Develop and test Kids First sequencing experiment conformance resources

[liberaliscomputing]

Develop and test Kids First sequencing experiment conformance resources. Consider the following steps:

• [x] Consult with the followings about the discussed specification
  • FHIR Task
  • KFDRC FHIR model mapping spreadsheet
  • KFDRC FHIR ERD
• [ ] Create a new kfdrc-sequencing-experiment profile
• [x] (Optional) Create any necessary Extensions for added attributes
• [x] (Optional) Create SearchParameters for the above Extensions
• [x] (Optional) Create any necessary CodeSystems or ValueSets
• [x] (Optional) Bind the above ValueSets to the new Extensions
• [x] Create example resources
• [x] Validate the above resources with the FHIR IG publisher
• [x] Test ingest and search

[liberaliscomputing]

During the meeting on 09-21-2020, the followings were discussed:

• KFDRC sequencing will be represented as follows:

KFDRC Entity	KFDRC Attribute	FHIR Profile	FHIR Attribute	FHIR Data Type	FHIR Target Reference
sequencing_experiment	experiment_date	Task	authoredOn	dateTime	Not Applicable
sequencing_experiment	sequencing_center_id	Task	owner	valueReference	Organization
biospecimen	biospecimen_id	Task	input	valueReference	Specimen
sequencing_experiment	experiment_strategy	Task	input	valueCodeableConcept	Not Applicable
sequencing_experiment	instrument_model	Task	input	valueCodeableConcept	Not Applicable
sequencing_experiment	is_paried_end	Task	input	valueBoolean	Not Applicable
sequencing_experiment	library_name	Task	input	valueString	Not Applicable
sequencing_experiment	library_prep	Task	input	valueCodeableConcept	Not Applicable
sequencing_experiment	library_selection	Task	input	valueCodeableConcept	Not Applicable
sequencing_experiment	platform	Task	input	valueCodeableConcept	Not Applicable
genomic_file	genomic_file_id	Task	output	valueReference	DocumentReference
sequencing_experiment	sequencing_experiment_id	Task	output	valueReference	Observation
genomic_file	genomic_file_id	Observation	focus	valueReference	DocumentReference
genomic_file	is_harmonized	Observation	component	valueBoolean	Not Applicable
genomic_file	paired_end	Observation	component	valueInteger	Not Applicable
genomic_file	reference_genome	Observation	component	valueCodeableConcept	Not Applicable
sequencing_experiment	max_insert_size	Observation	component	valueQuantity	Not Applicable
sequencing_experiment	mean_depth	Observation	component	valueQuantity	Not Applicable
sequencing_experiment	mean_insert_size	Observation	component	valueQuantity	Not Applicable
sequencing_experiment	mean_read_length	Observation	component	valueQuantity	Not Applicable
sequencing_experiment	total_reads	Observation	component	valueQuantity	Not Applicable

• Hold off creating any CodeSystems and ValueSets at the moment. Instead use KF attribute names and enumerations as follows:

{
  "resourceType": "Task",
  "input": [
  {
      "type": {
        "text": "biospecimen"
      },
      "valueReference": {
        "reference": "Specimen/bs-001"
      }
    },
    {
      "type": {
        "text": "experiment_strategy"
      },
      "valueCodeableConcept": {
        "text": "WGS"
      }
    }
  ]
}

{
  "resourceType": "Observation",
  "component": [
    {
      "code": "paired_end",
      "valueInteger": 1
    },
    {
      "code": "reference_genome",
      "valueCodeableConcept": {
        "text": "hs37d5"
      }
    }
  ]
}