Datasets:

fhir4ds
/

omop-demo

Error code:   StreamingRowsError
Exception:    CastError
Message:      Couldn't cast
resourceType: string
id: string
status: string
class: struct<system: string, code: string>
  child 0, system: string
  child 1, code: string
subject: struct<reference: string, display: string>
  child 0, reference: string
  child 1, display: string
period: struct<start: timestamp[s], end: timestamp[s]>
  child 0, start: timestamp[s]
  child 1, end: timestamp[s]
group: list<item: struct<source: string, target: string, element: list<item: struct<code: string, target: l (... 56 chars omitted)
  child 0, item: struct<source: string, target: string, element: list<item: struct<code: string, target: list<item: s (... 44 chars omitted)
      child 0, source: string
      child 1, target: string
      child 2, element: list<item: struct<code: string, target: list<item: struct<code: string, equivalence: string>>>>
          child 0, item: struct<code: string, target: list<item: struct<code: string, equivalence: string>>>
              child 0, code: string
              child 1, target: list<item: struct<code: string, equivalence: string>>
                  child 0, item: struct<code: string, equivalence: string>
                      child 0, code: string
                      child 1, equivalence: string
gender: string
birthDate: timestamp[s]
name: list<item: struct<family: string, given: list<item: string>>>
  child 0, item: struct<family: string, given: list<item: string>>
      child 0, family: string
      child 1, given: list<item: string>
          child 0, item: string
deceasedDateTime: timestamp[s]
files: list<item: struct<path: string, bytes: int64, sha256: string>>
  child 0, item: struct<path: string, bytes: int64, sha256: string>
      child 0, path: string
      child 1, bytes: int64
      child 2, sha256: string
dataset: string
conceptmap: struct<resources: int64, groups: list<item: struct<source: string, elements: int64, classes: list<it (... 102 chars omitted)
  child 0, resources: int64
  child 1, groups: list<item: struct<source: string, elements: int64, classes: list<item: string>>>
      child 0, item: struct<source: string, elements: int64, classes: list<item: string>>
          child 0, source: string
          child 1, elements: int64
          child 2, classes: list<item: string>
              child 0, item: string
  child 2, elements: int64
  child 3, fields: list<item: string>
      child 0, item: string
  child 4, display_omitted: bool
  child 5, provenance: string
coverage: struct<cohort_unique_rxcuis: int64, covered_codes: int64, cohort_mentions: int64, resolved_mentions: (... 80 chars omitted)
  child 0, cohort_unique_rxcuis: int64
  child 1, covered_codes: int64
  child 2, cohort_mentions: int64
  child 3, resolved_mentions: int64
  child 4, pct: double
  child 5, cohort_unique_cvx: int64
  child 6, covered_cvx: int64
  child 7, note: string
to
{'dataset': Value('string'), 'files': List({'path': Value('string'), 'bytes': Value('int64'), 'sha256': Value('string')}), 'conceptmap': {'resources': Value('int64'), 'groups': List({'source': Value('string'), 'elements': Value('int64'), 'classes': List(Value('string'))}), 'elements': Value('int64'), 'fields': List(Value('string')), 'display_omitted': Value('bool'), 'provenance': Value('string')}, 'coverage': {'cohort_unique_rxcuis': Value('int64'), 'covered_codes': Value('int64'), 'cohort_mentions': Value('int64'), 'resolved_mentions': Value('int64'), 'pct': Value('float64'), 'cohort_unique_cvx': Value('int64'), 'covered_cvx': Value('int64'), 'note': Value('string')}}
because column names don't match
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/utils.py", line 149, in get_rows_or_raise
                  return get_rows(
                      dataset=dataset,
                  ...<4 lines>...
                      column_names=column_names,
                  )
                File "/src/libs/libcommon/src/libcommon/utils.py", line 272, in decorator
                  return func(*args, **kwargs)
                File "/src/services/worker/src/worker/utils.py", line 129, in get_rows
                  rows_plus_one = list(itertools.islice(safe_iter(ds, dataset=dataset), rows_max_number + 1))
                File "/src/services/worker/src/worker/utils.py", line 544, in safe_iter
                  yield from ds.decode(False) if ds.features else ds
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 3052, in __iter__
                  for key, example in ex_iterable:
                                      ^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2559, in __iter__
                  for key, pa_table in self._iter_arrow():
                                       ~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 2584, in _iter_arrow
                  for key, pa_table in self.ex_iterable._iter_arrow():
                                       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 558, in _iter_arrow
                  for key, pa_table in iterator:
                                       ^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/iterable_dataset.py", line 440, in _iter_arrow
                  for key, pa_table in self.generate_tables_fn(**gen_kwags):
                                       ~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 361, in _generate_tables
                  self._cast_table(pa_table, json_field_paths=json_field_paths),
                  ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.14/site-packages/datasets/packaged_modules/json/json.py", line 132, in _cast_table
                  pa_table = table_cast(pa_table, self.info.features.arrow_schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2381, in table_cast
                  return cast_table_to_schema(table, schema)
                File "/usr/local/lib/python3.14/site-packages/datasets/table.py", line 2309, in cast_table_to_schema
                  raise CastError(
                  ...<3 lines>...
                  )
              datasets.table.CastError: Couldn't cast
              resourceType: string
              id: string
              status: string
              class: struct<system: string, code: string>
                child 0, system: string
                child 1, code: string
              subject: struct<reference: string, display: string>
                child 0, reference: string
                child 1, display: string
              period: struct<start: timestamp[s], end: timestamp[s]>
                child 0, start: timestamp[s]
                child 1, end: timestamp[s]
              group: list<item: struct<source: string, target: string, element: list<item: struct<code: string, target: l (... 56 chars omitted)
                child 0, item: struct<source: string, target: string, element: list<item: struct<code: string, target: list<item: s (... 44 chars omitted)
                    child 0, source: string
                    child 1, target: string
                    child 2, element: list<item: struct<code: string, target: list<item: struct<code: string, equivalence: string>>>>
                        child 0, item: struct<code: string, target: list<item: struct<code: string, equivalence: string>>>
                            child 0, code: string
                            child 1, target: list<item: struct<code: string, equivalence: string>>
                                child 0, item: struct<code: string, equivalence: string>
                                    child 0, code: string
                                    child 1, equivalence: string
              gender: string
              birthDate: timestamp[s]
              name: list<item: struct<family: string, given: list<item: string>>>
                child 0, item: struct<family: string, given: list<item: string>>
                    child 0, family: string
                    child 1, given: list<item: string>
                        child 0, item: string
              deceasedDateTime: timestamp[s]
              files: list<item: struct<path: string, bytes: int64, sha256: string>>
                child 0, item: struct<path: string, bytes: int64, sha256: string>
                    child 0, path: string
                    child 1, bytes: int64
                    child 2, sha256: string
              dataset: string
              conceptmap: struct<resources: int64, groups: list<item: struct<source: string, elements: int64, classes: list<it (... 102 chars omitted)
                child 0, resources: int64
                child 1, groups: list<item: struct<source: string, elements: int64, classes: list<item: string>>>
                    child 0, item: struct<source: string, elements: int64, classes: list<item: string>>
                        child 0, source: string
                        child 1, elements: int64
                        child 2, classes: list<item: string>
                            child 0, item: string
                child 2, elements: int64
                child 3, fields: list<item: string>
                    child 0, item: string
                child 4, display_omitted: bool
                child 5, provenance: string
              coverage: struct<cohort_unique_rxcuis: int64, covered_codes: int64, cohort_mentions: int64, resolved_mentions: (... 80 chars omitted)
                child 0, cohort_unique_rxcuis: int64
                child 1, covered_codes: int64
                child 2, cohort_mentions: int64
                child 3, resolved_mentions: int64
                child 4, pct: double
                child 5, cohort_unique_cvx: int64
                child 6, covered_cvx: int64
                child 7, note: string
              to
              {'dataset': Value('string'), 'files': List({'path': Value('string'), 'bytes': Value('int64'), 'sha256': Value('string')}), 'conceptmap': {'resources': Value('int64'), 'groups': List({'source': Value('string'), 'elements': Value('int64'), 'classes': List(Value('string'))}), 'elements': Value('int64'), 'fields': List(Value('string')), 'display_omitted': Value('bool'), 'provenance': Value('string')}, 'coverage': {'cohort_unique_rxcuis': Value('int64'), 'covered_codes': Value('int64'), 'cohort_mentions': Value('int64'), 'resolved_mentions': Value('int64'), 'pct': Value('float64'), 'cohort_unique_cvx': Value('int64'), 'covered_cvx': Value('int64'), 'note': Value('string')}}
              because column names don't match

Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.

OMOP demo data (FHIR R4 → OMOP CDM v5.5)

Ready-to-stage NDJSON bundles for the SQL-on-FHIR Viewing Room's OMOP mapping gallery (fhir4ds). Each bundle is one FHIR R4 resource per line, including the ConceptMap resources that carry the vocabulary mappings.

Bundles

File	Contents	Rows
`patient-resources.ndjson`	25 Synthea patients + the gender/encounter-class ConceptMap supplements	26
`encounter-resources.ndjson`	25 patients + 1,284 encounters + supplements	1,310
`medication-resources.ndjson`	25 patients + 1,143 MedicationRequests + 318 Immunizations + one ConceptMap (108,683 mappings: RxNorm, CVX, and the gender/encounter-class/condition-category supplements)	1,487

ConceptMap shape

One standard FHIR ConceptMap resource carries every mapping, with one group per source vocabulary:

{"resourceType":"ConceptMap","id":"fhir4ds-omop-conceptmap","status":"active",
 "group":[{"source":"http://www.nlm.nih.gov/research/umls/rxnorm",
           "target":"urn:omop:concept",
           "element":[{"code":"<RxCUI>",
                       "target":[{"code":"<OMOP concept_id>","equivalence":"equal"}]}]},
          {"source":"http://hl7.org/fhir/sid/cvx", "target":"urn:omop:concept", "element":[ ... ]},
          {"source":"http://hl7.org/fhir/administrative-gender", ...},
          {"source":"http://terminology.hl7.org/CodeSystem/v3-ActCode", ...},
          {"source":"http://terminology.hl7.org/CodeSystem/condition-category", ...}]}

RxNorm group: 108,421 mappings covering the product-level RxNorm classes (Clinical Drug, Branded Drug, Quant Clinical Drug, Quant Branded Drug, Clinical Pack, Branded Pack, Clinical Drug Comp, Branded Drug Comp) from the OHDSI Athena vocabulary tables.
CVX group: 255 vaccine-code mappings (immunizations).
display is omitted — it is not needed for mapping and keeps the payload small. equivalence is retained because FHIR requires it (ConceptMap.group.element.target.equivalence is 1..1) and the ViewDefinition's mapping view filters on it.
Coverage: 100% of coded rows — all 54 cohort RxCUIs (1,143 of 1,143 mentions) and all 13 CVX codes resolve to OMOP concept IDs.
27 MedicationRequests with no medication code (medicationCodeableConcept is null in the Synthea output; there is no drug to represent) are not included: a drug exposure with no drug and no code has nothing to map.
No chunking: a single ConceptMap is used. (Earlier revisions chunked the map at 20 elements per resource to work around an O(N x payload) unnest lowering in the ViewDefinition engine; that engine issue is fixed, so 100k-element maps execute in well under a second.)

Why chunked resources?

The fhir4ds ViewDefinition engine's forEach unnest currently re-evaluates the collection per output row (O(N × payload) in DuckDB); a single monolithic 157k-element ConceptMap exhausts memory. Chunking to 20 elements per resource keeps each unnest small and loadable in the browser. An engine fix (single-pass, materialized unnest) is tracked in the fhir4ds backlog; once it lands, chunking becomes unnecessary.

Provenance & licensing

FHIR resources: generated by Synthea 4.0.0 (MIT), seed 20261026, Massachusetts, FHIR R4 export, 25 patients. Synthetic data carries no usage restrictions.
RxNorm ConceptMap: derived from the NLM RxNorm vocabulary (U.S. government work, public domain) as distributed in the OHDSI Athena vocabulary tables.

See MANIFEST.json for file sizes and SHA-256 hashes.

Downloads last month: 123

Total file size:

10 MB