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Merge pull request #29 from bmeg/improvement/uuid_cellosaurus
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cellosaurus mint ids
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@teslajoy
teslajoy committed Jun 18, 2024
2 parents ce52bd9 + 953760e commit e747625
Showing 1 changed file with 35 additions and 15 deletions.
50 changes: 35 additions & 15 deletions fhirizer/entity2fhir.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1632,6 +1632,9 @@ def cellosaurus_resource(path, out_dir):


def cellosaurus_fhir_mappping(cell_lines, verbose=False):
project_id = "CELLOSAURUS"
NAMESPACE_CELLOSAURUS = uuid3(NAMESPACE_DNS, 'cellosaurus.org')

patients = []
conditions = []
samples = []
Expand All @@ -1642,33 +1645,32 @@ def cellosaurus_fhir_mappping(cell_lines, verbose=False):
ident_list = []
for accession in cl["accession-list"]:
if accession["type"] == "primary":
patient_id = accession["value"].replace("_", "-")
patient_identifier = Identifier(**{"system": "https://www.cellosaurus.org/cell-line-primary-accession", "value": accession["value"]})
patient_id = utils.mint_id(identifier=patient_identifier, resource_type="Patient", project_id=project_id,
namespace=NAMESPACE_CELLOSAURUS)

ident_id = Identifier.construct()
ident_id.value = accession["value"]
ident_id.system = "https://www.cellosaurus.org/"
ident_list.append(ident_id)
ident_list.append(patient_identifier)
if patient_id:
for identifier in cl["name-list"]:
if identifier["type"] == "identifier":
patient_identifer = identifier["value"]
ident_identifier = Identifier.construct()
ident_identifier.value = patient_identifer
ident_identifier.system = "https://www.cellosaurus.org/"
ident_identifier.system = "https://www.cellosaurus.org/name-list"
ident_list.append(ident_identifier)

for xref in cl["xref-list"]:
if xref["database"] == "DepMap":
depmap_identifier = Identifier.construct()
depmap_identifier.value = xref["accession"]
# dep_map_url = xref["url"] # ex. https://depmap.org/portal/cell_line/ACH-000035"
depmap_identifier.system = "https://depmap.org/"
depmap_identifier.system = "https://depmap.org/cell_line"
ident_list.append(depmap_identifier)

if xref["database"] == "Cosmic":
cosmic_identifier = Identifier.construct()
cosmic_identifier.value = xref["accession"]
cosmic_identifier.system = "https://cancer.sanger.ac.uk/cosmic/"
cosmic_identifier.system = "https://cancer.sanger.ac.uk/cosmic/cell_line"
ident_list.append(cosmic_identifier)

if "sex" in cl.keys() and cl["sex"]:
Expand All @@ -1682,7 +1684,14 @@ def cellosaurus_fhir_mappping(cell_lines, verbose=False):
# add condition from disease-list
if "disease-list" in cl.keys():
for disease_annotation in cl["disease-list"]:
if "database" in disease_annotation.keys() and disease_annotation["database"] == "NCIt":
condition_identifier = Identifier(
**{"system": "https://www.cellosaurus.org/disease",
"value": disease_annotation["accession"]})
condition_id = utils.mint_id(identifier=condition_identifier, resource_type="Condition",
project_id=project_id,
namespace=NAMESPACE_CELLOSAURUS)

if "terminology" in disease_annotation.keys() and disease_annotation["terminology"] == "NCIt":
condition_clinicalstatus_code = CodeableConcept.construct()
condition_clinicalstatus_code.coding = [
{"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
Expand All @@ -1696,7 +1705,6 @@ def cellosaurus_fhir_mappping(cell_lines, verbose=False):
elif "label" in disease_annotation.keys():
display = disease_annotation["label"]
else:
print(disease_annotation)
display = "place_holder"

coding = {'system': "https://ncit.nci.nih.gov/", 'display': display, 'code': code}
Expand Down Expand Up @@ -1733,19 +1741,25 @@ def cellosaurus_fhir_mappping(cell_lines, verbose=False):

if onset_age:
conditions.append(Condition(
**{"id": disease_annotation["accession"], "code": cc, "subject": patient_ref,
**{"id": condition_id, "identifier": [condition_identifier] ,"code": cc, "subject": patient_ref,
"clinicalStatus": condition_clinicalstatus_code, "onsetAge": onset_age}))
else:
conditions.append(Condition(
**{"id": disease_annotation["accession"], "code": cc, "subject": patient_ref,
**{"id": condition_id, "identifier": [condition_identifier], "code": cc, "subject": patient_ref,
"clinicalStatus": condition_clinicalstatus_code}))

sample_parents_ref = []
# sample hierarchy
if "derived-from" in cl.keys() and cl["derived-from"]:
for parent_cell in cl["derived-from"]:
if "terminology" in parent_cell.keys() and parent_cell["terminology"] == "Cellosaurus":
parent_id = parent_cell["accession"].replace("_", "-")

parent_identifier = Identifier(
**{"system": "https://www.cellosaurus.org/cell-line-primary-accession",
"value": parent_cell["accession"]})
parent_id = utils.mint_id(identifier=parent_identifier, resource_type="Specimen",
project_id=project_id,
namespace=NAMESPACE_CELLOSAURUS)

parent_id_identifier = Identifier.construct()
parent_id_identifier.value = parent_cell["accession"]
Expand All @@ -1761,21 +1775,27 @@ def cellosaurus_fhir_mappping(cell_lines, verbose=False):
samples.append(parent_sample)
sample_parents_ref.append(Reference(**{"reference": "/".join(["Specimen", parent_id])}))

specimen_id = utils.mint_id(identifier=patient_identifier, resource_type="Specimen",
project_id=project_id,
namespace=NAMESPACE_CELLOSAURUS)

if sample_parents_ref:
samples.append(Specimen(
**{"id": patient_id, "subject": patient_ref, "identifier": ident_list,
**{"id": specimen_id, "subject": patient_ref, "identifier": ident_list,
"parent": sample_parents_ref}))
else:
samples.append(Specimen(
**{"id": patient_id, "subject": patient_ref, "identifier": ident_list}))
**{"id": specimen_id, "subject": patient_ref, "identifier": ident_list}))

return {"patients": patients, "conditions": conditions, "samples": samples}


def cellosaurus_to_fhir_ndjson(out_dir, obj):
patients = [orjson.loads(patient.json()) for patient in obj["patients"]]
samples = [orjson.loads(sample.json()) for sample in obj["samples"]]
samples = list({v['id']: v for v in samples}.values())
conditions = [orjson.loads(condition.json()) for condition in obj["conditions"]]
conditions = list({v['id']: v for v in conditions}.values())

if patients:
utils.fhir_ndjson(patients, os.path.join(out_dir, "Patient.ndjson"))
Expand Down

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