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Comment: Package 6 release notes

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Basic Construct

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titleupdated

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

true

New Endpoint

New Endpoint

API request templateAPI v2 Only?Return Latest Version Only?Description

/mdr/bc/packages



Get Biomedical Concept Package List

/mdr/bc/packages/{package}/biomedicalconcepts



Get Biomedical Concept List in a Package (example)

/mdr/bc/packages/{package}/biomedicalconcepts/{biomedicalconcept}



Get Biomedical Concept in a Package (example)

/mdr/bc/biomedicalconcepts

Status
subtle
colourGreen
titleNew Endpoint

(tick)

(tick)

Get Biomedical Concept List (example)

/mdr/bc/biomedicalconcepts/{biomedicalconcept}

Status
subtletrue
colourGreen
title

(tick)

(tick)

Get Biomedical Concept (example)

/mdr/bc/categories

Status
subtletrue
colourGreen
title

(tick)


Get Biomedical Concept Categories List (example)

/mdr/bc/biomedicalconcepts?category={category}

Status
subtletrue
colourGreen
titleNew Endpoint

(tick)

(tick)

Get List of Biomedical Concepts for a Given Category (example)

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

Green

subtle

API request templateAPI v2 Only?Return Latest Version Only?Description

/mdr/specializations/sdtm/packages



Get SDTM Dataset Specialization Package List

/mdr/specializations/sdtm/packages/{package}/datasetspecializations



Get SDTM Dataset Specialization List in a Package (example)

/mdr/specializations/sdtm/packages/{package}/datasetspecializations/{datasetspecialization}



Get SDTM Dataset Specialization in a Package (example)

/mdr/specializations/sdtm/datasetspecializations

Status
subtletrue
colourGreen
titleNew Endpoint

(tick)

(tick)

Get SDTM Dataset Specialization List (example)

/mdr/specializations/sdtm/datasetspecializations/{datasetspecialization}

Status
subtletrue
colour
titleNew Endpoint
(tick) (tick) Get SDTM Dataset Specialization (example)

/mdr/specializations/sdtm/domains

Status
true
colourGreen
titleNew Endpoint
(tick)
Get SDTM Dataset Specialization Domain List (example)

/mdr/specializations/sdtm/datasetspecializations?domain={domain}status

subtletrue
colourGreen
titleNew Endpoint

(tick)

(tick)

Get a List of SDTM Dataset Specializations for a Given Domain (example)

The following table shows the basic construct of API requests to obtain dataset specializations:

New Endpoint

API request templateAPI v2 Only?Return Latest Version Only?Description

/mdr/specializations/datasetspecializations?biomedicalconcept={biomedicalconcept}/mdr/specializations/datasetspecializations?biomedicalconcept={biomedicalconcept}

Status
subtletrue
colourGreen
title (tick) (tick) Get a List of Dataset Specializations that Specialize a Biomedical Concept (example)

This is a table of supported parameters:

ParameterDescription
packagePackage Identifier. An ISO 8601 date.
biomedicalconceptBiomedical Concept Identifier. A string.
datasetspecializationSDTM Dataset Specialization Identifier. A string.
categoryBiomedical Concept Category. A string.
domainIdentifier for Dataset Specialization Domain. Examples: AE, DM, VS. A string.

...

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example3
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Example 3

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titleNew

Get a list of all biomedical concepts across packages.

/mdr/bc/biomedicalconcepts

Code Block
languageyml
linenumberstrue
{
    "_links": {
        "biomedicalConcepts": [
            {
                "href": "/mdr/bc/biomedicalconcepts/C25298",
                "title": "Systolic Blood Pressure",
                "type": "Biomedical Concept"
            },
            ...
        ],
        "self": {
            "href": "/mdr/bc/biomedicalconcepts",
            "title": "Biomedical Concepts (latest version)",
            "type": "Biomedical Concept List"
        }
    }, 
    "name": "Biomedical Concepts (latest version)",
    "label": "Biomedical Concepts List"
}

Lines 3-10: A list of HATEOS links to biomedical concepts, excerpted to show Systolic Blood Pressure.
Each biomedical concept has 3 elements: href, title, and type.

For an in-depth explanation of HATEOS refer to In-depth: HATEOAS Implementation in CDISC Library API for more information about hypermedia links.

Section
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Get the latest version of the Systolic Blood Pressure biomedical concept.

/mdr/bc/biomedicalconcepts/C25298

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Example 4

status

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Code Block
languageyml
linenumberstrue
{
    "_links": {
        "parentBiomedicalConcept": {
            "href": "/mdr/bc/biomedicalconcepts/C54706",
            "title": "Blood Pressure",
            "type": "Biomedical Concept"
        },
        "parentPackage": {
            "href": "/mdr/bc/packages/2023-07-06/biomedicalconcepts",
            "title": "Biomedical Concept Package Effective 2023-07-06",
            "type": "Biomedical Concept Package"
        },
        "self": {
            "href": "/mdr/bc/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 that has the latest version of this biomedical concept, 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.
Code Block
languageyml
firstline19
linenumberstrue
"categories": [
    "Vital Signs"
],
Lines 19-21: A list of categories to which this biomedical concept belongs.
Code Block
languageyml
firstline22
linenumberstrue
"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.
Code Block
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firstline29
linenumberstrue
"dataElementConcepts": [
       {
           "conceptId": "C173522",
           "dataType": "decimal",
           "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=C49669",
           "ncitCode": "C49669",
           "shortName": "Unit of Pressure"
       },
       ...
   ],

Lines 29-50: 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 31-35: Vital Signs Result (Line 35) is the first data element concept on the list. 

Lines 38-47: Unit of Measure (Line 47) is the next data element concept on the list. An example set of values is provided in this example.

Code Block
languageyml
title51
linenumberstrue
    "conceptId": "C25298",
    "definition": "The maximum pressure exerted into the systemic arterial...",
    "href": "https://ncithesaurus.nci.nih.gov/...&code=C25298",
    "resultScales": [
        "Quantitative
    ],
    "ncitCode": "C25298",
    "shortName": "Systolic Blood Pressure",
    "synonyms": [
        "SYSBP"
    ]
}
Lines 51-61: Metadata about the biomedical concept.
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New

Get a list of all the biomedical concept categories.

/mdr/bc/categories

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example5
Example 5

Status
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title
Code Block
languageyml
linenumberstrue
{
    "_links": {          
         "self": {
             "href": "/mdr/bc/categories",
             "title": "Biomedical Concept Categories",
             "type": "Biomedical Concept Category List"
         }
         "categories": [
            {
                "name": "Vital Signs",
                "_links": {
                    "self": {
                        "href": "/mdr/bc/biomedicalconcepts?category=Vital%20Signs",
                        "title": "Biomedical Concepts Category (Vital Signs)",
                        "type": "Biomedical Concepts Category"
                    }
                }
            },
            ...
        ],
     },
    "name": "Biomedical Concept Categories",
    "label": "Biomedical Concept Categories List"
}

Lines 8-20: A list of HATEOS links to biomedical concept categories, excerpted to show Vital Signs.
Each biomedical concept category has 3 elements: href, title, and type.

For an in-depth explanation of HATEOS refer to In-depth: HATEOAS Implementation in CDISC Library API for more information about hypermedia links.

Section
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New

Get a list of the latest version of all biomedical concepts in the Vital Signs category.

/mdr/bc/biomedicalconcepts?category=Vital%20Signs

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example6
example6
Example 6

Status
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title
Code Block
languageyml
linenumberstrue
{
    "_links": {
        "biomedicalConcepts": [
            {
                "href": "/mdr/bc/biomedicalconcepts/C25298",
                "title": "Systolic Blood Pressure",
                "type": "Biomedical Concept"
            },
            ...
        ],
        "self": {
            "href": "/mdr/bc/biomedicalconcepts",
            "title": "Biomedical Concepts (latest version)",
            "type": "Biomedical Concept List"
        }
    },

Lines 3-10: A list of HATEOS links to biomedical concepts in the Vital Signs category, excerpted to show Systolic Blood Pressure.
Each biomedical concept has 3 elements: href, title, and type.

For an in-depth explanation of HATEOS refer to In-depth: HATEOAS Implementation in CDISC Library API for more information about hypermedia links.

Code Block
languageyml
linenumberstrue
    "name": "Biomedical Concepts (latest version)",
    "category": "Vital Signs",
    "label": "Biomedical Concepts List"
} 
Lines 17-20: Metadata about the biomedical concept category list.
Section
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Get the SDTM dataset specialization list from the package released on October 26, 2022.

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

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Example 7

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Code Block
languageyml
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{
    "_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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    "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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Example 9

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titleNew

Get a list of all SDTM dataset specializations across packages.

/mdr/specializations/sdtm/datasetspecializations

Code Block
languageyml
linenumberstrue
{
    "_links": {
        "datasetSpecializations": [
            {
                "href": "/mdr/specializations/sdtm/datasetspecializations/SYSBP",
                "title": "Systolic Blood Pressure",
                "type": "SDTM Dataset Specialization"
            },
            ...
        ],
        "self": {
            "href": "/mdr/specializations/sdtm/datasetspecializations",
            "title": "SDTM Dataset Specializations (latest version)",
            "type": "SDTM Dataset Specializations List"
        }
    },
    "name": "SDTM Dataset Specializations (latest version)",
    "label": "SDTM Dataset Specializations List"
}

Lines 3-10: A list of SDTM dataset specializations, excerpted to show Systolic Blood Pressure.
Each SDTM dataset specialization has 3 elements: href, title, and type. For Refer to In-depth: HATEOAS Implementation in CDISC Library API for more information about hypermedia links.
Section
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title

Get the latest version of the Systolic Blood Pressure SDTM Dataset Specialization.

/mdr/specializations/sdtm/datasetspecializations/SYSBP

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example10
example10
Example 10

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Code Block
languageyml
linenumberstrue
{
    "_links": {
        "parentBiomedicalConcept": {
            "href": "/mdr/bc/biomedicalconcepts/C25298",
            "title": "Systolic Blood Pressure",
            "type": "Biomedical Concept"
        },
        "parentPackage": {
            "href": "/mdr/specializations/sdtm/packages/2023-07-06/datasetspecializations",
            "title": "SDTM Dataset Specialization Package Effective 2023-07-06",
            "type": "SDTM Dataset Specialization Package"
        },
        "self": {
            "href": "/mdr/specializations/sdtm/datasetspecializations/SYSBP",
            "title": "Systolic Blood Pressure",
            "type": "SDTM Dataset Specialization"
        }
    },

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, Systolic Blood Pressure is the parent biomedical concept to this SDTM dataset specialization.  parentBiomedicalConcept  will not be present if no parent is available at the time of publication.
Code Block
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firstline19
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    "variables": [
        ...
        {
            "name": "VSORRESU",
            "dateElementConceptId": "C49669",
            "isNonStandard": false,
            "codelist": {
                "conceptId": "C66770",
                "submissionValue": "VSRESU",
                "href": "https://ncithesaurus.nci.nih.gov/...&code=C66770"
            },
            "assignedTerm": {
                "conceptId": "C49670",
                "value": "mmHg"
            },
            "role": "Qualifier",
            "relationship": {
                "subject": "VSORRESU",
                "linkingPhrase": "is the unit for the value in",
                "predicateTerm": "IS_UNIT_FOR",
                "object": "VSORRES"
            },
            "mandatoryVariable": true,
            "mandatoryValue": false,
            "vlmTarget": true
        },

Line 19: Beginning of a variable (or, data element) list that comprise this Systolic Blood Pressure SDTM dataset specialization.

Lines 21-44: VSORRESU (Line 21) is a variable on the list. codelist (Lines 33-37) shows controlled terminology metadata for this variable. relationship (Lines 27-32) shows how this variable is related to another variable in the format of (subject, predicate, object): VSORRESU IS_UNIT_FOR VSORRES.

Code Block
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firstline45
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        {
            "name": "VSSTRESN",
            "dateElementConceptId": "C173522",
            "isNonStandard": false,
            "role": "Qualifier",
            "dataType": "integer",
            "length": 3,
            "relationship": {
                "subject": "VSSTRESN",
                "linkingPhrase": "is the result of the test in",
                "predicateTerm": "IS_RESULT_OF",
                "object": "VSTESTCD"
            },
            "mandatoryVariable": false,
            "mandatoryValue": false,
            "vlmTarget": true
        },
        ...
],
Lines 45-61: VSSTRESN (Line 45) is the next variable on the list. It has an integer as datatype with a preconfigured length of 3. relationship (Lines 53-58) shows how this variable is related to another variable in the format of (subject, predicate, object): VSSTRESN IS_RESULT_OF VSTESTCD.
Code Block
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    "datasetSpecializationId": "SYSBP",
    "domain": "VS",
    "sdtmigStartVersion": "3-2",
    "sdtmigEndVersion": "",
    "shortName": "Systolic Blood Pressure",
    "source": "VS.VSTESTCD"
}
Lines 64-70: Metadata about the SDTM dataset specialization.
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example11
Example 11

Status
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titleNew

Get a list of all the SDTM dataset specialization domains.

/mdr/specializations/sdtm/domains

Code Block
languageyml
linenumberstrue
{
    "_links": {
        "self": {
            "href": "/mdr/specializations/sdtm/domains",
            "title": "SDTM Dataset Specializations Domains",
            "type": "SDTM Dataset Specializations Domains List"
        }
    "domains": [
        {
             "name": "VS"
             "_links": {
                "self": {
                    "href": "/mdr/specializations/sdtm/datasetspecializations?domain=VS",
                    "title": "SDTM Dataset Specialization Domain (VS)",
                    "type": "SDTM Dataset Specialization Domain"
                }
            },
        },
        ...
       ]
    },
    "name": "SDTM Dataset Specializations Domains",
    "label": "SDTM Dataset Specializations Domains List"
}

Lines 8-20: A list of HATEOS links to SDTM dataset specialization domains, excerpted to show VS.
Each biomedical concept category has 3 elements: href, title, and type.

For an in-depth explanation of HATEOS refer to In-depth: HATEOAS Implementation in CDISC Library API for more information about hypermedia links.

Section
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New

Get a list of the latest version of all SDTM dataset specializations in the VS domain.

/mdr/specializations/sdtm/datasetspecializations?domain=VS

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example12
example12
Example 12

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title
Code Block
languageyml
linenumberstrue
{
    "_links": {
        "datasetSpecializations": [
            {
                "href": "/mdr/specializations/sdtm/datasetspecializations/SYSBP",
                "title": "Systolic Blood Pressure",
                "type": "SDTM Dataset Specialization"
            },
            ...
        ],
        "self": {
            "href": "/mdr/specializations/sdtm/datasetspecializations",
            "title": "SDTM Dataset Specializations (latest version)",
            "type": "SDTM Dataset Specializations List"
        }
    },

Lines 3-10: A list of HATEOS links to SDTM dataset specializations in the VS domain, excerpted to show Systolic Blood Pressure.
Each biomedical concept has 3 elements: href, title, and type.

For an in-depth explanation of HATEOS refer to In-depth: HATEOAS Implementation in CDISC Library API for more information about hypermedia links.



Code Block
languageyml
linenumberstrue
    "name": "SDTM Dataset Specializations (latest version)",
    "label": "SDTM Dataset Specializations List",
    "domain": "VS"
}  
Lines 17-20: Metadata about the SDTM dataset specialization.
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New

Get a list of the latest version of all dataset specializations that specialize the Glucose Measurement biomedical concept.

/mdr/specializations/datasetspecializations?biomedicalconcept=C105585

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Example 13

Status
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title
Code Block
languageyml
linenumberstrue
{
    "_links": {
        "datasetSpecializations": {
            "sdtm": [
                {
                    "href": "/mdr/specializations/sdtm/datasetspecializations/GLUCBLD",
                    "title": "Glucose Concentration in Blood",
                    "type": "SDTM Dataset Specialization"
                },
                {
                    "href": "/mdr/specializations/sdtm/datasetspecializations/GLUCPL",
                    "title": "Glucose Concentration in Plasma",
                    "type": "SDTM Dataset Specialization"
                },
                {
                    "href": "/mdr/specializations/sdtm/datasetspecializations/GLUCSER",
                    "title": "Glucose Concentration in Serum",
                    "type": "SDTM Dataset Specialization"
                },
                {
                    "href": "/mdr/specializations/sdtm/datasetspecializations/GLUCURIN",
                    "title": "Glucose Concentration in Urine",
                    "type": "SDTM Dataset Specialization"
                }
            ]
        },
        "parentBiomedicalConcept": {
            "href": "/mdr/bc/biomedicalconcepts/C105585",
            "title": "Glucose Measurement",
            "type": "Biomedical Concept"
        },
        "self": {
            "href": "/mdr/specializations/datasetspecializations?biomedicalconcept=C105585",
            "title": "Dataset Specializations that specialize a Biomedical Concept",
            "type": "Dataset Specializations List"
        }
    },
    "name": "Dataset Specializations (latest version)",
    "label": "Dataset Specializations List"
}
Lines 4-25: A list of SDTM dataset specializations that specialize the Glucose Measurement biomedical concept (C105585).