Minutes Data Working Group 20 Apr 2021

Agenda

1. (Brad) Review the WG-joint work to build a sample FHIR representation of COVID grand challenge data. Suggested datasets:
   1. COVID-19 2020 Lung CT Lesion Segmentation Challenge - cannot get access
   2. Other sources: Center for Artificial Intelligence in Medicine & Imaging COVID-19 Data
2. (All) Review the discussion at Github on mixed datasets
3. (All) Review if there are any Github issues/discussions tagged with #DataWorkingGroup or that should be flagged for this group to discuss
4. (Wenqi) Updates from MONAI development

Notes

• Attendees: Brad, Raghav, Mona, Stephen
• There should be a library function to extract relevant meta tags from objects
  • E.g., DICOM tags; while there is a wealth of data in DICOM tags, depending on the use case, more may be needed
• Discussion of different representations of data
  • Re-iterated discussion that FHIR is likely not the right representation right now for training AI models, but may be appropriate for inference
  • There needs to be a mapping of different object types into a simplified format for consumption by MONAI, including FHIR -> simplified format
  • CSV (or TSV) is too simplified with a lossy destruction of data context (column meaning is human / arbitrarily decided)
  • It may make sense to have some form of converter of a format like FHIR or DICOM (or BIDS or etc) into a simplified format
  • It's a joint effort between Data and I/O to discuss further
  • Parked discussion until Thursday (joint meeting with Data, I/O and other WGs)
• Github Issues and Discussion topics now have the ability to be tagged to a particular WG

Action Items

• All should review issues and discussions and consider tagging them to Data WG where appropriate

Sample FHIR Representation (not discussed during meeting)

• Based on https://www.kaggle.com/hgunraj/covidxct?select=metadata.csv
• Example is not currently correct (it is a batch of batches; but the child batch elements do not match the correct objects)

Sample FHIR Object:

{
	"resourceType": "Bundle",
	"id": "sequence0",
	"meta": {
		"lastUpdated": "2021-04-19T08:00:00-04:00"
	},
	"type": "batch",
	"entry": [{
		"resourceType": "Bundle",
		"id": "cp_1068",
		"meta": {
			"lastUpdated": "2021-04-19T08:00:00-04:00"
		},
		"type": "batch",
		"entry": [{
				"resourceType": "Observation",
				"id": "endoscope_frame0",
				"text": {
					"status": "generated",
					"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>(human readable text)</p></div>"
				},
				"status": "final",
				"category": [{
					"coding": [{
						"system": "http://terminology.hl7.org/CodeSystem/observation-category",
						"code": "procedure",
						"display": "Procedure"
					}]
				}],
				"code": {
					"coding": [{
						"system": "urn:oid:2.16.840.1.113883.6.24",
						"code": "(appropriate code for endoscope)",
						"display": "(appropriate label for endoscope)"
					}]
				},
				"subject": {
					"reference": "Patient/12345678",
					"display": "SMITH, J (ID:12345678)"
				},
				"effectiveDateTime": "2020-08-01T08:00:00-04:00",
				"performer": [{
					"reference": "Practitioner/87654321",
					"display": "DOE, J"
				}],
				"device": {
					"display": "Endoscope"
				}
			},
			{
				"resourceType": "Observation",
				"id": "endoscope_frame0",
				"text": {
					"status": "generated",
					"div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p>(human readable text)</p></div>"
				},
				"status": "final",
				"category": [{
					"coding": [{
						"system": "http://terminology.hl7.org/CodeSystem/observation-category",
						"code": "procedure",
						"display": "Procedure"
					}]
				}],
				"code": {
					"coding": [{
						"system": "urn:oid:2.16.840.1.113883.6.24",
						"code": "(appropriate code for endoscope)",
						"display": "(appropriate label for endoscope)"
					}]
				},
				"subject": {
					"reference": "Patient/12345678",
					"display": "SMITH, J (ID:12345678)"
				},
				"effectiveDateTime": "2020-08-01T08:00:00-04:00",
				"performer": [{
					"reference": "Practitioner/87654321",
					"display": "DOE, J"
				}],
				"device": {
					"display": "Endoscope"
				}
			}
		]
	}]
}