEW_STATUS_NOT_CLASSIFIED_BY_SUBMITTER = 11; // corresponds to "classified by multiple submitters" SUBMITTER_REVIEW_STATUS_CLASSIFIED_BY_MULTIPLE_SUBMITTERS = 12; } // Enumeration describing zygosity. enum Zygosity { // unspecified zygosity ZYGOSITY_UNSPECIFIED = 0; // corresponds to "Homozygote" ZYGOSITY_HOMOZYGOTE = 1; // corresponds to "SingleHeterozygote" ZYGOSITY_SINGLE_HETEROZYGOTE = 2; // corresponds to "CompoundHeterozygote" ZYGOSITY_COMPOUND_HETEROZYGOTE = 3; // corresponds to "Hemizygote" ZYGOSITY_HEMIZYGOTE = 4; // corresponds to "not provided" ZYGOSITY_NOT_PROVIDED = 5; } // Enumeration describing assertion type attributes. enum Assertion { // unspecified assertion type attribute ASSERTION_UNSPECIFIED = 0; // corresponds to "variation to disease" ASSERTION_VARIATION_TO_DISEASE = 1; // corresponds to "variation to included disease" ASSERTION_VARIATION_TO_INCLUDED_DISEASE = 2; // corresponds to "variation in modifier gene to disease" ASSERTION_VARIATION_IN_MODIFIER_GENE_TO_DISEASE = 3; // corresponds to "confers sensitivity" ASSERTION_CONFERS_SENSITIVITY = 4; // corresponds to "confers resistance" ASSERTION_CONFERS_RESISTANCE = 5; // corresponds to "variant to named protein" ASSERTION_VARIANT_TO_NAMED_PROTEIN = 6; } // Enumeration describing aggregate germline review status value. enum AggregateGermlineReviewStatus { // unspecified aggregate germline review status value AGGREGATE_GERMLINE_REVIEW_STATUS_UNSPECIFIED = 0; // corresponds to "no classification provided" AGGREGATE_GERMLINE_REVIEW_STATUS_NO_CLASSIFICATION_PROVIDED = 1; // corresponds to "no assertion criteria provided" AGGREGATE_GERMLINE_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED = 2; // corresponds to "criteria provided, single submitter" AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER = 3; // corresponds to "criteria provided, multiple submitters, no conflicts" AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS = 4; // corresponds to "criteria provided, conflicting classifications" AGGREGATE_GERMLINE_REVIEW_STATUS_CRITERIA_PROVIDED_CONFLICTING_CLASSIFICATIONS = 5; // corresponds to "reviewed by expert panel" AGGREGATE_GERMLINE_REVIEW_STATUS_REVIEWED_BY_EXPERT_PANEL = 6; // corresponds to "practice guideline" AGGREGATE_GERMLINE_REVIEW_STATUS_PRACTICE_GUIDELINE = 7; // corresponds to "no classifications from unflagged records" AGGREGATE_GERMLINE_REVIEW_STATUS_NO_CLASSIFICATIONS_FROM_UNFLAGGED_RECORDS = 8; // corresponds to "no classification for the single variant" AGGREGATE_GERMLINE_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT = 9; } // Enumeration describing aggregate somatic clinical impact review status value. enum AggregateSomaticClinicalImpactReviewStatus { // unspecified aggregate somatic clinical impact review status value AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_UNSPECIFIED = 0; // corresponds to "no classification provided" AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_CLASSIFICATION_PROVIDED = 1; // corresponds to "no assertion criteria provided" AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED = 2; // corresponds to "criteria provided, single submitter" AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER = 3; // corresponds to "criteria provided, multiple submitters" AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS = 4; // corresponds to "reviewed by expert panel" AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_REVIEWED_BY_EXPERT_PANEL = 5; // corresponds to "practice guideline" AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_PRACTICE_GUIDELINE = 6; // corresponds to "no classifications from unflagged records" AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_CLASSIFICATIONS_FROM_UNFLAGGED_RECORDS = 7; // corresponds to "no classification for the single variant" AGGREGATE_SOMATIC_CLINICAL_IMPACT_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT = 8; } // Enumeration describing aggregate oncogenicity review status value. enum AggregateOncogenicityReviewStatus { // unspecified aggregate oncogenicity review status value AGGREGATE_ONCOGENICITY_REVIEW_STATUS_UNSPECIFIED = 0; // corresponds to "no classification provided" AGGREGATE_ONCOGENICITY_REVIEW_STATUS_NO_CLASSIFICATION_PROVIDED = 1; // corresponds to "no assertion criteria provided" AGGREGATE_ONCOGENICITY_REVIEW_STATUS_NO_ASSERTION_CRITERIA_PROVIDED = 2; // corresponds to "criteria provided, single submitter" AGGREGATE_ONCOGENICITY_REVIEW_STATUS_CRITERIA_PROVIDED_SINGLE_SUBMITTER = 3; // corresponds to "criteria provided, multiple submitters, no conflicts" AGGREGATE_ONCOGENICITY_REVIEW_STATUS_CRITERIA_PROVIDED_MULTIPLE_SUBMITTERS_NO_CONFLICTS = 4; // corresponds to "criteria provided, conflicting classifications" AGGREGATE_ONCOGENICITY_REVIEW_STATUS_CRITERIA_PROVIDED_CONFLICTING_CLASSIFICATIONS = 5; // corresponds to "reviewed by expert panel" AGGREGATE_ONCOGENICITY_REVIEW_STATUS_REVIEWED_BY_EXPERT_PANEL = 6; // corresponds to "practice guideline" AGGREGATE_ONCOGENICITY_REVIEW_STATUS_PRACTICE_GUIDELINE = 7; // corresponds to "no classifications from unflagged records" AGGREGATE_ONCOGENICITY_REVIEW_STATUS_NO_CLASSIFICATIONS_FROM_UNFLAGGED_RECORDS = 8; // corresponds to "no classification for the single variant" AGGREGATE_ONCOGENICITY_REVIEW_STATUS_NO_CLASSIFICATION_FOR_THE_SINGLE_VARIANT = 9; } // Enumeration describing origin. enum Origin { // unspecified origin ORIGIN_UNSPECIFIED = 0; // corresponds to "germline" ORIGIN_GERMLINE = 1; // corresponds to "somatic" ORIGIN_SOMATIC = 2; // corresponds to "de novo" ORIGIN_DE_NOVO = 3; // corresponds to "not provided" ORIGIN_NOT_PROVIDED = 4; // corresponds to "inherited" ORIGIN_INHERITED = 5; // corresponds to "maternal" ORIGIN_MATERNAL = 6; // corresponds to "paternal" ORIGIN_PATERNAL = 7; // corresponds to "uniparental" ORIGIN_UNIPARENTAL = 8; // corresponds to "biparental" ORIGIN_BIPARENTAL = 9; // corresponds to "not-reported" ORIGIN_NOT_REPORTED = 10; // corresponds to "tested-inconclusive" ORIGIN_TESTED_INCONCLUSIVE = 11; // corresponds to "unknown" ORIGIN_UNKNOWN = 12; // corresponds to "not applicable" ORIGIN_NOT_APPLICABLE = 13; // corresponds to "experimentally generated" ORIGIN_EXPERIMENTALLY_GENERATED = 14; } // Enumeration describing chromosome. enum Chromosome { // unspecified chromosome CHROMOSOME_UNSPECIFIED = 0; // corresponds to "1" CHROMOSOME_1 = 1; // corresponds to "2" CHROMOSOME_2 = 2; // corresponds to "3" CHROMOSOME_3 = 3; // corresponds to "4" CHROMOSOME_4 = 4; // corresponds to "5" CHROMOSOME_5 = 5; // corresponds to "6" CHROMOSOME_6 = 6; // corresponds to "7" CHROMOSOME_7 = 7; // corresponds to "8" CHROMOSOME_8 = 8; // corresponds to "9" CHROMOSOME_9 = 9; // corresponds to "10" CHROMOSOME_10 = 10; // corresponds to "11" CHROMOSOME_11 = 11; // corresponds to "12" CHROMOSOME_12 = 12; // corresponds to "13" CHROMOSOME_13 = 13; // corresponds to "14" CHROMOSOME_14 = 14; // corresponds to "15" CHROMOSOME_15 = 15; // corresponds to "16" CHROMOSOME_16 = 16; // corresponds to "17" CHROMOSOME_17 = 17; // corresponds to "18" CHROMOSOME_18 = 18; // corresponds to "19" CHROMOSOME_19 = 19; // corresponds to "20" CHROMOSOME_20 = 20; // corresponds to "21" CHROMOSOME_21 = 21; // corresponds to "22" CHROMOSOME_22 = 22; // corresponds to "X" CHROMOSOME_X = 23; // corresponds to "Y" CHROMOSOME_Y = 24; // corresponds to "MT" CHROMOSOME_MT = 25; // corresponds to "PAR" CHROMOSOME_PAR = 26; // corresponds to "Un" CHROMOSOME_UN = 27; } // Enumeration describing comment type. enum CommentType { // unspecified comment type COMMENT_TYPE_UNSPECIFIED = 0; // corresponds to "public" COMMENT_TYPE_PUBLIC = 1; // corresponds to "ConvertedByNCBI" COMMENT_TYPE_CONVERTED_BY_NCB = 2; // corresponds to "MissingFromAssembly" COMMENT_TYPE_MISSING_FROM_ASSEMBLY = 3; // corresponds to "GenomicLocationNotEstablished" COMMENT_TYPE_GENOMIC_LOCATION_NOT_ESTABLISHED = 4; // corresponds to "LocationOnGenomeAndProductNotAligned" COMMENT_TYPE_LOCATION_ON_GENOME_AND_PRODUCT_NOT_ALIGNED = 5; // corresponds to "DeletionComment" COMMENT_TYPE_DELETION_COMMENT = 6; // corresponds to "MergeComment" COMMENT_TYPE_MERGE_COMMENT = 7; // corresponds to "AssemblySpecificAlleleDefinition" COMMENT_TYPE_ASSEMBLY_SPECIFIC_ALLELE_DEFINITION = 8; // corresponds to "AlignmentGapMakesAppearInconsistent" COMMENT_TYPE_ALIGNMENT_GAP_MAKES_APPEAR_INCONSISTENT = 9; // corresponds to "ExplanationOfClassification" COMMENT_TYPE_EXPLANATION_OF_CLASSIFICATION = 10; // corresponds to "FlaggedComment" COMMENT_TYPE_FLAGGED_COMMENT = 11; } // Enumeration describing nucleotide sequence. enum NucleotideSequence { // unspecified nucleotide sequence NUCLEOTIDE_SEQUENCE_UNSPECIFIED = 0; // corresponds to "genomic, top-level" NUCLEOTIDE_SEQUENCE_GENOMIC_TOP_LEVEL = 1; // corresponds to "genomic, RefSeqGene" NUCLEOTIDE_SEQUENCE_GENOMIC_REF_SEQ_GENE = 2; // corresponds to "genomic" NUCLEOTIDE_SEQUENCE_GENOMIC = 3; // corresponds to "coding" NUCLEOTIDE_SEQUENCE_CODING = 4; // corresponds to "non-coding" NUCLEOTIDE_SEQUENCE_NON_CODING = 5; // corresponds to "protein" NUCLEOTIDE_SEQUENCE_PROTEIN = 6; } // Enumeration describing protein sequence. enum ProteinSequence { // unspecified protein sequence PROTEIN_SEQUENCE_UNSPECIFIED = 0; // corresponds to "protein" PROTEIN_SEQUENCE_PROTEIN = 1; } // Enumeration describing phenotype set. enum PhenotypeSetType { // unspecified phenotype set PHENOTYPE_SET_TYPE_UNSPECIFIED = 0; // corresponds to "Disease" PHENOTYPE_SET_TYPE_DISEASE = 1; // corresponds to "DrugResponse" PHENOTYPE_SET_TYPE_DRUG_RESPONSE = 2; // corresponds to "Finding" PHENOTYPE_SET_TYPE_FINDING = 3; // corresponds to "PhenotypeInstruction" PHENOTYPE_SET_TYPE_PHENOTYPE_INSTRUCTION = 4; // corresponds to "TraitChoice" PHENOTYPE_SET_TYPE_TRAIT_CHOICE = 5; } // Enumeration describing variation type. enum VariationType { // unspecified variation type VARIATION_TYPE_UNSPECIFIED = 0; // corresponds to "Diplotype" VARIATION_TYPE_DIPLOTYPE = 1; // corresponds to "CompoundHeterozygote" VARIATION_TYPE_COMPOUND_HETEROZYGOTE = 2; // corresponds to "Distinct chromosomes" VARIATION_TYPE_DISTINCT_CHROMOSOMES = 3; } // Enumeration describing evidence type. // // Corresponds to "EvidenceType" in XSD. enum EvidenceType { // unspecified evidence type EVIDENCE_TYPE_UNSPECIFIED = 0; // corresponds to "Genetic" EVIDENCE_TYPE_GENETIC = 1; // corresponds to "Experimental" EVIDENCE_TYPE_EXPERIMENTAL = 2; // corresponds to "Population" EVIDENCE_TYPE_POPULATION = 3; // corresponds to "Computational" EVIDENCE_TYPE_COMPUTATIONAL = 4; } // Enumeration describing method list. // // Corresponds to "MethodListType" in XSD. enum MethodListType { // unspecified method METHOD_LIST_TYPE_UNSPECIFIED = 0; // corresponds to "literature only" METHOD_LIST_TYPE_LITERATURE_ONLY = 1; // corresponds to "reference population" METHOD_LIST_TYPE_REFERENCE_POPULATION = 2; // corresponds to "case-control" METHOD_LIST_TYPE_CASE_CONTROL = 3; // corresponds to "clinical testing" METHOD_LIST_TYPE_CLINICAL_TESTING = 4; // corresponds to "in vitro" METHOD_LIST_TYPE_IN_VITRO = 5; // corresponds to "in vivo" METHOD_LIST_TYPE_IN_VIVO = 6; // corresponds to "research" METHOD_LIST_TYPE_RESEARCH = 7; // corresponds to "curation" METHOD_LIST_TYPE_CURATION = 8; // corresponds to "not provided" METHOD_LIST_TYPE_NOT_PROVIDED = 9; // corresponds to "provider interpretation" METHOD_LIST_TYPE_PROVIDER_INTERPRETATION = 10; // corresponds to "phenotyping only" METHOD_LIST_TYPE_PHENOTYPING_ONLY = 11; } // Enumeration describing HGVS types. enum HgvsType { // unspecified HGVS type HGVS_TYPE_UNSPECIFIED = 0; // corresponds to "coding" HGVS_TYPE_CODING = 1; // corresponds to "genomic" HGVS_TYPE_GENOMIC = 2; // corresponds to "genomic, top-level" HGVS_TYPE_GENOMIC_TOP_LEVEL = 3; // corresponds to "non-coding" HGVS_TYPE_NON_CODING = 4; // corresponds to "protein" HGVS_TYPE_PROTEIN = 5; } // Enumeration describing clinical features affected status. enum ClinicalFeaturesAffectedStatusType { // unspecified status CLINICAL_FEATURES_AFFECTED_STATUS_TYPE_UNSPECIFIED = 0; // corresponds to "present" CLINICAL_FEATURES_AFFECTED_STATUS_TYPE_PRESENT = 1; // corresponds to "absent" CLINICAL_FEATURES_AFFECTED_STATUS_TYPE_ABSENT = 2; // corresponds to "not tested" CLINICAL_FEATURES_AFFECTED_STATUS_TYPE_NOT_TESTED = 3; } // Enumeration describing haplotype variation types. enum HaploVariationType { // unspecified haplotype variation type HAPLO_VARIATION_TYPE_UNSPECIFIED = 0; // corresponds to "Haplotype" HAPLO_VARIATION_TYPE_HAPLOTYPE = 1; // corresponds to "Haplotype, single variant" HAPLO_VARIATION_TYPE_HAPLOTYPE_SINGLE_VARIANT = 2; // corresponds to "Variation" HAPLO_VARIATION_TYPE_VARIATION = 3; // corresponds to "Phase unknown" HAPLO_VARIATION_TYPE_PHASE_UNKNOWN = 4; // corresponds to "Haplotype defined by a single variant" HAPLO_VARIATION_TYPE_HAPLOTYPE_DEFINED_BY_SINGLE_VARIANT = 5; } // A structure to support reporting unformatted content, with type and // source specified. message Comment { // The comment's value. string value = 1; // The optional comment data source. optional string data_source = 2; // The comment's type. optional CommentType type = 3; } // This structure is used to represent how an object described in the // submission relates to objects in other databases. message Xref { // The name of the database. When there is an overlap with sequence // databases, that name is used. string db = 1; // The identifier used by the database. Being exported as a string // even though internally the database has rules for defining which datases use // integer identifers. string id = 2; // Used to differentiate between different types of identifiers that // a database may provide. optional string type = 3; // Optional URL to the database entry. optional string url = 4; // The status; defaults to "current". optional Status status = 5; } // Description of a citation. message Citation { // Local ID with source. message IdType { // The citation's value. string value = 1; // If there is an identifier, what database provides it. string source = 2; } /* nested elements */ // Optional list of IDs. repeated IdType ids = 1; // Optional URL. optional string url = 2; // Optional citation text. optional string citation_text = 3; /* attributes */ // This maintained distinct from publication types in PubMed and // established by GTR curators. The default is 'general'. optional string type = 4; // Corresponds to the abbreviation reported by GTR. optional string abbrev = 5; } // The attribute is a general element to represent a defined set of data // qualified by an enumerated set of types. For each attribute element, the value will // be a character string and is optional. Source shall be used to store identifiers for // supplied data from source other than the submitter (e.g. SequenceOntology). The data // submitted where Type="variation" shall be validated against sequence_alternation in // Sequence Ontology http://www.sequenceontology.org/. This is to be a generic version // of AttributeType and should be used with extension when it is used to specify Type // and its enumerations. message BaseAttribute { // The attribute's value; can be empty. optional string value = 1; // The optional integer value. optional int64 integer_value = 2; // The optional date value. optional google.protobuf.Timestamp date_value = 3; } // Description of a nucleotide sequence expression. // // Corresponds to `typeNucleotideSequenceExpression` message HgvsNucleotideExpression { // The expression values. string expression = 1; // The type of the nucleotide sequence. optional NucleotideSequence sequence_type = 2; // Optional sequence accession version. optional string sequence_accession_version = 3; // Optional sequence accession. optional string sequence_accession = 4; // Optional sequence version. optional int32 sequence_version = 5; // Optional description of the change. optional string change = 6; // Optional assembly information. optional string assembly = 7; // Optional submission information. optional string submitted = 8; // Optional MANE Select flag. optional bool mane_select = 9; // Optional MANE Plus Clinical flag. optional bool mane_plus_clinical = 10; } // Description of a protein sequence expression. // // Corresponds to `typeProteinSequenceExpression` in XSD. message HgvsProteinExpression { // The expression values. string expression = 1; // Optional sequence accession version. optional string sequence_accession_version = 2; // Optional sequence accession. optional string sequence_accession = 3; // Optional sequence version. optional int32 sequence_version = 4; // Optional description of the change. optional string change = 5; } // A structure to represent an HGVS expression for a nucleotide sequence // variant, along with the predicted protein change and the predicted molecular // consequence. Also used to represent only the protein change if that is all that has // been reported. // // Corresponds to `typeHVSExpression` in XSD. message HgvsExpression { /* nested elements */ // Optional nucleotide sequence expression. optional HgvsNucleotideExpression nucleotide_expression = 1; // Optional protein sequence expression. optional HgvsProteinExpression protein_expression = 2; // List of molecular consequences. repeated Xref molecular_consequences = 3; /* attributes */ // Type of HGVS expression. HgvsType type = 4; // Optional assembly. optional string assembly = 5; } // // Phenotype list details. // message PhenotypeListDetailsType { // // Local type for phenotype. // message Phenotype { // message XRefList { // repeated Xref xrefs = 1; // } // /* nested elements */ // repeated XRefList xref_list = 1; // /* attributes */ // // `name` attribute // string name = 2; // // `target_id` attribute // int64 target_id = 3; // // `AffectedStatus` attribute. // optional string affected_status = 4; // } // /* nested elements */ // // List phenotypes. // repeated Phenotype phenotypes = 1; // // List of phenotype details. // repeated PhenotypeDetails phenotype_details = 2; // /* attributes */ // // Type of the phenotype set. // PhenotypeSetType phenotype_set_type = 3; // } // Description of a software. message Software { // Name of the software. string name = 1; // Version of the software; optional. optional string version = 2; // Purpose of the software; optional. optional string purpose = 3; } // Description of the history of a record. // // Called ``typeDescriptionHistory`` in XSD. message DescriptionHistory { // The pathogenicity description. string description = 1; // The date of the description. optional google.protobuf.Timestamp dated = 2; } // Entry in an element set. // // Called ``SetElementSetType`` in XSD. message GenericSetElement { // The element's value. string value = 1; // The element's type. string type = 2; // List of citations. repeated Citation citations = 3; // List of xrefs. repeated Xref xrefs = 4; // List of comments. repeated Comment comments = 5; } // Common type for an entry in a set of attributes. // // Called ``typeAttributeSet`` in XSD. message AttributeSetElement { // Extend the BaseAttribute with a `type` field. message Attribute { // The base value. BaseAttribute base = 1; // The type of the attribute. string type = 2; } // The attribute value. Attribute attribute = 1; // List of xrefs. repeated Xref xrefs = 2; // List of citations. repeated Citation citations = 3; // List of comments. repeated Comment comments = 4; } // Type to describe traits in various places. message Trait { // Local type for trait relationship. message TraitRelationship { // Local enumeration for trait types. // // NB: only DrugResponseAndDisease is used in the XML. enum Type { // unspecified trait type TYPE_UNSPECIFIED = 0; // corresponds to "phenotype" TYPE_PHENOTYPE = 1; // corresponds to "Subphenotype" TYPE_SUBPHENOTYPE = 2; // corresponds to "DrugResponseAndDisease" TYPE_DRUG_RESPONSE_AND_DISEASE = 3; // corresponds to "co-occuring condition" TYPE_CO_OCCURING_CONDITION = 4; // corresponds to "Finding member" TYPE_FINDING_MEMBER = 5; } /* nested elements */ // Name(s) of the trait. repeated GenericSetElement names = 1; // Citation list. repeated Citation citations = 2; // Xref list. repeated Xref xrefs = 3; // Comment list. repeated Comment comments = 4; // Sources repeated string sources = 5; /* attributes */ // Trait type. Type type = 6; } // names repeated GenericSetElement names = 1; // symbols repeated GenericSetElement symbols = 2; // attributes repeated AttributeSetElement attributes = 3; // Trait relationships repeated TraitRelationship trait_relationships = 4; // Citation list. repeated Citation citations = 5; // Xref list. repeated Xref xrefs = 6; // Comment list. repeated Comment comments = 7; // Sources repeated string sources = 8; } // Describes an indication. // // NB: Called "IndicationType" in the XSD. message Indication { // Enumeration for the indication type. enum Type { // unspecified indication type. TYPE_UNSPECIFIED = 0; // corresponds to "Indication" TYPE_INDICATION = 1; } /* nested elements */ // Represents the value for the test indication as a name of a trait. repeated Trait traits = 1; // List of names. repeated GenericSetElement names = 2; // List of attributes. repeated AttributeSetElement attributes = 3; // List of xrefs. repeated Xref xrefs = 4; // List of citations. repeated Citation citations = 5; // List of comments. repeated Comment comments = 6; /* attributes */ // The type of indication. Type type = 7; } // A set of ``Trait`` objects. // // NB: Called "ClinAsserTraitSetType" in the XSD. message TraitSet { // Local type. enum Type { // unspecified type TYPE_UNSPECIFIED = 0; // corresponds to "Disease" TYPE_DISEASE = 1; // corresponds to "DrugResponse" TYPE_DRUG_RESPONSE = 2; // corresponds to "Finding" TYPE_FINDING = 3; // corresponds to "PhenotypeInstruction" TYPE_PHENOTYPE_INSTRUCTION = 4; // corresponds to "TraitChoice" TYPE_TRAIT_CHOICE = 5; } /* nested elements */ // The traits. repeated Trait traits = 1; // The names. repeated GenericSetElement names = 2; // The symbols. repeated GenericSetElement symbols = 3; // The attributes. repeated AttributeSetElement attributes = 4; // List of xrefs. repeated Xref xrefs = 5; // List of citations. repeated Citation citations = 6; // List of comments. repeated Comment comments = 7; /* attributes */ // The type. Type type = 8; // Date of last evaluation. optional google.protobuf.Timestamp date_last_evaluated = 9; // ID. optional int64 id = 10; // Whether contributes to aggregate classification. optional bool contributes_to_aggregate_classification = 11; // Lower level of evidence. optional bool lower_level_of_evidence = 12; // Explanation of or multiple conditions. optional string multiple_condition_explanation = 13; } // Aggregated germline classification info. // // Corresponds to ``typeAggregatedGermlineClassification`` in XSD. message AggregatedGermlineClassification { /* nested elements */ // The aggregate review status based on all germline submissions // for this record. AggregateGermlineReviewStatus review_status = 1; // We are not providing an enumeration for the values we report // for germline classification within the xsd. Details are in // https://github.com/ncbi/clinvar/ClassificationOnClinVar.md // optional string description = 2; // Explanation is used only when the description is 'conflicting // data from submitters' The element summarizes the conflict. optional Comment explanation = 3; // List of xrefs. repeated Xref xrefs = 4; // List of citations. repeated Citation citations = 5; // List of comments. repeated Comment comments = 6; // History information. repeated DescriptionHistory history_records = 7; // List of conditions. repeated TraitSet conditions = 8; /* attributes */ // Date of last evaluation. optional google.protobuf.Timestamp date_last_evaluated = 9; // Date of creation. google.protobuf.Timestamp date_created = 10; // Date of most recent submission. google.protobuf.Timestamp most_recent_submission = 11; // Number of submitters. optional int32 number_of_submitters = 12; // Number of submissions. optional int32 number_of_submissions = 13; } // Aggregated somatic clinical impact info. message AggregatedSomaticClinicalImpact { /* nested elements */ // The aggregate review status based on all somatic clinical // impact submissions for this record. AggregateSomaticClinicalImpactReviewStatus review_status = 1; // We are not providing an enumeration for the values we report // for somatic clinical impact classification within the xsd. Details are in // https://github.com/ncbi/clinvar/ClassificationOnClinVar.md optional string description = 2; // List of xrefs. repeated Xref xrefs = 3; // List of citations. repeated Citation citations = 4; // List of comments. repeated Comment comments = 5; // History information. repeated DescriptionHistory history_records = 6; // List of conditions. repeated TraitSet conditions = 7; /* attributes */ // Date of last evaluation. optional google.protobuf.Timestamp date_last_evaluated = 8; // Date of creation. google.protobuf.Timestamp date_created = 9; // Date of most recent submission. google.protobuf.Timestamp most_recent_submission = 10; // Number of submitters. optional int32 number_of_submitters = 11; // Number of submissions. optional int32 number_of_submissions = 12; } // Aggregated oncogenicity classification info. message AggregatedOncogenicityClassification { /* nested elements */ // The aggregate review status based on all somatic clinical // impact submissions for this record. AggregateOncogenicityReviewStatus review_status = 1; // We are not providing an enumeration for the values we report // for somatic clinical impact classification within the xsd. Details are in // https://github.com/ncbi/clinvar/ClassificationOnClinVar.md optional string description = 2; // List of xrefs. repeated Xref xrefs = 3; // List of citations. repeated Citation citations = 4; // List of comments. repeated Comment comments = 5; // History information. repeated DescriptionHistory history_records = 6; // List of conditions. repeated TraitSet conditions = 7; /* attributes */ // Date of last evaluation. optional google.protobuf.Timestamp date_last_evaluated = 8; // Date of creation. google.protobuf.Timestamp date_created = 9; // Date of most recent submission. google.protobuf.Timestamp most_recent_submission = 10; // Number of submitters. optional int32 number_of_submitters = 11; // Number of submissions. optional int32 number_of_submissions = 12; } // Used to bundle different types of Classifications (germline, // oncogenic, somatic clinical impact) ; Supports summary as // well as submission details. // // NB: called "typeAggregateClassificationSet" in XSD. message AggregateClassificationSet { // The aggregate germline classification. optional AggregatedGermlineClassification germline_classification = 1; // The aggregate somatic clinical impact. optional AggregatedSomaticClinicalImpact somatic_clinical_impact = 2; // The aggregate oncogenicity classification. optional AggregatedOncogenicityClassification oncogenicity_classification = 3; } // Describes the clinical significance of a variant. // // Corresponds to `ClinicalSignificanceType` in XSD. message ClinicalSignificance { /* contained elements */ // The optional review status. optional SubmitterReviewStatus review_status = 1; // Structure used to support old data of AlleleDescriptionSet // within Co-occurenceSet. // // NB: unused in XML optional string description = 2; // Optional explanatory comment. // // Explanation is used only when the description is 'conflicting // data from submitters' The element summarizes the conflict. // // NB: unused in XML optional Comment explanation = 3; // Optional list of xrefs. repeated Xref xrefs = 4; // Optional list of citations. repeated Citation citations = 5; // Optional list of comments. repeated Comment comments = 6; /* attributes */ // Date of last evaluation. // // NB: unused in XML optional google.protobuf.Timestamp date_last_evaluated = 7; } // This is to be used within co-occurrence set. // // Corresponds to `typeAlleleDescr` in XSD. message AlleleDescription { // Enumeration for relative orientation. // // NB: unused in XML enum RelativeOrientation { // unspecified relative orientation RELATIVE_ORIENTATION_UNSPECIFIED = 0; // corresponds to "cis" RELATIVE_ORIENTATION_CIS = 1; // corresponds to "trans" RELATIVE_ORIENTATION_TRANS = 2; // corresponds to "unknown" RELATIVE_ORIENTATION_UNKNOWN = 3; } // The name of the allele. string name = 1; // Optional relative orientation. // // NB: Unused in XML optional RelativeOrientation relative_orientation = 2; // Optional zygosity. optional Zygosity zygosity = 3; // Optional clinical significance. // // Corresponds to `ClinicalSignificanceType` in XSD. optional ClinicalSignificance clinical_significance = 4; } // A structure to support reporting of an accession, its version, the // date its status changed, and text describing that change. // // Corresponds to `typeRecordHistory` in XSD. message RecordHistory { /* nested elements */ // Optional comment on the history record. optional Comment comment = 1; /* attributes */ // The accession. string accession = 2; // The version. int32 version = 3; // The date the record. google.protobuf.Timestamp date_changed = 4; // Attribute @VaritionID is only populated for VCV, where @Accession // is like VCV000000009 optional int64 variation_id = 5; } // Report classification of a variant for a SCV. // // Corresponds to `ClassificationTypeSCV` in XSD. message ClassificationScv { // Clinical impact of a somatic variatn. message SomaticClinicalImpact { // The somatic clinical impact value. string value = 1; /* attributes */ // Type of the clinical impact assertion. optional string clinical_impact_assertion_type = 2; // Clinical impact significance. optional string clinical_impact_clinical_significance = 3; // Name of the drug for the therapeutic assertion. optional string drug_for_therapeutic_assertion = 4; } // Classification score description. message ClassificationScore { // The score's value. double value = 1; // The score's type; optional. optional string type = 2; } /* nested elements */ // The field's review status. SubmitterReviewStatus review_status = 1; // The germline classification; mutually exlusive with `somatic_clinical_impact` // and `oncogenicity_classification`. optional string germline_classification = 2; // Information on the clinical impact; mutually exlusive with `germline_classification` // and `oncogenicity_classification`. optional SomaticClinicalImpact somatic_clinical_impact = 3; // The oncogenicity classification; mutually exlusive with `germline_classification` // and `oncogenicity_classification`. optional string oncogenicity_classification = 4; // Optional explanation of classification. optional string explanation_of_classification = 5; // List of classification scores. repeated ClassificationScore classification_scores = 6; // List of xrefs. repeated Xref xrefs = 7; // List of citations. repeated Citation citations = 8; // List of comments. repeated Comment comments = 9; /* attributes */ // Date of last evaluation. optional google.protobuf.Timestamp date_last_evaluated = 10; } // Set of attributes for the primary submitter. Any addtional submitters // are captured in the AdditionalSubmitters element. message SubmitterIdentifiers { // Name of submitter. string submitter_name = 1; // Organization ID. int64 org_id = 2; // Organization category. string org_category = 3; // Organization abbreviation; optional. optional string org_abbreviation = 4; } // Definition of a species. message Species { // Name of the species. string name = 1; // Optional taxonomy ID. optional int32 taxonomy_id = 2; } // Interpreted condition for an RCV record. // // Corresponds to `typeRCVInterpretedCondition` in XSD. message ClassifiedCondition { // Condition value. string value = 1; // Database name. optional string db = 2; // Identifier in database. optional string id = 3; } // Inside ClinicalAssertion, a structure to support reporting of an // accession, its version, the date its status changed, and text describing that // change. // // Corresponds to `typeClinicalAssertionRecordHistory` in XSD. message ClinicalAssertionRecordHistory { // Optional comment. optional Comment comment = 1; // Accession. string accession = 2; // Optional version. optional int32 version = 3; // Date of the record. google.protobuf.Timestamp date_changed = 4; } // Description of a functional consequence. // // Corresponds to `typeFunctionalConsequence` in XSD. message FunctionalConsequence { /* nested elements */ // List of xrefs. repeated Xref xrefs = 1; // List of citations. repeated Citation citations = 2; // List of comments. repeated Comment comments = 3; /* attributes */ // Value of functional consequence. string value = 4; } // Type for the tag `GeneralCitations`. message GeneralCitations { // List of xrefs. repeated Xref xrefs = 1; // List of citations. repeated Citation citations = 2; } // This refers to the zygosity of the variant being asserted. message Cooccurrence { // Optional zygosity. optional Zygosity zygosity = 1; // The allele descriptions. repeated AlleleDescription allele_descriptions = 2; // The optional count. optional int32 count = 3; } // A structure to support reporting the name of a submitter, its // organization id, and its abbreviation and type. message Submitter { // Enumeration of submitter kind. enum Type { // unspecified submitter type TYPE_UNSPECIFIED = 0; // corresponds to "primary" TYPE_PRIMARY = 1; // corresponds to "secondary" TYPE_SECONDARY = 2; // corresponds to "behalf" TYPE_BEHALF = 3; } // The submitter's identifier. SubmitterIdentifiers submitter_identifiers = 1; // The submitter type. Type type = 2; } // Haploinsufficiency/Triplosensitivity of gene. message DosageSensitivity { /* nested elements */ // Value. string value = 1; /* attributes */ // Optional last evaluated date. optional google.protobuf.Timestamp last_evaluated = 2; // URL to ClinGen. optional string clingen = 3; } // A name with an optional type. // // Corresponds to `typeNames` in XSD. message OtherName { // The name's value. string value = 1; // The name's type. optional string type = 2; } // A structure to support reporting of an accession, its version, the // date it was deleted and a free-text summary of why it was deleted. // // Corresponds to `typeDeletedSCV`. message DeletedScv { // The accession. string accession = 1; // The version. int32 version = 2; // The date of deletion. google.protobuf.Timestamp date_deleted = 3; } // There can be multiple types of location, and the locations may have // identifiers in other databases. // // Corresponds to `typeLocation` in XSD. message Location { // Local type for sequence location. message SequenceLocation { // Local enum for the assembly status. enum AssemblyStatus { // unspecified assembly status ASSEMBLY_STATUS_UNSPECIFIED = 0; // corresponds to "current" ASSEMBLY_STATUS_CURRENT = 1; // corresponds to "previous" ASSEMBLY_STATUS_PREVIOUS = 2; } // forDisplay value. optional bool for_display = 1; // Name of assembly. string assembly = 2; // Chromosomeof variant. Chromosome chr = 3; // Optional chromosome accession. optional string accession = 4; // Outer start position. optional uint32 outer_start = 5; // Inner start position. optional uint32 inner_start = 6; // Start position. optional uint32 start = 7; // Stop position. optional uint32 stop = 8; // Inner stop position. optional uint32 inner_stop = 9; // Outer stop position. optional uint32 outer_stop = 10; // Display start position. optional uint32 display_start = 11; // Display stop position. optional uint32 display_stop = 12; // Strand. optional string strand = 13; // Variant length. optional uint32 variant_length = 14; // Reference allele. optional string reference_allele = 15; // Alternate allele. optional string alternate_allele = 16; // Assembly accession version. optional string assembly_accession_version = 17; // Assembly status. optional AssemblyStatus assembly_status = 18; // Position in VCF. optional uint32 position_vcf = 19; // Reference allele in VCF. optional string reference_allele_vcf = 20; // Alternate allele in VCF. optional string alternate_allele_vcf = 21; // For display length. optional uint32 for_display_length = 22; } // Cytogenetic location is maintained independent of sequence // location, and can be submitted or computed from the sequence location. // // Between 0 and 4 entries. repeated string cytogenetic_locations = 1; // Location on a defined sequence, with reference and alternate // allele, and start /stop values depending on the specificity with which the // variant location is known. The number system of offset 1, and // right-justified to be consistent with HGVS location data. repeated SequenceLocation sequence_locations = 2; // The location of the variant relative to features within the gene. repeated string gene_locations = 3; // List of xrefs. repeated Xref xrefs = 4; } // Description of a SCV. // // Corresponds to "typeSCV" in XSD. message Scv { // Optional title. optional string title = 1; // Accession. string accession = 2; // Version. int32 version = 3; } // // Description of a list of indications. // // // // Corresponds to `IndicationListType` in XSD. // message Indications { // // The indication may be a set of phenotypic descriptions. // message Indication { // // Xrefs. // repeated Xref xrefs = 1; // // Name of the indication. // string name = 2; // // Target ID. // int64 target_id = 3; // } // // Type of the phenotype. // PhenotypeSetType phenotype_set_type = 1; // } // // Description of a pharma. // message PharmaType { // // Local type for drug response. // message DrugResponse { // // // The phenotype details. // // repeated PhenotypeListDetailsType phenotype_details = 1; // // Xref list. // repeated Xref xrefs = 1; // // Name of drug. // string drug_name = 2; // // Target ID. // int64 target_id = 3; // } // // Drug responses. // repeated DrugResponse drug_responses = 1; // } // // Description of a single method. // // // // Corresponds to `typeMethodRefs` in XSD. // message MethodWithXrefs { // // Name of the method. // string method_name = 1; // // Xrefs. // repeated Xref xrefs = 2; // } // Structure to describe attributes of any family data in an observation. // If the details of the number of families and the de-identified pedigree id are not // available, use FamilyHistory to describe what type of family data is available. Can // also be used to report 'Yes' or 'No' if there are no more details. // // Corresponds to "FamilyInfo" in XSD. message FamilyData { /* nested elements */ // Optional family history. optional string family_history = 1; /* attributes */ // Number of families. optional int32 num_families = 2; // Number of families with variant. optional int32 num_families_with_variant = 3; // Number of families with segregation observed. optional int32 num_families_with_segregation_observed = 4; // Pedigree ID. optional string pedigree_id = 5; // Segregation oberved (yes, no, number) optional string segregation_observed = 6; } // Description of a sample. // // Corresponds to `typeSample` in XSD. message Sample { // Local type for sample description. message SampleDescription { // Description of sample. optional Comment description = 1; // Citation. optional Citation citation = 2; } // Local enumeration for presence in normal tissue. enum SomaticVariantInNormalTissue { // unspecified presence SOMATIC_VARIANT_IN_NORMAL_TISSUE_UNSPECIFIED = 0; // corresponds to "present" SOMATIC_VARIANT_IN_NORMAL_TISSUE_PRESENT = 1; // corresponds to "absent" SOMATIC_VARIANT_IN_NORMAL_TISSUE_ABSENT = 2; // corresponds to "not tested" SOMATIC_VARIANT_IN_NORMAL_TISSUE_NOT_TESTED = 3; } // Local enumeration for an age unit. enum AgeUnit { // unspecified age unit AGE_UNIT_UNSPECIFIED = 0; // corresponds to "days" AGE_UNIT_DAYS = 1; // corresponds to "weeks" AGE_UNIT_WEEKS = 2; // corresponds to "months" AGE_UNIT_MONTHS = 3; // corresponds to "years" AGE_UNIT_YEARS = 4; // corresponds to "weeks gestation" AGE_UNIT_WEEKS_GESTATION = 5; // corresponds to "months gestation" AGE_UNIT_MONTHS_GESTATION = 6; } // Local enumeration for an age type. enum AgeType { // unspecified age type AGE_TYPE_UNSPECIFIED = 0; // corresponds to "minimum" AGE_TYPE_MINIMUM = 1; // corresponds to "maximum" AGE_TYPE_MAXIMUM = 2; // corresponds to "single" AGE_TYPE_SINGLE = 3; } // Local enumeration for the affected status. enum AffectedStatus { // unspecified affected status AFFECTED_STATUS_UNSPECIFIED = 0; // corresponds to "yes" AFFECTED_STATUS_YES = 1; // corresponds to "no" AFFECTED_STATUS_NO = 2; // corresponds to "not provided" AFFECTED_STATUS_NOT_PROVIDED = 3; // corresponds to "unknown" AFFECTED_STATUS_UNKNOWN = 4; // corresponds to "not applicable" AFFECTED_STATUS_NOT_APPLICABLE = 5; } // Local type for an age. message Age { // The age value. int32 value = 1; // The age unit. AgeUnit unit = 2; // The age type. AgeType type = 3; } // Local enumeration for gender. enum Gender { // unspecified gender GENDER_UNSPECIFIED = 0; // corresponds to "male" GENDER_MALE = 1; // corresponds to "female" GENDER_FEMALE = 2; // corresponds to "mixed" GENDER_MIXED = 3; } // Local enumeration for SourceType. enum SourceType { // unspecified source type SOURCE_TYPE_UNSPECIFIED = 0; // corresponds to "submitter-generated" SOURCE_TYPE_SUBMITTER_GENERATED = 1; // corresponds to "data mining" SOURCE_TYPE_DATA_MINING = 2; } // The sample description. optional SampleDescription sample_description = 1; // The sample origin. optional Origin origin = 2; // Sample ethnicity. optional string ethnicity = 3; // Sample geographic origin. optional string geographic_origin = 4; // Sample tissue. optional string tissue = 5; // Presence of variant in normal tissue. optional SomaticVariantInNormalTissue somatic_variant_in_normal_tissue = 6; // Somatic variant allele fraction. optional string somatic_variant_allele_fraction = 7; // Cell line name. optional string cell_line = 8; // Species. optional Species species = 9; // Age (range), max. size of 2. repeated Age ages = 10; // Strain. optional string strain = 11; // Affected status. optional AffectedStatus affected_status = 12; // Denominator, total individuals included in this observation set. optional int32 numer_tested = 13; // Denominator, total males included in this observation set. optional int32 number_males = 14; // Denominator, total females included in this observation set. optional int32 number_females = 15; // Denominator, total number chromosomes tested. Number affected // and unaffected are captured in the element NumberObserved. optional int32 number_chr_tested = 16; // Gender should be used ONLY if explicit values are not // available for number of males or females, and there is a need to indicate // that the genders in the sample are known. optional Gender gender = 17; // Family information. optional FamilyData family_data = 18; // Optional proband ID. optional string proband = 19; // Optional indication. optional Indication indication = 20; // List of citations. repeated Citation citations = 21; // List of xrefs. repeated Xref xrefs = 22; // List of comments. repeated Comment comments = 23; // Source type. optional SourceType source_type = 24; } // Details of a method used to generate variant calls or predict/report // functional consequence. The name of the platform should represent a sequencer or an // array, e.g. sequencing or array , e.g. capillary, 454, Helicos, Solexa, SOLiD. This // structure should also be used if the method is 'Curation'. // // Corresponds to `MethodType` in XSD. message Method { // Local enumeration for result types. enum ResultType { // unspecified result type RESULT_TYPE_UNSPECIFIED = 0; // corresponds to "number of occurrences" RESULT_TYPE_NUMBER_OF_OCCURRENCES = 1; // corresponds to "p value" RESULT_TYPE_P_VALUE = 2; // corresponds to "odds ratio" RESULT_TYPE_ODDS_RATIO = 3; // corresponds to "variant call" RESULT_TYPE_VARIANT_CALL = 4; } // Local enumeration for SourceType. enum SourceType { // unspecified source type SOURCE_TYPE_UNSPECIFIED = 0; // corresponds to "submitter-generated" SOURCE_TYPE_SUBMITTER_GENERATED = 1; // corresponds to "data mining" SOURCE_TYPE_DATA_MINING = 2; // corresponds to "data review" SOURCE_TYPE_DATA_REVIEW = 3; } // Local type for method attribute. message MethodAttribute { // Local enumeration of attribute type. enum AttributeType { // unspecified attribute type ATTRIBUTE_TYPE_UNSPECIFIED = 0; // corresponds to "Location" ATTRIBUTE_TYPE_LOCATION = 1; // corresponds to "ControlsAppropriate" ATTRIBUTE_TYPE_CONTROLS_APPROPRIATE = 2; // corresponds to "MethodAppropriate" ATTRIBUTE_TYPE_METHOD_APPROPRIATE = 3; // corresponds to "TestName" ATTRIBUTE_TYPE_TEST_NAME = 4; // corresponds to "StructVarMethod" ATTRIBUTE_TYPE_STRUCT_VAR_METHOD_TYPE = 5; // corresponds to "ProbeAccession" ATTRIBUTE_TYPE_PROBE_ACCESSION = 6; } // The base value. BaseAttribute base = 1; // The attribute type. AttributeType type = 2; } // Local type for observation method attribute. message ObsMethodAttribute { // Local enumeration for attribute type. enum AttributeType { // unspecified attribute type ATTRIBUTE_TYPE_UNSPECIFIED = 0; // corresponds to "MethodResult" ATTRIBUTE_TYPE_METHOD_RESULT = 1; // corresponds to "TestingLaboratory" ATTRIBUTE_TYPE_TESTING_LABORATORY = 2; } // The base value. BaseAttribute base = 1; // The attribute type. AttributeType type = 2; // Optional comments. repeated Comment comments = 3; } // Platform name. optional string name_platform = 1; // Platform type. optional string type_platform = 2; // Method purpose. optional string purpose= 3; // Method result type. optional ResultType result_type = 4; // Smallest reported. optional string min_reported = 5; // Largest reported. optional string max_reported = 6; // Reference standard. optional string reference_standard = 7; // List of citations. repeated Citation citations = 8; // List of xrefs. repeated Xref xrefs = 9; // Free text to enrich the description of the method and to // provide information not captured in specific fields. optional string description = 10; // List of softwares used. repeated Software software = 11; // Source type. optional SourceType source_type = 12; // Method type. MethodListType method_type = 13; // Method attribute. repeated MethodAttribute method_attributes = 14; // ObsMethodAttribute is used to indicate an attribute specific // to a particular method in conjunction with a particular observation . repeated ObsMethodAttribute obs_method_attributes = 15; } // This is a record per variant (Measure/@ID,AlleleID) as submitted for // accessioning in an SCV. // // Corresponds to "typeAlleleSCV" in XSD. message AlleleScv { // Local type for Gene. message Gene { /* nested elements */ // Gene name. optional string name = 1; // Used to set key words for retrieval or // display about a gene, such as genes listed by the // ACMG guidelines. repeated string properties = 2; // Used for gene specific identifiers // such as MIM number, Gene ID, HGNC ID, etc. repeated Xref xrefs = 3; /* attributes */ // Optional gene symbol. optional string symbol = 4; // Relationship between gene and variant. optional GeneVariantRelationship relationship_type = 5; } // Local type for MolecularConsequence. message MolecularConsequence { /* nested elements */ // Xref list. repeated Xref xrefs = 1; // Citation list. repeated Citation citations = 2; // Comment list. repeated Comment comments = 3; /* attributes */ // RS id. optional int64 rs = 4; // Optional HGVS expression. optional string hgvs = 5; // Optional SO id. optional string so_id = 6; // Function. string function = 7; } /* nested elements */ // 0 to many genes (and related data ) related to the allele // being reported. repeated Gene genes = 1; // Name provided by the submitter. OtherName name = 2; // Variant type. optional string variant_type = 3; // Location. optional Location location = 4; // List of other names. repeated OtherName other_names = 5; // Single letter representation of the amino acid change and its // location. repeated string protein_changes = 6; // List of xrefs. repeated Xref xrefs = 7; // List of citations. repeated Citation citations = 8; // List of comments. repeated Comment comments = 9; // Currently redundant with the MolecularConsequence element of // the HGVS element? repeated MolecularConsequence molecular_consequences = 10; // Functional consequences. repeated FunctionalConsequence functional_consequences = 11; // Attributes. repeated AttributeSetElement attributes = 12; /* attributes */ // Allele ID. optional int64 allele_id = 13; } // This is a record of a haplotype in SCV. // // Corresponds to `typeHaplotypeSCV` in XSD. message HaplotypeScv { // The list of alleles in the haplotype. repeated AlleleScv simple_alleles = 1; // The preferred representation of the haplotype. optional string name = 2; // Names other than 'preferred' used for the haplotype. repeated OtherName other_names = 3; // Classification of the variant. optional AggregateClassificationSet classifications = 4; // Functional consequences of the variant. repeated FunctionalConsequence functional_consequences = 5; // List of attributes. repeated AttributeSetElement attributes = 6; // List of citations. repeated Citation citations = 7; // List of cross-references. repeated Xref xrefs = 8; // List of comments. repeated Comment comments = 9; // Variation ID. optional int64 variation_id = 10; // Number of copies. optional int32 number_of_copies = 11; // Number of chromosomes. optional int32 number_of_chromosomes = 12; } // Used to report genotypes, be they simple or complex diplotypes. // // Corresponds to "typeGenotypeSCV" in XSD. message GenotypeScv { /* nested elements */ // Simple alleles; mutually exclusive with `haplotypes`. repeated AlleleScv simple_alleles = 1; // Haplotype; mutually exclusive with `simple_alleles`. // // Allows more than 2 haplotypes per genotype to support // representation of ploidy. repeated HaplotypeScv haplotypes = 2; // Optional name. optional string name = 3; // Other names used for the genotype. repeated OtherName other_names = 4; // The variation type. VariationType variation_type = 5; // Functional consequences. repeated FunctionalConsequence functional_consequences = 6; // Attributes. repeated AttributeSetElement attributes = 7; // List of citations. repeated Citation citations = 8; // List of xrefs. repeated Xref xrefs = 9; // List of comments. repeated Comment comments = 10; /* attributes */ // Variation ID. optional int64 variation_id = 11; } // // Observation of one piece of evidence. // message typeEvidenceObservation { // // // Method of data capture, not method of evaluation. // // repeated MethodWithXrefs methods = 1; // // Modes of inheritance. // repeated string modes_of_inheritance = 1; // // List of citations. // repeated Citation citations = 2; // // Comments. // repeated Comment comments = 3; // // // Observed phenotypes. // // repeated PhenotypeListDetailsType observed_phenotypes = 5; // // // Indications. // // repeated Indications indications = 6; // // The submitter's identifiers. // repeated Submitter submitter_identifiers = 4; // // Families. // optional string families = 5; // // Individuals. // optional string individuals = 6; // // Segregation. // optional string segregations = 7; // // Other gene. // optional string other_gene = 8; // // Same gene. // optional string same_gene = 9; // // Evident type. // EvidenceType evidence_type = 10; // // Allele frequency. // optional string allele_frequency = 11; // // Allele origin. // optional string allele_origin = 12; // // Ethnicity. // optional string ethnicity = 13; // // Geographic origin. // optional string geographic_origin = 14; // } // Documents in what populations or samples an allele or genotype has // been observed relative to the described trait. Summary observations can be // registered per submitted assertion, grouped by common citation, study type, origin, // ethnicity, tissue, cell line, and species data. Not all options are valid per study // type, but these will not be validated in the xsd. // // Corresponds to `ObservationSet` in XSD. message ObservedIn { // Local enum for the method type. enum MethodType { // unspecified method type METHOD_TYPE_UNSPECIFIED = 0; // corresponds to "literature only" METHOD_TYPE_LITERATURE_ONLY = 1; // corresponds to "reference population" METHOD_TYPE_REFERENCE_POPULATION = 2; // corresponds to "case-control" METHOD_TYPE_CASE_CONTROL = 3; // corresponds to "clinical testing" METHOD_TYPE_CLINICAL_TESTING = 4; // corresponds to "in vitro" METHOD_TYPE_IN_VITRO = 5; // corresponds to "in vivo" METHOD_TYPE_IN_VIVO = 6; // corresponds to "inferred from source" METHOD_TYPE_INFERRED_FROM_SOURCE = 7; // corresponds to "research" METHOD_TYPE_RESEARCH = 8; } // Local struct for attributes based on `BaseAttribute`. message ObservedDataAttribute { // Local enum for the observed data type. enum Type { // unspecified observed data attribute type TYPE_UNSPECIFIED = 0; // corresponds to "Description" TYPE_DESCRIPTION = 1; // corresponds to "VariantAlleles" TYPE_VARIANT_ALLELES = 2; // corresponds to "SubjectsWithVariant" TYPE_SUBJECTS_WITH_VARIANT = 3; // corresponds to "SubjectsWithDifferentCausativeVariant" TYPE_SUBJECTS_WITH_DIFFERENT_CAUSATIVE_VARIANT = 4; // corresponds to "VariantChromosomes" TYPE_VARIANT_CHROMOSOMES = 5; // corresponds to "IndependentObservations" TYPE_INDEPENDENT_OBSERVATIONS = 6; // corresponds to "SingleHeterozygote" TYPE_SINGLE_HETEROZYGOUS = 7; // corresponds to "CompoundHeterozygote" TYPE_COMPOUND_HETEROZYGOUS = 8; // corresponds to "Homozygote" TYPE_HOMOZYGOUS = 9; // corresponds to "Hemizygote" TYPE_HEMIZYGOUS = 10; // corresponds to "NumberMosaic" TYPE_NUMBER_MOSAIC = 11; // corresponds to "ObservedUnspecified" TYPE_OBSERVED_UNSPECIFIED = 12; // corresponds to "AlleleFrequency" TYPE_ALLELE_FREQUENCY = 13; // corresponds to "SecondaryFinding" TYPE_SECONDARY_FINDING = 14; // corresponds to "GenotypeAndMOIConsistent" TYPE_GENOTYPE_AND_MOI_CONSISTENT = 15; // corresponds to "UnaffectedFamilyMemberWithCausativeVariant" TYPE_UNAFFECTED_FAMILY_MEMBER_WITH_CAUSATIVE_VARIANT = 16; // corresponds to "HetParentTransmitNormalAllele" TYPE_HET_PARENT_TRANSMIT_NORMAL_ALLELE = 17; // corresponds to "CosegregatingFamilies" TYPE_COSEGREGATING_FAMILIES = 18; // corresponds to "InformativeMeioses" TYPE_INFORMATIVE_MEIOSES = 19; // corresponds to "SampleLocalID" TYPE_SAMPLE_LOCAL_ID = 20; // corresponds to "SampleVariantID" TYPE_SAMPLE_VARIANT_ID = 21; // corresponds to "FamilyHistory" TYPE_FAMILY_HISTORY = 22; // corresponds to "NumFamiliesWithVariant" TYPE_NUM_FAMILIES_WITH_VARIANT = 23; // corresponds to "NumFamiliesWithSegregationObserved" TYPE_NUM_FAMILIES_WITH_SEGREGATION_OBSERVED = 24; // corresponds to "SegregationObserved" TYPE_SEGREGATION_OBSERVED = 25; } // base BaseAttribute base = 1; // type Type type = 2; } // This is an AttributeSet, there will be 1 attribute supported // by optional citations, xrefs and comment. There must be at least one // ObservedData Set, but can be any number. For each ObservedData set the // Attribute will be either decimal or string depending on type. The value will // be stored here, but decimals will be entered to the database as a string. message ObservedData { // Attributes. repeated ObservedDataAttribute attributes = 1; // Severity. optional Severity severity = 2; // Citation list. repeated Citation citations = 3; // Xref list. repeated Xref xrefs = 4; // Comment list. repeated Comment comments = 5; } // Sample. Sample sample = 1; // Observed data. repeated ObservedData observed_data = 2; // Co-occurence set. repeated Cooccurrence cooccurrence_sets = 3; // TraitSet. optional TraitSet trait_set = 4; // Citation list. repeated Citation citations = 5; // Xref list. repeated Xref xrefs = 6; // Comment list. repeated Comment comments = 7; } // A clinical assertion as submitted (SCV record). // // Corresponds to `MeasureTraitType` in XSD and `` in XML message ClinicalAssertion { // Local type for ClinVarSubmissionID. message ClinvarSubmissionId { // The identifier provided by the submitter to facilitate // identification of records corresponding to their submissions. If not // provided by a submitter, NCBI generates one. If provided by // submitter, that is represented in localKeyIsSubmitted. string local_key = 1; // Optional title. optional string title = 2; // Optional indication whether local key has been submitted. optional bool local_key_is_submitted = 3; // Optional assembly of submission. optional string submitted_assembly = 4; } // Local type for attribute set. message AttributeSetElement { // Local enum for types. enum Type { // unspecified type TYPE_UNSPECIFIED = 0; // Corresponds to "ModeOfInheritance" TYPE_MODE_OF_INHERITANCE = 1; // Corresponds to "Penetrance" TYPE_PENETRANCE = 2; // Corresponds to "AgeOfOnset" TYPE_AGE_OF_ONSET = 3; // Corresponds to "Severity" TYPE_SEVERITY = 4; // Corresponds to "ClassificationHistory" TYPE_CLASSIFICATION_HISTORY = 5; // Corresponds to "SeverityDescription" TYPE_SEVERITY_DESCRIPTION = 6; // Corresponds to "AssertionMethod" TYPE_ASSERTION_METHOD = 7; } // The base value. BaseAttribute attribute = 1; // The type of the attribute. Type type = 2; // List of xrefs. repeated Xref xrefs = 3; // List of citations. repeated Citation citations = 4; // List of comments. repeated Comment comments = 5; } // Local type for `ClinVarAccession` message ClinvarAccession { // Accession. string accession = 1; // Version. int32 version = 2; // The submitter's identifier. SubmitterIdentifiers submitter_identifiers = 3; // The date that the latest update to the submitted // record (SCV) became public in ClinVar. optional google.protobuf.Timestamp date_updated = 4; // DateCreated is the date when the record first became // public in ClinVar. optional google.protobuf.Timestamp date_created = 5; } // Local enum for record status. enum RecordStatus { // unspecified record status RECORD_STATUS_UNSPECIFIED = 0; // corresponds to "current" RECORD_STATUS_CURRENT = 1; // corresponds to "replaced" RECORD_STATUS_REPLACED = 2; // corresponds to "removed" RECORD_STATUS_REMOVED = 3; } /* nested elements */ // The ClinVar submission ID. ClinvarSubmissionId clinvar_submission_id = 1; // The ClinVar SCV accessions. ClinvarAccession clinvar_accession = 2; // Optional list of additional submitters. repeated Submitter additional_submitters = 3; // Record status. RecordStatus record_status = 4; // Replaces; mutually exclusive with replaceds repeated string replaces = 5; // Replaced list; mutually exclusive with replaces repeated ClinicalAssertionRecordHistory replaceds = 6; // SCV classification. ClassificationScv classifications = 7; // The assertion. Assertion assertion = 8; // Attributes. repeated AttributeSetElement attributes = 9; // Observed in. repeated ObservedIn observed_ins = 10; // Allele in SCV; mutually exclusive with haplotype/genotype. optional AlleleScv simple_allele = 11; // Haplotype in SCV; mutually exclusive with allele/genotype. optional HaplotypeScv haplotype = 12; // Genotype in SCV; mutually exclusive with allele/haplotype. optional GenotypeScv genotype = 13; // The trait set. TraitSet trait_set = 14; // List of citations. repeated Citation citations = 15; // Optional study name. optional string study_name = 16; // Optional study description. optional string study_description = 17; // List of comments. repeated Comment comments = 18; // List of submissions. repeated string submission_names = 19; /* attributes */ // Date of creation. google.protobuf.Timestamp date_created = 20; // Date of creation. google.protobuf.Timestamp date_last_updated = 21; // Date of creation. google.protobuf.Timestamp submission_date = 22; // ID. optional uint64 id = 23; // Whether it is an FDA recognized database. optional bool fda_recognized_database = 24; } // This is a record per variant (Measure/@ID,AlleleID). // // Corresponds to "typeAllele" in XSD. message Allele { // Local type for Gene. message Gene { /* nested elements */ // Gene's locations. repeated Location locations = 1; // OMIM ID. repeated uint64 omims = 2; // Haploinsuffiency. optional DosageSensitivity haploinsufficiency = 3; // Triplosensitivity. optional DosageSensitivity triplosensitivity = 4; // Used to set key words for retrieval or // display about a gene, such as genes listed by the // ACMG guidelines. repeated string properties = 5; /* attributes */ // Optional gene symbol. optional string symbol = 6; // Full gene name. string full_name = 7; // Gene ID. int64 gene_id = 8; // Optional HGNC ID. optional string hgnc_id = 9; // Source of gene (calculated or submitted). string source = 10; // Relationship between gene and variant. optional GeneVariantRelationship relationship_type = 11; } // Local type for allele frequency. message AlleleFrequency { // Value. double value = 1; // Source. string source = 2; // URL. optional string url = 3; } // Local type for GlobalMinorAlleleFrequency. message GlobalMinorAlleleFrequency { // Value. double value = 1; // Source. string source = 2; // Minor allele. optional string minor_allele = 3; // URL. optional string url = 4; } // Local type for allele name. message Name { // The name's value. string value = 1; // The name's type. optional string type = 2; } /* nested elements */ // Gene list. repeated Gene genes = 1; // Name. string name = 2; // Canonical SPDI. optional string canonical_spdi = 3; // Variant type(s). repeated string variant_types = 4; // Location. repeated Location locations = 5; // List of other names. repeated OtherName other_names = 6; // These are the single-letter representations of the protein change. repeated string protein_changes = 7; // List of HGVS expressions. repeated HgvsExpression hgvs_expressions = 8; // Aggregated classifications. optional AggregateClassificationSet classifications = 9; // List of xrefs. repeated Xref xrefs = 10; // List of comments. repeated Comment comments = 11; // List of functional consequences. repeated FunctionalConsequence functional_consequences = 12; // Allele frequencies. repeated AlleleFrequency allele_frequencies = 13; // Global minor allele frequencies. optional GlobalMinorAlleleFrequency global_minor_allele_frequency = 14; /* attributes */ // Allele ID. int64 allele_id = 15; // Variation ID. int64 variation_id = 16; } // This is a record of one or more simple alleles on the same chromosome // molecule. // // Corresponds to `typeHaplotype` in XSD message Haplotype { // The list of alleles in the haplotype. repeated Allele simple_alleles = 1; // The preferred representation of the haplotype. string name = 2; // The type of the haplotype. HaploVariationType variation_type = 3; // Names other than 'preferred' used for the haplotype. repeated OtherName other_names = 4; // List of all the HGVS expressions valid for, or used to submit, // a variant. repeated HgvsExpression hgvs_expressions = 5; // Classifications of the variant. optional AggregateClassificationSet classifications = 6; // Functional consequences of the variant. repeated FunctionalConsequence functional_consequences = 7; // List of cross-references. repeated Xref xrefs = 8; // List of comments. repeated Comment comments = 9; // Variation ID. int64 variation_id = 10; // Number of copies. optional int32 number_of_copies = 11; // Number of chromosomes. optional int32 number_of_chromosomes = 12; } // This element is used for alleles that were not directly part of a // submission but were part of a complex submission. They have no direct submitted // classification, but are being reported for a complete representation of all alleles // in ClinVar. Compare to ClassifiedRecord. message IncludedRecord { // Local type for tag `ClassifiedVariation`. message ClassifiedVariation { // Variation ID. int64 variation_id = 1; // Optional accession. optional string accession = 2; // Version. int32 version = 3; } // Simple allele; mutually exclusive with haplotype. optional Allele simple_allele = 1; // Haplotype; mutually exclusive with simple_allele. optional Haplotype haplotype = 2; // Aggregate classification sets. optional AggregateClassificationSet classifications = 3; // List of submitted records. repeated Scv submitted_classifications = 4; // Maintains the list of classified variants represented in // this submission, although not submitted with an Classification // independently. repeated ClassifiedVariation classified_variations = 5; // List of general citations. repeated GeneralCitations general_citations = 6; } // Used to report genotypes, be they simple or complex diplotypes. // // Corresponds to "typeGenotype" in XSD. message Genotype { /* nested elements */ // Simple allele; mutually exclusive with `haplotype`. repeated Allele simple_alleles = 1; // Haplotype; mutually exclusive with `simple_allele`. // // Allows more than 2 haplotypes per genotype to support // representation of ploidy. repeated Haplotype haplotypes = 2; // Optional name. string name = 3; // The variation type. VariationType variation_type = 4; // Names other than 'preferred' used for the Genotype. repeated OtherName other_names = 5; // HGVS descriptions. repeated HgvsExpression hgvs_expressions = 6; // Functional consequences. repeated FunctionalConsequence functional_consequences = 7; // Aggregated classifications. optional AggregateClassificationSet classifications = 8; // List of xrefs. repeated Xref xrefs = 9; // List of citations. repeated Citation citations = 10; // List of comments. repeated Comment comments = 11; // Attributes. repeated AttributeSetElement attributes = 12; /* attributes */ // Variation ID. optional int64 variation_id = 13; } // Corresponds to "typeRCV" in XSD. message RcvAccession { // Local type for ClassifiedConditionList. message ClassifiedConditionList { /* nested elements */ // List of interpreted conditions. repeated ClassifiedCondition classified_conditions = 1; /* attributes */ // Trait set ID. optional int64 trait_set_id = 2; } // Local type for GermlineClassification. // // The aggregate review status based on // all germline submissions for this record. message GermlineClassification { // Local type for Description. message Description { // The description. string value = 1; /* attributes */ // The date of the description. optional google.protobuf.Timestamp date_last_evaluated = 2; // The number of submissions. optional uint32 submission_count = 3; } // The aggregate review status based on // all somatic clinical impact submissions for this // record. AggregateGermlineReviewStatus review_status = 1; // The oncogenicity description. Description description = 2; } // Local type for SomaticClinicalImpact. // // The aggregate review status based on // all somatic clinical impact submissions for this // record. message SomaticClinicalImpact { // Local type for Description. message Description { // The description. string value = 1; /* attributes */ // Clinical impact assertion type. optional string clinical_impact_assertion_type = 2; // Clinical impact significance optional string clinical_impact_clinical_significance = 3; // The date of the description. optional google.protobuf.Timestamp date_last_evaluated = 4; // The number of submissions. optional uint32 submission_count = 5; } // The aggregate review status based on // all somatic clinical impact submissions for this // record. AggregateSomaticClinicalImpactReviewStatus review_status = 1; // The oncogenicity description. repeated Description descriptions = 2; } // Local type for OncogenicityClassification. message OncogenicityClassification { // Local type for Description. message Description { // The description. string value = 1; /* attributes */ // The date of the description. optional google.protobuf.Timestamp date_last_evaluated = 2; // The number of submissions. optional uint32 submission_count = 3; } // The aggregate review status based on // all oncogenic submissions for this record. AggregateOncogenicityReviewStatus review_status = 1; // The oncogenicity description. Description description = 2; } // Local type for RCV classifications. message RcvClassifications { // Germline classification. optional GermlineClassification germline_classification = 1; // Somatic clinical impact. optional SomaticClinicalImpact somatic_clinical_impact = 2; // Oncogenicity classification. optional OncogenicityClassification oncogenicity_classification = 3; } /* nested elements */ // The list of classified conditions. optional ClassifiedConditionList classified_condition_list = 1; // The list of RCV classifications. RcvClassifications rcv_classifications = 2; // The list of RCV accessions this record has replaced. repeated RecordHistory replaceds = 3; /* attributes */ // Optional title. optional string title = 4; // Accession. string accession = 5; // Version. int32 version = 6; } // This element is restricted to variation records for which an explicit // classification was submitted. Compare to IncludedRecord, which provides aggregate // information about variants that are part of another submission, but for which // ClinVar has *not* received a submission specific to that variant independently. message ClassifiedRecord { // Local type for tag `RCVList`. message RcvList { // The RCV record. repeated RcvAccession rcv_accessions = 1; // The number of submissions (SCV accessions) referencing the VariationID. optional int32 submission_count = 2; // The number of idependent observations. optional int32 independent_observations = 3; } // Local type for the attribute `@MappingType`. enum MappingType { // unspecified mapping type MAPPING_TYPE_UNSPECIFIED = 0; // corresponds to "Name" MAPPING_TYPE_NAME = 1; // corresponds to "Xref" MAPPING_TYPE_XREF = 2; } // Local type for the tag `TraitMapping`. message TraitMapping { // Local type for the tag "MedGen" message Medgen { // Name. string name = 1; // CUI. string cui = 2; } /* nested elements */ repeated Medgen medgens = 1; /* attributes */ // ID of clinical assertion. int64 clinical_assertion_id = 2; // The trait type. string trait_type = 3; // The mapping type. MappingType mapping_type = 4; // The mapping value. string mapping_value = 5; // The mapping reference. string mapping_ref = 6; } // Describes a single sequence change relative to a // contiguous region of a chromosome or the mitochondrion. // // Mutually exclusive with `haplotype` and `genotype`. optional Allele simple_allele = 1; // Describes multiple sequence changes on one of the // chromosomes of a homologous pair or on the mitochondrion. // // Mutually exclusive with `simple_allele` and `genotype`. optional Haplotype haplotype = 2; // Describes the combination of sequence changes on each // chromosome of a homologous pair. // // Mutually exclusive with `simple_allele` and `haplotype`. optional Genotype genotype = 3; // List of RCV records. RcvList rcv_list = 4; // List of classifications. AggregateClassificationSet classifications = 5; // List of clinical assertions. repeated ClinicalAssertion clinical_assertions = 6; // This element is used to report how each user-submitted // trait name was mapped to a MedGen CUI identifier and a preferred name. // The structure may be used in the future to report, when a trait is // identified by a source's identifier (e.g. MIM number), the preferred // name used by that source at the time of submission. For MappingType // XRef, MappingRef is the database name and MappingValue is the database's // identifier. For MappingType Name, MappingRef is Alternate or Preferred, // and MappingValue is the submitted name of the trait. ClinicalAssertionID // is an integer identifier that corresponds 1:1 to the SCV assigned to the // submission. repeated TraitMapping trait_mappings = 7; // List of deleted SCVs. repeated DeletedScv deleted_scvs = 8; // List of general citations. repeated GeneralCitations general_citations = 9; } // This element groups the set of data specific to a VariationArchive // record, namely the summary data of what has been submitted about a // VariationID AND for Classified records only, the content each // submission (SCV) provided. // // Type for the `` type. message VariationArchive { // Enumeration for `@RecordType`. enum RecordType { // unspecified record type RECORD_TYPE_UNSPECIFIED = 0; // corresponds to "included" RECORD_TYPE_INCLUDED = 1; // corresponds to "classified" RECORD_TYPE_CLASSIFIED = 2; } // Enumeration for `@RecordStatus`. enum RecordStatus { // unspecified record status RECORD_STATUS_UNSPECIFIED = 0; // corresponds to "current" RECORD_STATUS_CURRENT = 1; // corresponds to "previous" RECORD_STATUS_PREVIOUS = 2; // corresponds to "replaced" RECORD_STATUS_REPLACED = 3; // correspodns to "deleted" RECORD_STATUS_DELETED = 4; } /* attributes */ // Numeric variation ID. int64 variation_id = 1; // This is ClinVar's name for the variant. ClinVar uses this term in // its web displays string variation_name = 2; // Type of the variant. string variation_type = 3; // DateCreated is the date when the record first became public in // ClinVar. google.protobuf.Timestamp date_created = 4; // The date the record was last updated in the public database. The // update may be a change to one of the submitted records (SCVs) or // annotation added to the aggregate record by NCBI staff. This date // is independent of a version change; annotated added by NCBI may // change without representing a change in the version. google.protobuf.Timestamp date_last_updated = 5; // This date is of the most recent submitted record (SCV) for the // VCV; it may reflect a new submitted record or an update to a submitted record. google.protobuf.Timestamp most_recent_submission = 6; // Accession assigned to the variant, or set of variants, that was // Classified string accession = 7; // Version of record and suffix for accession. int32 version = 8; // Number of submitters in record. int32 number_of_submitters = 9; // Number of submissions in record. int32 number_of_submissions = 10; // Record type. RecordType record_type = 11; /* contained elements */ // The record's status. RecordStatus record_status = 12; // Pointer to the replacing record; optional. RecordHistory replaced_by = 13; // The list of VCV accessions this record has replaced. repeated RecordHistory replaceds = 14; // Comment on the record; optional. Comment comment = 15; // Specification of the species. Species species = 16; // This element describes the classification of a single // allele, haplotype, or genotype based on all submissions to ClinVar. This // differs from the element IncludedRecord, which describes simple alleles // or haplotypes, referenced in ClassifiedRecord, but for which no explicit // classification was submitted. Once that variation is described, details // are added about the phenotypes being classified, the classification, the // submitters providing the classifications, and all supported evidence. // // NB: mutually exclusive with `included_record`. optional ClassifiedRecord classified_record = 17; // This element describes a single allele or haplotype // included in submissions to ClinVar, but for which no explicit // classification was submitted. It also references the submissions and the // Classified records that include them. // // NB: mutually exclusive with `classified_record`. optional IncludedRecord included_record = 18; } // The element to group each VariationArchive element in the release // // Type for the `` tag. message ClinvarVariationRelease { /* attributes */ // The current release. google.protobuf.Timestamp release_date = 1; /* contained elements */ // List of `` tags. repeated VariationArchive variation_archives = 2; }