org.opencb.biodata.models.variant.avro.EvidenceProtocol Maven / Gradle / Ivy
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/**
* Autogenerated by Avro
*
* DO NOT EDIT DIRECTLY
*/
package org.opencb.biodata.models.variant.avro;
@SuppressWarnings("all")
@org.apache.avro.specific.AvroGenerated
public interface EvidenceProtocol {
public static final org.apache.avro.Protocol PROTOCOL = org.apache.avro.Protocol.parse("{\"protocol\":\"EvidenceProtocol\",\"namespace\":\"org.opencb.biodata.models.variant.avro\",\"types\":[{\"type\":\"record\",\"name\":\"EvidenceSource\",\"doc\":\"The source of an evidence.\",\"fields\":[{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Name of source\"},{\"name\":\"version\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Version of source\"},{\"name\":\"date\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The source date.\"}]},{\"type\":\"record\",\"name\":\"EvidenceSubmission\",\"doc\":\"The submission information\",\"fields\":[{\"name\":\"submitter\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The submitter\"},{\"name\":\"date\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The submission date\"},{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The submission id\"}]},{\"type\":\"record\",\"name\":\"SomaticInformation\",\"doc\":\"The somatic information.\",\"fields\":[{\"name\":\"primarySite\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The primary site\"},{\"name\":\"siteSubtype\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The primary site subtype\"},{\"name\":\"primaryHistology\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The primary histology\"},{\"name\":\"histologySubtype\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The histology subtype\"},{\"name\":\"tumourOrigin\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The tumour origin\"},{\"name\":\"sampleSource\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The sample source, e.g. blood-bone marrow, cell-line, pancreatic\"}]},{\"type\":\"enum\",\"name\":\"ModeOfInheritance\",\"doc\":\"An enumeration for the different mode of inheritances:\\n\\n* `monoallelic_not_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, not imprinted\\n* `monoallelic_maternally_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, maternally imprinted (paternal allele expressed)\\n* `monoallelic_paternally_imprinted`: MONOALLELIC, autosomal or pseudoautosomal, paternally imprinted (maternal allele expressed)\\n* `monoallelic`: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown\\n* `biallelic`: BIALLELIC, autosomal or pseudoautosomal\\n* `monoallelic_and_biallelic`: BOTH monoallelic and biallelic, autosomal or pseudoautosomal\\n* `monoallelic_and_more_severe_biallelic`: BOTH monoallelic and biallelic, autosomal or pseudoautosomal (but BIALLELIC mutations cause a more SEVERE disease form), autosomal or pseudoautosomal\\n* `xlinked_biallelic`: X-LINKED: hemizygous mutation in males, biallelic mutations in females\\n* `xlinked_monoallelic`: X linked: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)\\n* `mitochondrial`: MITOCHONDRIAL\\n* `unknown`: Unknown\\n* `NA`: Not applicable\",\"symbols\":[\"monoallelic\",\"monoallelic_not_imprinted\",\"monoallelic_maternally_imprinted\",\"monoallelic_paternally_imprinted\",\"biallelic\",\"monoallelic_and_biallelic\",\"monoallelic_and_more_severe_biallelic\",\"xlinked_biallelic\",\"xlinked_monoallelic\",\"mitochondrial\",\"unknown\",\"NA\"]},{\"type\":\"record\",\"name\":\"HeritableTrait\",\"doc\":\"The entity representing a phenotype and its inheritance pattern.\",\"fields\":[{\"name\":\"trait\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The trait (e.g.: HPO term, MIM term, DO term etc.)\"},{\"name\":\"inheritanceMode\",\"type\":[\"null\",\"ModeOfInheritance\"],\"doc\":\"The mode of inheritance\"}]},{\"type\":\"enum\",\"name\":\"FeatureTypes\",\"doc\":\"The feature types\",\"symbols\":[\"regulatory_region\",\"gene\",\"transcript\",\"protein\"]},{\"type\":\"record\",\"name\":\"GenomicFeature\",\"doc\":\"The genomic feature\",\"fields\":[{\"name\":\"featureType\",\"type\":[\"null\",\"FeatureTypes\"],\"doc\":\"Feature Type\"},{\"name\":\"ensemblId\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Feature used, this should be a feature ID from Ensembl, (i.e, ENST00000544455)\"},{\"name\":\"xrefs\",\"type\":[\"null\",{\"type\":\"map\",\"values\":{\"type\":\"string\",\"avro.java.string\":\"String\"},\"avro.java.string\":\"String\"}],\"doc\":\"Others IDs. Fields like the HGNC symbol if available should be added here\"}]},{\"type\":\"enum\",\"name\":\"ClinicalSignificance\",\"doc\":\"Mendelian variants classification with ACMG terminology as defined in Richards, S. et al. (2015). Standards and\\n guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College\\n of Medical Genetics and Genomics and the Association for Molecular Pathology. Genetics in Medicine, 17(5),\\n 405–423. https://doi.org/10.1038/gim.2015.30.\\n\\n Classification for pharmacogenomic variants, variants associated to\\n disease and somatic variants based on the ACMG recommendations and ClinVar classification\\n (https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/).\\n\\n* `benign_variant` : Benign variants interpreted for Mendelian disorders\\n* `likely_benign_variant` : Likely benign variants interpreted for Mendelian disorders with a certainty of at least 90%\\n* `pathogenic_variant` : Pathogenic variants interpreted for Mendelian disorders\\n* `likely_pathogenic_variant` : Likely pathogenic variants interpreted for Mendelian disorders with a certainty of at\\nleast 90%\\n* `uncertain_significance` : Uncertain significance variants interpreted for Mendelian disorders. Variants with\\nconflicting evidences should be classified as uncertain_significance\",\"symbols\":[\"benign\",\"likely_benign\",\"VUS\",\"likely_pathogenic\",\"pathogenic\",\"uncertain_significance\"]},{\"type\":\"enum\",\"name\":\"DrugResponseClassification\",\"doc\":\"Pharmacogenomics drug response variant classification\",\"symbols\":[\"responsive\",\"altered_sensitivity\",\"reduced_sensitivity\",\"increased_sensitivity\",\"altered_resistance\",\"increased_resistance\",\"reduced_resistance\",\"increased_risk_of_toxicity\",\"reduced_risk_of_toxicity\",\"altered_toxicity\",\"adverse_drug_reaction\",\"indication\",\"contraindication\",\"dosing_alteration\",\"increased_dose\",\"reduced_dose\",\"increased_monitoring\",\"increased_efficacy\",\"reduced_efficacy\",\"altered_efficacy\"]},{\"type\":\"enum\",\"name\":\"TraitAssociation\",\"doc\":\"Association of variants to a given trait.\\n* `established_risk_allele` : Established risk allele for variants associated to disease\\n* `likely_risk_allele` : Likely risk allele for variants associated to disease\\n* `uncertain_risk_allele` : Uncertain risk allele for variants associated to disease\\n* `protective` : Protective allele\",\"symbols\":[\"established_risk_allele\",\"likely_risk_allele\",\"uncertain_risk_allele\",\"protective\"]},{\"type\":\"enum\",\"name\":\"TumorigenesisClassification\",\"doc\":\"Variant classification according to its relation to cancer aetiology.\\n* `driver` : Driver variants\\n* `passenger` : Passenger variants\\n* `modifier` : Modifier variants\",\"symbols\":[\"driver\",\"passenger\",\"modifier\"]},{\"type\":\"enum\",\"name\":\"EvidenceImpact\",\"doc\":\"Evidence of pathogenicity and benign impact as defined in Richards, S. et al. (2015). Standards and guidelines for the interpretation\\n of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and\\n the Association for Molecular Pathology. Genetics in Medicine, 17(5), 405–423. https://doi.org/10.1038/gim.2015.30\\n\\nEvidence of pathogenicity:\\n* `very_strong`:\\n - PVS1 null variant (nonsense, frameshift, canonical ±1 or 2 splice sites, initiation codon, single or multiexon\\n deletion) in a gene where LOF is a known mechanism of disease\\n* `strong`:\\n - PS1 Same amino acid change as a previously established pathogenic variant regardless of nucleotide change\\n - PS2 De novo (both maternity and paternity confirmed) in a patient with the disease and no family history\\n - PS3 Well-established in vitro or in vivo functional studies supportive of a damaging effect on the gene or gene\\n product\\n - PS4 The prevalence of the variant in affected individuals is significantly increased compared with the prevalence\\n in controls\\n* `moderate`:\\n - PM1 Located in a mutational hot spot and/or critical and well-established functiona","l domain (e.g., active site of\\n an enzyme) without benign variation\\n - PM2 Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes\\n Project, or Exome Aggregation Consortium\\n - PM3 For recessive disorders, detected in trans with a pathogenic variant\\n - PM4 Protein length changes as a result of in-frame deletions/insertions in a nonrepeat region or stop-loss\\n variants\\n - PM5 Novel missense change at an amino acid residue where a different missense change determined to be pathogenic\\n has been seen before\\n - PM6 Assumed de novo, but without confirmation of paternity and maternity\\n* `supporting`:\\n - PP1 Cosegregation with disease in multiple affected family members in a gene definitively known to cause the\\n disease\\n - PP2 Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are\\n a common mechanism of disease\\n - PP3 Multiple lines of computational evidence support a deleterious effect on the gene or gene product\\n (conservation, evolutionary, splicing impact, etc.)\\n - PP4 Patient’s phenotype or family history is highly specific for a disease with a single genetic etiology\\n - PP5 Reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory\\n to perform an independent evaluation\\n\\nEvidence of benign impact:\\n* `stand_alone`:\\n - BA1 Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation\\n Consortium\\n* `strong`:\\n - BS1 Allele frequency is greater than expected for disorder\\n - BS2 Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked\\n (hemizygous) disorder, with full penetrance expected at an early age\\n - BS3 Well-established in vitro or in vivo functional studies show no damaging effect on protein function or\\n splicing\\n - BS4 Lack of segregation in affected members of a family\\n* `supporting`:\\n - BP1 Missense variant in a gene for which primarily truncating variants are known to cause disease\\n - BP2 Observed in trans with a pathogenic variant for a fully penetrant dominant gene/disorder or observed in cis\\n with a pathogenic variant in any inheritance pattern\\n - BP3 In-frame deletions/insertions in a repetitive region without a known function\\n - BP4 Multiple lines of computational evidence suggest no impact on gene or gene product (conservation,\\n evolutionary, splicing impact, etc.)\\n - BP5 Variant found in a case with an alternate molecular basis for disease\\n - BP6 Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to\\n perform an independent evaluation\\n - BP7 A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice\\n consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved\",\"symbols\":[\"very_strong\",\"strong\",\"moderate\",\"supporting\",\"stand_alone\"]},{\"type\":\"enum\",\"name\":\"EthnicCategory\",\"doc\":\"This is the list of ethnics in ONS16\\n\\n* `D`: Mixed: White and Black Caribbean\\n* `E`: Mixed: White and Black African\\n* `F`: Mixed: White and Asian\\n* `G`: Mixed: Any other mixed background\\n* `A`: White: British\\n* `B`: White: Irish\\n* `C`: White: Any other White background\\n* `L`: Asian or Asian British: Any other Asian background\\n* `M`: Black or Black British: Caribbean\\n* `N`: Black or Black British: African\\n* `H`: Asian or Asian British: Indian\\n* `J`: Asian or Asian British: Pakistani\\n* `K`: Asian or Asian British: Bangladeshi\\n* `P`: Black or Black British: Any other Black background\\n* `S`: Other Ethnic Groups: Any other ethnic group\\n* `R`: Other Ethnic Groups: Chinese\\n* `Z`: Not stated\",\"symbols\":[\"D\",\"E\",\"F\",\"G\",\"A\",\"B\",\"C\",\"L\",\"M\",\"N\",\"H\",\"J\",\"K\",\"P\",\"S\",\"R\",\"Z\"]},{\"type\":\"enum\",\"name\":\"Penetrance\",\"doc\":\"Penetrance assumed in the analysis\",\"symbols\":[\"complete\",\"incomplete\"]},{\"type\":\"enum\",\"name\":\"VariantFunctionalEffect\",\"doc\":\"Variant effect with Sequence Ontology terms.\\n\\n* `SO_0002052`: dominant_negative_variant (http://purl.obolibrary.org/obo/SO_0002052)\\n* `SO_0002053`: gain_of_function_variant (http://purl.obolibrary.org/obo/SO_0002053)\\n* `SO_0001773`: lethal_variant (http://purl.obolibrary.org/obo/SO_0001773)\\n* `SO_0002054`: loss_of_function_variant (http://purl.obolibrary.org/obo/SO_0002054)\\n* `SO_0001786`: loss_of_heterozygosity (http://purl.obolibrary.org/obo/SO_0001786)\\n* `SO_0002055`: null_variant (http://purl.obolibrary.org/obo/SO_0002055)\",\"symbols\":[\"dominant_negative_variant\",\"gain_of_function_variant\",\"lethal_variant\",\"loss_of_function_variant\",\"loss_of_heterozygosity\",\"null_variant\"]},{\"type\":\"enum\",\"name\":\"AlleleOrigin\",\"doc\":\"Variant origin.\\n\\n* `SO_0001781`: de novo variant. http://purl.obolibrary.org/obo/SO_0001781\\n* `SO_0001778`: germline variant. http://purl.obolibrary.org/obo/SO_0001778\\n* `SO_0001775`: maternal variant. http://purl.obolibrary.org/obo/SO_0001775\\n* `SO_0001776`: paternal variant. http://purl.obolibrary.org/obo/SO_0001776\\n* `SO_0001779`: pedigree specific variant. http://purl.obolibrary.org/obo/SO_0001779\\n* `SO_0001780`: population specific variant. http://purl.obolibrary.org/obo/SO_0001780\\n* `SO_0001777`: somatic variant. http://purl.obolibrary.org/obo/SO_0001777\",\"symbols\":[\"de_novo_variant\",\"germline_variant\",\"maternal_variant\",\"paternal_variant\",\"pedigree_specific_variant\",\"population_specific_variant\",\"somatic_variant\"]},{\"type\":\"enum\",\"name\":\"Confidence\",\"doc\":\"Confidence based on the Confidence Information Ontology\\n\\n* `CIO_0000029`: high confidence level http://purl.obolibrary.org/obo/CIO_0000029\\n* `CIO_0000031`: low confidence level http://purl.obolibrary.org/obo/CIO_0000031\\n* `CIO_0000030`: medium confidence level http://purl.obolibrary.org/obo/CIO_0000030\\n* `CIO_0000039`: rejected http://purl.obolibrary.org/obo/CIO_0000039\",\"symbols\":[\"low_confidence_level\",\"medium_confidence_level\",\"high_confidence_level\",\"rejected\"]},{\"type\":\"enum\",\"name\":\"ConsistencyStatus\",\"doc\":\"The consistency of evidences for a given phenotype. This aggregates all evidences for a given phenotype and all\\n evidences with no phenotype associated (e.g.: in silico impact prediction, population frequency).\\n This is based on the Confidence Information Ontology terms.\\n\\n* `CIO_0000033`: congruent, all evidences are consistent. http://purl.obolibrary.org/obo/CIO_0000033\\n* `CIO_0000034`: conflict, there are conflicting evidences. This should correspond to a `VariantClassification` of\\n`uncertain_significance` for mendelian disorders. http://purl.obolibrary.org/obo/CIO_0000034\\n* `CIO_0000035`: strongly conflicting. http://purl.obolibrary.org/obo/CIO_0000035\\n* `CIO_0000036`: weakly conflicting. http://purl.obolibrary.org/obo/CIO_0000036\",\"symbols\":[\"congruent\",\"conflict\",\"weakly_conflicting\",\"strongly_conflicting\"]},{\"type\":\"record\",\"name\":\"Property\",\"doc\":\"A property in the form of name-value pair.\\n Names are restricted to ontology ids, they should be checked against existing ontologies in resources like\\n Ontology Lookup Service.\",\"fields\":[{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The ontology term id or accession in OBO format ${ONTOLOGY_ID}:${TERM_ID} (http://www.obofoundry.org/id-policy.html)\"},{\"name\":\"name\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The ontology term name\"},{\"name\":\"value\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Optional value for the ontology term, the type of the value is not checked\\n (i.e.: we could set the pvalue term to \\\"significant\\\" or to \\\"0.0001\\\")\"}]},{\"type\":\"record\",\"name\":\"VariantClassification\",\"doc\":\"The variant classification according to different properties.\",\"fields\":[{\"name\":\"clinicalSignificance\",\"type\":[\"null\",\"ClinicalSignificance\"],\"doc\":\"The variant's clinical significance.\"},{\"name\":\"drugResponseClassification\",\"type\":[\"null\",\"DrugResponseClassification\"],\"doc\":\"The variant's pharmacogenomics classi","fication.\"},{\"name\":\"traitAssociation\",\"type\":[\"null\",\"TraitAssociation\"],\"doc\":\"The variant's trait association.\"},{\"name\":\"tumorigenesisClassification\",\"type\":[\"null\",\"TumorigenesisClassification\"],\"doc\":\"The variant's tumorigenesis classification.\"},{\"name\":\"functionalEffect\",\"type\":[\"null\",\"VariantFunctionalEffect\"],\"doc\":\"The variant functional effect\"}]},{\"type\":\"record\",\"name\":\"EvidenceEntry\",\"doc\":\"An entry for an evidence\",\"fields\":[{\"name\":\"source\",\"type\":\"EvidenceSource\",\"doc\":\"Source of the evidence\"},{\"name\":\"submissions\",\"type\":{\"type\":\"array\",\"items\":\"EvidenceSubmission\"},\"doc\":\"The list of submissions\",\"default\":[]},{\"name\":\"somaticInformation\",\"type\":[\"null\",\"SomaticInformation\"],\"doc\":\"The somatic information\"},{\"name\":\"url\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"URL of source if any\"},{\"name\":\"id\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"ID of record in the source\"},{\"name\":\"assembly\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"The reference genome assembly\"},{\"name\":\"alleleOrigin\",\"type\":[\"null\",{\"type\":\"array\",\"items\":\"AlleleOrigin\"}],\"doc\":\"List of allele origins\"},{\"name\":\"heritableTraits\",\"type\":{\"type\":\"array\",\"items\":\"HeritableTrait\"},\"doc\":\"Heritable traits associated to this evidence\",\"default\":[]},{\"name\":\"genomicFeatures\",\"type\":{\"type\":\"array\",\"items\":\"GenomicFeature\"},\"doc\":\"The transcript to which the evidence refers\",\"default\":[]},{\"name\":\"variantClassification\",\"type\":[\"null\",\"VariantClassification\"],\"doc\":\"The variant classification\"},{\"name\":\"impact\",\"type\":[\"null\",\"EvidenceImpact\"],\"doc\":\"Impact of evidence. Should be coherent with the classification of impact if provided.\"},{\"name\":\"confidence\",\"type\":[\"null\",\"Confidence\"],\"doc\":\"The curation confidence.\"},{\"name\":\"consistencyStatus\",\"type\":[\"null\",\"ConsistencyStatus\"],\"doc\":\"The consistency status. This is applicable to complex evidences (e.g.: ClinVar)\"},{\"name\":\"ethnicity\",\"type\":\"EthnicCategory\",\"doc\":\"Ethnicity\"},{\"name\":\"penetrance\",\"type\":[\"null\",\"Penetrance\"],\"doc\":\"The penetrance of the phenotype for this genotype. Value in the range [0, 1]\"},{\"name\":\"variableExpressivity\",\"type\":[\"null\",\"boolean\"],\"doc\":\"Variable expressivity of a given phenotype for the same genotype\"},{\"name\":\"description\",\"type\":[\"null\",{\"type\":\"string\",\"avro.java.string\":\"String\"}],\"doc\":\"Evidence description\"},{\"name\":\"additionalProperties\",\"type\":{\"type\":\"array\",\"items\":\"Property\"},\"doc\":\"A list of additional properties in the form name-value.\",\"default\":[]},{\"name\":\"bibliography\",\"type\":{\"type\":\"array\",\"items\":{\"type\":\"string\",\"avro.java.string\":\"String\"}},\"doc\":\"Bibliography\",\"default\":[]}]}],\"messages\":{}}");
@SuppressWarnings("all")
public interface Callback extends EvidenceProtocol {
public static final org.apache.avro.Protocol PROTOCOL = org.opencb.biodata.models.variant.avro.EvidenceProtocol.PROTOCOL;
}
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