phenopackets 0.2.2-post0

Rust bindings for Phenopacket Schema
Documentation 
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id: "comprehensive-phenopacket-id"
subject:
  id: "14 year-old boy"
  alternateIds:
  - "boy"
  - "patient"
  - "proband"
  dateOfBirth: "1970-01-02T10:17:36.000000100Z"
  timeAtLastEncounter:
    age:
      iso8601duration: "P14Y"
  sex: "MALE"
  karyotypicSex: "XY"
  taxonomy:
    id: "NCBITaxon:9606"
    label: "homo sapiens"
phenotypicFeatures:
- type:
    id: "HP:0001558"
    label: "Decreased fetal movement"
  onset:
    ontologyClass:
      id: "HP:0011461"
      label: "Fetal onset"
  evidence:
  - evidenceCode:
      id: "ECO:0000033"
      label: "author statement supported by traceable reference"
    reference:
      id: "PMID:30808312"
      description: "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria:\
        \ a case report."
- type:
    id: "HP:0031910"
    label: "Abnormal cranial nerve physiology"
  excluded: true
  evidence:
  - evidenceCode:
      id: "ECO:0000033"
      label: "author statement supported by traceable reference"
    reference:
      id: "PMID:30808312"
      description: "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria:\
        \ a case report."
- type:
    id: "HP:0011463"
    label: "Macroscopic hematuria"
  modifiers:
  - id: "HP:0031796"
    label: "Recurrent"
  onset:
    age:
      iso8601duration: "P14Y"
  evidence:
  - evidenceCode:
      id: "ECO:0000033"
      label: "author statement supported by traceable reference"
    reference:
      id: "PMID:30808312"
      description: "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria:\
        \ a case report."
- type:
    id: "HP:0001270"
    label: "Motor delay"
  severity:
    id: "HP:0012825"
    label: "Mild"
  onset:
    ontologyClass:
      id: "HP:0011463"
      label: "Childhood onset"
biosamples:
- id: "biosample-id"
  individualId: "14 year-old boy"
  description: "Muscle biopsy of 14 year-old boy"
  sampledTissue:
    id: "UBERON:0003403"
    label: "skin of forearm"
  taxonomy:
    id: "NCBITaxon:9606"
    label: "homo sapiens"
  timeOfCollection:
    age:
      iso8601duration: "P14Y"
  histologicalDiagnosis:
    id: "NCIT:C38757"
    label: "Negative Finding"
  tumorProgression:
    id: "NCIT:C3677"
    label: "Benign Neoplasm"
  tumorGrade:
    id: "NCIT:C28076"
    label: "Disease Grade Qualifier"
  diagnosticMarkers:
  - id: "NCIT:C68748"
    label: "HER2/Neu Positive"
  materialSample:
    id: "EFO:0009655"
    label: "abnormal sample"
interpretations:
- id: "comprehensive-phenopacket-id"
  progressStatus: "SOLVED"
  diagnosis:
    disease:
      id: "OMIM:101600"
      label: "PFEIFFER SYNDROME"
    genomicInterpretations:
    - subjectOrBiosampleId: "14 year-old boy"
      interpretationStatus: "CAUSATIVE"
      variantInterpretation:
        variationDescriptor:
          expressions:
          - syntax: "hgvs"
            value: "NM_001848.2:c.877G>A"
          allelicState:
            id: "GENO:0000135"
            label: "heterozygous"
diseases:
- term:
    id: "OMIM:101600"
    label: "PFEIFFER SYNDROME"
  onset:
    ontologyClass:
      id: "HP:0003577"
      label: "Congenital onset"
files:
- uri: "file://data/genomes/P000001C"
  individualToFileIdentifiers:
    "14 year-old boy": "P000001C"
  fileAttributes:
    genomeAssembly: "GRCh38.p13"
    fileFormat: "vcf"
    description: "Whole genome sequencing VCF output"
metaData:
  created: "2022-10-03T16:39:04.000123456Z"
  createdBy: "Peter R."
  submittedBy: "PhenopacketLab"
  resources:
  - id: "hp"
    name: "human phenotype ontology"
    url: "http://purl.obolibrary.org/obo/hp.owl"
    version: "2018-03-08"
    namespacePrefix: "HP"
    iriPrefix: "http://purl.obolibrary.org/obo/HP_"
  - id: "geno"
    name: "Genotype Ontology"
    url: "http://purl.obolibrary.org/obo/geno.owl"
    version: "19-03-2018"
    namespacePrefix: "GENO"
    iriPrefix: "http://purl.obolibrary.org/obo/GENO_"
  - id: "pubmed"
    name: "PubMed"
    namespacePrefix: "PMID"
    iriPrefix: "https://www.ncbi.nlm.nih.gov/pubmed/"
  - id: "ncit"
    name: "NCI Thesaurus"
    url: "http://purl.obolibrary.org/obo/ncit.owl"
    version: "20-03-2020"
    namespacePrefix: "NCIT"
    iriPrefix: "http://purl.obolibrary.org/obo/NCIT_"
  phenopacketSchemaVersion: "2.0.0"
  externalReferences:
  - id: "PMID:30808312"
    description: "COL6A1 mutation leading to Bethlem myopathy with recurrent hematuria:\
      \ a case report."