def yield_practitioners(eng, table):
for row in make_select(eng, table, CONCEPT.INVESTIGATOR.NAME):
name = get(row, CONCEPT.INVESTIGATOR.NAME)
if not name:
continue
retval = {
"resourceType":
RESOURCE_TYPE,
"id":
make_identifier(RESOURCE_TYPE, name),
"meta": {
"profile":
["http://hl7.org/fhir/StructureDefinition/Practitioner"]
},
"identifier": [{
"system":
"https://kf-api-dataservice.kidsfirstdrc.org/investigators?name=",
"value": name,
}],
"name": [{
"text": name
}],
}
yield retval, name
def yield_kfdrc_vital_statuses(eng, table, study_id, kfdrc_patients):
for row in make_select(
eng,
table,
CONCEPT.PARTICIPANT.ID,
CONCEPT.OUTCOME.EVENT_AGE_DAYS,
CONCEPT.OUTCOME.VITAL_STATUS,
):
participant_id = get(row, CONCEPT.PARTICIPANT.ID)
event_age_days = get(row, CONCEPT.OUTCOME.EVENT_AGE_DAYS)
vital_status = get(row, CONCEPT.OUTCOME.VITAL_STATUS)
status = clinical_status.get(vital_status)
if not participant_id or not status:
continue
retval = {
"resourceType":
RESOURCE_TYPE,
"id":
make_identifier(RESOURCE_TYPE, participant_id, vital_status,
event_age_days),
"meta": {
"profile": [
"http://fhir.kids-first.io/StructureDefinition/kfdrc-vital-status"
]
},
"status":
"preliminary",
"code": {
"coding": [{
"code": "263493007",
"system": "http://snomed.info/sct",
"display": "Clinical status",
}],
"text":
"Clinical status",
},
"subject": {
"reference": f'Patient/{kfdrc_patients[participant_id]["id"]}'
},
"valueCodeableConcept": {
"coding": [status],
"text": vital_status
},
}
if event_age_days:
retval.setdefault("extension", []).append({
"url":
"http://fhir.kids-first.io/StructureDefinition/age-at-event",
"valueAge": {
"value": int(event_age_days),
"unit": "d",
"system": "http://unitsofmeasure.org",
"code": "days",
},
})
yield retval
def yield_groups(eng, table, study_id, kfdrc_patients):
df = pd.DataFrame([
dict(row) for row in make_select(
eng,
table,
CONCEPT.FAMILY.ID,
CONCEPT.PARTICIPANT.SPECIES,
CONCEPT.PARTICIPANT.ID,
)
])
for family_id, group in df.groupby(CONCEPT.FAMILY.ID):
if not family_id:
continue
retval = {
"resourceType":
RESOURCE_TYPE,
"id":
make_identifier(RESOURCE_TYPE, study_id, family_id),
"meta": {
"profile": ["http://hl7.org/fhir/StructureDefinition/Group"]
},
"identifier": [{
"system":
f"https://kf-api-dataservice.kidsfirstdrc.org/families?study_id={study_id}&external_id=",
"value": family_id,
}],
"actual":
True,
}
for _, row in group.iterrows():
species = get(row, CONCEPT.PARTICIPANT.SPECIES)
participant_id = get(row, CONCEPT.PARTICIPANT.ID)
if not participant_id:
continue
retval["type"] = group_type.get(species) or "person"
retval.setdefault("member", []).append({
"entity": {
"reference":
f'Patient/{kfdrc_patients[participant_id]["id"]}'
}
})
if not isinstance(retval.get("member"), list):
continue
yield retval, family_id
def yield_practitioner_roles(eng, table, practitioners, organizations):
for row in make_select(
eng,
table,
CONCEPT.INVESTIGATOR.ID,
CONCEPT.INVESTIGATOR.INSTITUTION,
CONCEPT.INVESTIGATOR.NAME,
):
investigator_id = get(row, CONCEPT.INVESTIGATOR.ID)
institution = get(row, CONCEPT.INVESTIGATOR.INSTITUTION)
name = get(row, CONCEPT.INVESTIGATOR.NAME)
if not all((institution, name)):
continue
retval = {
"resourceType":
RESOURCE_TYPE,
"id":
make_identifier(RESOURCE_TYPE, institution, name),
"meta": {
"profile":
["http://hl7.org/fhir/StructureDefinition/PractitionerRole"]
},
"practitioner": {
"reference": f'Practitioner/{practitioners[name]["id"]}'
},
"organization": {
"reference": f'Organization/{organizations[institution]["id"]}'
},
"code": [{
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/practitioner-role",
"code": "researcher",
"display": "Researcher",
}]
}],
}
if investigator_id:
retval.setdefault("identifier", []).append({
"system":
"https://kf-api-dataservice.kidsfirstdrc.org/investigators?external_id=",
"value":
investigator_id,
})
yield retval, (institution, name)
def yield_organizations(eng, table):
for row in make_select(eng, table, CONCEPT.INVESTIGATOR.INSTITUTION):
institution = get(row, CONCEPT.INVESTIGATOR.INSTITUTION)
if not institution:
continue
retval = {
"resourceType": RESOURCE_TYPE,
"id": make_identifier(RESOURCE_TYPE, institution),
"meta": {
"profile":
["http://hl7.org/fhir/StructureDefinition/Organization"]
},
"name": institution,
}
yield retval, institution
def yield_kfdrc_patient_relations(eng, table, kfdrc_patients):
df = pd.DataFrame(
[
dict(row)
for row in make_select(
eng,
table,
CONCEPT.FAMILY_RELATIONSHIP.PERSON1.ID,
CONCEPT.FAMILY_RELATIONSHIP.PERSON2.ID,
CONCEPT.FAMILY_RELATIONSHIP.RELATION_FROM_1_TO_2,
)
]
)
for person2_id, group in df.groupby(CONCEPT.FAMILY_RELATIONSHIP.PERSON2.ID):
retval = kfdrc_patients.get(person2_id)
if not retval:
continue
for _, row in group.iterrows():
person1_id = get(row, CONCEPT.FAMILY_RELATIONSHIP.PERSON1.ID)
relation = get(
row, CONCEPT.FAMILY_RELATIONSHIP.RELATION_FROM_1_TO_2
)
retval.setdefault("extension", []).append(
{
"url": "http://fhir.kids-first.io/StructureDefinition/relation",
"extension": [
{
"url": "subject",
"valueReference": {
"reference": f'{RESOURCE_TYPE}/{kfdrc_patients[person1_id]["id"]}'
},
},
relation_dict[relation],
],
}
)
yield retval, person2_id
def yield_kfdrc_patients(eng, table, study_id):
for row in make_select(
eng,
table,
CONCEPT.PARTICIPANT.ID,
CONCEPT.PARTICIPANT.ETHNICITY,
CONCEPT.PARTICIPANT.RACE,
CONCEPT.PARTICIPANT.SPECIES,
CONCEPT.PARTICIPANT.GENDER,
):
participant_id = get(row, CONCEPT.PARTICIPANT.ID)
ethnicity = get(row, CONCEPT.PARTICIPANT.ETHNICITY)
race = get(row, CONCEPT.PARTICIPANT.RACE)
species = get(row, CONCEPT.PARTICIPANT.SPECIES)
gender = get(row, CONCEPT.PARTICIPANT.GENDER)
if not participant_id:
continue
retval = {
"resourceType":
RESOURCE_TYPE,
"id":
make_identifier(RESOURCE_TYPE, study_id, participant_id),
"meta": {
"profile": [
"http://fhir.kids-first.io/StructureDefinition/kfdrc-patient"
]
},
"identifier": [{
"system":
f"https://kf-api-dataservice.kidsfirstdrc.org/participants?study_id={study_id}&external_id=",
"value": participant_id,
}],
}
if ethnicity:
if omb_ethnicity_category.get(ethnicity):
retval.setdefault("extension", []).append({
"url":
"http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity",
"extension": [
omb_ethnicity_category[ethnicity],
{
"url": "text",
"valueString": ethnicity
},
],
})
if race:
if omb_race_category.get(race):
retval.setdefault("extension", []).append({
"url":
"http://hl7.org/fhir/us/core/StructureDefinition/us-core-race",
"extension": [
omb_race_category[race],
{
"url": "text",
"valueString": race
},
],
})
if species:
if species_dict.get(species):
retval.setdefault("extension",
[]).append(species_dict[species])
if gender:
if administrative_gender.get(gender):
retval["gender"] = administrative_gender[gender]
yield retval, participant_id
def yield_kfdrc_specimens(eng, table, study_id, kfdrc_patients):
for row in make_select(
eng,
table,
CONCEPT.PARTICIPANT.ID,
CONCEPT.BIOSPECIMEN.ID,
CONCEPT.BIOSPECIMEN.EVENT_AGE_DAYS,
CONCEPT.BIOSPECIMEN.CONCENTRATION_MG_PER_ML,
CONCEPT.BIOSPECIMEN.COMPOSITION,
CONCEPT.BIOSPECIMEN.VOLUME_UL,
):
participant_id = get(row, CONCEPT.PARTICIPANT.ID)
biospecimen_id = get(row, CONCEPT.BIOSPECIMEN.ID)
event_age_days = get(row, CONCEPT.BIOSPECIMEN.EVENT_AGE_DAYS)
concentration_mg_per_ml = get(
row, CONCEPT.BIOSPECIMEN.CONCENTRATION_MG_PER_ML)
composition = get(row, CONCEPT.BIOSPECIMEN.COMPOSITION)
volume_ul = get(row, CONCEPT.BIOSPECIMEN.VOLUME_UL)
if not all((participant_id, biospecimen_id)):
continue
retval = {
"resourceType":
RESOURCE_TYPE,
"id":
make_identifier(RESOURCE_TYPE, study_id, biospecimen_id),
"meta": {
"profile": [
"http://fhir.kids-first.io/StructureDefinition/kfdrc-specimen"
]
},
"identifier": [{
"system":
f"http://kf-api-dataservice.kidsfirstdrc.org/biospecimens?study_id={study_id}&external_aliquot_id=",
"value": biospecimen_id,
}],
"subject": {
"reference": f'Patient/{kfdrc_patients[participant_id]["id"]}'
},
}
if event_age_days:
retval.setdefault("extension", []).append({
"url":
"http://fhir.kids-first.io/StructureDefinition/age-at-event",
"valueAge": {
"value": int(event_age_days),
"unit": "d",
"system": "http://unitsofmeasure.org",
"code": "days",
},
})
if concentration_mg_per_ml:
retval.setdefault("extension", []).append({
"url":
"http://fhir.kids-first.io/StructureDefinition/concentration",
"valueQuantity": {
"value": float(concentration_mg_per_ml),
"unit": "mg/mL",
},
})
if composition:
retval["type"] = {
"coding": [specimen_type[composition]],
"text": composition,
}
if volume_ul:
retval.setdefault("collection", {})["quantity"] = {
"unit": "uL",
"value": float(volume_ul),
}
yield retval, biospecimen_id
def yield_kfdrc_research_studies(eng, table, target_service_id, organizations,
practitioner_roles, groups):
for row in make_select(
eng,
table,
CONCEPT.STUDY.ID,
CONCEPT.INVESTIGATOR.INSTITUTION,
CONCEPT.INVESTIGATOR.NAME,
CONCEPT.STUDY.ATTRIBUTION,
CONCEPT.STUDY.SHORT_NAME,
CONCEPT.STUDY.AUTHORITY,
CONCEPT.STUDY.NAME,
):
study_id = get(row, CONCEPT.STUDY.ID)
institution = get(row, CONCEPT.INVESTIGATOR.INSTITUTION)
investigator_name = get(row, CONCEPT.INVESTIGATOR.NAME)
study_name = get(row, CONCEPT.STUDY.NAME)
attribution = get(row, CONCEPT.STUDY.ATTRIBUTION)
short_name = get(row, CONCEPT.STUDY.SHORT_NAME)
if not all((study_id, institution, investigator_name, study_name)):
continue
retval = {
"resourceType":
RESOURCE_TYPE,
"id":
make_identifier(RESOURCE_TYPE, study_id),
"meta": {
"profile": [
"http://fhir.kids-first.io/StructureDefinition/kfdrc-research-study"
]
},
"identifier": [
{
"system":
"https://kf-api-dataservice.kidsfirstdrc.org/studies",
"value": target_service_id,
},
{
"system":
"https://kf-api-dataservice.kidsfirstdrc.org/studies?external_id=",
"value": study_id,
},
],
"extension": [{
"url":
"http://fhir.kids-first.io/StructureDefinition/related-organization",
"extension": [{
"url": "organization",
"valueReference": {
"reference":
f'Organization/{organizations[institution]["id"]}'
},
}],
}],
"title":
study_name,
"status":
"completed",
"principalInvestigator": {
"reference":
f'PractitionerRole/{practitioner_roles[(institution, investigator_name)]["id"]}'
},
}
if attribution:
retval["identifier"].append({"value": attribution})
if short_name:
retval["extension"].append({
"url":
"http://fhir.kids-first.io/StructureDefinition/display-name",
"valueString": short_name,
})
if groups:
retval["enrollment"] = [{
"reference": f'Group/{group["id"]}'
} for group in groups.values()]
yield retval
def yield_kfdrc_conditions(eng, table, study_id, kfdrc_patients):
for row in make_select(
eng,
table,
CONCEPT.PARTICIPANT.ID,
CONCEPT.DIAGNOSIS.NAME,
CONCEPT.DIAGNOSIS.EVENT_AGE_DAYS,
CONCEPT.DIAGNOSIS.MONDO_ID,
CONCEPT.DIAGNOSIS.NCIT_ID,
CONCEPT.DIAGNOSIS.ICD_ID,
):
participant_id = get(row, CONCEPT.PARTICIPANT.ID)
name = get(row, CONCEPT.DIAGNOSIS.NAME)
event_age_days = get(row, CONCEPT.DIAGNOSIS.EVENT_AGE_DAYS)
mondo = get(row, CONCEPT.DIAGNOSIS.MONDO_ID)
ncit = get(row, CONCEPT.DIAGNOSIS.NCIT_ID)
icd = get(row, CONCEPT.DIAGNOSIS.ICD_ID)
if not all((participant_id, name)):
continue
retval = {
"resourceType":
RESOURCE_TYPE,
"id":
make_identifier(RESOURCE_TYPE, study_id, participant_id, name,
event_age_days),
"meta": {
"profile": [
"http://fhir.kids-first.io/StructureDefinition/kfdrc-condition"
]
},
"category": [{
"coding": [{
"system":
"http://terminology.hl7.org/CodeSystem/condition-category",
"code": "encounter-diagnosis",
"display": "Encounter Diagnosis",
}]
}],
"code": {
"text": name
},
"subject": {
"reference": f'Patient/{kfdrc_patients[participant_id]["id"]}'
},
}
if event_age_days:
retval.setdefault("extension", []).append({
"url":
"http://fhir.kids-first.io/StructureDefinition/age-at-event",
"valueAge": {
"value": int(event_age_days),
"unit": "d",
"system": "http://unitsofmeasure.org",
"code": "days",
},
})
if mondo:
retval["code"].setdefault("coding", []).append({
"system": "http://purl.obolibrary.org/obo/mondo.owl",
"code": mondo,
})
if ncit:
retval["code"].setdefault("coding", []).append({
"system": "http://purl.obolibrary.org/obo/ncit.owl",
"code": ncit
})
if icd:
retval["code"].setdefault("coding", []).append({
"system": "http://hl7.org/fhir/sid/icd-10",
"code": icd
})
yield retval
def yield_kfdrc_phenotypes(eng, table, study_id, kfdrc_patients):
for row in make_select(
eng,
table,
CONCEPT.PARTICIPANT.ID,
CONCEPT.PHENOTYPE.NAME,
CONCEPT.PHENOTYPE.HPO_ID,
CONCEPT.PHENOTYPE.EVENT_AGE_DAYS,
CONCEPT.PHENOTYPE.OBSERVED,
):
participant_id = get(row, CONCEPT.PARTICIPANT.ID)
name = get(row, CONCEPT.PHENOTYPE.NAME)
hpo = get(row, CONCEPT.PHENOTYPE.HPO_ID)
event_age_days = get(row, CONCEPT.PHENOTYPE.EVENT_AGE_DAYS)
observed = get(row, CONCEPT.PHENOTYPE.OBSERVED)
if not all(
(participant_id, name, hpo)) or not interpretation.get(observed):
continue
retval = {
"resourceType":
RESOURCE_TYPE,
"id":
make_identifier(
RESOURCE_TYPE,
study_id,
participant_id,
name,
observed,
event_age_days,
),
"meta": {
"profile": [
"http://fhir.kids-first.io/StructureDefinition/kfdrc-phenotype"
]
},
"status":
"preliminary",
"code": {
"coding": [{
"code": hpo
}],
"text": name
},
"subject": {
"reference": f'Patient/{kfdrc_patients[participant_id]["id"]}'
},
"interpretation": [{
"coding": [interpretation[observed]],
"text": observed
}],
}
if event_age_days:
retval.setdefault("extension", []).append({
"url":
"http://fhir.kids-first.io/StructureDefinition/age-at-event",
"valueAge": {
"value": int(event_age_days),
"unit": "d",
"system": "http://unitsofmeasure.org",
"code": "days",
},
})
yield retval