Phenopacket-squamous-cell-esophageal-carcinoma.yaml

metaData:
  created: '2021-05-14T10:35:00Z'
  createdBy: anonymous biocurator
  phenopacketSchemaVersion: 2.0.0
  resources:
  - id: ncit
    iriPrefix: http://purl.obolibrary.org/obo/NCIT_
    name: NCI Thesaurus
    namespacePrefix: NCIT
    url: http://purl.obolibrary.org/obo/ncit.owl
    version: 21.05d
  - id: efo
    iriPrefix: http://purl.obolibrary.org/obo/EFO_
    name: Experimental Factor Ontology
    namespacePrefix: EFO
    url: http://www.ebi.ac.uk/efo/efo.owl
    version: 3.34.0
  - id: uberon
    iriPrefix: http://purl.obolibrary.org/obo/UBERON_
    name: Uber-anatomy ontology
    namespacePrefix: UBERON
    url: http://purl.obolibrary.org/obo/uberon.owl
    version: '2021-07-27'
  - id: ncbitaxon
    iriPrefix: http://purl.obolibrary.org/obo/NCBITaxon_
    name: NCBI organismal classification
    namespacePrefix: NCBITaxon
    url: http://purl.obolibrary.org/obo/ncbitaxon.owl
    version: '2021-06-10'
biosamples:
- id: biosample 1
  individualId: proband A
  procedure:
    code:
      id: NCIT:C15189
      label: Biopsy
  sampledTissue:
    id: NCIT:C12389
    label: Esophagus
  timeOfCollection:
    age:
      iso8601duration: P49Y2M
  tumorProgression:
    id: NCIT:C4813
    label: Recurrent Malignant Neoplasm
- diagnosticMarkers:
    NCIT:C131711:
      id: NCIT:C131711
      label: Human Papillomavirus-18 Positive
  histologicalDiagnosis:
    id: NCIT:C4024
    label: Esophageal Squamous Cell Carcinoma
  id: biosample 2
  individualId: proband A
  procedure:
    code:
      id: NCIT:C15189
      label: Biopsy
  sampledTissue:
    id: NCIT:C139196
    label: Esophageal Lymph Node
  timeOfCollection:
    age:
      iso8601duration: P48Y3M
  tumorProgression:
    id: NCIT:C84509
    label: Primary Malignant Neoplasm
- id: biosample 3
  individualId: proband A
  procedure:
    code:
      id: NCIT:C15189
      label: Biopsy
  sampledTissue:
    id: NCIT:C12468
    label: Lung
  timeOfCollection:
    age:
      iso8601duration: P50Y7M
  tumorProgression:
    id: NCIT:C3261
    label: Metastatic Neoplasm
diseases:
- clinicalTnmFinding:
    NCIT:C48724:
      id: NCIT:C48724
      label: T2 Stage Finding
    NCIT:C48706:
      id: NCIT:C48706
      label: N1 Stage Finding
    NCIT:C48699:
      id: NCIT:C48699
      label: M0 Stage Finding
  excluded: false
  term:
    id: NCIT:C4024
    label: Esophageal Squamous Cell Carcinoma
id: arbitrary.id
subject:
  id: proband A
  karyotypicSex: UNKNOWN_KARYOTYPE
  sex: MALE
  timeAtLastEncounter:
    age:
      iso8601duration: P38Y