Parquet on FHIR

This specification defines a method for representing FHIR data within the Apache Parquet format.

Rather than defining a schema for each of the resource types within FHIR, it defines a method for deriving a schema from a resource definition.

This format is intended to be a lossless representation of FHIR. For example, FHIR JSON converted to this format should be able to be regenerated from the format without any loss of data.

The format is intended to define the structure and types of the schema without requiring all fields to be present. A data set that populates only a few elements for a resource can be represented by a schema with only those fields in the Parquet schema.

It is the intent that multiple Parquet tables could exist for the same resource that have different fields in their schemas, and that these schemas could be merged to produce a single table with the union of those fields.

Resource type

The schema for a Parquet table SHALL be derived from a single base FHIR resource definition.

The schema SHALL contain a field named resourceType with a primitive type of binary and a logical type of STRING, and it SHALL be set to a type from the FHIR resource types value set (http://hl7.org/fhir/ValueSet/resource-types).

All rows within the table SHALL contain the same value for the "resourceType" field.

Field optionality

The only field that must be present within the table is the resourceType field. It MUST always be in the schema of any table that complies with this specification, and also marked as required within the schema.

All other fields can be optionally included in the schema as needed to represent the data set. Consuming applications SHALL be able to tolerate the absence of any field within the schema except for resourceType.

All fields in the schema other than the resourceType field SHALL be marked as optional.

Primitive elements

The value of each primitive element within a resource definition is represented as a field within the schema with the same name.

The Parquet primitive and logical types of the value field SHALL be determined by the element type according to the following table:

FHIR type	Parquet primitive type	Parquet logical type
base64Binary	binary
boolean	boolean
canonical	binary	STRING
code	binary	STRING
date	binary	STRING
dateTime	binary	STRING
decimal	binary	STRING
id	binary	STRING
instant	binary	STRING
integer	INT32	INT(32, true)
integer64	INT64	INT(64, true)
markdown	binary	STRING
oid	binary	STRING
positiveInt	INT32	INT(32, false)
string	binary	STRING
time	binary	STRING
unsignedInt	INT32	INT(32, false)
uri	binary	STRING
url	binary	STRING
uuid	binary	STRING

The format of the data stored within each field SHALL comply with the rules defined in the Data Types section of the FHIR specification.

Here is an example of a simple Patient resource:

{
  "resourceType": "Patient",
  "id": "example",
  "birthDate": "1970-01-01"
}

This example could be accommodated within the following schema:

message Patient {
  required binary resourceType (STRING);
  optional binary id (STRING);
  optional binary birthDate (STRING);
}

Repeating elements

Any element that has a maximum cardinality greater than one (1) SHALL be represented as a group containing a repeated list field.

Here is an example of a repeating element within the AllergyIntolerance resource:

{
  "resourceType": "AllergyIntolerance",
  "category": [
    "food",
    "environment"
  ]
}

This example could be accommodated within the following schema:

message AllergyIntolerance {
  required binary resourceType (STRING);
  optional group category (LIST) {
    repeated group list {
      optional binary element (STRING);
    }
  }
}

Choice types

If an element has a choice type (i.e. it can have more than one data type), it SHALL be represented as with a field for each of its valid types.

The name of each field SHALL follow the format value[type], where [type] is the name of the type in upper camel case.

Here is an example of an element with a choice type in two different Patient resource:

{
  "resourceType": "Patient",
  "multipleBirthBoolean": false
}

{
  "resourceType": "Patient",
  "multipleBirthInteger": 2
}

These examples could be accommodated within the following schema:

message Patient {
  required binary resourceType (STRING);
  optional boolean multipleBirthBoolean;
  optional int32 multipleBirthInteger (INT(32, true));
}

Complex and backbone elements

Each complex and backbone element within a resource definition SHALL be represented as a group within the schema with the same name. The group SHALL contain a field for each of the child elements.

Here is an example of a Reference element within the Condition resource:

{
  "resourceType": "Condition",
  "subject": {
    "reference": "Patient/123"
  }
}

This example could be accommodated within the following schema:

message Condition {
  required binary resourceType (STRING);
  optional group subject {
    optional binary reference (STRING);
  }
}

Extensions

Extensions at the resource level and within complex elements SHALL be represented as a group within the schema with the name extension.

The extension group SHALL contain fields for each of the elements within the Extension data type, as per the rules in the Complex and backbone elements section.

Here is an example of a Patient resource with an extension at the root level:

{
  "resourceType": "Patient",
  "extension": [
    {
      "url": "http://hl7.org.au/fhir/StructureDefinition/indigenous-status",
      "valueCoding": {
        "system": "https://healthterminologies.gov.au/fhir/CodeSystem/australian-indigenous-status-1",
        "code": "1",
        "display": "Aboriginal but not Torres Strait Islander origin"
      }
    }
  ]
}

This example could be accommodated within the following schema:

message Patient {
  required binary resourceType (STRING);
  optional group extension (LIST) {
    repeated group list {
      optional group element {
        optional binary url (STRING);
        optional group valueCoding {
          optional binary code (STRING);
          optional binary display (STRING);
          optional binary system (STRING);
        }
      }
    }
  }
}

Primitive extensions and internal identifiers

Extensions and the internal identifier of each primitive element can be represented within the schema as a field within the schema with the same name prepended with an underscore.

This field is represented as a group within the schema that can contain the following fields:

Field name	Parquet primitive type	Parquet logical type
id	binary	STRING
extension	group	As per the Extension data type (Complex and backbone elements)

Here is an example of a Patient resource with a primitive element that has an id and an extension:

{
  "resourceType": "Patient",
  "birthDate": "1970-01-01",
  "_birthDate": {
    "id": "1",
    "extension": [
      {
        "url": "http://hl7.org/fhir/StructureDefinition/patient-birthTime",
        "valueDateTime": "1970-01-01T00:00:00Z"
      }
    ]
  }
}

This example could be accommodated within the following schema:

message Patient {
  required binary resourceType (STRING);
  optional binary birthDate (STRING);
  optional group _birthDate {
    optional binary id (STRING);
    optional group extension {
      optional binary url (STRING);
      optional binary valueDateTime (STRING);
    }
  }
}

Annotations

Annotations are a mechanism for including derived forms of element values that may be useful for querying the data.

An annotated field is the name of the annotated element, prefixed by two underscores (__) and suffixed by an underscore and the name of the annotation (_[annotation name]).

Each annotation defined in this specification provides a name and a description of the data type or schema for that field.

Non-standard annotations can be included in the format provided that their names do not collide with the annotations defined in this specification.

Date ranges

Any element with the date or dateTime data type can be annotated with range annotations.

The start annotation describes the earliest instant that is considered to be included in the value.

The end annotation describes the latest instant that is considered to be included in the value.

For example, a value of 2014-06-01T12:05Z would have a start of 2014-06-01T12:05:00.000Z and an end of 2014-06-01T12:05:59.999Z at millisecond precision.

Both the start and end annotations use the int96 Parquet primitive type, and the TIMESTAMP(isAdjustedToUTC=true, unit=MILLIS) logical type.

Here is an example of a schema that can accommodate Patient resources with the birthDate element populated, along with annotation fields to store the range.

message Patient {
  required binary resourceType (STRING);
  optional binary birthDate (STRING);
  optional int96 __birthDate_start (TIMESTAMP(isAdjustedToUTC=true, unit=MILLIS));
  optional int96 __birthDate_end (TIMESTAMP(isAdjustedToUTC=true, unit=MILLIS));

Decimal values

The original values of decimals are stored as strings to preserve the precision and scale of the original data.

Elements with a decimal type can use the numeric to store the value in a numeric form.

The numeric annotation uses the fixed_len_byte_array(16) Parquet primitive type, and the DECIMAL(precision=38, scale=6) logical type.

Here is an example of a schema that can accommodate Observation resources with an annotated decimal value:

message Observation {
  required binary resourceType (STRING);
  optional binary valueDecimal (STRING);
  optional fixed_len_byte_array(16) __valueDecimal_numeric (DECIMAL(precision=38, scale=6));
}

Quantity unit canonicalization

Elements of type Quantity can be annotated with the canonical annotation to add canonical unit and value information. This can assist with comparison of Quantity values at query time.

For example, temperature observations in Celsius or Fahrenheit could be canonicalized to Kelvin.

The canonical annotation is represented as a group within the schema that can contain the following fields:

Field name	Parquet primitive type	Parquet logical type
value	fixed_len_byte_array(16)	DECIMAL(precision=38, scale=6)
code	binary	STRING

Examples

Patient

Here is an example of a Patient resource:

{
  "resourceType": "Patient",
  "id": "bennelong-anne",
  "meta": {
    "profile": [
      "http://hl7.org.au/fhir/core/StructureDefinition/au-core-patient"
    ]
  },
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Patient bennelong-anne</b></p><a name=\"bennelong-anne\"> </a><a name=\"hcbennelong-anne\"> </a><a name=\"hcbennelong-anne-en-AU\"> </a><p style=\"border: 1px #661aff solid; background-color: #e6e6ff; padding: 10px;\">Mrs. Anne Mary Bennelong(official) Female, DoB: 1968-10-11 ( Medicare Number:\u00a06951449677)</p><hr/><table class=\"grid\"><tr><td style=\"background-color: #f3f5da\" title=\"Ways to contact the Patient\">Contact Detail</td><td colspan=\"3\"><ul><li>ph: 0491 572 665(Mobile)</li><li>4 Brisbane Street Brisbane QLD 4112 AU (home)</li></ul></td></tr><tr><td style=\"background-color: #f3f5da\" title=\"Language spoken\">Language:</td><td colspan=\"3\"><span title=\"Codes:{urn:ietf:bcp:47 yub}\">Yugambal</span></td></tr><tr><td style=\"background-color: #f3f5da\" title=\"This extension applies to the Patient, Person, and RelatedPerson resources and is used to indicate whether a person identifies as being of Aboriginal or Torres Strait Islander origin.\"><a href=\"https://build.fhir.org/ig/hl7au/au-fhir-base/StructureDefinition-indigenous-status.html\">Australian Indigenous Status</a></td><td colspan=\"3\">australian-indigenous-status-1 1: Aboriginal but not Torres Strait Islander origin</td></tr></table></div>"
  },
  "extension": [
    {
      "url": "http://hl7.org.au/fhir/StructureDefinition/indigenous-status",
      "valueCoding": {
        "system": "https://healthterminologies.gov.au/fhir/CodeSystem/australian-indigenous-status-1",
        "code": "1",
        "display": "Aboriginal but not Torres Strait Islander origin"
      }
    }
  ],
  "identifier": [
    {
      "type": {
        "coding": [
          {
            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
            "code": "MC"
          }
        ],
        "text": "Medicare Number"
      },
      "system": "http://ns.electronichealth.net.au/id/medicare-number",
      "value": "6951449677"
    }
  ],
  "name": [
    {
      "use": "official",
      "text": "Mrs. Anne Mary Bennelong",
      "family": "Bennelong",
      "given": [
        "Anne"
      ],
      "prefix": [
        "Mrs"
      ]
    }
  ],
  "telecom": [
    {
      "system": "phone",
      "value": "0491 572 665",
      "use": "mobile"
    }
  ],
  "gender": "female",
  "birthDate": "1968-10-11",
  "address": [
    {
      "use": "home",
      "line": [
        "4 Brisbane Street"
      ],
      "city": "Brisbane",
      "state": "QLD",
      "postalCode": "4112",
      "country": "AU"
    }
  ],
  "communication": [
    {
      "language": {
        "coding": [
          {
            "system": "urn:ietf:bcp:47",
            "code": "yub"
          }
        ],
        "text": "Yugambal"
      }
    }
  ]
}

This is a Parquet schema that complies with this specification and can accommodate the example Patient resource:

message Patient {
  required binary resourceType (STRING);
  optional binary id (STRING);
  optional group meta {
    optional group profile (LIST) {
      repeated group list {
        optional binary element (STRING);
      }
    }
  }
  optional group text {
    optional binary div (STRING);
    optional binary status (STRING);
  }
  optional group extension (LIST) {
    repeated group list {
      optional group element {
        optional binary url (STRING);
        optional group valueCoding {
          optional binary code (STRING);
          optional binary display (STRING);
          optional binary system (STRING);
        }
      }
    }
  }
  optional group identifier (LIST) {
    repeated group list {
      optional group element {
        optional binary system (STRING);
        optional group type {
          optional group coding (LIST) {
            repeated group list {
              optional group element {
                optional binary code (STRING);
                optional binary system (STRING);
              }
            }
          }
          optional binary text (STRING);
        }
        optional binary value (STRING);
      }
    }
  }
  optional group name (LIST) {
    repeated group list {
      optional group element {
        optional binary family (STRING);
        optional group given (LIST) {
          repeated group list {
            optional binary element (STRING);
          }
        }
        optional group prefix (LIST) {
          repeated group list {
            optional binary element (STRING);
          }
        }
        optional binary text (STRING);
        optional binary use (STRING);
      }
    }
  }
  optional group telecom (LIST) {
    repeated group list {
      optional group element {
        optional binary system (STRING);
        optional binary use (STRING);
        optional binary value (STRING);
      }
    }
  }
  optional binary gender (STRING);
  optional binary birthDate (STRING);
  optional int96 __birthDate_start (TIMESTAMP(isAdjustedToUTC=true, unit=MILLIS));
  optional int96 __birthDate_end (TIMESTAMP(isAdjustedToUTC=true, unit=MILLIS));
  optional group address (LIST) {
    repeated group list {
      optional group element {
        optional binary city (STRING);
        optional binary country (STRING);
        optional group line (LIST) {
          repeated group list {
            optional binary element (STRING);
          }
        }
        optional binary postalCode (STRING);
        optional binary state (STRING);
        optional binary use (STRING);
      }
    }
  }
  optional group communication (LIST) {
    repeated group list {
      optional group element {
        optional group language {
          optional group coding (LIST) {
            repeated group list {
              optional group element {
                optional binary code (STRING);
                optional binary system (STRING);
              }
            }
          }
          optional binary text (STRING);
        }
      }
    }
  }
}

Observation

Here is an example of an Observation resource:

{
  "resourceType": "Observation",
  "id": "bodytemp-1",
  "meta": {
    "profile": [
      "http://hl7.org.au/fhir/core/StructureDefinition/au-core-bodytemp"
    ]
  },
  "text": {
    "status": "generated",
    "div": "<div xmlns=\"http://www.w3.org/1999/xhtml\"><p class=\"res-header-id\"><b>Generated Narrative: Observation bodytemp-1</b></p><a name=\"bodytemp-1\"> </a><a name=\"hcbodytemp-1\"> </a><a name=\"hcbodytemp-1-en-AU\"> </a><p><b>status</b>: Final</p><p><b>category</b>: <span title=\"Codes:{http://terminology.hl7.org/CodeSystem/observation-category vital-signs}\">Vital Signs</span></p><p><b>code</b>: <span title=\"Codes:{http://loinc.org 8310-5}, {http://snomed.info/sct 386725007}\">Body temperature</span></p><p><b>subject</b>: <a href=\"Patient-bennelong-anne.html\">Mrs. Anne Mary Bennelong(official) Female, DoB: 1968-10-11 ( Medicare Number:\u00a06951449677)</a></p><p><b>effective</b>: 2022-02-10</p><p><b>value</b>: 36.5 C<span style=\"background: LightGoldenRodYellow\"> (Details: UCUM  codeCel = 'Cel')</span></p></div>"
  },
  "status": "final",
  "category": [
    {
      "coding": [
        {
          "system": "http://terminology.hl7.org/CodeSystem/observation-category",
          "code": "vital-signs",
          "display": "Vital Signs"
        }
      ],
      "text": "Vital Signs"
    }
  ],
  "code": {
    "coding": [
      {
        "system": "http://loinc.org",
        "code": "8310-5",
        "display": "Body temperature"
      },
      {
        "system": "http://snomed.info/sct",
        "code": "386725007"
      }
    ],
    "text": "Body temperature"
  },
  "subject": {
    "reference": "Patient/bennelong-anne"
  },
  "effectiveDateTime": "2022-02-10",
  "valueQuantity": {
    "value": 36.5,
    "unit": "C",
    "system": "http://unitsofmeasure.org",
    "code": "Cel"
  }
}

This is a Parquet schema that complies with this specification and can accommodate the example Observation resource:

message Observation {
  required binary resourceType (STRING);
  optional binary id (STRING);
  optional group meta {
    optional group profile (LIST) {
      repeated group list {
        optional binary element (STRING);
      }
    }
  }
  optional group text {
    optional binary div (STRING);
    optional binary status (STRING);
  }
  optional binary status (STRING);
  optional group category (LIST) {
    repeated group list {
      optional group element {
        optional group coding (LIST) {
          repeated group list {
            optional group element {
              optional binary code (STRING);
              optional binary display (STRING);
              optional binary system (STRING);
            }
          }
        }
        optional binary text (STRING);
      }
    }
  }
  optional group code {
    optional group coding (LIST) {
      repeated group list {
        optional group element {
          optional binary code (STRING);
          optional binary display (STRING);
          optional binary system (STRING);
        }
      }
    }
    optional binary text (STRING);
  }
  optional group subject {
    optional binary reference (STRING);
  }
  optional binary effectiveDateTime (STRING);
  optional int96 __effectiveDateTime_start (TIMESTAMP(isAdjustedToUTC=true, unit=MILLIS));
  optional int96 __effectiveDateTime_end (TIMESTAMP(isAdjustedToUTC=true, unit=MILLIS));
  optional group valueQuantity {
    optional binary code (STRING);
    optional binary system (STRING);
    optional binary unit (STRING);
    optional binary value (STRING);
    optional fixed_len_byte_array(16) __value_numeric (DECIMAL(precision=38, scale=6));
  }
  optional group __valueQuantity_canonical {
    optional binary code (STRING);
    optional binary system (STRING);
    optional binary unit (STRING);
    optional binary value (STRING);
    optional fixed_len_byte_array(16) __value_numeric (DECIMAL(precision=38, scale=6));
  }
}

Name		Name	Last commit message	Last commit date
Latest commit History 15 Commits
.prettierrc.json		.prettierrc.json
CITATION.cff		CITATION.cff
LICENSE		LICENSE
README.md		README.md

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Repository files navigation

Parquet on FHIR

Resource type

Field optionality

Primitive elements

Repeating elements

Choice types

Complex and backbone elements

Extensions

Primitive extensions and internal identifiers

Annotations

Date ranges

Decimal values

Quantity unit canonicalization

Examples

Patient

Observation

About

Releases 1

Packages

License

aehrc/parquet-on-fhir

Folders and files

Latest commit

History

Repository files navigation

Parquet on FHIR

Resource type

Field optionality

Primitive elements

Repeating elements

Choice types

Complex and backbone elements

Extensions

Primitive extensions and internal identifiers

Annotations

Date ranges

Decimal values

Quantity unit canonicalization

Examples

Patient

Observation

About

Resources

License

Stars

Watchers

Forks

Releases 1

Packages 0

Packages