Update a dataset corresponding to the given ID

PUT

/datasets/{id}

Update a dataset corresponding to the given ID. The dataset must already exist.

Parameters

Path Parameters

id

required

string

Request Body ^required

A full dataset, including all persons within it

object

persons

Array

Any of:

object

object

gender_concept_id

required

Use the gender or sex value present in the data under the assumption that it is the biological sex at birth. If the source data captures gender identity it should be stored in the OBSERVATION table. Accepted gender concepts. Please refer to the THEMIS repository for detailed conventions on how to populate this field. This field is meant to capture the biological sex at birth of the Person. This field should not be used to study gender identity issues.

integer

year_of_birth

For data sources with date of birth, the year should be extracted. If no year of birth is available all the person’s data should be dropped from the CDM instance. For additional information on how to populate this field, please refer to the THEMIS repository. Compute age using year_of_birth.

integer

month_of_birth

For data sources that provide the precise date of birth, the month should be extracted and stored in this field.

integer

day_of_birth

For data sources that provide the precise date of birth, the day should be extracted and stored in this field.

integer

birth_datetime

This field is not required but highly encouraged. For data sources that provide the precise datetime of birth, that value should be stored in this field. For more information on how to populate this field, please refer to the THEMIS repository.

string

nullable

race_concept_id

required

This field captures race or ethnic background of the person. Only use this field if you have information about race or ethnic background. The Vocabulary contains Concepts about the main races and ethnic backgrounds in a hierarchical system. Due to the imprecise nature of human races and ethnic backgrounds, this is not a perfect system. Mixed races are not supported. If a clear race or ethnic background cannot be established, use Concept_Id.

integer

ethnicity_concept_id

required

This field captures Ethnicity as defined by the Office of Management and Budget (OMB) of the US Government - it distinguishes only between “Hispanic” and “Not Hispanic”. Races and ethnic backgrounds are not stored here. Only use this field if you have US-based data and a source of this information. Do not attempt to infer Ethnicity from the race or ethnic background of the Person.

integer

location_id

The location refers to the physical address of the person. This field should capture the last known location of the person. Put the location_id from the LOCATION table here that represents the most granular location information for the person. For additional information on how to populate this field, please refer to the THEMIS repository.

integer

nullable

provider_id

The Provider refers to the last known primary care provider (General Practitioner). Put the provider_id from the PROVIDER table of the last known general practitioner of the person. If there are multiple providers, it is up to the ETL to decide which to put here.

integer

nullable

care_site_id

The Care Site refers to where the Provider typically provides the primary care.

integer

nullable

person_source_value

Use this field to link back to persons in the source data. This is typically used for error checking of ETL logic. Some use cases require the ability to link back to persons in the source data. This field allows for the storing of the person value as it appears in the source. This field is not required but strongly recommended.

string

gender_source_value

This field is used to store the biological sex of the person from the source data. It is not intended for use in standard analytics but for reference only. Put the assigned sex at birth of the person as it appears in the source data.

string

nullable

gender_source_concept_id

Due to the small number of options, this tends to be zero. If the source data codes assigned sex at birth in a non-standard vocabulary, store the concept_id here.

integer

nullable

race_source_value

This field is used to store the race of the person from the source data. It is not intended for use in standard analytics but for reference only. Put the race of the person as it appears in the source data.

string

nullable

race_source_concept_id

Due to the small number of options, this tends to be zero. If the source data codes race in an OMOP supported vocabulary store the concept_id here.

integer

nullable

ethnicity_source_value

This field is used to store the ethnicity of the person from the source data. It is not intended for use in standard analytics but for reference only. If the person has an ethnicity other than the OMB standard of “Hispanic” or “Not Hispanic” store that value from the source data here.

string

nullable

ethnicity_source_concept_id

Due to the small number of options, this tends to be zero. If the source data codes ethnicity in an OMOP supported vocabulary, store the concept_id here.

integer

nullable

unknown

object

gender_concept_id

required

Use the gender or sex value present in the data under the assumption that it is the biological sex at birth. If the source data captures gender identity it should be stored in the OBSERVATION table. Accepted gender concepts. Please refer to the THEMIS repository for detailed conventions on how to populate this field. This field is meant to capture the biological sex at birth of the Person. This field should not be used to study gender identity issues.

integer

year_of_birth

For data sources with date of birth, the year should be extracted. If no year of birth is available all the person’s data should be dropped from the CDM instance. For additional information on how to populate this field, please refer to the THEMIS repository. Compute age using year_of_birth.

integer

month_of_birth

For data sources that provide the precise date of birth, the month should be extracted and stored in this field.

integer

day_of_birth

For data sources that provide the precise date of birth, the day should be extracted and stored in this field.

integer

birth_datetime

This field is not required but highly encouraged. For data sources that provide the precise datetime of birth, that value should be stored in this field. For more information on how to populate this field, please refer to the THEMIS repository.

string

nullable

race_concept_id

required

This field captures race or ethnic background of the person. Only use this field if you have information about race or ethnic background. The Vocabulary contains Concepts about the main races and ethnic backgrounds in a hierarchical system. Due to the imprecise nature of human races and ethnic backgrounds, this is not a perfect system. Mixed races are not supported. If a clear race or ethnic background cannot be established, use Concept_Id.

integer

ethnicity_concept_id

required

This field captures Ethnicity as defined by the Office of Management and Budget (OMB) of the US Government - it distinguishes only between “Hispanic” and “Not Hispanic”. Races and ethnic backgrounds are not stored here. Only use this field if you have US-based data and a source of this information. Do not attempt to infer Ethnicity from the race or ethnic background of the Person.

integer

location_id

The location refers to the physical address of the person. This field should capture the last known location of the person. Put the location_id from the LOCATION table here that represents the most granular location information for the person. For additional information on how to populate this field, please refer to the THEMIS repository.

integer

nullable

provider_id

The Provider refers to the last known primary care provider (General Practitioner). Put the provider_id from the PROVIDER table of the last known general practitioner of the person. If there are multiple providers, it is up to the ETL to decide which to put here.

integer

nullable

care_site_id

The Care Site refers to where the Provider typically provides the primary care.

integer

nullable

person_source_value

Use this field to link back to persons in the source data. This is typically used for error checking of ETL logic. Some use cases require the ability to link back to persons in the source data. This field allows for the storing of the person value as it appears in the source. This field is not required but strongly recommended.

string

gender_source_value

This field is used to store the biological sex of the person from the source data. It is not intended for use in standard analytics but for reference only. Put the assigned sex at birth of the person as it appears in the source data.

string

nullable

gender_source_concept_id

Due to the small number of options, this tends to be zero. If the source data codes assigned sex at birth in a non-standard vocabulary, store the concept_id here.

integer

nullable

race_source_value

This field is used to store the race of the person from the source data. It is not intended for use in standard analytics but for reference only. Put the race of the person as it appears in the source data.

string

nullable

race_source_concept_id

Due to the small number of options, this tends to be zero. If the source data codes race in an OMOP supported vocabulary store the concept_id here.

integer

nullable

ethnicity_source_value

This field is used to store the ethnicity of the person from the source data. It is not intended for use in standard analytics but for reference only. If the person has an ethnicity other than the OMB standard of “Hispanic” or “Not Hispanic” store that value from the source data here.

string

nullable

ethnicity_source_concept_id

Due to the small number of options, this tends to be zero. If the source data codes ethnicity in an OMOP supported vocabulary, store the concept_id here.

integer

nullable

person_id

required

Any person linkage that needs to occur to uniquely identify Persons ought to be done prior to writing this table. This identifier can be the original id from the source data provided if it is an integer, otherwise it can be an autogenerated number. It is assumed that every person with a different unique identifier is in fact a different person and should be treated independently.

integer

info

Dataset information object that can contain various metadata fields

object

dataset_description

A complete description of the dataset.

string

key

additional properties

any

string

Responses

200

Updated dataset information

object

id

string

info

Dataset information object that can contain various metadata fields

object

dataset_description

A complete description of the dataset.

string

key

additional properties

any

400

The request was not processed, as the request parameters did not adhere to the specification

object

query

Error object container

object

error

required

Name/type of the error that occurred

string

ServerError

message

required

Message explaining why the error occurred

string

An unspecified server error occurred

query

object

error

InvalidInput

message

FOO is not an acceptable field

401

The request was not processed, as the request was missing an authentication token

object

query

Error object container

object

error

required

Name/type of the error that occurred

string

ServerError

message

required

Message explaining why the error occurred

string

An unspecified server error occurred

query

object

error

InvalidInput

message

FOO is not an acceptable field

403

The request was not processed, as the user in the given authentication token does not have sufficient privileges to proceed

object

query

Error object container

object

error

required

Name/type of the error that occurred

string

ServerError

message

required

Message explaining why the error occurred

string

An unspecified server error occurred

query

object

error

InvalidInput

message

FOO is not an acceptable field

404

The request was not processed, as the requested object was not found

object

query

Error object container

object

error

required

Name/type of the error that occurred

string

ServerError

message

required

Message explaining why the error occurred

string

An unspecified server error occurred

query

object

error

NotFound

message

The requested resource could not be located

default

Unspecified server error encountered

object

query

Error object container

object

error

required

Name/type of the error that occurred

string

ServerError

message

required

Message explaining why the error occurred

string

An unspecified server error occurred