Info

title	News and updates

2023-07-06: Package 4 (package 2023-07-06), new versioned APIs
2023-04-04: Package 3 (package 2023-03-31)
2023-02-13: Package 2 (package 2023-02-13)
2022-12-07: Initial version (package 2022-10-26)

Table of Contents

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Note

title	Changes to API Endpoint Responses for CDISC Biomedical Concepts and SDTM Dataset Specializations

API endpoint responses for CDISC Biomedical Concepts and SDTM Dataset Specializations have changed due to the evolution of the Biomedical Concepts data model. As a result, all API endpoints will be versioned. The original, pre-existing API endpoints will remain available in API v1.

New API endpoints have been developed and are available in API v2. On July 6, 2023, all new and revised API endpoints for CDISC Biomedical Concepts and SDTM Dataset Specializations will be included in API v2.

Starting July 6, 2023, all API requests will need to include a version. For example,

Old API endpoint:

/mdr/bc/packages/2022-10-26/biomedicalconcepts/C64547

New API endpoints

/cosmos/v1/mdr/bc/packages/2022-10-26/biomedicalconcepts/C64547 /cosmos/v2/mdr/bc/packages/2022-10-26/biomedicalconcepts/C64547

A version must be specified. If a user does not specify a version, a 404 API response code (Not Found) will be returned. All documentation for the CDISC Library API can be found at https://api.developer.library.cdisc.org/. Users should use their existing cdiscID login credentials.

Info

title	Release Notes 2023-07-06

CDISC Biomedical Concepts (BCs) include a two layered approach:

Conceptual/abstract layer that provides standards-agnostic, unambiguous semantic definition largely based on NCIt concepts.
Implementation layer based on valid CDISC dataset specializations that provide value level metadata definitions that facilitate metadata-driven automation.

~300 draft CDISC BCs and SDTM Dataset Specializations are now retrievable via the CDISC Library API, including laboratory tests, vital signs, microbiology specimen tests, electrocardiogram measurements and findings, concomitant medications, procedures, adverse events, medical history, disposition events, biospecimen events and demographics . Public Review is planned for later this year.

CDISC BCs and SDTM Dataset Specializations for RECIST 1.1 disease response criteria are also included in the package release as draft, pending Public Review.

CDISC BCs and SDTM Dataset Specializations are focused on addressing some of the true needs of implementers. For example, SDTM Dataset Specializations can be considered pre-configured building blocks that can be used to generate value level metadata, which is an important part of Define-XML. The Digital Data Flow project uses CDISC BCs to facilitate an efficient, metadata-driven study design process.

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Introduction

CDISC biomedical concepts and dataset specializations are currently supported standards. These include an abstract conceptual layer, aligned with NCI terminology, which is linked to a simplified implementation layer of pre-configured SDTM dataset specializations.Information for additional specializations, such as CDASH data collections, will be added when they become available.

The biomedical concepts and dataset specializations are informative content. They will start to fill gaps such as semantics, variable relationships and value level metadata. Key objectives are to reduce variability in standards implementations, increase metadata-driven automation and reduce barriers to operational implementation.

CDISC biomedical concepts and dataset specializations will be released in incremental packages. The first package was released on October 26, 2022. Subsequent packages have been released and are now available via CDISC Library APIs (see News and Updates).

Please use CDISC Jira for comments and feedback.

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Base URL for API Endpoints

Status

colour	Green
title	New

The base URL for the API is:

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https://library.cdisc.org/api/cosmos/v2

Or, this one for legacy support:

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https://library.cdisc.org/api/cosmos/v1

Note that there has not been a target sunset date established yet

Introduction

Status

colour	Yellow
title	Updated

CDISC biomedical concepts and dataset specializations are currently supported standards. These include an abstract conceptual layer, aligned with NCI terminology, which is linked to a simplified implementation layer of pre-configured SDTM dataset specializations.Information for additional specializations, such as CDASH data collections, will be added when they become available.

The biomedical concepts and dataset specializations are informative content. They will start to fill gaps such as semantics, variable relationships and value level metadata. Key objectives are to reduce variability in standards implementations, increase metadata-driven automation and reduce barriers to operational implementation.

CDISC biomedical concepts and dataset specializations will be released in incremental packages. The first package was released on October 26, 2022. Subsequent packages have been released and are now available via CDISC Library APIs (see News and Updates).

Please use CDISC Jira for comments and feedback.

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Model & Schema

The model and schema describing the CDISC biomedical concepts and SDTM dataset specializations can be found on GitHub.

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Basic Construct

The following table shows the basic construct of API request to obtain biomedical concepts:

API request template	Description
`/mdr/bc/packages`	Get Biomedical Concept Package List
`/mdr/bc/packages/{package}/biomedicalconcepts`	Get Biomedical Concept List
`/mdr/bc/packages/{package}/biomedicalconcepts/{biomedicalconcept}`	Get Biomedical Concept

The following table shows the basic construct of API request to obtain SDTM specializations:

API request template	Description
`/mdr/specializations/sdtm/packages`	Get SDTM Dataset Specialization Package List
`/mdr/specializations/sdtm/packages/{package}/datasetspecializations`	Get SDTM Dataset Specialization List
`/mdr/specializations/sdtm/packages/{package}/datasetspecializations/{datasetspecialization}`	Get SDTM Dataset Specialization

This is a table of supported parameters:

Parameter	Description
package	Package Identifier. An ISO 8601 date.
biomedicalconcept	Biomedical Concept Identifier. A string.
datasetspecialization	SDTM Dataset Specialization Identifier. A string.

Noteinfo
Some examples are slightly modified to provide a better visual and flow. . The examples are reflective of v2 endpoints.

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Example 1

Get biomedical concept list from the package released on October 26, 2022.

/mdr/bc/packages/2022-10-26/biomedicalconcepts

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{
    "_links": {
         "self": {
            "href": "/mdr/bc/packages/2022-10-26/biomedicalconcepts",
            "title": "Biomedical Concepts",
            "type": "Biomedical Concept List"
        },
        "biomedicalConcepts": [
            {
                "href": "/mdr/bc/packages/2022-10-26/biomedicalconcepts/C25298",
                "title": "Systolic Blood Pressure",
                "type": "Biomedical Concept"
            },
            ...
        ],
     },

Lines 8-15: A list of biomedical concepts matching the package parameter, excerpted to show Systolic Blood Pressure. Each biomedical concept has 3 elements: href, title, and type. For Refer to In-depth: HATEOAS Implementation in CDISC Library API for more information about hypermedia links.

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    "effectiveDate": "2022-10-26",
    "label": "Biomedical Concept Package Effective 2022-10-26",
    "name": "Biomedical Concepts 2022-10-26",
    "version": "2022-10-26"
}

Lines 17-20: Metadata about the biomedical concept list.

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Example 2

Status

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title	Updated

Get Get the one Systolic Blood Pressure biomedical concept from the package released on October 26, 2022.

/mdr/bc/packages/2022-10-26/biomedicalconcepts/C25298

Code Block

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{
    "_links": {
        "parentBiomedicalConcept": {
            "href": "/mdr/bc/packages/2022-10-26/biomedicalconcepts/C54706",
            "title": "Blood Pressure",
            "type": "Biomedical Concept"
        },
        "parentPackage": {
            "href": "/mdr/bc/packages/2022-10-26/biomedicalconcepts",
            "title": "Biomedical Concept Package Effective 2022-10-26",
            "type": "Biomedical Concept Package"
        },
        "self": {
            "href": "/mdr/bc/packages/2022-10-26/biomedicalconcepts/C25298",
            "title": "Systolic Blood Pressure",
            "type": "Biomedical Concept"
        }
    },

Lines 2-18: A list of HATEOAS links to related resources, such as self, parent package, and parent biomedical concept. A note on parent biomedical concept: In this example, Blood Pressure is the parent to Systolic Blood Pressure. parentBiomedicalConcept will not be present for topmost biomedical concepts.

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language	yml
firstline	19
linenumbers	true

     "categorycategories": [
        "Vital Signs"
    ],

Lines 19-21: A list of categories to which this biomedical concept belongs.

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firstline	22
linenumbers	true

    "coding": [
        {
            "code": "8480-6",
            "system": "http://loinc.org/",
            "systemName": "LOINC"
        }
    ],

Lines 22-28: A list of external code systems to which this biomedical concept relates.

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theme	Confluence
firstline	29
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    "dataElementConcepts": [
        {
            "conceptId": "C173522",
            "dataType": "integer",
            "href": "https://ncithesaurus.nci.nih.gov/...&code=C173522",
            "ncitCode": "C173522",
            "shortName": "Vital Signs Result"
        },
        {
            "conceptId": "C49669",
            "dataType": "string",
            "exampleSet": [
                "cmHg",
                "mmHG",
                "Pascal"
            ],
            "href": "https://ncithesaurus.nci.nih.gov/...&code=code=C49669",
            "ncitCode": "C49669",
                   "shortName": "Unit of Pressure"
        },
        ...
    ],

Lines 29-4850: A list of data element concepts that comprise this biomedical concept. The href value points to an NCI EVS Thesaurus resource where definition of this data element can be found via the concept code (or, commonly known as c-code).

Lines 3031-35: Vital Signs Result (Line 3435) is the first data element concept on the list.

Lines 3638-4647: Unit of Measure (Line 4547) is the next data element concept on the list. An example set of values is provided in this example.

Code Block

language	yml
firstline	4951
linenumbers	true

    "conceptId": "C25298",
    "definition": "The maximum pressure exerted into the systemic arterial...",
    "href": "https://ncithesaurus.nci.nih.gov/...&code=C25298",
    "resultScaleresultScales": [
        "Quantitative"
    ],
    "ncitCode": "C25298",
    "shortName": "Systolic Blood Pressure",
    "synonymsynonyms": [
        "SYSBP"
    ]
}

Lines 5051-5661: Metadata about the biomedical concept.

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Example 3

Get SDTM dataset specialization list from the package released on October 26, 2022.

/mdr/specializations/sdtm/packages/2022-10-26/datasetspecializationdatasetspecializations

Code Block

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linenumbers	true

{
    "_links": {
        "self": {
            "href": "/mdr/specializations/sdtm/...datasetspecializations",
            "title": "SDTM Dataset Specializations",
            "type": "SDTM Dataset Specialization list"
        },
        "datasetSpecializations": [
            {
                "href": "/mdr/specializations/sdtm/...datasetspecializations/SYSBP",
                "title": "Systolic Blood Pressure",
                "type": "SDTM Dataset Specialization"
            },
            ...
        ]
    },

Lines 8-15: A list of SDTM dataset specializations matching the package parameter, excerpted to show Systolic Blood Pressure. Note the specialization type is set to "SDTM Dataset Specialization".

Code Block

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firstline	17
linenumbers	true

    "effectiveDate": "2022-10-26",
    "label": "SDTM Dataset Specialization Package Effective 2022-10-26",
    "name": "SDTM Dataset Specializations 2022-10-26",
    "version": "2022-10-26"
}

Lines 17-20: Metadata about the SDTM dataset specialization list.

...

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