avro.variantAnnotation.avdl Maven / Gradle / Ivy
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@namespace("org.opencb.biodata.models.variant.avro")
protocol VariantAnnotations {
import idl "evidence.avdl";
// DEPRECATED: to be removed next release
@javaAnnotation("Deprecated")
enum ExpressionCall {UP, DOWN}
record GeneDrugInteraction {
union { null, string } geneName;
union { null, string } drugName;
union { null, string } source;
union { null, string } studyType;
union { null, string } type;
union { null, string } interactionType;
union { null, string } chemblId;
union { null, array } publications;
}
record Expression {
union { null, string } geneName;
union { null, string } transcriptId;
union { null, string } experimentalFactor;
union { null, string } factorValue;
union { null, string } experimentId;
union { null, string } technologyPlatform;
union { null, ExpressionCall} expression;
union { null, float } pvalue;
}
record Constraint {
union { null, string } source;
union { null, string } method;
union { null, string } name;
union { null, double } value;
}
record GeneMirnaTarget {
union { null, string } id;
union { null, string } name;
union { null, string } biotype;
}
record GeneTraitAssociation {
string id;
string name;
union { null, string } hpo;
union { null, float } score;
union { null, int } numberOfPubmeds;
union { null, array } associationTypes;
union { null, array } sources;
string source;
}
record PopulationFrequency {
string study;
string population;
string refAllele;
string altAllele;
float refAlleleFreq;
float altAlleleFreq;
union { null, int } refAlleleCount;
union { null, int } altAlleleCount;
union { null, float } refHomGenotypeFreq;
union { null, float } hetGenotypeFreq;
union { null, float } altHomGenotypeFreq;
union { null, int } refHomGenotypeCount;
union { null, int } hetGenotypeCount;
union { null, int } altHomGenotypeCount;
}
record SequenceOntologyTerm {
string accession;
string name;
}
record ProteinFeature {
union { null, string } id;
int start;
int end;
union { null, string } type;
union { null, string } description;
}
record Score {
double score;
string source;
union { null, string } description;
}
record ProteinVariantAnnotation {
union { null, string } uniprotAccession = null;
union { null, string } uniprotName = null;
union { null, string } proteinId = null; // Ensembl or RefSeq protein ID
union { null, int } position;
union { null, string } reference;
union { null, string } alternate;
union { null, string } uniprotVariantId;
union { null, string } functionalDescription;
union { null, array } substitutionScores;
union { null, array } keywords;
union { null, array } features;
}
record ExonOverlap {
union { null, string } number;
union { null, float } percentage;
}
record SpliceScores {
string source;
map scores;
}
record ConsequenceType {
union { null, string } geneId;
union { null, string } geneName;
// DEPRECATED: duplicate of geneId, to be removed next release
@javaAnnotation("Deprecated")
union { null, string } ensemblGeneId;
// DEPRECATED: duplicate of transcriptId, to be removed next release
@javaAnnotation("Deprecated")
union { null, string } ensemblTranscriptId;
union { null, string } transcriptId; // Ensembl or RefSeq ID depending on field 'source'
union { null, array } hgvs;
union { null, string } strand;
union { null, string } biotype;
union { null, string } source;
union { null, array } exonOverlap;
union { null, array } spliceScores;
// DEPRECATED: replaced by transcriptFlags
//@javaAnnotation("Deprecated")
//union { null, array } transcriptAnnotationFlags;
union { null, array } transcriptFlags;
union { null, int } cdnaPosition;
union { null, int } cdsPosition;
union { null, string } codon;
union { null, ProteinVariantAnnotation } proteinVariantAnnotation;
array sequenceOntologyTerms;
}
record Xref {
union { null, string } id;
union { null, string } source;
}
record Cytoband {
union { null, string } chromosome;
union { null, string } stain;
union { null, string } name;
union { null, int } start;
union { null, int } end;
}
record Repeat {
union { null, string } id;
union { null, string } chromosome;
union { null, int } start;
union { null, int } end;
union { null, int } period;
union { null, int } consensusSize;
union { null, float } copyNumber;
union { null, float } percentageMatch;
union { null, float } score;
union { null, string } sequence;
union { null, string } source;
}
record Drug {
union { null, string } therapeuticContext;
union { null, string } pathway;
union { null, string } effect;
union { null, string } association;
union { null, string } status;
union { null, string } evidence;
union { null, array } bibliography;
}
record PharmacogenomicsAlleles {
union { null, string } allele;
union { null, string } annotation;
union { null, string } description;
}
record PharmacogenomicsClinicalAnnotation {
union { null, string } variantId;
union { null, array } geneNames;
union { null, array } phenotypes;
union { null, array } phenotypeTypes;
union { null, string } confidence;
union { null, string } score;
union { null, string } url;
union { null, string } summary;
union { null, array } pubmed;
union { null, array } alleles;
}
record Pharmacogenomics {
union { null, string } id;
union { null, string } name;
union { null, string } source;
union { null, array } types;
union { null, string } smiles;
union { null, string } inChI;
union { null, array } annotations;
}
record GeneCancerAssociation {
union { null, string } id;
union { null, string } source;
union { null, string } tier;
union { null, boolean } somatic;
union { null, boolean } germline;
union { null, array } somaticTumourTypes;
union { null, array } germlineTumourTypes;
union { null, array } syndromes;
union { null, array } tissues;
union { null, array } modeOfInheritance;
union { null, array } roleInCancer;
union { null, array } mutationTypes;
union { null, array } translocationPartners;
}
record GwasAssociationStudyTraitScores {
union { null, double } pValue;
union { null, double } pValueMlog;
union { null, string } pValueText;
union { null, double } orBeta;
union { null, string } percentCI;
}
record OntologyTermAnnotation {
union { null, string } id;
union { null, string } name;
union { null, string } description;
union { null, string } source;
union { null, string } url;
union { null, map } attributes;
}
record GwasAssociationStudyTrait {
union { null, string } diseaseTrait;
union { null, array } strongestSnpRiskAllele;
union { null, array } ontologies;
union { null, array } scores;
}
record GwasAssociationStudy {
union { null, string } pubmedid;
union { null, string } study;
union { null, string } studyAccession;
union { null, string } initialSampleSizeDescription;
union { null, int } initialSampleSize;
union { null, string } platform;
union { null, string } genotypingTechnology;
union { null, array } traits;
}
record GwasAssociation {
union { null, string } source;
union { null, string } region;
union { null, string } snpId;
union { null, string } riskAllele;
union { null, double } riskAlleleFrequency;
union { null, array } studies;
}
record CancerHotspotAlternateAnnotation {
union { null, string } aminoacidAlternate;
union { null, int } count;
union { null, map } sampleCount;
}
record CancerHotspotVariantAnnotation {
union { null, string } geneName;
union { null, string } proteinId;
union { null, int } aminoacidPosition;
union { null, string } aminoacidReference;
union { null, string } cancerType;
union { null, map } scores;
union { null, map } cancerTypeCount;
union { null, map } organCount;
union { null, array } variants;
union { null, string } source;
}
record AdditionalAttribute {
map attribute;
}
record VariantAnnotation {
union { null, string } chromosome;
union { null, int } start;
union { null, int } end;
union { null, string } reference;
union { null, string } alternate;
// DEPRECATED: to be removed next release
@javaAnnotation("Deprecated")
union { null, string } ancestralAllele;
union { null, string } id;
union { null, array } xrefs;
union { null, array } hgvs;
union { null, string } displayConsequenceType;
array consequenceTypes = [];
union { null, array } populationFrequencies;
union { null, string } minorAllele;
union { null, float } minorAlleleFreq;
union { null, array } conservation;
// DEPRECATED: to be removed next release
@javaAnnotation("Deprecated")
union { null, array } geneExpression;
union { null, array } geneTraitAssociation;
union { null, array } geneDrugInteraction;
union { null, array } geneConstraints;
union { null, array } geneMirnaTargets;
union { null, array } geneCancerAssociations;
union { null, array } traitAssociation;
union { null, array } pharmacogenomics;
union { null, array } gwas;
union { null, array } cancerHotspots;
union { null, array } functionalScore;
union { null, array } cytoband;
union { null, array } repeat;
union { null, array } drugs;
union { null, map } additionalAttributes = null;
}
}