5511 lines
317 KiB
HTML
5511 lines
317 KiB
HTML
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<meta xmlns:ncbi-portal="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" name="ncbi_app" content="gtr" /><meta xmlns:ncbi-portal="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" name="ncbi_pdid" content="static" />
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<title>GTR Submission API</title>
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The NCBI web site requires JavaScript to function.
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<div role="navigation" aria-label="access keys">
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<div class="header">
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<div class="gtr_logo"><a href="/gtr" title="Genetic Testing Registry">NIH Genetic Testing Registry</a></div>
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<div><div class="header_con2"><div id="searchBox" class="smallSearchBox"><form id="formSearch" data-selected-scope="docs" action="https://www.ncbi.nlm.nih.gov/gtr/" method="get"><div class="formFields noWrap"><label for="gtr_term" class="ui-helper-hidden-accessible">Search term</label><input id="gtr_term" name="term" type="text" data-jig="ncbiautocomplete" value="all[sb]" data-jigconfig="maxListLimit: 15" data-dictionary="gtr_allgtr" /><select name="scope" class="scope_sel" id="scope"><option value="gtr">All GTR</option><option value="conditions">Conditions/Phenotypes</option><option value="genes">Genes</option><option value="tests">Human Tests</option><option value="testsmicrobe">Microbe Tests</option><option value="labs">Labs</option></select><button type="submit" id="submitSearchButton" class="gtr-button-submit ui-ncbibutton-blue">Search</button><a href="/gtr/tests/advanced/" id="go-to-advanced-search">Advanced search for tests</a></div></form></div></div></div>
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</div>
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<div class="nav_and_browser">
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<div class="localnav"><ul class="jig-ncbilocalnav">
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<li><a href="#">Overview</a><ul>
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<li><a href="/gtr/docs/about/">About GTR</a></li>
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<li><a title="Submission overview" href="/gtr/docs/submit/">Submission to GTR</a></li>
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<li><a title="Resources included in GTR and where to locate a genetics professional" href="/gtr/docs/resources/">GTR resources</a></li>
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<li><a title="Frequently asked questions" href="/gtr/docs/faq/">FAQ</a></li>
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<li><a href="https://www.nih.gov/institutes-nih/nih-office-director">NIH Office of the Director</a></li>
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<li><a href="/gtr/docs/outreach/">Community outreach</a></li>
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<li><a href="/gtr/docs/maintenance_use/">Data use and maintenance</a></li>
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<li><a href="/clinvar/nomenclature/">Terminology</a></li>
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<li><a href="/gtr/docs/linkcriteria/">Web link criteria</a></li>
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<li><a href="/gtr/docs/linking/">How to create links to GTR</a></li>
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</ul>
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</li>
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<li><a href="#">Lab Submission</a><ul>
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<li><a href="/gtr/docs/login/">Login</a></li>
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<li><a title="Overview of how to submit novel laboratory information" href="/gtr/docs/submit/add_lab/">Register a new lab</a></li>
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<li><a title="Instructions for performing the annual review" href="/gtr/docs/annual_review/">Annual review</a></li>
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<li><a title="Instructions for managing the group account for submitters" href="/gtr/docs/manage_permissions/">Groups: Manage person permissions</a></li>
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<li><a title="Instructions for submitters about updating and deleting records" href="/gtr/docs/manage_records/">Manage records</a></li>
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</ul>
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</li>
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<li><a href="#">Genetic Test Submission</a><ul>
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<li><a title="Overview of genetic test submissions" href="/gtr/docs/submit/">Getting started</a></li>
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<li><a title="Instructions for clinical genetic test submissions" href="/gtr/docs/submit/add_test/">Clinical tests</a></li>
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<li><a title="Instructions for spreadsheet submissions for clinical genetic tests" href="/gtr/docs/fulltest/">Clinical tests by spreadsheet</a></li>
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<li><a title="Instructions for API submissions for clinical genetic tests" href="/gtr/docs/gtr_api_http/">Clinical tests by api</a></li>
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<li><a title="Instructions for research genetic test submissions" href="/gtr/docs/submit/add_research/">Research tests</a></li>
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</ul>
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</li>
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<li><a href="#">Microbe Test Submission</a><ul>
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<li><a title="Overview of microbe test submissions" href="/gtr/docs/microbe_test/">Getting started</a></li>
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<li><a title="Instructions for clinical microbe test submissions" href="/gtr/docs/submit/add_microbe_clinical/">Clinical tests</a></li>
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<li><a title="Instructions for spreadsheet submissions for clinical microbe tests" href="/gtr/docs/microbe_fulltest/">Clinical tests by spreadsheet</a></li>
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<li><a title="Instructions for API submissions for clinical microbe tests" href="/gtr/docs/gtr_api_http/">Clinical tests by api</a></li>
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<li><a title="Instructions for research microbe test submissions" href="/gtr/docs/submit/add_microbe_research/">Research tests</a></li>
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</ul>
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</li>
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<li><a href="#">Search GTR</a><ul>
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<li><a title="How to use and search the GTR website" href="/gtr/docs/help/">Search tips</a></li>
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<li><a href="/gtr/docs/advanced_search">Advanced search</a></li>
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<li><a href="/gtr/docs/common_searches/">Common searches</a></li>
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<li><a href="https://www.youtube.com/playlist?list=PL7dF9e2qSW0a1b37gVee-pYFZ4AEOGvqw">YouTube library</a>
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<span id="shared-content-1"></span></li>
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</ul>
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</li>
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</ul></div>
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</div>
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<!-- was itemctrl -->
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<div class="container">
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<div id="maincontent" class="content col twelve_col last">
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<div class="col1">
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<div><div id="static-page-tools"><div style="display:inline-block;"><form id="form-helpdocs" action="/gtr/docs/" method="get"><label class="ui-helper-hidden-accessible" for="helpdocs-search-term">Search GTR Help Documents</label><input autocomplete="off" value="" placeholder="Search GTR Help Documents" name="term" id="helpdocs-search-term" style="width:30em;" /><button id="search">Search GTR help documents</button></form></div><ul><li class="print"><a href="#" id="print-this" title="Print this document">Print this document</a></li></ul></div>
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<span id="api_contents">
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<div class="toc_sidebar api_scroll">
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<p data-target="h1_csa">GTR Submission API</p>
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<p data-target="h2_setup">Account Setup</p>
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<p data-target="h2_api_submit_data">Data Submission</p>
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<p data-target="h2_api_re_code">Submission Status HTTP Return Codes</p>
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<p data-target="h2_schema_raw">Submission schema</p>
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<p data-target="h2_schema_desc">Submission description</p>
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<p data-target="h2_summary_raw">Summary response schema</p>
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<p data-target="h2_summary_desc">Summary response description</p>
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<p data-target="h2_sample">Sample Submission Script</p>
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<p data-target="h2_check_status">Checking the Submission Status</p>
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<p data_target="h2_sample_submission_files">Sample Submission Files</p>
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</div>
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<div class="api_main_content">
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<h1 id="h1_csa">GTR Submission API</h1>
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<div id="api_intro"><p>
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GTR uses the NCBI <a target="_blank" href="https://submit.ncbi.nlm.nih.gov/api/v1/docs/">Submission Portal Public API</a> which is organized around REST and JSON for data exchange. This page documents how the API can be used to upload GTR test submission data and query its status.
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</p></div>
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<h2 id="h2_setup">Account Setup</h2>
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<h3 id="h3_acct">Create a New API Service Account</h3>
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<div id="new_account">
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<p>To get started, send a request to GTR staff (<a target="_blank" href="mailto:tkt-tryhd@ncbi.nlm.nih.gov?subject=Create%20a%20GTR%20API%20service%20account">tkt-tryhd@ncbi.nlm.nih.gov</a>) to create an API service account. Once the service account has been created, create an API key.</p>
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</div>
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<h3 id="h3_api_key">Create an API Key</h3>
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<div id="new_api_key">
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<ol start="1" type="1">
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<li>In the group account for your lab, click on the API Access tab.<br />
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<img src="/core/assets/gtr/images/api_sub_portal_2.jpg" alt="New service account screenshot" />
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</li>
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<li>In the service account, click 'Get new key for service account'.
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</li>
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<li>A new key will be created. Please take note of the key because you will not see the key again. The key will look something like this:<br />
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<pre>abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZzyxwvutsrqpo</pre>
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</li>
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<li>If you lose the key, you can create a new key.<br />
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<img src="/core/assets/gtr/images/api_sub_portal_4.png" alt="New service account screenshot" />
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</li>
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<li>Use this key for your submission.</li>
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</ol>
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</div>
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<h2 id="h2_api_submit_data">Data Submission</h2>
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<div id="submitting_data">
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<p>You can submit a test by uploading a JSON file via http using the following URL:<br />
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<pre>https://submit.ncbi.nlm.nih.gov/api/v1/submissions/</pre></p>
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<p>To check the response, use the following URL:<br />
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<pre>https://submit.ncbi.nlm.nih.gov/api/v1/submissions/SUBnnnnnn/actions/</pre></p>
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<h3 id="h3_submission_dryrun_mode">Dry Run Mode</h3>
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<p>To perform a dry run without creating a submission, include a query string, dry-run=true in the URL:<br />
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<pre>https://submit.ncbi.nlm.nih.gov/api/v1/submissions/?dry-run=true</pre></p>
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<p>In dry run mode, the submission file is validated against the JSON schema. If the file is valid, it will return HTTP status 204, but no submission-id is created (see <a target="_blank" href="gtr/docs/gtr_api_http.xml#h2_api_re_code">API Submission Status HTTP Return Codes</a>).</p>
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<h3 id="h3_submission_test_mode">Test Mode</h3>
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<p>To validate data prior to submission, use the following URL:<br />
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<pre>https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions</pre></p>
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<p>To check the response, use the following URL:<br />
|
|
<pre>https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions/SUBnnnnnn/actions/</pre></p>
|
|
</div>
|
|
<h3 id="h3_api_sub_other">API Submission Related to Other Modes of Submission</h3>
|
|
<div id="api_related_others">
|
|
<p>Tests can be submitted to GTR in three modes: Submission Portal wizard, submission spreadsheet, and GTR API. Here are the rules that govern by which mode a test can be submitted:</p>
|
|
<ul>
|
|
<li>Any test submitted by SP wizard and/or submission spreadsheet can be updated via API. The original submission will be deleted, so it will not be visible under 'Tests in this lab' on the Submission Portal lab home page. A new SUBID will be created in the API Submissions table (see below).</li>
|
|
<li>Any test added/updated by API will not be available for updating via Submission Portal wizard or submission spreadsheet.</li>
|
|
<li>Tests submitted by API will not be available for downloading via spreadsheet format.</li>
|
|
</ul>
|
|
|
|
<h4 id="h4_api_sub_table">API Submissions Table</h4>
|
|
<p>On the Submission Portal home page for your lab, the API Submissions table, located below 'Tests in this Lab' will display the list of submissions, with the most recent submission at the top of the list.<br />
|
|
<img src="/core/assets/gtr/images/api_sub_table.png" alt="New service account screenshot" />
|
|
</p>
|
|
|
|
<h4 id="h4_api_expect">What to Expect when you Submit a Test via API</h4>
|
|
<div>
|
|
<ul>
|
|
<li>First, the submission pipeline performs validation of the submitted file against the schema.
|
|
<ul>
|
|
<li>Success
|
|
<ul>
|
|
<li>For any action (add, update, or delete): a submission identifier (SUBID) is created for the submitted file.</li>
|
|
<li>For actions 'update' or 'delete': If a test that was submitted originally using the Submission Wizard or spreadsheet is updated or deleted using the API, it will no longer be listed under 'Tests in this Lab' on the Submission Portal home page. Instead there is a new grid to view API Submissions located below 'Tests in this Lab'.</li>
|
|
</ul>
|
|
</li>
|
|
<li>Failure
|
|
<ul><li>For any action (add, update, or delete): No SUBID is created.<br />
|
|
Note: See 'Checking the Submission Status'</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
<li>Next, the system attempts to process the submission to the GTR database.
|
|
<ul>
|
|
<li>Success
|
|
<ul>
|
|
<li>Action 'add': GTR test (new accession GTR000######) is added to the db and will be available.</li>
|
|
<li>Action 'update': Existing GTR test is updated in db.</li>
|
|
<li>Action 'delete': Existing GTR test is deleted in db.</li>
|
|
</ul>
|
|
</li>
|
|
<li>Failure
|
|
<ul>
|
|
<li>Action 'add': no GTR test (no accession) will be added to the database.</li>
|
|
<li>Action 'update': the GTR test is not updated.</li>
|
|
<li>Action 'delete': the GTR test is not deleted.</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
<h2 id="h2_api_re_code">Submission Status HTTP Return Codes</h2>
|
|
<div id="api_sub_status_return_code">
|
|
<p>The <a target="_blank" href="https://developer.mozilla.org/en-US/docs/Web/HTTP/Status">HTTP status return codes</a> are shown below, indicating whether or not the API call is successful.</p>
|
|
<p>The key property in the response is actions[0].status and the possible values are:</p>
|
|
<ul>
|
|
<li>submitted: The submission has been received and is waiting to be validated.</li>
|
|
<li>error: The submission failed. A file URLs will be available in actions[0].responses[].files In actions[0].responses[0].message there will be more information for severity, errorCode, and text. severity will also be error and the errorCode will be 1 or 2. An errorCode of 1 indicates partial success which means that some records in the batch failed while others succeeded. An errorCode of 2 indicates that all records in the batch failed.</li>
|
|
<li>processing: The submission is being validated and should be done soon. For actions[0].responses[0].message, severity is info and errorCode is null</li>
|
|
<li>success: Submission was successful.</li>
|
|
</ul>
|
|
<p>If actions[0].status is not error, then for actions[0].responses[0].message, severity is info and errorCode is null.</p>
|
|
</div>
|
|
<div>
|
|
<table class="http_return">
|
|
<colgroup>
|
|
<col width="20%" />
|
|
<col width="80%" />
|
|
</colgroup>
|
|
<thead>
|
|
<tr>
|
|
<th>HTTP Code</th>
|
|
<th>Meaning</th>
|
|
</tr>
|
|
</thead>
|
|
<tbody>
|
|
<tr>
|
|
<td><code class="bold">201</code></td>
|
|
<td>The request succeeded, and a new SUBID was created as a result.<br />
|
|
Example with a status of "submitted":
|
|
<pre class="example">
|
|
{
|
|
"actions": [
|
|
{
|
|
"id": "SUB788098-1",
|
|
"targetDb": "GTR",
|
|
"status": "submitted",
|
|
"updated": "2022-08-29T12:46:21.160474Z",
|
|
"responses": []
|
|
}
|
|
]
|
|
}
|
|
</pre>
|
|
Example with a status of "processing":
|
|
<pre class="example">
|
|
{
|
|
"actions": [
|
|
{
|
|
"id": "SUB788098-1",
|
|
"targetDb": "GTR",
|
|
"status": "processing",
|
|
"updated": "2022-08-29T12:47:04.602679Z",
|
|
"responses": [
|
|
{
|
|
"status": "processing",
|
|
"message": {
|
|
"severity": "info",
|
|
"errorCode": null,
|
|
"text": "Your GTR submission processing status is \"In processing\"."
|
|
},
|
|
"files": [],
|
|
"objects": [
|
|
{
|
|
"targetDb": "GTR",
|
|
"accession": null,
|
|
"content": null
|
|
}
|
|
]
|
|
}
|
|
]
|
|
}
|
|
]
|
|
}
|
|
</pre>
|
|
Example with a status of "success":
|
|
<pre class="example">
|
|
{
|
|
"actions": [
|
|
{
|
|
"id": "SUB786329-1",
|
|
"targetDb": "GTR",
|
|
"status": "processed",
|
|
"updated": "2022-08-12T13:57:51.283336Z",
|
|
"responses": [
|
|
{
|
|
"status": "processed",
|
|
"message": {
|
|
"severity": "info",
|
|
"errorCode": null,
|
|
"text": "Your GTR submission processing status is \"success\". Please find the details in the file referenced by actions[0].responses[0].files[0].url."
|
|
},
|
|
"files": [
|
|
{"url": "https://dsubmit.ncbi.nlm.nih.gov/api/2.0/files/ih6akl6x/sub786329-report.json/?format=attachment"}
|
|
],
|
|
"objects": [
|
|
{
|
|
"targetDb": "GTR",
|
|
"accession": "GTR000597177",
|
|
"content": null
|
|
}
|
|
]
|
|
}
|
|
]
|
|
}
|
|
]
|
|
}
|
|
</pre>
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code class="bold">400</code></td>
|
|
<td>The request failed.
|
|
<pre class="example">
|
|
{
|
|
"submissionID": "SUB782594",
|
|
"submissionDate": "2022-07-25",
|
|
"processingStatus": "Error",
|
|
"errors": [
|
|
{
|
|
"input": [
|
|
{
|
|
"field": "fdaReviews.reviewCategoryDesignation",
|
|
"value": null
|
|
}
|
|
],
|
|
"userMessage": [
|
|
"The value is not in the allowed list."
|
|
]
|
|
}
|
|
]
|
|
}
|
|
</pre>
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code class="bold">429</code></td>
|
|
<td>Too many requests. Wait for a number of seconds specified in the response header, then try and submit the request again.
|
|
</td>
|
|
</tr>
|
|
<tr>
|
|
<td><code class="bold">500-599</code></td>
|
|
<td>Example of server error
|
|
<pre class="example">
|
|
{
|
|
"file": "clinical_exome.json",
|
|
"status": 500,
|
|
"message": "Unexpected error occurred",
|
|
"eventId": "19ed9257b98349fa94baba94e15ba7e8"
|
|
}
|
|
</pre>
|
|
</td>
|
|
</tr>
|
|
</tbody>
|
|
</table>
|
|
</div>
|
|
<h2 id="h2_schema_raw">Submission schema</h2>
|
|
<p>You can download the schema here: <a target="_blank" href="https://github.com/ncbi/gtr/blob/master/api/gtr_api_submission_schema.json">https://github.com/ncbi/gtr/blob/master/api/gtr_api_submission_schema.json</a></p>
|
|
<div class="api_scroll"><pre>
|
|
{
|
|
<span class="quotedn">"$schema"</span>: <span class="quotedv">"http://json-schema.org/draft-07/schema#"</span>,
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"title"</span>: <span class="quotedv">"GTR test submission"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"GTR API submission schema"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"humanTest"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Human clinical test - add or update"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"action",
|
|
"labTestName",
|
|
"testPurposes",
|
|
"testPerformanceLocations",
|
|
"methods",
|
|
"analyticalValidity",
|
|
"testTargetsAssociated"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"action"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value to add a new test or update an existing test."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"add",
|
|
"update"
|
|
]
|
|
},
|
|
<span class="quotedn">"analyticalValidity"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Quantitative information about analytical sensitivity, analytical specificity, accuracy, and/or precision of this test."</span>
|
|
},
|
|
<span class="quotedn">"assayLimitations"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Test limitations that affect the value of the test for its intended use, such as the limit of detection and test restrictions."</span>
|
|
},
|
|
<span class="quotedn">"caps"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Set of mjaor category, sub-category and test code to specify, if College of American Pathologists (CAP) is chosen as Provider for proficiency testing."</span>,
|
|
<span class="quotedn">"minItems"</span>: 0,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"capCategory"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Relevant sub-category, if major CAP category is selected."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/capCategoryEnum"</span>
|
|
},
|
|
<span class="quotedn">"capTest"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Relevant test code, if major CAP category is selected."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/capTestEnum"</span>
|
|
},
|
|
<span class="quotedn">"majorCapCategory"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Category to specify, if College of American Pathologists (CAP) is chosen as Provider for proficiency testing"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/majorCapCategoryEnum"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"citationsForAnalyticalValidity"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations supporting the analytical validity statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForAssayLimitations"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations supporting the assay limitation statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForClinicalValidity"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations used to evaluate the clinical validity of the test; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForInternalTestValidationMethod"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations to support internal test validation method statement; for PubMed ID use format 'PMID: 23193275';; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForTargetPopulation"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations supporting statements provided in 'Target population for this test'; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForTestingStrategy"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations for the testing strategy/algorithm; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForTestProcedureOrProtocol"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations supporting the test protocol; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"clinicalUtilities"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Likelihood of the test to significantly improve patient outcomes."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"category"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Clinical utility category value"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Avoidance of invasive testing",
|
|
"Establish or confirm diagnosis",
|
|
"Guidance for management",
|
|
"Guidance for selecting a drug therapy and/or dose",
|
|
"Lifestyle planning",
|
|
"Predictive risk information for patient and/or family members",
|
|
"Reproductive decision-making",
|
|
"Sufficient research has not been conducted to demonstrate the utility of the test"
|
|
]
|
|
},
|
|
<span class="quotedn">"citations"</span>: {
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"otherCategory"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if category is not in the enum list."</span>
|
|
},
|
|
<span class="quotedn">"url"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The URL to display references to support a clinical utility choice."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"allOf"</span>: [
|
|
{
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"category"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherCategory"
|
|
]
|
|
}
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"anyOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"url"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"citations"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"clinicalValidity"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Clinical sensitivity and specificity, description of the population(s) assessed, and the number of specimens used to calculate clinical validity."</span>
|
|
},
|
|
<span class="quotedn">"commentForTestPerformanceLocation"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If any part of the test is performed externally, a description about where it is performed and any other information."</span>
|
|
},
|
|
<span class="quotedn">"cptCodes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Molecular pathology Current Procedural Terminology (CPT\u00ae) code - 'MoPath' code - from the American Medical Association (AMA) that describes the test."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"fdaReviews"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Has the test been reviewed by the FDA?"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"fdaApplicationNumber"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If FDA reviewed, FDA application number."</span>
|
|
},
|
|
<span class="quotedn">"noReviewCategoryDesignation"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If no FDA review, FDA category designation"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"FDA exercises enforcement discretion",
|
|
"Not Applicable"
|
|
]
|
|
},
|
|
<span class="quotedn">"otherRegulatoryStatus"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if fdaRegulatoryStatus value is not in the status enum list."</span>
|
|
},
|
|
<span class="quotedn">"otherReviewItem"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if FDA reviewed item is not in the item enum list."</span>
|
|
},
|
|
<span class="quotedn">"regulatoryStatus"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If FDA reviewed, FDA regulatory status from enum list."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"FDA cleared/approved",
|
|
"FDA exempt",
|
|
"Not submitted",
|
|
"Pending"
|
|
]
|
|
},
|
|
<span class="quotedn">"reviewCategoryDesignation"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If FDA review, FDA category designation."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"IUO - Investigational Use Only. The performance characteristics of this product have not been established.",
|
|
"IVD - In Vitro Device.",
|
|
"RUO - Research Use Only. Not for use in diagnostic procedures."
|
|
]
|
|
},
|
|
<span class="quotedn">"reviewed"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"boolean"</span>
|
|
},
|
|
<span class="quotedn">"reviewItem"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If FDA reviewed, item under reviewed."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"ASR - Analyte Specific Reagent(s)",
|
|
"Assay(s)",
|
|
"IVDMIA - In Vitro Diagnostic Multivariate Index Assay(s)",
|
|
"Instrument(s)",
|
|
"Test kit(s)"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"reviewed"</span>: {
|
|
<span class="quotedn">"const"</span>: true
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"not"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"reviewCategoryDesignation",
|
|
"noReviewCategoryDesignation"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"allOf"</span>: [
|
|
{
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"reviewItem"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherReviewItem"
|
|
]
|
|
}
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"regulatoryStatus"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherRegulatoryStatus"
|
|
]
|
|
}
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"reviewCategoryDesignation"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"gtrAccession"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"GTR accession number, for an existing GTR test."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/gtrAccessionType"</span>
|
|
},
|
|
<span class="quotedn">"howToOrder"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Description of the test ordering procedure."</span>
|
|
},
|
|
<span class="quotedn">"informedConsentRequired"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Whether the lab reqires informed consent prior to performing the test."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Decline to answer",
|
|
"Required",
|
|
"Not required",
|
|
"Based on applicable state law"
|
|
]
|
|
},
|
|
<span class="quotedn">"internalTestValidationMethod"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Explanation of how the lab validates the test."</span>
|
|
},
|
|
<span class="quotedn">"labTestName"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The name of the test to be displayed in GTR."</span>
|
|
},
|
|
<span class="quotedn">"labTestShortName"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Shortened name or mneumonic used by the lab to identify the test."</span>
|
|
},
|
|
<span class="quotedn">"loincCodes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Logical Observation Identifiers Names and Codes."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"manufactureTestName"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The manufacturer's name for the test, if a commercial test or kit was used."</span>
|
|
},
|
|
<span class="quotedn">"methods"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Set of method category and primary methodology used in the test; the major method categories for the test which will be inferred from the methodCategory are: (1) Molecular Genetics, (2) Biochemical Genetics, and (3) Cytogenetics."</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"instruments"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Instrument(s) used for the method."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"name"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Name of instrument used."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/humanTestInstrumentEnum"</span>
|
|
},
|
|
<span class="quotedn">"otherInstrument"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if the instrument used is not in the instrument enum list."</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"name"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherInstrument"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"method"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Primary methodology for the test"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/humanTestMethodEnum"</span>
|
|
},
|
|
<span class="quotedn">"methodCategory"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"General category to which the test method belongs"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/humanTestMethodCategoryEnum"</span>
|
|
},
|
|
<span class="quotedn">"otherMethod"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if method is not in the method enum list."</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"allOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"methodCategory"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"method"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherMethod"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"nysClep"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"NYS Clinical Laboratory Evaluation Program"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"status"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"NYS CLEP status"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Approved",
|
|
"Exempt",
|
|
"Grandfathered",
|
|
"Pending"
|
|
]
|
|
},
|
|
<span class="quotedn">"testApprovalNumber"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"NYS CLEP test approval number"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
},
|
|
<span class="quotedn">"orderURL"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The URL for ordering the test."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
},
|
|
<span class="quotedn">"platforms"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The platform used for the test, usually a commercial product (catalog number or set of numbers) with pre-defined test targets used in the test."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"name"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Name of commercial platform or kit with predefined test targets."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/humanTestPlatformEnum"</span>
|
|
},
|
|
<span class="quotedn">"otherPlatform"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if platform used is not in the enum list."</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"name"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherPlatform"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"posttestGeneticCounselingRequired"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Requirement by the laboratory for genetic counseling after performing the test in order to release the test results."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Decline to answer",
|
|
"Required",
|
|
"Not required"
|
|
]
|
|
},
|
|
<span class="quotedn">"pretestGeneticCounselingRequired"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Requirement by the laboratory for genetic counseling prior to performing the test."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Decline to answer",
|
|
"Required",
|
|
"Not required"
|
|
]
|
|
},
|
|
<span class="quotedn">"proficiencyTesting"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Periodic internal or external evaluation of the test to corroborate the accuracy of test results."</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"citationsForMethodDescription"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations to support the proficiency testing method statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"method"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The type of proficiency testing that is performed, from enum list. "</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Alternative Assessment",
|
|
"Formal PT program",
|
|
"Inter-Laboratory",
|
|
"Intra-Laboratory"
|
|
]
|
|
},
|
|
<span class="quotedn">"methodDescription"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"A description of the proficiency testing method used."</span>
|
|
},
|
|
<span class="quotedn">"otherMethod"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if method is not in the method enum list."</span>
|
|
},
|
|
<span class="quotedn">"otherProvider"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if provider is not in the provider enum list."</span>
|
|
},
|
|
<span class="quotedn">"provider"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Provider for proficiency testing, from enum list."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"American College of Medical Genetics / College of American Pathologists, ACMG/CAP",
|
|
"American College of Physicians - Medical Laboratory Evaluation, ACP MLE",
|
|
"Association for Molecular Pathology, AMP",
|
|
"Belgian Official EKE Schemes, GLP Monitoring Programme",
|
|
"Canadian External Quality Assessment Laboratory, CEQAL",
|
|
"Centers for Disease Control and Prevention Newborn Screening Quality Assurance Program, CDC DLS",
|
|
"Clinical Pathology Accreditation (UK) Ltd., CPA",
|
|
"College of American Pathologists, CAP",
|
|
"European Concerted Action on Thrombosis External Quality Assessment Program, ECAT EQAP",
|
|
"European Molecular Genetics Quality Network, EMQN",
|
|
"European Research Network for the Evaluation and Improvement of Screening Diagnosis and Treatment of Inherited Metabolic Disorders - External Quality Assessment Schemes, ERNDIM EQAS",
|
|
"External Quality Assessment for Molecular Genetic Testing for Phenylketonuria, EQA-PKU",
|
|
"Human Genetic Society of Australasia, HGSA",
|
|
"Institute for Standardization and Documentation in the Medical Laboratory, INSTAND",
|
|
"Pacific Northwest Regional Genetics Group, PacNoRGG",
|
|
"Society for Inherited Metabolic Disorders, SIMD"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForMethodDescription"
|
|
]
|
|
},
|
|
<span class="quotedn">"not"</span>: {
|
|
<span class="quotedn">"anyOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"method",
|
|
"otherMethod"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"provider",
|
|
"otherProvider"
|
|
]
|
|
}
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"methodDescription"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"searchTerms"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Keywords by which users can search for the test."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"specimen"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Specimen sample allowed for the test."</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"otherSource"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"sources"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Specimen sample source, from enum list"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Amniocytes",
|
|
"Amniotic fluid",
|
|
"Bone marrow",
|
|
"Buccal swab",
|
|
"Buffy coat",
|
|
"Cell culture",
|
|
"Cell-free DNA",
|
|
"Cerebrospinal fluid",
|
|
"Chorionic villi",
|
|
"Cord blood",
|
|
"Cystic hygroma fluid",
|
|
"Dried blood spot (DBS) card",
|
|
"Fetal blood",
|
|
"Fibroblasts",
|
|
"Fresh tissue",
|
|
"Frozen tissue",
|
|
"Isolated DNA",
|
|
"Nasal aspirates",
|
|
"Nasopharyngeal washes",
|
|
"Oropharyngeal swab",
|
|
"Paraffin block",
|
|
"Peripheral (whole) blood",
|
|
"Plasma",
|
|
"Product of conception (POC)",
|
|
"Saliva",
|
|
"Serum",
|
|
"Skin",
|
|
"Sputum",
|
|
"Urine",
|
|
"White blood cell prep"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"url"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The URL at lab's website that describes specimen requirements and/or collection protocol."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
},
|
|
<span class="quotedn">"targetPopulation"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Segment(s) of the population that should be tested for the condition or phenotype and why."</span>
|
|
},
|
|
<span class="quotedn">"testAdditionalServices"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Additional test service offered in conjunction with the test."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"additionalService"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"additionalService"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If applicable, additional laboratory service from enum list."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Custom Prenatal Testing",
|
|
"Custom mutation-specific/Carrier testing"
|
|
]
|
|
},
|
|
<span class="quotedn">"comment"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Enter helpful information regarding the test service, such as how to request the service, limitations, etc."</span>
|
|
},
|
|
<span class="quotedn">"orderCode"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Order code for additional test service"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
}
|
|
},
|
|
<span class="quotedn">"testCodeURL"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The URL for information on codes (e.g. CPT, ICD-9, ICD-10)."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
},
|
|
<span class="quotedn">"testComment"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Optional textual description of the test."</span>
|
|
},
|
|
<span class="quotedn">"testContactPersons"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Lab person name in the format: first-name last-name. The lab person should be in the lab personnel list."</span>,
|
|
<span class="quotedn">"minLength"</span>: 1
|
|
}
|
|
},
|
|
<span class="quotedn">"testContactPolicies"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Laboratory policy regarding who may contact lab (e.g., patients and/or health care providers) and when during the testing process the laboratory will discuss tests with patients."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.",
|
|
"Post-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.",
|
|
"Pre-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families."
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"testDevelopment"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Information about how the test is developed."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"FDA-reviewed (has FDA test name)",
|
|
"Manufactured (research use only; not FDA-reviewed)",
|
|
"Modified FDA (has FDA-reviewed entry, but with lab modifications/field changes)",
|
|
"Test developed by laboratory (no manufacturer test name)"
|
|
]
|
|
},
|
|
<span class="quotedn">"testingStrategy"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Description of the clinical testing strategy, not the test procedure; can include prior testing requirements"</span>
|
|
},
|
|
<span class="quotedn">"testOrderCode"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The test order code, commonly found on the laboratory's requisition form, test menu or test catalog."</span>
|
|
},
|
|
<span class="quotedn">"testPerformanceLocations"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Locations for test performance."</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Entire test performed in-house",
|
|
"Interpretation performed at an outside lab",
|
|
"Interpretation performed both in-house and at an outside lab",
|
|
"Interpretation performed in-house",
|
|
"Report generated at an outside lab",
|
|
"Report generated both in-house and at an outside lab",
|
|
"Report generated in-house",
|
|
"Specimen preparation performed at an outside lab",
|
|
"Specimen preparation performed both in-house and at an outside lab",
|
|
"Specimen preparation performed in-house",
|
|
"Wet lab work performed at an outside lab",
|
|
"Wet lab work performed both in-house and at an outside lab",
|
|
"Wet lab work performed in-house"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"testProcedureOrProtocol"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Summary of the methodology, including specific steps for each method used in the assay."</span>
|
|
},
|
|
<span class="quotedn">"testPurposes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Purpose of the test"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Diagnosis",
|
|
"Drug Response",
|
|
"Monitoring",
|
|
"Mutation Confirmation",
|
|
"Pre-implantation genetic diagnosis",
|
|
"Pre-symptomatic",
|
|
"Predictive",
|
|
"Prognostic",
|
|
"Recurrence",
|
|
"Risk Assessment",
|
|
"Screening",
|
|
"Therapeutic management"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"testResultsConfirmation"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Information about whether results are confirmed and if so, how."</span>
|
|
},
|
|
<span class="quotedn">"testServices"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"comment"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Helpful information regarding the test service, e.g. how to request the service"</span>
|
|
},
|
|
<span class="quotedn">"orderCode"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Order code for test service"</span>
|
|
},
|
|
<span class="quotedn">"otherService"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if test service is not in the enum list."</span>
|
|
},
|
|
<span class="quotedn">"testService"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Laboratory service that is offered in conjunction with the test, from enum list"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Clinical Testing/Confirmation of Mutations Identified Previously",
|
|
"Confirmation of research findings",
|
|
"Custom Balanced Chromosome Rearrangement Studies",
|
|
"Custom Deletion/Duplication Testing",
|
|
"Custom Sequence Analysis",
|
|
"Data Storage and Backup",
|
|
"Genetic counseling",
|
|
"Identity Testing",
|
|
"Marker Chromosome Identification",
|
|
"Maternal cell contamination study (MCC)",
|
|
"Preimplantation Genetic Diagnosis (PGD)",
|
|
"Result interpretation",
|
|
"Specimen Source Identification",
|
|
"Uniparental Disomy (UPD) Testing",
|
|
"X-Chromosome Inactivation Studies"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"testService"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherService"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"testTargetsAssociated"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Category describing the condition(s)/phenotype(s) associated with the test target(s) in the test"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"conditionsOrPhenotypes",
|
|
"origins",
|
|
"targetsTested"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"conditionsOrPhenotypes"</span>: {
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/humanTestConditionsOrPhenotypes"</span>
|
|
},
|
|
<span class="quotedn">"origins"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"For a given condition or phenotype, whether the test target is germline or somatic or both."</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Germline",
|
|
"Somatic"
|
|
]
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"targetsTested"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The analytes, chromosomal or mitochondrial regions, genes and variations, or proteins that are measured in the test."</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"analytes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Name of analyte"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"chromosomalRegionOrMitochondrions"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Chromosomal region/mitochondrion (for example, '11q15' or 'm.7446-m.7514')"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"genes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Gene, example, 'CDKN2A' or 'CFTR'"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"geneWithRefSeqAndExons"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Relevant reference sequences and exons for each associated reference sequence."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"gene",
|
|
"refSeq"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"exons"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"For exon range, example 3, 5, 9-12; f the range includes all exons, add (All), example 1-5 (All); if a subset is tested, enumerate the exons tested."</span>
|
|
},
|
|
<span class="quotedn">"gene"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Gene, example, 'CDKN2A' or 'CFTR'"</span>
|
|
},
|
|
<span class="quotedn">"refSeq"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Associated reference sequence."</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
}
|
|
},
|
|
<span class="quotedn">"geneWithVariants"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Relevant gene variant; format is HGVS expression (preferred), or the allele name."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"gene",
|
|
"variant"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"citationsForClinicalSignificance"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations used to support the clinical significance of the variant; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"gene"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Gene, example, 'CDKN2A' or 'CFTR'"</span>
|
|
},
|
|
<span class="quotedn">"variant"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"variantClinicalSignificance"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value for clinical significance of variant from enum list"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/clinicalSignificanceEnum"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForClinicalSignificance"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"variantClinicalSignificance"
|
|
]
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"proteins"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Protein; example, 'Hemoglobin subunit beta' or 'Adenomatous polyposis coli protein'"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"analytes"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"chromosomalRegionOrMitochondrions"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"genes"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"proteins"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"geneWithVariants"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"geneWithRefSeqAndExons"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
}
|
|
},
|
|
<span class="quotedn">"testTargetUnassociated"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Category describing condition(s)/phenotype(s) and/or test target(s) that are not associated"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"origins"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"conditionsOrPhenotypes"</span>: {
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/humanTestConditionsOrPhenotypes"</span>
|
|
},
|
|
<span class="quotedn">"origins"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"For a given condition or phenotype, whether the test target is germline or somatic or both."</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Germline",
|
|
"Somatic"
|
|
]
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"targetsTested"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The analytes, chromosomal or mitochondrial regions, genes and variations, or proteins that are measured in the test."</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"analytes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Name of analyte"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"chromosomalRegionOrMitochondrions"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Chromosomal region/mitochondrion (for example, '11q15' or 'm.7446-m.7514')"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"genes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Gene, example, 'CDKN2A' or 'CFTR'"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"geneWithRefSeqAndExons"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Relevant reference sequences and exons for each associated reference sequence."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"gene",
|
|
"refSeq"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"exons"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"For exon range, example 3, 5, 9-12; f the range includes all exons, add (All), example 1-5 (All); if a subset is tested, enumerate the exons tested."</span>
|
|
},
|
|
<span class="quotedn">"gene"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Gene, example, 'CDKN2A' or 'CFTR'"</span>
|
|
},
|
|
<span class="quotedn">"refSeq"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Associated reference sequence."</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
}
|
|
},
|
|
<span class="quotedn">"geneWithVariants"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Relevant gene variant; format is HGVS expression (preferred), or the allele name."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"gene",
|
|
"variant"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"citationsForClinicalSignificance"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations used to support the clinical significance of the variant; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"gene"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Gene, example, 'CDKN2A' or 'CFTR'"</span>
|
|
},
|
|
<span class="quotedn">"variant"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"variantClinicalSignificance"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value for clinical significance of variant from enum list"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/clinicalSignificanceEnum"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForClinicalSignificance"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"variantClinicalSignificance"
|
|
]
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"proteins"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Protein; example, 'Hemoglobin subunit beta' or 'Adenomatous polyposis coli protein'"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"anyOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"analytes"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"chromosomalRegionOrMitochondrions"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"genes"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"proteins"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"geneWithVariants"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"geneWithRefSeqAndExons"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"anyOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"conditionsOrPhenotypes"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"targetsTested"
|
|
]
|
|
}
|
|
]
|
|
},
|
|
<span class="quotedn">"testURL"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The URL for the test."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
},
|
|
<span class="quotedn">"vus"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Variant of Unknown Significance"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"areFamilyMembersRecruitedWithoutCharge"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Whether the lab offers testing for a variant of unknown significance to family members free of charge; for example, to affected individuals and/or presumed obligate carriers to help determine clinical significance of a VUS."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Not provided",
|
|
"Yes",
|
|
"No",
|
|
"Decline to answer"
|
|
]
|
|
},
|
|
<span class="quotedn">"commentsAboutRecontactingOrderingPhysican"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"An explanation about how the lab monitors and addresses reinterpretation of genetic tests results over time, after issuing the report; for example, time limit if any, whether the laboratory systematically re-evaluates prior interpretations and generate new reports, or whether the person ordering the test needs to periodically recontact the laboratory to inquire about changes in test interpretation."</span>
|
|
},
|
|
<span class="quotedn">"commentsAboutRecruitingFamilyMembers"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Explanation of who is eligible to testing free of charge and how the lab does it; for example, is the testing offered to affected individuals and/or presumed obligate carriers to help determine clinical significance of a VUS."</span>
|
|
},
|
|
<span class="quotedn">"labPolicyOnReportingNovelVariations"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"A description of how the lab reports novel variations."</span>
|
|
},
|
|
<span class="quotedn">"protocolForInterpretingVariationAsVUS"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Method used by the lab to interpret a variation as VUS."</span>
|
|
},
|
|
<span class="quotedn">"researchPerformedAfterClinicalTestingIsComplete"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"An explanation or information about any research testing being performed using the submitted sample; for example, research testing is allowed under IRB approved protocols or the patient would have to sign an informed consent for the research protocol; if the protocol is registered in clinicaltials.gov, you can enter that information here."</span>
|
|
},
|
|
<span class="quotedn">"softwareUsedToInterpretNovelVariations"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Software used by the lab to interpret novel variations."</span>
|
|
},
|
|
<span class="quotedn">"willLabRecontactOrderingPhysicanIfVariantInterpretationChanges"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Whether the lab contacts the ordering physician after testing and initial report, if a variant interpretation changes."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Not provided",
|
|
"Yes",
|
|
"No",
|
|
"Decline to answer"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
},
|
|
<span class="quotedn">"whoCanOrder"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"One or more types of individuals able to order the test."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Genetic Counselor",
|
|
"Health Care Provider",
|
|
"In-State Patients",
|
|
"Licensed Dentist",
|
|
"Licensed Physician",
|
|
"Nurse Practitioner",
|
|
"Out-of-State Patients",
|
|
"Physician Assistant",
|
|
"Public Health Mandate",
|
|
"Registered Nurse"
|
|
]
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"allOf"</span>: [
|
|
{
|
|
<span class="quotedn">"else"</span>: {
|
|
<span class="quotedn">"not"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"gtrAccession"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"action"</span>: {
|
|
<span class="quotedn">"const"</span>: <span class="quotedv">"update"</span>
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"gtrAccession"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForTargetPopulation"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"targetPopulation"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForTestingStrategy"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"testingStrategy"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForTestProcedureOrProtocol"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"testProcedureOrProtocol"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForAnalyticalValidity"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"analyticalValidity"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForClinicalValidity"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"clinicalValidity"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForAssayLimitations"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"assayLimitations"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForInternalTestValidationMethod"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"internalTestValidationMethod"
|
|
]
|
|
}
|
|
}
|
|
]
|
|
},
|
|
<span class="quotedn">"microbeTest"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Add or update a clinical microbe test."</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"action",
|
|
"labTestName",
|
|
"testPurposes",
|
|
"testPerformanceLocations",
|
|
"methods",
|
|
"analyticalValidity",
|
|
"testTargets",
|
|
"conditionsOrPhenotypes"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"action"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Specify to add a new test or update an existing test."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"add",
|
|
"update"
|
|
]
|
|
},
|
|
<span class="quotedn">"analyticalValidity"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Quantitative information about analytical sensitivity, analytical specificity, accuracy, and/or precision of this test."</span>
|
|
},
|
|
<span class="quotedn">"assayLimitations"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Test limitations that affect the value of the test for its intended use, such as the limit of detection and test restrictions."</span>
|
|
},
|
|
<span class="quotedn">"caps"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Set of mjaor category, sub-category and test code to specify, if College of American Pathologists (CAP) is chosen as Provider for proficiency testing"</span>,
|
|
<span class="quotedn">"minItems"</span>: 0,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"capCategory"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Relevant sub-category, if major CAP category is selected."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/capCategoryEnum"</span>
|
|
},
|
|
<span class="quotedn">"capTest"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Relevant test code, if major CAP category is selected."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/capTestEnum"</span>
|
|
},
|
|
<span class="quotedn">"majorCapCategory"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Category to specify, if College of American Pathologists (CAP) is chosen as Provider for proficiency testing"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/majorCapCategoryEnum"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"citationsForAnalyticalValidity"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations supporting the analytical validity statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForAssayLimitations"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations supporting the assay limitation statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForClinicalValidity"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations used to evaluate the clinical validity of the test; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForInternalTestValidationMethod"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations to support internal test validation method statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForMinimalMicrobeLoadTestCanDetect"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations supporting the minimal microbial load s statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForPPVAndNPV"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations used to evaluate PPV/NPV of the test; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForTargetPopulation"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations supporting statements provided in 'Target population for this test'; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForTestingStrategy"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations for the testing strategy/algorithm; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"citationsForTestProcedureOrProtocol"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations supporting the test protocol; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"clinicalUtilities"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Likelihood of the test is to significantly improve patient outcomes."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"category"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Clinical utility category value"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Avoidance of invasive testing",
|
|
"Establish or confirm diagnosis",
|
|
"Guidance for management",
|
|
"Guidance for selecting a drug therapy and/or dose",
|
|
"Lifestyle planning",
|
|
"Sufficient research has not been conducted to demonstrate the utility of the test"
|
|
]
|
|
},
|
|
<span class="quotedn">"citations"</span>: {
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"otherCategory"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if category is not in the enum list."</span>
|
|
},
|
|
<span class="quotedn">"url"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The URL to display references to support a clinical utility choice."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"allOf"</span>: [
|
|
{
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"category"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherCategory"
|
|
]
|
|
}
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"anyOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"url"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"citations"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"clinicalValidity"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"A measure of how consistently and accurately the test detects or predicts the intermediate or final outcomes of interest. Clinical sensitivity and specificity, description of the population(s) assessed, and the number of specimens are used to calculate clinical validity."</span>
|
|
},
|
|
<span class="quotedn">"commentForTestPerformanceLocation"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If any part of the test is performed externally, describe here which part(s) and where part(s) are performed."</span>
|
|
},
|
|
<span class="quotedn">"commentsAboutTestInterpretation"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"conditionsOrPhenotypes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The condition or phenotype relevant to the eligibility criteria and/or study aims for the test, provided as either a database identifier or a name."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"type"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Infectious disease",
|
|
"disease",
|
|
"pharmacological response"
|
|
]
|
|
},
|
|
<span class="quotedn">"acronyms"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Your laboratory's preferred acronym for the condition."</span>,
|
|
<span class="quotedn">"minItems"</span>: 0,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"citationsForPrevalence"</span>: {
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"id"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"labPreferredAcronym"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The acronym for the condition or phenotype that is referred to by the laboratory."</span>
|
|
},
|
|
<span class="quotedn">"labPreferredName"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The preferred name of the condition or phenotype that is referred to by the laboratory."</span>
|
|
},
|
|
<span class="quotedn">"name"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Name of condition or phenotype."</span>
|
|
},
|
|
<span class="quotedn">"ontologyDb"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Databases supporting the classification and standardized nomenclature and coding of human conditions and phenotypes with a genetic basis: OMIM - Online Mendelian Inheritance in Man\u00ae; MedGen - Medical Genetics resource (National Center for Biotechnology Information; NCBI); HPO - Human Phenotype Ontology (The Jackson Laboratory); Orphanet (Orphanet / INSERM); MeSH - Medical Subject Headings (NCBI); MONDO (EMBL - EBI); select from enum list."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"OMIM",
|
|
"MedGen",
|
|
"HPO",
|
|
"Orphanet",
|
|
"MeSH",
|
|
"MONDO"
|
|
]
|
|
},
|
|
<span class="quotedn">"prevalenceDescription"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Prevalence or the most current estimated number of cases of the disease in the population."</span>
|
|
},
|
|
<span class="quotedn">"prevalenceURL"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"URL for prevalence claim."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
},
|
|
<span class="quotedn">"synonyms"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The synonym of the condition or phenotype."</span>,
|
|
<span class="quotedn">"minItems"</span>: 0,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"allOf"</span>: [
|
|
{
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"ontologyDb",
|
|
"id"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"name"
|
|
]
|
|
}
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"dependencies"</span>: {
|
|
<span class="quotedn">"id"</span>: [
|
|
"ontologyDb"
|
|
],
|
|
<span class="quotedn">"ontologyDb"</span>: [
|
|
"id"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForPrevalence"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"prevalenceDescription"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"prevalenceURL"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"prevalenceDescription"
|
|
]
|
|
}
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"cptCodes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Molecular pathology Current Procedural Terminology (CPT\u00ae) code - 'MoPath' code - from the American Medical Association (AMA) that describes the test."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"fdaReviews"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Has the test been reviewed by the FDA?"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"fdaApplicationNumber"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If FDA reviewed, FDA application number."</span>
|
|
},
|
|
<span class="quotedn">"noReviewCategoryDesignation"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If no FDA review, specify FDA category designation"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"EUA - Emergency Use Authorization",
|
|
"FDA exercises enforcement discretion",
|
|
"Not Applicable"
|
|
]
|
|
},
|
|
<span class="quotedn">"otherRegulatoryStatus"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If fdaRegulatoryStatus value is not in the status enum list, please specify."</span>
|
|
},
|
|
<span class="quotedn">"otherReviewItem"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If FDA reviewed item is not in the item enum list, please specify."</span>
|
|
},
|
|
<span class="quotedn">"regulatoryStatus"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If FDA reviewed, FDA regulatory status from enum list."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"FDA cleared/approved",
|
|
"FDA exempt",
|
|
"Not submitted",
|
|
"Pending"
|
|
]
|
|
},
|
|
<span class="quotedn">"reviewCategoryDesignation"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If FDA review, specify FDA category designation"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"IUO - Investigational Use Only. The performance characteristics of this product have not been established.",
|
|
"IVD - In Vitro Device.",
|
|
"RUO - Research Use Only. Not for use in diagnostic procedures."
|
|
]
|
|
},
|
|
<span class="quotedn">"reviewed"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"boolean"</span>
|
|
},
|
|
<span class="quotedn">"reviewItem"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If FDA reviewed, item under reviewed."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"ASR - Analyte Specific Reagent(s)",
|
|
"Assay(s)",
|
|
"IVDMIA - In Vitro Diagnostic Multivariate Index Assay(s)",
|
|
"Instrument(s)",
|
|
"Test kit(s)"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"reviewed"</span>: {
|
|
<span class="quotedn">"const"</span>: true
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"not"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"reviewCategoryDesignation",
|
|
"noReviewCategoryDesignation"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"allOf"</span>: [
|
|
{
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"reviewItem"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherReviewItem"
|
|
]
|
|
}
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"regulatoryStatus"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherRegulatoryStatus"
|
|
]
|
|
}
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"reviewCategoryDesignation"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"gtrAccession"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"If this test has been registered previously in the GTR, enter the GTR accession number here. This is required for update."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/gtrAccessionType"</span>
|
|
},
|
|
<span class="quotedn">"howLongMicrobePresentAfterTherapy"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"howToOrder"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Description of the test ordering procedure."</span>
|
|
},
|
|
<span class="quotedn">"informedConsentRequired"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Whether the lab reqires informed consent prior to performing the test."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Decline to answer",
|
|
"Required",
|
|
"Not required",
|
|
"Based on applicable state law"
|
|
]
|
|
},
|
|
<span class="quotedn">"internalTestValidationMethod"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Explanation of how the lab validates the test."</span>
|
|
},
|
|
<span class="quotedn">"labTestName"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The name of the test to be displayed in GTR."</span>
|
|
},
|
|
<span class="quotedn">"labTestShortName"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Shortened name or mneumonic used by the lab to identify the test."</span>
|
|
},
|
|
<span class="quotedn">"loincCodes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Logical Observation Identifiers Names and Codes."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"manufactureTestName"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The manufacturer's name for the test, if a commercial test or kit was used."</span>
|
|
},
|
|
<span class="quotedn">"methods"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Set of method category and primary methodology used in the test; the major method categories for the test which will be inferred from the methodCategory are: (1) Molecular Genetics, and (2) Serology"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"instruments"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Instrument(s) used for the method."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"name"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Name of instrument used."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/microbeTestInstrumentEnum"</span>
|
|
},
|
|
<span class="quotedn">"otherInstrument"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if instrument used is not in the instrument enum list."</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"name"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherInstrument"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"method"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Primary methodology for the test"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/microbeTestMethodEnum"</span>
|
|
},
|
|
<span class="quotedn">"methodCategory"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"General category to which the test method belongs"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/microbeTestMethodCategoryEnum"</span>
|
|
},
|
|
<span class="quotedn">"otherMethod"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if method is not in the method enum list."</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"allOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"methodCategory"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"method"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherMethod"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"minimalMicrobeLoadTestCanDetect"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Limit of detection or the microbe load below which the test cannot reliably detect the microbe; e.g., viral loads < 20 copies/ml cannot be reliably detected and will be reported as 'below the limit of detection')."</span>
|
|
},
|
|
<span class="quotedn">"nysClep"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"NYS Clinical Laboratory Evaluation Program"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"status"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"NYS CLEP status"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Approved",
|
|
"Exempt",
|
|
"Grandfathered",
|
|
"Pending"
|
|
]
|
|
},
|
|
<span class="quotedn">"testApprovalNumber"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"NYS CLEP test approval number"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
},
|
|
<span class="quotedn">"orderURL"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The URL for ordering the test."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
},
|
|
<span class="quotedn">"platforms"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The platform used for the test, usually a commercial product (catalog number or set of numbers) with pre-defined test targets used in the test."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"name"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Name of commercial platform or kit with predefined test targets."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/microbeTestPlatformEnum"</span>
|
|
},
|
|
<span class="quotedn">"otherPlatform"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if platform used is not in the enum list."</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"name"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherPlatform"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"positiveAndNegativePredictiveValuesOrPPVAndNPV"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Positive Predictive Value (PPV) is the probability of true disease when the result is positive. Negative Predictive Value (NPV) is the probability of no disease when the result is negative"</span>
|
|
},
|
|
<span class="quotedn">"proficiencyTesting"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Periodic internal or external evaluation of the test to corroborate the accuracy of test results."</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"citationsForMethodDescription"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations to support the proficiency testing method statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)"</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"method"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The type of proficiency testing that is performed, from enum list. "</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Alternative Assessment",
|
|
"Formal PT program",
|
|
"Inter-Laboratory",
|
|
"Intra-Laboratory"
|
|
]
|
|
},
|
|
<span class="quotedn">"methodDescription"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"A description of the proficiency testing method used."</span>
|
|
},
|
|
<span class="quotedn">"otherMethod"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if method is not in the method enum list."</span>
|
|
},
|
|
<span class="quotedn">"otherProvider"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if provider is not in the provider enum list."</span>
|
|
},
|
|
<span class="quotedn">"provider"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"American College of Physicians - Medical Laboratory Evaluation, ACP MLE",
|
|
"Association for Molecular Pathology, AMP",
|
|
"Belgian Official EKE Schemes, GLP Monitoring Programme",
|
|
"Canadian External Quality Assessment Laboratory, CEQAL",
|
|
"Centers for Disease Control and Prevention Newborn Screening Quality Assurance Program, CDC DLS",
|
|
"Clinical Pathology Accreditation (UK) Ltd., CPA",
|
|
"College of American Pathologists, CAP",
|
|
"European Concerted Action on Thrombosis External Quality Assessment Program, ECAT EQAP",
|
|
"European Molecular Genetics Quality Network, EMQN",
|
|
"European Research Network for the Evaluation and Improvement of Screening Diagnosis and Treatment of Inherited Metabolic Disorders - External Quality Assessment Schemes, ERNDIM EQAS",
|
|
"External Quality Assessment for Molecular Genetic Testing for Phenylketonuria, EQA-PKU",
|
|
"Human Genetic Society of Australasia, HGSA",
|
|
"Institute for Standardization and Documentation in the Medical Laboratory, INSTAND",
|
|
"Pacific Northwest Regional Genetics Group, PacNoRGG",
|
|
"Society for Inherited Metabolic Disorders, SIMD"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForMethodDescription"
|
|
]
|
|
},
|
|
<span class="quotedn">"not"</span>: {
|
|
<span class="quotedn">"anyOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"method",
|
|
"otherMethod"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"provider",
|
|
"otherProvider"
|
|
]
|
|
}
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"methodDescription"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"researchPerformedAfterClinicalTestingIsComplete"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"sampleRequirement"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Instructions for proper processing of the sample, including collection, sample container, volume, storage, temperature, causes for rejection, days that samples may or may not be received."</span>
|
|
},
|
|
<span class="quotedn">"searchTerms"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Keywords by which users can search for the test."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"specimen"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Specimen sample allowed for the test."</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"otherSource"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if specimen source is not in the provider enum list"</span>
|
|
},
|
|
<span class="quotedn">"sources"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Specimen sample source, from enum list"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Amniotic fluid",
|
|
"Bone marrow",
|
|
"Bronchoalveolar lavage",
|
|
"Buccal swab",
|
|
"Buffy coat",
|
|
"Cell culture",
|
|
"Cerebrospinal fluid",
|
|
"Chorionic villi",
|
|
"Cord blood",
|
|
"Fetal blood",
|
|
"Fresh tissue",
|
|
"Frozen tissue",
|
|
"Nasal aspirates",
|
|
"Nasal swab",
|
|
"Nasopharyngeal (NP) swab",
|
|
"Nasopharyngeal washes",
|
|
"Oropharyngeal swab",
|
|
"Paraffin block",
|
|
"Peripheral (whole) blood",
|
|
"Plasma",
|
|
"Product of conception (POC)",
|
|
"Saliva",
|
|
"Serum",
|
|
"Skin",
|
|
"Sputum",
|
|
"Throat swab",
|
|
"Urine",
|
|
"White blood cell prep"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"url"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The URL at lab's website that describes specimen requirements and/or collection protocol."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
},
|
|
<span class="quotedn">"targetPopulation"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Segment(s) of the population that should be tested for the condition or phenotype and why."</span>
|
|
},
|
|
<span class="quotedn">"testCodeURL"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The URL for information on codes (e.g. CPT, ICD-9, ICD-10)."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
},
|
|
<span class="quotedn">"testComment"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Optional textual description of the test."</span>
|
|
},
|
|
<span class="quotedn">"testContactPersons"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Lab person name in the format: first-name last-name. The lab person should be in the lab personnel list."</span>,
|
|
<span class="quotedn">"minLength"</span>: 1
|
|
}
|
|
},
|
|
<span class="quotedn">"testContactPolicies"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Laboratory policy regarding who may contact lab (e.g., patients and/or health care providers) and when during the testing process the laboratory will discuss tests with patients."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss testing options with their health care provider.",
|
|
"Post-test email/phone consultation regarding test results and interpretation is provided to patients/families.",
|
|
"Pre-test email/phone consultation regarding test results and interpretation is provided to patients/families."
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"testDevelopment"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Information about how the test is developed."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"FDA-reviewed (has FDA test name)",
|
|
"Manufactured (research use only; not FDA-reviewed)",
|
|
"Modified FDA (has FDA-reviewed entry, but with lab modifications/field changes)",
|
|
"Test developed by laboratory (no manufacturer test name)"
|
|
]
|
|
},
|
|
<span class="quotedn">"testingStrategy"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Description of the clinical testing strategy, not the test procedure; can include prior testing requirements"</span>
|
|
},
|
|
<span class="quotedn">"testOrderCode"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The test order code, commonly found on the laboratory's requisition form, test menu or test catalog."</span>
|
|
},
|
|
<span class="quotedn">"testPerformanceLocations"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Locations for test performance."</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Entire test performed in-house",
|
|
"Interpretation performed at an outside lab",
|
|
"Interpretation performed both in-house and at an outside lab",
|
|
"Interpretation performed in-house",
|
|
"Report generated at an outside lab",
|
|
"Report generated both in-house and at an outside lab",
|
|
"Report generated in-house",
|
|
"Specimen preparation performed at an outside lab",
|
|
"Specimen preparation performed both in-house and at an outside lab",
|
|
"Specimen preparation performed in-house",
|
|
"Wet lab work performed at an outside lab",
|
|
"Wet lab work performed both in-house and at an outside lab",
|
|
"Wet lab work performed in-house"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"testProcedureOrProtocol"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Summary of the methodology, including specific steps for each method used in the assay."</span>
|
|
},
|
|
<span class="quotedn">"testPurposes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Purpose of the test."</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Diagnosis",
|
|
"Drug Response",
|
|
"Microbe identification",
|
|
"Monitoring",
|
|
"Predictive",
|
|
"Recurrence",
|
|
"Screening",
|
|
"Therapeutic management",
|
|
"Viral load"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"testResultsConfirmation"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Information about whether results are confirmed and if so, how."</span>
|
|
},
|
|
<span class="quotedn">"testServices"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Laboratory service that is offered in conjunction with the test, from enum list"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"comment"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Helpful information regarding the test service, e.g., how to request the service."</span>
|
|
},
|
|
<span class="quotedn">"orderCode"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Order code for test service"</span>
|
|
},
|
|
<span class="quotedn">"otherService"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if test service is not in the enum list"</span>
|
|
},
|
|
<span class="quotedn">"testService"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Data Storage and Backup",
|
|
"Result interpretation"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"testService"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"otherService"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"testTargets"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The microorganism(s) and their genes, variants, proteins, analytes, and/or extrachromosomal or nucleic acid sequences that are measured in the test."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"microbeType",
|
|
"organism"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"analytes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Microbial analyte(s) measured in the test."</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"chromosomalRegionOrMitochondrions"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Microbial chromosomal region, mitochondrion, extrachromosomal elements, and/or nucleic acid sequences measured in the test."</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"genes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Microbial gene(s) measured in the test."</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"microbeType"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Type of microorganism, from the enum list."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"bacterium",
|
|
"fungus",
|
|
"microbe",
|
|
"protozoan",
|
|
"virus"
|
|
]
|
|
},
|
|
<span class="quotedn">"organism"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Name of the microorganism."</span>
|
|
},
|
|
<span class="quotedn">"proteins"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Microbial protein(s) measured in the test."</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"variants"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Microbial gene variant(s) measured in the test."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"genes",
|
|
"variant"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"genes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"variant"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"anyOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"genes"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"variants"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"analytes"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"chromosomalRegionOrMitochondrions"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"proteins"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"testURL"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The URL for the test."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
},
|
|
<span class="quotedn">"turnaroundTime"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The usual number of hours or days between the time a specimen is received and a result is released. Specify the time unit (e.g. 2-3 days)."</span>
|
|
},
|
|
<span class="quotedn">"whoCanOrder"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"One or more types of individuals who are able to order the test."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Genetic Counselor",
|
|
"Health Care Provider",
|
|
"In-State Patients",
|
|
"Licensed Dentist",
|
|
"Licensed Physician",
|
|
"Nurse Practitioner",
|
|
"Out-of-State Patients",
|
|
"Physician Assistant",
|
|
"Public Health Mandate",
|
|
"Registered Nurse"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"zCode"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Z-Code Identifier for this test. 5-character alpha-numeric code associated with certain molecular diagnostics (MDx) tests used in addition to the CPT code, to help payers and providers clearly understand which test is being ordered, performed, and billed."</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"allOf"</span>: [
|
|
{
|
|
<span class="quotedn">"else"</span>: {
|
|
<span class="quotedn">"not"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"gtrAccession"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"action"</span>: {
|
|
<span class="quotedn">"const"</span>: <span class="quotedv">"update"</span>
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"gtrAccession"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForTargetPopulation"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"targetPopulation"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForTestingStrategy"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"testingStrategy"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForTestProcedureOrProtocol"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"testProcedureOrProtocol"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForAnalyticalValidity"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"analyticalValidity"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForClinicalValidity"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"clinicalValidity"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForAssayLimitations"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"assayLimitations"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForInternalTestValidationMethod"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"internalTestValidationMethod"
|
|
]
|
|
}
|
|
}
|
|
]
|
|
},
|
|
<span class="quotedn">"testDeletion"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Delete a previously registered human clinical test or clinical microbe test."</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"gtrAccession"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"gtrAccession"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The GTR test accession number to be deleted."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/gtrAccessionType"</span>
|
|
},
|
|
<span class="quotedn">"reason"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Reason for deleting the test."</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
}
|
|
},
|
|
<span class="quotedn">"$id"</span>: <span class="quotedv">"https://submit.ncbi.nlm.nih.gov/gtr/v0.0.1/test.schema.json"</span>,
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"definitions"</span>: {
|
|
<span class="quotedn">"capCategoryEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"10q (PTEN) deletion",
|
|
"ABO grouping",
|
|
"ABO subgroup typing",
|
|
"Acid-fast smear",
|
|
"Acylcarnitines, qualitative and quantitative",
|
|
"Adenovirus",
|
|
"Adenovirus (Not 40/41) antigen",
|
|
"Adenovirus 40/41",
|
|
"Adenovirus antigen",
|
|
"Adenovirus viral load",
|
|
"Adrenocorticotropic hormone (ACTH)",
|
|
"Allele detection (genotype)",
|
|
"Alpha-1 antitrypsin",
|
|
"Alpha-1 antitrypsin genotyping",
|
|
"Alpha-thalassemia",
|
|
"Amino acids, qualitative and quantitative",
|
|
"Anti-A titer",
|
|
"Anti-B titer",
|
|
"Anti-D titer",
|
|
"Anti-DNA antibody (ds)",
|
|
"Anti-Jo-1 (antihistidyl t-RNA synthetase)",
|
|
"Anti-LKM",
|
|
"Anti-RNP antibody",
|
|
"Anti-SSA antibody",
|
|
"Anti-SSA/SSB antibody",
|
|
"Anti-SSB antibody",
|
|
"Anti-Saccharomyces cerevisiae antibody, IgG and IgA",
|
|
"Anti-Scl-70 (anti-DNA topoisomerase)",
|
|
"Anti-Sm antibody",
|
|
"Anti-Sm/RNP antibody",
|
|
"Antibodies to tick-transmitted disease organisms",
|
|
"Antibody detection",
|
|
"Antibody identification",
|
|
"Anticardiolipin antibody",
|
|
"Anticentromere antibody",
|
|
"Antichromatin antibody",
|
|
"Antifilamentous actin (f-acting) IgG antibody",
|
|
"Antifungal susceptibility testing",
|
|
"Antigen detection (DFA)",
|
|
"Antigen detection (EIA)",
|
|
"Antiglomerular basement membrane (GBM), IgG antibody",
|
|
"Antihistone antibody",
|
|
"Antimicrobial susceptibility testing",
|
|
"Antimitochondrial antibody",
|
|
"Antimycobacterial susceptibility testing",
|
|
"Antineutrophil cytoplasmic antibody (ANCA, anti-MPO, anti-PR3)",
|
|
"Antinuclear antibody (ANA)",
|
|
"Antiparietal cell antibody",
|
|
"Antiphosphatidylserine antibody",
|
|
"Antiribosomal-P antibody",
|
|
"Antismooth muscle antibody",
|
|
"Antistreptolysin O (ASO)",
|
|
"Antithyroglobulin antibody",
|
|
"Antithyroid microsomal antibody",
|
|
"Antithyroid peroxidase antibody",
|
|
"Apolipoprotein E (APOE) genotyping",
|
|
"BCR/ABL1 p190",
|
|
"BCR/ABL1 p210",
|
|
"BK viral load",
|
|
"BK virus",
|
|
"BRAF",
|
|
"BRAF testing for HNPCC",
|
|
"BRCA1/2",
|
|
"Bacterial antigen detection",
|
|
"Bacterial identification",
|
|
"Bacterial vaginosis detection",
|
|
"Beta-2-glycoprotein I",
|
|
"Beta-2-microglobulin",
|
|
"Beta-thalassemia",
|
|
"Blood culture bacterial detection",
|
|
"Bloom syndrome",
|
|
"Bordetella parapertussis",
|
|
"Bordetella pertussis",
|
|
"Bordetella pertussis/parapertussis",
|
|
"Brain/Glioma Tissue: 1p/19q",
|
|
"Breast Cancer: HER2 gene amplification",
|
|
"C-reactive protein",
|
|
"C. difficile",
|
|
"CA 125",
|
|
"CA 15-3",
|
|
"CA 19-9",
|
|
"CA 27.29",
|
|
"CA 72-4",
|
|
"CD34+",
|
|
"CMA analysis for constitutional abnormality",
|
|
"CMV viral load",
|
|
"CYP2C19",
|
|
"CYP2C9",
|
|
"CYP2D6",
|
|
"CYP3A4",
|
|
"CYP3A5",
|
|
"Calcitonin",
|
|
"Campylobacter",
|
|
"Canavan",
|
|
"Candida sp.",
|
|
"Carnitine, qualitative and quantitative",
|
|
"Ceruloplasmin",
|
|
"Chlamydia trachomatis culture",
|
|
"Chromosome abnormality",
|
|
"Clostridium difficile toxin",
|
|
"Compatibility testing",
|
|
"Complement C3",
|
|
"Complement C4",
|
|
"Connexin 26",
|
|
"Coronavirus/Rhinovirus",
|
|
"Cryptococcal antigen detection",
|
|
"Cryptosporidium",
|
|
"Culture",
|
|
"Cystic fibrosis",
|
|
"Cytogenetics, validated material",
|
|
"Cytomegalovirus",
|
|
"Cytomegalovirus (CMV) - IgG, IgM and total antibodies",
|
|
"Cytomegalovirus antigen",
|
|
"DMD/Becker",
|
|
"DNA content and cell cycle analysis",
|
|
"DNA extraction and amplification from formalin-fixed, paraffin-embedded (FFPE) tissue",
|
|
"DNA sequence interpretation",
|
|
"DNA sequencing",
|
|
"EBV viral load",
|
|
"EGFR",
|
|
"Educational challenge",
|
|
"Educational challenge, ungraded",
|
|
"Educational paper challenge for constitutional or neoplastic abnormality",
|
|
"Electronic crossmatch",
|
|
"Entamoeba histolytica",
|
|
"Enterococcus",
|
|
"Enterotoxigenic E. coli (ETEC) LT/ST",
|
|
"Enterovirus",
|
|
"Epstein-Barr virus",
|
|
"Epstein-Barr virus (EBV)",
|
|
"Epstein-Barr virus (EBV) - VCA - IgG, IgM EBNA - IgG, IgM and total antibodies - EA - IgG",
|
|
"Escherichia coli 0157",
|
|
"FISH for constitutional abnormality",
|
|
"FISH for neoplastic disorder",
|
|
"FISH for urothelial carcinoma",
|
|
"Factor II",
|
|
"Factor V",
|
|
"Factor V Leiden",
|
|
"Familial dysautonomia",
|
|
"Fanconi anemia complementation group C",
|
|
"Fecal suspension (Giardia and/or Cryptosporidium immunoassay and mod. acid-fast stain)",
|
|
"Fecal suspension (wet mount)",
|
|
"Flow cytometry, interpretation only",
|
|
"Fragile X",
|
|
"Free beta hCG",
|
|
"Friedreich ataxia",
|
|
"GC culture",
|
|
"Galactomannan - Aspergillus",
|
|
"Gardnerella vaginalis",
|
|
"Gastrointestinal stromal tumor (GIST)",
|
|
"Gaucher",
|
|
"Giardia",
|
|
"Giemsa-stained blood smear",
|
|
"Glycogen storage disease type 1A",
|
|
"Glycosaminoglycans (mucopolysaccharides), qualitative and quantitative",
|
|
"Gram stain",
|
|
"Gram-negative organisms",
|
|
"Gram-negative rods",
|
|
"Group A Streptococcus antigen detection",
|
|
"Group B Streptococcus detection",
|
|
"HBV viral load",
|
|
"HCV genotyping",
|
|
"HCV viral load",
|
|
"HCV, qualitative",
|
|
"HER2 (ERBB2) gene amplification (bright field)",
|
|
"HHV6 viral load",
|
|
"HIV genotyping",
|
|
"HIV-RNA viral load",
|
|
"HLA-B*5701",
|
|
"HLA-B27 typing",
|
|
"Haptoglobin",
|
|
"Helicobacter pylori antigen detection",
|
|
"Helicobacter pylori, IgG antibody",
|
|
"Helocobacter pylori - IgG, IgA and total antibodies",
|
|
"Hemochromatosis",
|
|
"Hemoglobin S/C",
|
|
"Herpes simplex virus",
|
|
"Herpes simplex virus (HSV) - IgG antibody",
|
|
"Herpes simplex virus (HSV) antigen",
|
|
"Human herpesvirus 6",
|
|
"Human herpesvirus 8",
|
|
"Human metapneumovirus",
|
|
"Human papillomavirus",
|
|
"Human papillomavirus (HPV)",
|
|
"Huntington",
|
|
"IDH1, IDH2",
|
|
"IL-10",
|
|
"IL-2",
|
|
"IL-6",
|
|
"IL-8",
|
|
"IL28B 9rs12979860)",
|
|
"Identification of gram-negative organisms",
|
|
"Identification of gram-positive organisms",
|
|
"IgA",
|
|
"IgA kappa",
|
|
"IgA kappa/lambda ratio and ratio interpretation",
|
|
"IgA lambda",
|
|
"IgD",
|
|
"IgE",
|
|
"IgG",
|
|
"IgG kappa",
|
|
"IgG kappa/lambda ratio and ratio interpretation",
|
|
"IgG lambda",
|
|
"IgG subclass",
|
|
"IgM",
|
|
"IgM kappa",
|
|
"IgM kappa/lambda ratio and ratio interpretation",
|
|
"IgM lambda",
|
|
"India Ink",
|
|
"Infectious mononucleosis",
|
|
"Influenza A",
|
|
"Influenza A antigen",
|
|
"Influenza B",
|
|
"Influenza B antigen",
|
|
"Influenza virus",
|
|
"Interferon (IFN)-gamma",
|
|
"Interleukin (IL)-1 beta",
|
|
"Interpretation",
|
|
"JC virus",
|
|
"KIT",
|
|
"KOH preparation/calcofluor white",
|
|
"KRAS",
|
|
"Kappa/Lambda (IGK/IGL)",
|
|
"Karyotype",
|
|
"Legionella pneumophila antigen detection",
|
|
"Legionella pneumophila/Chlamydophila pneumoniae",
|
|
"Leukemia/lymphoma",
|
|
"Live organisms",
|
|
"Lymphocyte immunophenotyping",
|
|
"Lymphoid malignancy genotyping: IGH",
|
|
"Lymphoid malignancy genotyping: IGH/BCL2 major",
|
|
"Lymphoid malignancy genotyping: IGH/BCL2 minor",
|
|
"Lymphoid malignancy genotyping: IGH/CCND1",
|
|
"Lymphoid malignancy genotyping: IGK",
|
|
"Lymphoid malignancy genotyping: TRB",
|
|
"Lymphoid malignancy genotyping: TRG",
|
|
"Lymphoma Tissue: BCL2",
|
|
"Lymphoma Tissue: BCL6 (3q27) gene rearrangement",
|
|
"Lymphoma Tissue: MALT1 (18q21) gene rearrangement",
|
|
"M. tuberculosis",
|
|
"MCAD",
|
|
"MECP2 genotyping",
|
|
"MGMT",
|
|
"MRSA/MSSA detection",
|
|
"Metastatic colorectal carcinoma",
|
|
"Methicillin-resistant Staphylococcus aureus",
|
|
"Methylene tetrahydrofolate reductase (MTHFR) 677C>T and 1298A>C",
|
|
"Microsatellite instability testing (DNA amplification)",
|
|
"Mitochondrial DNA deletion syndromes",
|
|
"Mitochondrial cytopathies",
|
|
"Mold and yeast identification",
|
|
"Molecular HLA-A, -B, and -C typing (Class I)",
|
|
"Molecular HLA-DR, -DQ, and -DP typing (Class II)",
|
|
"Molecular typing (bacterial isolates)",
|
|
"Mucolipidosis IV",
|
|
"Multiple endocrine neoplasia type 2 (MEN2)",
|
|
"Mumps - IgG",
|
|
"Mycobacterial culture",
|
|
"Mycobacterial identification",
|
|
"Mycobacterium tuberculosis",
|
|
"Mycobacterium tuberculosis detection",
|
|
"Mycoplasma pneumoniae",
|
|
"Mycoplasma pneumoniae - IgG, IgM and total antibodies",
|
|
"Myeloid malignancy genotyping: CBFB/MYH11",
|
|
"Myeloid malignancy genotyping: FLT3 ITD",
|
|
"Myeloid malignancy genotyping: FLT3 TKD",
|
|
"Myeloid malignancy genotyping: JAK2 c.1849G>T (p.V617F)",
|
|
"Myeloid malignancy genotyping: NPM1",
|
|
"Myeloid malignancy genotyping: PML/RARA",
|
|
"Myeloid malignancy genotyping: RUNX1/RUNX1T1",
|
|
"Myotonic dystrophy",
|
|
"Niemann-Pick disease type A",
|
|
"Non-small cell lung adenocarcinoma",
|
|
"Norovirus",
|
|
"Norovirus GI/GII",
|
|
"Nucleic acid amplification (NAA)",
|
|
"Online assessment of percent neoplastic cellularity",
|
|
"Organic acids, qualitative and quantitative",
|
|
"PAPP-A",
|
|
"PCP stain",
|
|
"PDGFRA",
|
|
"PML/RARA",
|
|
"Parainfluenza antigen",
|
|
"Parainfluenza virus",
|
|
"Parvovirus B19",
|
|
"Plasminogen activator inhibitor (PAI)-1",
|
|
"Prader-Willi/Angelman syndrome",
|
|
"Prealbumin (transthyretin)",
|
|
"Preserved slide (for permanent stain)",
|
|
"Prothrombin",
|
|
"Rapid group A Streptococcus antigen detection",
|
|
"Red blood cell antigen typing",
|
|
"Red cell antigen genotype with predictive phenotype",
|
|
"Respiratory syncytial virus (RSV)",
|
|
"Respiratory syncytial virus (RSV) antigen",
|
|
"Rh typing",
|
|
"RhD",
|
|
"Rheumatoid factor",
|
|
"Rhinovirus/Enterovirus",
|
|
"Rifampin resistance",
|
|
"Rotavirus",
|
|
"Rotavirus A",
|
|
"Rotavirus antigen",
|
|
"Rubella (IgG)",
|
|
"Rubeola virus (English measles) - IgG antibody",
|
|
"SLCO1B1",
|
|
"Salmonella",
|
|
"Sarcoma translocation (RT-PCR)",
|
|
"Serological detection of specific fungal antibodies",
|
|
"Shiga toxin",
|
|
"Shiga-like toxin producing E. coli (STEC) stx1/stx2",
|
|
"Shigella",
|
|
"Solid Tumor: DDIT3 (CHOP) (12q13) gene rearrangement",
|
|
"Solid Tumor: EWSR1 (22q12) gene rearrangement",
|
|
"Solid Tumor: FOXO1",
|
|
"Solid Tumor: MDM2",
|
|
"Spinal muscular atrophy",
|
|
"Spinocerebellar ataxia",
|
|
"Staphylococcus",
|
|
"Streptococcus pneumoniae antigen detection",
|
|
"Syphilis",
|
|
"Tay-Sachs",
|
|
"Thin/thick blood film sets",
|
|
"Throat culture",
|
|
"Thyroglobulin",
|
|
"Tick, mite and arthropod identification",
|
|
"Total hCG",
|
|
"Total kappa/lambda ratio",
|
|
"Toxoplasma gondii - IgG, IgM and total antibodies",
|
|
"Transferrin",
|
|
"Trichomonas vaginalis",
|
|
"Tumor necrosis factor (TNF)-alpha",
|
|
"UGT1A1",
|
|
"Urine culture",
|
|
"VKORC1",
|
|
"Vancomycin-resistant Enterococcus",
|
|
"Vancomycin-resistant Enterococcus (VRE) detection",
|
|
"Varicella-zoster antigen",
|
|
"Varicella-zoster virus",
|
|
"Varicella-zoster virus - IgG and total antibodies",
|
|
"Vascular endothelial growth factor (VEGF)",
|
|
"Viral isolation/identification",
|
|
"Worm identification",
|
|
"Yeast",
|
|
"Yeast identification",
|
|
"hCG, serum"
|
|
]
|
|
},
|
|
<span class="quotedn">"capTestEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"AAT",
|
|
"ABOSG",
|
|
"ABT",
|
|
"ABT1",
|
|
"ABT2",
|
|
"ABT3",
|
|
"ACA",
|
|
"ACL",
|
|
"AHT",
|
|
"ANA",
|
|
"APC",
|
|
"APOE",
|
|
"APS",
|
|
"ARP",
|
|
"ASC",
|
|
"ASO",
|
|
"B27",
|
|
"BCS",
|
|
"BGL",
|
|
"BGL1",
|
|
"BOR",
|
|
"BP",
|
|
"BRAF",
|
|
"BSTE",
|
|
"BSTN",
|
|
"BSTS",
|
|
"BV",
|
|
"CAMP",
|
|
"CDF2",
|
|
"CDF5",
|
|
"CRP",
|
|
"CTKN",
|
|
"CY",
|
|
"CYBK",
|
|
"CYCGH",
|
|
"CYF",
|
|
"CYH",
|
|
"CYI",
|
|
"CYJ",
|
|
"CYK",
|
|
"CYL",
|
|
"CYM",
|
|
"D",
|
|
"D5",
|
|
"D6",
|
|
"D8",
|
|
"D9",
|
|
"DEX",
|
|
"DL",
|
|
"DML",
|
|
"E",
|
|
"E1",
|
|
"EGFR",
|
|
"EXM",
|
|
"EXM2",
|
|
"F",
|
|
"F1",
|
|
"F3",
|
|
"FCN",
|
|
"FGAL",
|
|
"FL",
|
|
"FL1",
|
|
"FL2",
|
|
"FL3",
|
|
"FL4",
|
|
"FP1B",
|
|
"FP1T",
|
|
"FSER",
|
|
"FSM",
|
|
"G",
|
|
"GIP",
|
|
"GLI",
|
|
"GNBC",
|
|
"GPBC",
|
|
"HBVL",
|
|
"HBVL5",
|
|
"HC1",
|
|
"HC2",
|
|
"HC3",
|
|
"HC4",
|
|
"HC6",
|
|
"HC6X",
|
|
"HC7",
|
|
"HCA",
|
|
"HCG",
|
|
"HCV2",
|
|
"HGM",
|
|
"HIV",
|
|
"HIVG",
|
|
"HPS",
|
|
"HPV",
|
|
"HV2",
|
|
"ID1",
|
|
"ID1T",
|
|
"ID2",
|
|
"ID3",
|
|
"IDN",
|
|
"IDO",
|
|
"IDR",
|
|
"IG/IGX",
|
|
"IL",
|
|
"IM",
|
|
"IMD1",
|
|
"IMD2",
|
|
"IMD3",
|
|
"IND",
|
|
"ISH",
|
|
"ISH2",
|
|
"J",
|
|
"J1",
|
|
"JAT",
|
|
"JATE1",
|
|
"JE1",
|
|
"KIT",
|
|
"KRAS",
|
|
"LBAS",
|
|
"LKM",
|
|
"MC1",
|
|
"MC2",
|
|
"MC3",
|
|
"MC4",
|
|
"MC5",
|
|
"MGL1",
|
|
"MGL2",
|
|
"MGL3",
|
|
"MGL4",
|
|
"MGL5",
|
|
"MHO, MHO1",
|
|
"MHO2, MHO3",
|
|
"MHO5",
|
|
"ML",
|
|
"MRD",
|
|
"MRD1",
|
|
"MRD2",
|
|
"MRS",
|
|
"MRS5",
|
|
"MSI",
|
|
"MTBR",
|
|
"MTP",
|
|
"NEO",
|
|
"P",
|
|
"P3",
|
|
"P4",
|
|
"P5",
|
|
"PCP1",
|
|
"PCP2",
|
|
"PCP3",
|
|
"PCP4",
|
|
"PGx",
|
|
"PGx1",
|
|
"PGx2",
|
|
"PNA1",
|
|
"PNA2",
|
|
"PNA3",
|
|
"PNA4",
|
|
"QF",
|
|
"RAG",
|
|
"RDS",
|
|
"RETT",
|
|
"RF/RFX",
|
|
"RUB/RUBX",
|
|
"S2",
|
|
"S4",
|
|
"S5",
|
|
"SARC",
|
|
"SBAS",
|
|
"SEC",
|
|
"SEC1",
|
|
"SP",
|
|
"SP1",
|
|
"SPN",
|
|
"ST",
|
|
"TM",
|
|
"TMO",
|
|
"TMX",
|
|
"TPM",
|
|
"TTD",
|
|
"TVAG",
|
|
"VLS",
|
|
"VLS2",
|
|
"VR1",
|
|
"VR2",
|
|
"VR3",
|
|
"VR3M",
|
|
"VR4",
|
|
"VRE",
|
|
"VS",
|
|
"VS1",
|
|
"WID"
|
|
]
|
|
},
|
|
<span class="quotedn">"citationsType"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"minItems"</span>: 0,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"clinicalSignificanceEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Affects",
|
|
"Benign",
|
|
"Likely benign",
|
|
"Likely pathogenic",
|
|
"Pathogenic",
|
|
"Uncertain significance",
|
|
"association",
|
|
"association not found",
|
|
"confers sensitivity",
|
|
"conflicting data from submitters",
|
|
"drug response",
|
|
"not provided",
|
|
"other",
|
|
"protective",
|
|
"risk factor"
|
|
]
|
|
},
|
|
<span class="quotedn">"gtrAccessionType"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"pattern"</span>: <span class="quotedv">"^GTR[0123456789]{9}$"</span>
|
|
},
|
|
<span class="quotedn">"humanTestConditionsOrPhenotypes"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The condition or phenotype relevant to the eligibility criteria and/or study aims for the test, provided as either a database identifier or a name."</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"type"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"blood group",
|
|
"disease",
|
|
"named protein variant",
|
|
"pharmacological response"
|
|
]
|
|
},
|
|
<span class="quotedn">"acronyms"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Your laboratory's preferred acronym for the condition."</span>,
|
|
<span class="quotedn">"minItems"</span>: 0,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
},
|
|
<span class="quotedn">"citationsForPrevalence"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Citations to support the prevalence statement. Provide PubMed ID when available (example 'PMID: 23193275')."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/citationsType"</span>
|
|
},
|
|
<span class="quotedn">"diseaseMechanism"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Disease mechanism for the relationship of condition to test target."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"gain of function",
|
|
"loss of function"
|
|
]
|
|
},
|
|
<span class="quotedn">"id"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"labPreferredAcronym"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The acronym for the condition or phenotype that is referred to by the laboratory."</span>
|
|
},
|
|
<span class="quotedn">"labPreferredName"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The preferred name of the condition or phenotype that is referred to by the laboratory."</span>
|
|
},
|
|
<span class="quotedn">"modeOfInheritance"</span>: {
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value for mode of inheritance for the condition from enum list."</span>,
|
|
<span class="quotedn">"$ref"</span>: <span class="quotedv">"#/definitions/modeOfInheritanceEnum"</span>
|
|
},
|
|
<span class="quotedn">"name"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Name of condition or phenotype"</span>
|
|
},
|
|
<span class="quotedn">"ontologyDb"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Databases supporting the classification and standardized nomenclature and coding of human conditions and phenotypes with a genetic basis: OMIM - Online Mendelian Inheritance in Man\u00ae; MedGen - Medical Genetics resource (National Center for Biotechnology Information; NCBI); HPO - Human Phenotype Ontology (The Jackson Laboratory); Orphanet (Orphanet / INSERM); MeSH - Medical Subject Headings (NCBI); MONDO (EMBL - EBI); select from enum list."</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"OMIM",
|
|
"MedGen",
|
|
"HPO",
|
|
"Orphanet",
|
|
"MeSH",
|
|
"MONDO"
|
|
]
|
|
},
|
|
<span class="quotedn">"otherDiseaseMechanism"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if disease mechanism is not in the enum list."</span>
|
|
},
|
|
<span class="quotedn">"otherModeOfInheritance"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Value if mode of inheritance is not in the enum list."</span>
|
|
},
|
|
<span class="quotedn">"prevalenceDescription"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Prevalence or the most current estimated number of cases of the disease in the population."</span>
|
|
},
|
|
<span class="quotedn">"prevalenceURL"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"URL for prevalence claim."</span>,
|
|
<span class="quotedn">"format"</span>: <span class="quotedv">"uri"</span>
|
|
},
|
|
<span class="quotedn">"primary"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"boolean"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The flag of whether the name of the condition or phenotype is primary in the test. Each test can have only one primary condition or phenotype."</span>
|
|
},
|
|
<span class="quotedn">"synonyms"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The synonym of the condition or phenotype."</span>,
|
|
<span class="quotedn">"minItems"</span>: 0,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>
|
|
},
|
|
<span class="quotedn">"uniqueItems"</span>: true
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"allOf"</span>: [
|
|
{
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"ontologyDb",
|
|
"id"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"name"
|
|
]
|
|
}
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"dependencies"</span>: {
|
|
<span class="quotedn">"id"</span>: [
|
|
"ontologyDb"
|
|
],
|
|
<span class="quotedn">"ontologyDb"</span>: [
|
|
"id"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"not"</span>: {
|
|
<span class="quotedn">"anyOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"modeOfInheritance",
|
|
"otherModeOfInheritance"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"diseaseMechanism",
|
|
"otherDiseaseMechanism"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"citationsForPrevalence"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"prevalenceDescription"
|
|
]
|
|
}
|
|
},
|
|
{
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"prevalenceURL"
|
|
]
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"prevalenceDescription"
|
|
]
|
|
}
|
|
}
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"humanTestInstrumentEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Affymetrix GeneChip Scanner 3000 7G Whole-Genome Association System",
|
|
"Affymetrix GeneTitan\u00ae MC",
|
|
"Affymetrix HotStart-IT Probe qPCR Master Mix with UDG (2X)",
|
|
"Agilent 2100 Bioanalyzer",
|
|
"Agilent SureSelect",
|
|
"Applied Biosystems 3730 capillary sequencing instrument",
|
|
"Applied Biosystems 7900HT Sequence Detection System",
|
|
"Applied Biosystems SOLiD v4 System Sequencer",
|
|
"BeadXpress\u00ae Reader",
|
|
"BioRad CFX384",
|
|
"BioRad CFX96",
|
|
"Covaris S2 Sonicator",
|
|
"GenMark Diagnostics eSensor XT-8 system",
|
|
"Illumina Genome AnalyzerIIx and Genome AnalyzerIIe",
|
|
"Illumina HiScan\u2122SQ system",
|
|
"Illumina HiSeq\u21222000 system",
|
|
"PerkinElmer Victor3 1420 Multilabel Plate Reader",
|
|
"Qiagen AutoPure LS",
|
|
"Qiagen QIAcube",
|
|
"Roche LightCycler 480",
|
|
"Tecan Genesis Robotic Workstation 150"
|
|
]
|
|
},
|
|
<span class="quotedn">"humanTestMethodCategoryEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Analyte",
|
|
"Chromosome breakage studies",
|
|
"Deletion/duplication analysis",
|
|
"Detection of homozygosity",
|
|
"Enzyme assay",
|
|
"FISH-interphase",
|
|
"FISH-metaphase",
|
|
"Fluorescence in situ hybridization (FISH)",
|
|
"Immunohistochemistry",
|
|
"Karyotyping",
|
|
"Linkage analysis",
|
|
"Methylation analysis",
|
|
"Microsatellite instability testing (MSI)",
|
|
"Multicolor FISH (M-FISH)/Spectral Karyotyping\u2122 (SKY\u2122)",
|
|
"Mutation scanning of select exons",
|
|
"Mutation scanning of the entire coding region",
|
|
"Protein analysis",
|
|
"Protein expression",
|
|
"RNA analysis",
|
|
"Sequence analysis of select exons",
|
|
"Sequence analysis of the entire coding region",
|
|
"Sister chromatid exchange",
|
|
"Targeted variant analysis",
|
|
"Uniparental disomy study (UPD)"
|
|
]
|
|
},
|
|
<span class="quotedn">"humanTestMethodEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Allele-specific primer extension (ASPE)",
|
|
"Alternative splicing detection",
|
|
"Bi-directional Sanger Sequence Analysis",
|
|
"C-banding",
|
|
"Chemiluminescent Immunoassay (CIA)",
|
|
"Chromatin Immunoprecipitation on ChIP",
|
|
"Comparative Genomic Hybridization",
|
|
"DamID",
|
|
"Digital / Virtual karyotyping",
|
|
"Digital microfluidic microspheres",
|
|
"Enzymatic levels",
|
|
"Enzyme activity",
|
|
"Enzyme-Linked Immunosorbent Assays (ELISA)",
|
|
"Flow cytometry",
|
|
"Fluorescence in situ hybridization (FISH)",
|
|
"Fluorometry",
|
|
"Fusion genes microarrays",
|
|
"G-banding",
|
|
"Gas chromatography\u2013mass spectrometry (GC-MS)",
|
|
"Gene expression profiling",
|
|
"GeneID",
|
|
"Gold nanoparticle probe technology",
|
|
"High-performance liquid chromatography (HPLC)",
|
|
"Liquid chromatography-tandem mass spectrometry (LC-MS/MS)",
|
|
"Liquid chromatography\u2013mass spectrometry (LC-MS)",
|
|
"Metabolite levels",
|
|
"Methylation-specific PCR",
|
|
"Microarray",
|
|
"Multiplex Ligation-dependent Probe Amplification (MLPA)",
|
|
"Next-Generation (NGS)/Massively parallel sequencing (MPS)",
|
|
"Oligonucleotide Ligation Assay (OLA)",
|
|
"Oligonucleotide hybridization-based DNA sequencing",
|
|
"PCR",
|
|
"PCR with allele specific hybridization",
|
|
"PCR-RFLP with Southern hybridization",
|
|
"Protein truncation test",
|
|
"Pyrosequencing",
|
|
"Q-banding",
|
|
"Quantitative PCR (qPCR)",
|
|
"R-banding",
|
|
"RFLP",
|
|
"RT-LAMP",
|
|
"RT-PCR",
|
|
"RT-PCR with gel analysis",
|
|
"RT-qPCR",
|
|
"SNP Detection",
|
|
"Silver staining",
|
|
"Spectral karyotyping (SKY)",
|
|
"T-banding",
|
|
"Tandem mass spectrometry (MS/MS)",
|
|
"Tetra-nucleotide repeat by PCR or Southern Blot",
|
|
"Tiling Arrays",
|
|
"Trinucleotide repeat by PCR or Southern Blot",
|
|
"Uni-directional Sanger sequencing"
|
|
]
|
|
},
|
|
<span class="quotedn">"humanTestPlatformEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Affymetrix CytoScan HD Array",
|
|
"Affymetrix Gene Profiling Array cGMP U133 P2",
|
|
"Affymetrix GeneChip Human Genome U133 Plus 2.0 Array",
|
|
"Affymetrix GeneChip Human Mitochondrial Resequencing Array 2.0",
|
|
"Affymetrix Genome-Wide Human SNP Array 6.0",
|
|
"Affymetrix QuantiGene 2.0 Assay",
|
|
"Agilent Human CpG Island Microarray Kit, 1x244K",
|
|
"Agilent Human ENCODE ChIP-on-chip Microarray",
|
|
"Agilent Human miRNA Microarray Kit Release 16.0, 8x60K",
|
|
"Agilent SurePrint G3 Human CGH Microarray Kit, 2x400K",
|
|
"Amersham CodeLink UniSet Human I Bioarray",
|
|
"Illumina Infinium HD HumanCytoSNP-12",
|
|
"Life Technologies TaqMan OpenArray MicroRNA Panels",
|
|
"NimbleGen CGH 3-plex ISCA Plus Cytogenetic Array",
|
|
"None/not applicable",
|
|
"Oxford Gene Technology CytoSure DMD (4x44k)",
|
|
"Oxford Gene Technology CytoSure ISCA UPD (4x180k)",
|
|
"Oxford Gene Technology CytoSure ISCA v2 (4x180k)",
|
|
"Oxford Gene Technology CytoSure ISCA v2 (4x44k)",
|
|
"Oxford Gene Technology CytoSure ISCA v2 (8x60k)",
|
|
"Oxford Gene Technology CytoSure Syndrome Plus v2 (2x105k)"
|
|
]
|
|
},
|
|
<span class="quotedn">"majorCapCategoryEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"ABO Subgroup Typing",
|
|
"Alpha-1 Antitrypsin (SERPINA1) Genotyping",
|
|
"Anti-HCV, Rapid Methods, Waived",
|
|
"Anti-Saccharomyces cerevisiae Antibody",
|
|
"Antibody Titer",
|
|
"Antichromatin Antibody",
|
|
"Antifilamentous Actin IgG Antibody",
|
|
"Antihistone Antibody",
|
|
"Antimitochondrial M2 Antibody",
|
|
"Antiparietal Cell Antibody",
|
|
"Antiphosphatidylserine Antibody",
|
|
"Antiphospholipid Antibody",
|
|
"Antiribosomal-P Antibody",
|
|
"Apolipoprotein E Genotyping",
|
|
"Bacterial Antigen Detection",
|
|
"Bacterial Detection in Platelets",
|
|
"Bacterial Detection in Platelets, Rapid",
|
|
"Bacterial Strain Typing",
|
|
"Bacterial Vaginosis",
|
|
"Bacteriology",
|
|
"Biochemical Genetics",
|
|
"Blood Culture",
|
|
"Blood Culture Panels for Molecular Multiplex Testing",
|
|
"Blood Parasite",
|
|
"Bordetella pertussis/parapertussis Molecular",
|
|
"C. difficile Detection",
|
|
"C. trachomatis and N. gonorrhoeae",
|
|
"CAP/NSH HistoQIP",
|
|
"CAP/NSH HistoQIP - IHC",
|
|
"CD117, CD20 Immunohistochemistry Tissue Microarray",
|
|
"Campylobacter",
|
|
"Candida Culture",
|
|
"Chlamydia trachomatis",
|
|
"Cord Blood and Stem Cell Processing",
|
|
"Cytogenetics",
|
|
"Cytogenomic Microarray Analysis",
|
|
"Cytokines",
|
|
"DNA Mismatch Repair",
|
|
"DNA Purification from FFPET",
|
|
"Defective DNA Mismatch Repair/HNPCC",
|
|
"Direct Antiglobulin Testing",
|
|
"ER/PgR Immunohistochemistry Tissue Microarray",
|
|
"Eluate Survey",
|
|
"Expanded Bacteriology",
|
|
"First Trimester Maternal Screening",
|
|
"Flow Cytometry",
|
|
"Fluorescence in Situ Hybridization (FISH)",
|
|
"Fluorescence in Situ Hybridization (FISH) for Paraffin-Embedded Tissue",
|
|
"Fungal Serology",
|
|
"Fungal Smear",
|
|
"GC, Throat and Urine Cultures",
|
|
"Galactomannan",
|
|
"Gastric HER2",
|
|
"Gastrointestinal Panel for Molecular Multiplex Testing",
|
|
"Glioma",
|
|
"Gram Stain",
|
|
"Group B Strep Detection",
|
|
"HER2 Immunohistochemistry",
|
|
"HIV Viral Load",
|
|
"HLA Crossmatching, Antibody Screen, and Antibody Identification (Class I)",
|
|
"HLA Crossmatching, Antibody Screen, and Antibody Identification (Class I/II) Combinations",
|
|
"HLA Crossmatching, Antibody Screen, and Antibody Identification (Class II)",
|
|
"HLA Disease Association, Drug Risk",
|
|
"HLA Molecular Typing",
|
|
"HLA Serologic Typing (Class I/II)",
|
|
"HLA-B27 Typing",
|
|
"Heavy Chain/Light Chain Analysis",
|
|
"Helicobacter pylori Antigen, Stool",
|
|
"Hemoglobinopathies, Molecular Methods",
|
|
"Hepatitis Viral Load",
|
|
"Herpes Simplex Virus",
|
|
"Human Papillomavirus",
|
|
"Human Papillomavirus (High Risk) for Cytology",
|
|
"Immunohistochemistry",
|
|
"Immunohistochemistry Tissue Microarray Series",
|
|
"Immunology ANA, ASO, CRP, HCG, IM, RF/RFX, RUB/RUBX, IL",
|
|
"Immunology, General",
|
|
"Immunology, Special; Limited",
|
|
"In Situ Hybridization",
|
|
"India Ink",
|
|
"Infectious Disease Respiratory Panel for Molecular Multiplex Testing",
|
|
"Infectious Disease Serology",
|
|
"Influenza A, Influenza B and RSV by NAA",
|
|
"Inherited Metabolic Diseases",
|
|
"Limited Bacteriology",
|
|
"Limited Mycobacteriology",
|
|
"Liver-Kidney Microsomal Antibody (Anti-LKM)",
|
|
"M. tuberculosis-Stimulated Infection Detection",
|
|
"Methicillin-Resistant Staphylococcus aureus Screen",
|
|
"Microbiology Combination",
|
|
"Minimal Residual Disease",
|
|
"Molecular Genetics",
|
|
"Molecular Genetics Sequencing",
|
|
"Molecular Hematologic Oncology",
|
|
"Molecular MTB Detection and Resistance",
|
|
"Monitoring Engraftment",
|
|
"Multigene Tumor Panel",
|
|
"Mycobacteriology",
|
|
"Mycology",
|
|
"Neoplastic Cellularity",
|
|
"Next-Generation Sequencing - Hematologic Malignancies",
|
|
"Next-Generation Sequencing - Solid Tumors",
|
|
"Next-Generation Sequencing Bioinformatics",
|
|
"Nucleic Acid Amplification, Organisms",
|
|
"Nucleic Acid Amplification, Respiratory",
|
|
"Nucleic Acid Amplification, Viruses",
|
|
"Nucleic Acid Testing",
|
|
"PNA FISH",
|
|
"Parasitology",
|
|
"Parentage/Relationship Testing",
|
|
"Pharmacogenetics",
|
|
"Platelet Serology",
|
|
"Pneumocystis jirovecii",
|
|
"Rapid Anti-HIV; Rapid Anti-HIV, Waived",
|
|
"Rapid Strep A Antigen Detection",
|
|
"Red Blood Cell Antigen Genotyping",
|
|
"Red Blood Cell Antigen Typing",
|
|
"Rett Syndrome (MECP2) Genotyping",
|
|
"Rheumatic Disease Special Serologies",
|
|
"Sarcoma Translocation",
|
|
"Shiga Toxin",
|
|
"Solid Tumors - Other",
|
|
"Stool Pathogen",
|
|
"Syphilis Serology",
|
|
"Throat Culture/Rapid Strep Combination",
|
|
"Thrombophilia Mutations",
|
|
"Tick-Transmitted Diseases",
|
|
"Ticks, Mites and Other Arthropods",
|
|
"Transfusion Medicine Automated",
|
|
"Transfusion Medicine Automated, Electronic Crossmatch",
|
|
"Transfusion Medicine Educational Challenges",
|
|
"Transfusion Medicine, Comprehensive/Limited",
|
|
"Transfusion Medicine, Electronic Crossmatch",
|
|
"Trichomonas vaginalis, Molecular",
|
|
"Tumor Markers",
|
|
"Urine Colony Count; Urine Colony Count Combination",
|
|
"Vaginitis Screen",
|
|
"Vancomycin-Resistant Enterococcus",
|
|
"Viral Load",
|
|
"Viral Markers - Series 1",
|
|
"Viral Markers - Series 2",
|
|
"Viral Markers - Series 3",
|
|
"Viral Markers - Seriest 4",
|
|
"Viral Markers - Seriest 5",
|
|
"Viral Markers - Seriest 6",
|
|
"Virology Antigen Detection (DFA)",
|
|
"Virology Antigen Detection (Non-DFA)",
|
|
"Virology Culture",
|
|
"Worm Identification",
|
|
"Yeast"
|
|
]
|
|
},
|
|
<span class="quotedn">"microbeTestInstrumentEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Abbott ID NOW\u2122",
|
|
"Affymetrix GeneChip Scanner 3000 7G Whole-Genome Association System",
|
|
"Affymetrix GeneTitan\u00ae MC",
|
|
"Affymetrix HotStart-IT Probe qPCR Master Mix with UDG (2X)",
|
|
"Agilent 2100 Bioanalyzer",
|
|
"Agilent SureSelect",
|
|
"Applied Biosystems 3730 capillary sequencing instrument",
|
|
"Applied Biosystems 7900HT Sequence Detection System",
|
|
"Applied Biosystems SOLiD v4 System Sequencer",
|
|
"BeadXpress\u00ae Reader",
|
|
"BioFireDx FilmArray",
|
|
"BioRad CFX384",
|
|
"BioRad CFX96",
|
|
"Cobas\u00ae 6800 / 8800 System",
|
|
"Covaris S2 Sonicator",
|
|
"GenMark Diagnostics eSensor XT-8 system",
|
|
"Illumina Genome AnalyzerIIx and Genome AnalyzerIIe",
|
|
"Illumina HiScan\u2122SQ system",
|
|
"Illumina HiSeq\u21222000 system",
|
|
"PerkinElmer Victor3 1420 Multilabel Plate Reader",
|
|
"Qiagen AutoPure LS",
|
|
"Qiagen QIAcube",
|
|
"Roche LightCycler 480",
|
|
"Tecan Genesis Robotic Workstation 150"
|
|
]
|
|
},
|
|
<span class="quotedn">"microbeTestMethodCategoryEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Antibody assay",
|
|
"Antigen assay",
|
|
"Combination antibody and antigen assay",
|
|
"Mutation scanning of select exons",
|
|
"Mutation scanning of the entire coding region",
|
|
"RNA analysis",
|
|
"Sequence analysis of select exons",
|
|
"Sequence analysis of the entire coding region",
|
|
"Targeted variant analysis"
|
|
]
|
|
},
|
|
<span class="quotedn">"microbeTestMethodEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Allele-specific primer extension (ASPE)",
|
|
"Alternative splicing detection",
|
|
"Antibody detection",
|
|
"Antigen detection",
|
|
"Bi-directional Sanger Sequence Analysis",
|
|
"Chemiluminescent Immunoassay (CIA)",
|
|
"Combination antibody and antigen detection",
|
|
"Comparative Genomic Hybridization",
|
|
"Digital microfluidic microspheres",
|
|
"Enzymatic levels",
|
|
"Enzyme activity",
|
|
"Enzyme-Linked Immunosorbent Assays (ELISA)",
|
|
"Flow cytometry",
|
|
"Fluorescence in situ hybridization (FISH)",
|
|
"Fluorometry",
|
|
"Gas chromatography\u2013mass spectrometry (GC-MS)",
|
|
"GeneID",
|
|
"Gold nanoparticle probe technology",
|
|
"High-performance liquid chromatography (HPLC)",
|
|
"Liquid chromatography-tandem mass spectrometry (LC-MS/MS)",
|
|
"Liquid chromatography\u2013mass spectrometry (LC-MS)",
|
|
"Metabolite levels",
|
|
"Methylation-specific PCR",
|
|
"Microarray",
|
|
"Multiplex Ligation-dependent Probe Amplification (MLPA)",
|
|
"Multiplex PCR",
|
|
"Multiplex real-time PCR",
|
|
"Next-Generation (NGS)/Massively parallel sequencing (MPS)",
|
|
"Nucleic acid amplification test (NAAT)",
|
|
"Oligonucleotide Ligation Assay (OLA)",
|
|
"Oligonucleotide hybridization-based DNA sequencing",
|
|
"PCR",
|
|
"PCR with allele specific hybridization",
|
|
"PCR-RFLP with Southern hybridization",
|
|
"Pyrosequencing",
|
|
"Quantitative PCR (qPCR)",
|
|
"RFLP",
|
|
"RT-LAMP",
|
|
"RT-PCR",
|
|
"RT-PCR with gel analysis",
|
|
"RT-qPCR",
|
|
"SNP Detection",
|
|
"Tandem mass spectrometry (MS/MS)",
|
|
"Tiling Arrays",
|
|
"Uni-directional Sanger sequencing",
|
|
"Viral load"
|
|
]
|
|
},
|
|
<span class="quotedn">"microbeTestPlatformEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Abbott ID NOW\u2122 COVID-19",
|
|
"Affymetrix CytoScan HD Array",
|
|
"Affymetrix Gene Profiling Array cGMP U133 P2",
|
|
"Affymetrix GeneChip Human Genome U133 Plus 2.0 Array",
|
|
"Affymetrix GeneChip Human Mitochondrial Resequencing Array 2.0",
|
|
"Affymetrix Genome-Wide Human SNP Array 6.0",
|
|
"Affymetrix QuantiGene 2.0 Assay",
|
|
"Agilent Human CpG Island Microarray Kit, 1x244K",
|
|
"Agilent Human ENCODE ChIP-on-chip Microarray",
|
|
"Agilent Human miRNA Microarray Kit Release 16.0, 8x60K",
|
|
"Agilent SurePrint G3 Human CGH Microarray Kit, 2x400K",
|
|
"Amersham CodeLink UniSet Human I Bioarray",
|
|
"BioFireDx FilmArray Pneumonia Panel plus",
|
|
"Cobas\u00ae SARS-CoV-2 Test",
|
|
"Illumina Infinium HD HumanCytoSNP-12",
|
|
"Life Technologies TaqMan OpenArray MicroRNA Panels",
|
|
"LightMix\u00ae Modular Assays",
|
|
"NimbleGen CGH 3-plex ISCA Plus Cytogenetic Array",
|
|
"None/not applicable",
|
|
"Oxford Gene Technology CytoSure DMD (4x44k)",
|
|
"Oxford Gene Technology CytoSure ISCA UPD (4x180k)",
|
|
"Oxford Gene Technology CytoSure ISCA v2 (4x180k)",
|
|
"Oxford Gene Technology CytoSure ISCA v2 (4x44k)",
|
|
"Oxford Gene Technology CytoSure ISCA v2 (8x60k)",
|
|
"Oxford Gene Technology CytoSure Syndrome Plus v2 (2x105k)",
|
|
"RIDA\u00aeGENE Bacterial Stool Panel",
|
|
"RIDA\u00aeGENE Viral Stool Panel III",
|
|
"ZEUS Borrelia Modified Two-Tiered Testing\u2122 (MTTT) for Lyme Disease"
|
|
]
|
|
},
|
|
<span class="quotedn">"modeOfInheritanceEnum"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"Autosomal dominant inheritance",
|
|
"Autosomal dominant inheritance with maternal imprinting",
|
|
"Autosomal dominant inheritance with paternal imprinting",
|
|
"Autosomal recessive inheritance",
|
|
"Autosomal unknown",
|
|
"Codominant",
|
|
"Genetic anticipation",
|
|
"Mitochondrial inheritance",
|
|
"Multifactorial inheritance",
|
|
"Oligogenic inheritance",
|
|
"Sex-limited autosomal dominant",
|
|
"Somatic mutation",
|
|
"Sporadic",
|
|
"Unknown mechanism",
|
|
"X-linked dominant inheritance",
|
|
"X-linked inheritance",
|
|
"X-linked recessive inheritance",
|
|
"Y-linked inheritance"
|
|
]
|
|
}
|
|
},
|
|
<span class="quotedn">"oneOf"</span>: [
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"humanTest"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"microbeTest"
|
|
]
|
|
},
|
|
{
|
|
<span class="quotedn">"required"</span>: [
|
|
"testDeletion"
|
|
]
|
|
}
|
|
]
|
|
}
|
|
</pre></div>
|
|
<h2 id="h2_schema_desc">Submission description</h2>
|
|
<span class="propertyOpenAll">Expand all</span>
|
|
<span class="propertyCloseAll">Collapse all</span>
|
|
<div class="json_schema">
|
|
<div class="property_description">GTR API submission schema</div><div class="property">
|
|
<span class="propertyName"><code>humanTest</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">Human clinical test - add or update</div><div class="property">
|
|
<span class="propertyName"><code>action</code></span>
|
|
<span class="propertyAttr">string, required, enumeration</span><div class="property_description">Value to add a new test or update an existing test.</div><div class="property_enum"><b>Allowed values</b>: <code>"add", "update"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>analyticalValidity</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">Quantitative information about analytical sensitivity, analytical specificity, accuracy, and/or precision of this test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>assayLimitations</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Test limitations that affect the value of the test for its intended use, such as the limit of detection and test restrictions.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>caps</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Set of mjaor category, sub-category and test code to specify, if College of American Pathologists (CAP) is chosen as Provider for proficiency testing.</div><div class="property">
|
|
<span class="propertyName"><code>capCategory</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Relevant sub-category, if major CAP category is selected.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>capTest</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Relevant test code, if major CAP category is selected.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>majorCapCategory</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Category to specify, if College of American Pathologists (CAP) is chosen as Provider for proficiency testing</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForAnalyticalValidity</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations supporting the analytical validity statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForAssayLimitations</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations supporting the assay limitation statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForClinicalValidity</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations used to evaluate the clinical validity of the test; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForInternalTestValidationMethod</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations to support internal test validation method statement; for PubMed ID use format 'PMID: 23193275';; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForTargetPopulation</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations supporting statements provided in 'Target population for this test'; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForTestingStrategy</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations for the testing strategy/algorithm; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://).</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForTestProcedureOrProtocol</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations supporting the test protocol; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>clinicalUtilities</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Likelihood of the test to significantly improve patient outcomes.</div><div class="property">
|
|
<span class="propertyName"><code>category</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Clinical utility category value</div><div class="property_enum"><b>Allowed values</b>: <code>"Avoidance of invasive testing", "Establish or confirm diagnosis", "Guidance for management", "Guidance for selecting a drug therapy and/or dose", "Lifestyle planning", "Predictive risk information for patient and/or family members", "Reproductive decision-making", "Sufficient research has not been conducted to demonstrate the utility of the test"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citations</code></span>
|
|
<span class="propertyAttr">None, optional</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherCategory</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if category is not in the enum list.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>url</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The URL to display references to support a clinical utility choice.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>clinicalValidity</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Clinical sensitivity and specificity, description of the population(s) assessed, and the number of specimens used to calculate clinical validity.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>commentForTestPerformanceLocation</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">If any part of the test is performed externally, a description about where it is performed and any other information.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>cptCodes</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Molecular pathology Current Procedural Terminology (CPT®) code - 'MoPath' code - from the American Medical Association (AMA) that describes the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>fdaReviews</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Has the test been reviewed by the FDA?</div><div class="property">
|
|
<span class="propertyName"><code>fdaApplicationNumber</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">If FDA reviewed, FDA application number.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>noReviewCategoryDesignation</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">If no FDA review, FDA category designation</div><div class="property_enum"><b>Allowed values</b>: <code>"FDA exercises enforcement discretion", "Not Applicable"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherRegulatoryStatus</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if fdaRegulatoryStatus value is not in the status enum list.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherReviewItem</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if FDA reviewed item is not in the item enum list.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>regulatoryStatus</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">If FDA reviewed, FDA regulatory status from enum list.</div><div class="property_enum"><b>Allowed values</b>: <code>"FDA cleared/approved", "FDA exempt", "Not submitted", "Pending"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>reviewCategoryDesignation</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">If FDA review, FDA category designation.</div><div class="property_enum"><b>Allowed values</b>: <code>"IUO - Investigational Use Only. The performance characteristics of this product have not been established.", "IVD - In Vitro Device.", "RUO - Research Use Only. Not for use in diagnostic procedures."</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>reviewed</code></span>
|
|
<span class="propertyAttr">boolean, optional</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>reviewItem</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">If FDA reviewed, item under reviewed.</div><div class="property_enum"><b>Allowed values</b>: <code>"ASR - Analyte Specific Reagent(s)", "Assay(s)", "IVDMIA - In Vitro Diagnostic Multivariate Index Assay(s)", "Instrument(s)", "Test kit(s)"</code></div>
|
|
</div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>gtrAccession</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">GTR accession number, for an existing GTR test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>howToOrder</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Description of the test ordering procedure.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>informedConsentRequired</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Whether the lab reqires informed consent prior to performing the test.</div><div class="property_enum"><b>Allowed values</b>: <code>"Decline to answer", "Required", "Not required", "Based on applicable state law"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>internalTestValidationMethod</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Explanation of how the lab validates the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>labTestName</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">The name of the test to be displayed in GTR.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>labTestShortName</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Shortened name or mneumonic used by the lab to identify the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>loincCodes</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Logical Observation Identifiers Names and Codes.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>manufactureTestName</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The manufacturer's name for the test, if a commercial test or kit was used.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>methods</code></span>
|
|
<span class="propertyAttr">array, required, 1 or more items</span><div class="property_description">Set of method category and primary methodology used in the test; the major method categories for the test which will be inferred from the methodCategory are: (1) Molecular Genetics, (2) Biochemical Genetics, and (3) Cytogenetics.</div><div class="property">
|
|
<span class="propertyName"><code>instruments</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Instrument(s) used for the method.</div><div class="property">
|
|
<span class="propertyName"><code>name</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Name of instrument used.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherInstrument</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if the instrument used is not in the instrument enum list.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>method</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Primary methodology for the test</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>methodCategory</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">General category to which the test method belongs</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherMethod</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if method is not in the method enum list.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>nysClep</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">NYS Clinical Laboratory Evaluation Program</div><div class="property">
|
|
<span class="propertyName"><code>status</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">NYS CLEP status</div><div class="property_enum"><b>Allowed values</b>: <code>"Approved", "Exempt", "Grandfathered", "Pending"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testApprovalNumber</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">NYS CLEP test approval number</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>orderURL</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The URL for ordering the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>platforms</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">The platform used for the test, usually a commercial product (catalog number or set of numbers) with pre-defined test targets used in the test.</div><div class="property">
|
|
<span class="propertyName"><code>name</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Name of commercial platform or kit with predefined test targets.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherPlatform</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if platform used is not in the enum list.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>posttestGeneticCounselingRequired</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Requirement by the laboratory for genetic counseling after performing the test in order to release the test results.</div><div class="property_enum"><b>Allowed values</b>: <code>"Decline to answer", "Required", "Not required"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>pretestGeneticCounselingRequired</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Requirement by the laboratory for genetic counseling prior to performing the test.</div><div class="property_enum"><b>Allowed values</b>: <code>"Decline to answer", "Required", "Not required"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>proficiencyTesting</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">Periodic internal or external evaluation of the test to corroborate the accuracy of test results.</div><div class="property">
|
|
<span class="propertyName"><code>citationsForMethodDescription</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations to support the proficiency testing method statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>method</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">The type of proficiency testing that is performed, from enum list. </div><div class="property_enum"><b>Allowed values</b>: <code>"Alternative Assessment", "Formal PT program", "Inter-Laboratory", "Intra-Laboratory"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>methodDescription</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">A description of the proficiency testing method used.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherMethod</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if method is not in the method enum list.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherProvider</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if provider is not in the provider enum list.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>provider</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Provider for proficiency testing, from enum list.</div><div class="property_enum"><b>Allowed values</b>: <code>"American College of Medical Genetics / College of American Pathologists, ACMG/CAP", "American College of Physicians - Medical Laboratory Evaluation, ACP MLE", "Association for Molecular Pathology, AMP", "Belgian Official EKE Schemes, GLP Monitoring Programme", "Canadian External Quality Assessment Laboratory, CEQAL", "Centers for Disease Control and Prevention Newborn Screening Quality Assurance Program, CDC DLS", "Clinical Pathology Accreditation (UK) Ltd., CPA", "College of American Pathologists, CAP", "European Concerted Action on Thrombosis External Quality Assessment Program, ECAT EQAP", "European Molecular Genetics Quality Network, EMQN", "European Research Network for the Evaluation and Improvement of Screening Diagnosis and Treatment of Inherited Metabolic Disorders - External Quality Assessment Schemes, ERNDIM EQAS", "External Quality Assessment for Molecular Genetic Testing for Phenylketonuria, EQA-PKU", "Human Genetic Society of Australasia, HGSA", "Institute for Standardization and Documentation in the Medical Laboratory, INSTAND", "Pacific Northwest Regional Genetics Group, PacNoRGG", "Society for Inherited Metabolic Disorders, SIMD"</code></div>
|
|
</div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>searchTerms</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Keywords by which users can search for the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>specimen</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">Specimen sample allowed for the test.</div><div class="property">
|
|
<span class="propertyName"><code>otherSource</code></span>
|
|
<span class="propertyAttr">string, optional</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>sources</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Specimen sample source, from enum list</div><div class="property_enum"><b>Allowed values</b>: <code>"Amniocytes", "Amniotic fluid", "Bone marrow", "Buccal swab", "Buffy coat", "Cell culture", "Cell-free DNA", "Cerebrospinal fluid", "Chorionic villi", "Cord blood", "Cystic hygroma fluid", "Dried blood spot (DBS) card", "Fetal blood", "Fibroblasts", "Fresh tissue", "Frozen tissue", "Isolated DNA", "Nasal aspirates", "Nasopharyngeal washes", "Oropharyngeal swab", "Paraffin block", "Peripheral (whole) blood", "Plasma", "Product of conception (POC)", "Saliva", "Serum", "Skin", "Sputum", "Urine", "White blood cell prep"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>url</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The URL at lab's website that describes specimen requirements and/or collection protocol.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>targetPopulation</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Segment(s) of the population that should be tested for the condition or phenotype and why.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testAdditionalServices</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Additional test service offered in conjunction with the test.</div><div class="property">
|
|
<span class="propertyName"><code>additionalService</code></span>
|
|
<span class="propertyAttr">string, required, enumeration</span><div class="property_description">If applicable, additional laboratory service from enum list.</div><div class="property_enum"><b>Allowed values</b>: <code>"Custom Prenatal Testing", "Custom mutation-specific/Carrier testing"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>comment</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Enter helpful information regarding the test service, such as how to request the service, limitations, etc.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>orderCode</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Order code for additional test service</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testCodeURL</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The URL for information on codes (e.g. CPT, ICD-9, ICD-10).</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testComment</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Optional textual description of the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testContactPersons</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Lab person name in the format: first-name last-name. The lab person should be in the lab personnel list.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testContactPolicies</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Laboratory policy regarding who may contact lab (e.g., patients and/or health care providers) and when during the testing process the laboratory will discuss tests with patients.</div><div class="property_enum"><b>Allowed values</b>: <code>"Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss genetic testing options with their health care provider.", "Post-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families.", "Pre-test email/phone consultation regarding genetic test results and interpretation is provided to patients/families."</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testDevelopment</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Information about how the test is developed.</div><div class="property_enum"><b>Allowed values</b>: <code>"FDA-reviewed (has FDA test name)", "Manufactured (research use only; not FDA-reviewed)", "Modified FDA (has FDA-reviewed entry, but with lab modifications/field changes)", "Test developed by laboratory (no manufacturer test name)"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testingStrategy</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Description of the clinical testing strategy, not the test procedure; can include prior testing requirements</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testOrderCode</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The test order code, commonly found on the laboratory's requisition form, test menu or test catalog.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testPerformanceLocations</code></span>
|
|
<span class="propertyAttr">array, required, 1 or more items</span><div class="property_description">Locations for test performance.</div><div class="property_enum"><b>Allowed values</b>: <code>"Entire test performed in-house", "Interpretation performed at an outside lab", "Interpretation performed both in-house and at an outside lab", "Interpretation performed in-house", "Report generated at an outside lab", "Report generated both in-house and at an outside lab", "Report generated in-house", "Specimen preparation performed at an outside lab", "Specimen preparation performed both in-house and at an outside lab", "Specimen preparation performed in-house", "Wet lab work performed at an outside lab", "Wet lab work performed both in-house and at an outside lab", "Wet lab work performed in-house"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testProcedureOrProtocol</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Summary of the methodology, including specific steps for each method used in the assay.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testPurposes</code></span>
|
|
<span class="propertyAttr">array, required, 1 or more items</span><div class="property_description">Purpose of the test</div><div class="property_enum"><b>Allowed values</b>: <code>"Diagnosis", "Drug Response", "Monitoring", "Mutation Confirmation", "Pre-implantation genetic diagnosis", "Pre-symptomatic", "Predictive", "Prognostic", "Recurrence", "Risk Assessment", "Screening", "Therapeutic management"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testResultsConfirmation</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Information about whether results are confirmed and if so, how.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testServices</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property">
|
|
<span class="propertyName"><code>comment</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Helpful information regarding the test service, e.g. how to request the service</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>orderCode</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Order code for test service</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherService</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if test service is not in the enum list.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testService</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Laboratory service that is offered in conjunction with the test, from enum list</div><div class="property_enum"><b>Allowed values</b>: <code>"Clinical Testing/Confirmation of Mutations Identified Previously", "Confirmation of research findings", "Custom Balanced Chromosome Rearrangement Studies", "Custom Deletion/Duplication Testing", "Custom Sequence Analysis", "Data Storage and Backup", "Genetic counseling", "Identity Testing", "Marker Chromosome Identification", "Maternal cell contamination study (MCC)", "Preimplantation Genetic Diagnosis (PGD)", "Result interpretation", "Specimen Source Identification", "Uniparental Disomy (UPD) Testing", "X-Chromosome Inactivation Studies"</code></div>
|
|
</div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testTargetsAssociated</code></span>
|
|
<span class="propertyAttr">array, required, 1 or more items</span><div class="property_description">Category describing the condition(s)/phenotype(s) associated with the test target(s) in the test</div><div class="property">
|
|
<span class="propertyName"><code>conditionsOrPhenotypes</code></span>
|
|
<span class="propertyAttr">None, required</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>origins</code></span>
|
|
<span class="propertyAttr">array, required, 1 or more items</span><div class="property_description">For a given condition or phenotype, whether the test target is germline or somatic or both.</div><div class="property_enum"><b>Allowed values</b>: <code>"Germline", "Somatic"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>targetsTested</code></span>
|
|
<span class="propertyAttr">object, required</span><div class="property_description">The analytes, chromosomal or mitochondrial regions, genes and variations, or proteins that are measured in the test.</div><div class="property">
|
|
<span class="propertyName"><code>analytes</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Name of analyte</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>chromosomalRegionOrMitochondrions</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Chromosomal region/mitochondrion (for example, '11q15' or 'm.7446-m.7514')</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>genes</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Gene, example, 'CDKN2A' or 'CFTR'</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>geneWithRefSeqAndExons</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Relevant reference sequences and exons for each associated reference sequence.</div><div class="property">
|
|
<span class="propertyName"><code>exons</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">For exon range, example 3, 5, 9-12; f the range includes all exons, add (All), example 1-5 (All); if a subset is tested, enumerate the exons tested.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>gene</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">Gene, example, 'CDKN2A' or 'CFTR'</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>refSeq</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">Associated reference sequence.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>geneWithVariants</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Relevant gene variant; format is HGVS expression (preferred), or the allele name.</div><div class="property">
|
|
<span class="propertyName"><code>citationsForClinicalSignificance</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations used to support the clinical significance of the variant; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>gene</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">Gene, example, 'CDKN2A' or 'CFTR'</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>variant</code></span>
|
|
<span class="propertyAttr">string, required</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>variantClinicalSignificance</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Value for clinical significance of variant from enum list</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>proteins</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Protein; example, 'Hemoglobin subunit beta' or 'Adenomatous polyposis coli protein'</div></div>
|
|
</div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testTargetUnassociated</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">Category describing condition(s)/phenotype(s) and/or test target(s) that are not associated</div><div class="property">
|
|
<span class="propertyName"><code>conditionsOrPhenotypes</code></span>
|
|
<span class="propertyAttr">None, optional</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>origins</code></span>
|
|
<span class="propertyAttr">array, required, 1 or more items</span><div class="property_description">For a given condition or phenotype, whether the test target is germline or somatic or both.</div><div class="property_enum"><b>Allowed values</b>: <code>"Germline", "Somatic"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>targetsTested</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">The analytes, chromosomal or mitochondrial regions, genes and variations, or proteins that are measured in the test.</div><div class="property">
|
|
<span class="propertyName"><code>analytes</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Name of analyte</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>chromosomalRegionOrMitochondrions</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Chromosomal region/mitochondrion (for example, '11q15' or 'm.7446-m.7514')</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>genes</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Gene, example, 'CDKN2A' or 'CFTR'</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>geneWithRefSeqAndExons</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Relevant reference sequences and exons for each associated reference sequence.</div><div class="property">
|
|
<span class="propertyName"><code>exons</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">For exon range, example 3, 5, 9-12; f the range includes all exons, add (All), example 1-5 (All); if a subset is tested, enumerate the exons tested.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>gene</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">Gene, example, 'CDKN2A' or 'CFTR'</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>refSeq</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">Associated reference sequence.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>geneWithVariants</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Relevant gene variant; format is HGVS expression (preferred), or the allele name.</div><div class="property">
|
|
<span class="propertyName"><code>citationsForClinicalSignificance</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations used to support the clinical significance of the variant; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>gene</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">Gene, example, 'CDKN2A' or 'CFTR'</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>variant</code></span>
|
|
<span class="propertyAttr">string, required</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>variantClinicalSignificance</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Value for clinical significance of variant from enum list</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>proteins</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Protein; example, 'Hemoglobin subunit beta' or 'Adenomatous polyposis coli protein'</div></div>
|
|
</div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testURL</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The URL for the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>vus</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">Variant of Unknown Significance</div><div class="property">
|
|
<span class="propertyName"><code>areFamilyMembersRecruitedWithoutCharge</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Whether the lab offers testing for a variant of unknown significance to family members free of charge; for example, to affected individuals and/or presumed obligate carriers to help determine clinical significance of a VUS.</div><div class="property_enum"><b>Allowed values</b>: <code>"Not provided", "Yes", "No", "Decline to answer"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>commentsAboutRecontactingOrderingPhysican</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">An explanation about how the lab monitors and addresses reinterpretation of genetic tests results over time, after issuing the report; for example, time limit if any, whether the laboratory systematically re-evaluates prior interpretations and generate new reports, or whether the person ordering the test needs to periodically recontact the laboratory to inquire about changes in test interpretation.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>commentsAboutRecruitingFamilyMembers</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Explanation of who is eligible to testing free of charge and how the lab does it; for example, is the testing offered to affected individuals and/or presumed obligate carriers to help determine clinical significance of a VUS.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>labPolicyOnReportingNovelVariations</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">A description of how the lab reports novel variations.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>protocolForInterpretingVariationAsVUS</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Method used by the lab to interpret a variation as VUS.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>researchPerformedAfterClinicalTestingIsComplete</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">An explanation or information about any research testing being performed using the submitted sample; for example, research testing is allowed under IRB approved protocols or the patient would have to sign an informed consent for the research protocol; if the protocol is registered in clinicaltials.gov, you can enter that information here.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>softwareUsedToInterpretNovelVariations</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Software used by the lab to interpret novel variations.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>willLabRecontactOrderingPhysicanIfVariantInterpretationChanges</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Whether the lab contacts the ordering physician after testing and initial report, if a variant interpretation changes.</div><div class="property_enum"><b>Allowed values</b>: <code>"Not provided", "Yes", "No", "Decline to answer"</code></div>
|
|
</div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>whoCanOrder</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">One or more types of individuals able to order the test.</div><div class="property_enum"><b>Allowed values</b>: <code>"Genetic Counselor", "Health Care Provider", "In-State Patients", "Licensed Dentist", "Licensed Physician", "Nurse Practitioner", "Out-of-State Patients", "Physician Assistant", "Public Health Mandate", "Registered Nurse"</code></div>
|
|
</div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>microbeTest</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">Add or update a clinical microbe test.</div><div class="property">
|
|
<span class="propertyName"><code>action</code></span>
|
|
<span class="propertyAttr">string, required, enumeration</span><div class="property_description">Specify to add a new test or update an existing test.</div><div class="property_enum"><b>Allowed values</b>: <code>"add", "update"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>analyticalValidity</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">Quantitative information about analytical sensitivity, analytical specificity, accuracy, and/or precision of this test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>assayLimitations</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Test limitations that affect the value of the test for its intended use, such as the limit of detection and test restrictions.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>caps</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Set of mjaor category, sub-category and test code to specify, if College of American Pathologists (CAP) is chosen as Provider for proficiency testing</div><div class="property">
|
|
<span class="propertyName"><code>capCategory</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Relevant sub-category, if major CAP category is selected.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>capTest</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Relevant test code, if major CAP category is selected.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>majorCapCategory</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Category to specify, if College of American Pathologists (CAP) is chosen as Provider for proficiency testing</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForAnalyticalValidity</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations supporting the analytical validity statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForAssayLimitations</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations supporting the assay limitation statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForClinicalValidity</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations used to evaluate the clinical validity of the test; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForInternalTestValidationMethod</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations to support internal test validation method statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForMinimalMicrobeLoadTestCanDetect</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations supporting the minimal microbial load s statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForPPVAndNPV</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations used to evaluate PPV/NPV of the test; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForTargetPopulation</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations supporting statements provided in 'Target population for this test'; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForTestingStrategy</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations for the testing strategy/algorithm; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://).</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForTestProcedureOrProtocol</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations supporting the test protocol; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>clinicalUtilities</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Likelihood of the test is to significantly improve patient outcomes.</div><div class="property">
|
|
<span class="propertyName"><code>category</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Clinical utility category value</div><div class="property_enum"><b>Allowed values</b>: <code>"Avoidance of invasive testing", "Establish or confirm diagnosis", "Guidance for management", "Guidance for selecting a drug therapy and/or dose", "Lifestyle planning", "Sufficient research has not been conducted to demonstrate the utility of the test"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citations</code></span>
|
|
<span class="propertyAttr">None, optional</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherCategory</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if category is not in the enum list.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>url</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The URL to display references to support a clinical utility choice.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>clinicalValidity</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">A measure of how consistently and accurately the test detects or predicts the intermediate or final outcomes of interest. Clinical sensitivity and specificity, description of the population(s) assessed, and the number of specimens are used to calculate clinical validity.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>commentForTestPerformanceLocation</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">If any part of the test is performed externally, describe here which part(s) and where part(s) are performed.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>commentsAboutTestInterpretation</code></span>
|
|
<span class="propertyAttr">string, optional</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>conditionsOrPhenotypes</code></span>
|
|
<span class="propertyAttr">array, required, 0 or more items</span><div class="property_description">The condition or phenotype relevant to the eligibility criteria and/or study aims for the test, provided as either a database identifier or a name.</div><div class="property">
|
|
<span class="propertyName"><code>acronyms</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Your laboratory's preferred acronym for the condition.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>citationsForPrevalence</code></span>
|
|
<span class="propertyAttr">None, optional</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>id</code></span>
|
|
<span class="propertyAttr">string, optional</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>labPreferredAcronym</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The acronym for the condition or phenotype that is referred to by the laboratory.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>labPreferredName</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The preferred name of the condition or phenotype that is referred to by the laboratory.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>name</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Name of condition or phenotype.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>ontologyDb</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Databases supporting the classification and standardized nomenclature and coding of human conditions and phenotypes with a genetic basis: OMIM - Online Mendelian Inheritance in Man®; MedGen - Medical Genetics resource (National Center for Biotechnology Information; NCBI); HPO - Human Phenotype Ontology (The Jackson Laboratory); Orphanet (Orphanet / INSERM); MeSH - Medical Subject Headings (NCBI); MONDO (EMBL - EBI); select from enum list.</div><div class="property_enum"><b>Allowed values</b>: <code>"OMIM", "MedGen", "HPO", "Orphanet", "MeSH", "MONDO"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>prevalenceDescription</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Prevalence or the most current estimated number of cases of the disease in the population.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>prevalenceURL</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">URL for prevalence claim.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>synonyms</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">The synonym of the condition or phenotype.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>type</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_enum"><b>Allowed values</b>: <code>"Infectious disease", "disease", "pharmacological response"</code></div>
|
|
</div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>cptCodes</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Molecular pathology Current Procedural Terminology (CPT®) code - 'MoPath' code - from the American Medical Association (AMA) that describes the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>fdaReviews</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Has the test been reviewed by the FDA?</div><div class="property">
|
|
<span class="propertyName"><code>fdaApplicationNumber</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">If FDA reviewed, FDA application number.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>noReviewCategoryDesignation</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">If no FDA review, specify FDA category designation</div><div class="property_enum"><b>Allowed values</b>: <code>"EUA - Emergency Use Authorization", "FDA exercises enforcement discretion", "Not Applicable"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherRegulatoryStatus</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">If fdaRegulatoryStatus value is not in the status enum list, please specify.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherReviewItem</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">If FDA reviewed item is not in the item enum list, please specify.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>regulatoryStatus</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">If FDA reviewed, FDA regulatory status from enum list.</div><div class="property_enum"><b>Allowed values</b>: <code>"FDA cleared/approved", "FDA exempt", "Not submitted", "Pending"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>reviewCategoryDesignation</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">If FDA review, specify FDA category designation</div><div class="property_enum"><b>Allowed values</b>: <code>"IUO - Investigational Use Only. The performance characteristics of this product have not been established.", "IVD - In Vitro Device.", "RUO - Research Use Only. Not for use in diagnostic procedures."</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>reviewed</code></span>
|
|
<span class="propertyAttr">boolean, optional</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>reviewItem</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">If FDA reviewed, item under reviewed.</div><div class="property_enum"><b>Allowed values</b>: <code>"ASR - Analyte Specific Reagent(s)", "Assay(s)", "IVDMIA - In Vitro Diagnostic Multivariate Index Assay(s)", "Instrument(s)", "Test kit(s)"</code></div>
|
|
</div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>gtrAccession</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">If this test has been registered previously in the GTR, enter the GTR accession number here. This is required for update.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>howLongMicrobePresentAfterTherapy</code></span>
|
|
<span class="propertyAttr">string, optional</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>howToOrder</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Description of the test ordering procedure.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>informedConsentRequired</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Whether the lab reqires informed consent prior to performing the test.</div><div class="property_enum"><b>Allowed values</b>: <code>"Decline to answer", "Required", "Not required", "Based on applicable state law"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>internalTestValidationMethod</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Explanation of how the lab validates the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>labTestName</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">The name of the test to be displayed in GTR.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>labTestShortName</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Shortened name or mneumonic used by the lab to identify the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>loincCodes</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Logical Observation Identifiers Names and Codes.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>manufactureTestName</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The manufacturer's name for the test, if a commercial test or kit was used.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>methods</code></span>
|
|
<span class="propertyAttr">array, required, 1 or more items</span><div class="property_description">Set of method category and primary methodology used in the test; the major method categories for the test which will be inferred from the methodCategory are: (1) Molecular Genetics, and (2) Serology</div><div class="property">
|
|
<span class="propertyName"><code>instruments</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Instrument(s) used for the method.</div><div class="property">
|
|
<span class="propertyName"><code>name</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Name of instrument used.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherInstrument</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if instrument used is not in the instrument enum list.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>method</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Primary methodology for the test</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>methodCategory</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">General category to which the test method belongs</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherMethod</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if method is not in the method enum list.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>minimalMicrobeLoadTestCanDetect</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Limit of detection or the microbe load below which the test cannot reliably detect the microbe; e.g., viral loads &lt; 20 copies/ml cannot be reliably detected and will be reported as 'below the limit of detection').</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>nysClep</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">NYS Clinical Laboratory Evaluation Program</div><div class="property">
|
|
<span class="propertyName"><code>status</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">NYS CLEP status</div><div class="property_enum"><b>Allowed values</b>: <code>"Approved", "Exempt", "Grandfathered", "Pending"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testApprovalNumber</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">NYS CLEP test approval number</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>orderURL</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The URL for ordering the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>platforms</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">The platform used for the test, usually a commercial product (catalog number or set of numbers) with pre-defined test targets used in the test.</div><div class="property">
|
|
<span class="propertyName"><code>name</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Name of commercial platform or kit with predefined test targets.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherPlatform</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if platform used is not in the enum list.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>positiveAndNegativePredictiveValuesOrPPVAndNPV</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Positive Predictive Value (PPV) is the probability of true disease when the result is positive. Negative Predictive Value (NPV) is the probability of no disease when the result is negative</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>proficiencyTesting</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">Periodic internal or external evaluation of the test to corroborate the accuracy of test results.</div><div class="property">
|
|
<span class="propertyName"><code>citationsForMethodDescription</code></span>
|
|
<span class="propertyAttr">None, optional</span><div class="property_description">Citations to support the proficiency testing method statement; for PubMed ID use format 'PMID: 23193275'; for URL, begin with the protocol (e.g. https://)</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>method</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">The type of proficiency testing that is performed, from enum list. </div><div class="property_enum"><b>Allowed values</b>: <code>"Alternative Assessment", "Formal PT program", "Inter-Laboratory", "Intra-Laboratory"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>methodDescription</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">A description of the proficiency testing method used.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherMethod</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if method is not in the method enum list.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherProvider</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if provider is not in the provider enum list.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>provider</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_enum"><b>Allowed values</b>: <code>"American College of Physicians - Medical Laboratory Evaluation, ACP MLE", "Association for Molecular Pathology, AMP", "Belgian Official EKE Schemes, GLP Monitoring Programme", "Canadian External Quality Assessment Laboratory, CEQAL", "Centers for Disease Control and Prevention Newborn Screening Quality Assurance Program, CDC DLS", "Clinical Pathology Accreditation (UK) Ltd., CPA", "College of American Pathologists, CAP", "European Concerted Action on Thrombosis External Quality Assessment Program, ECAT EQAP", "European Molecular Genetics Quality Network, EMQN", "European Research Network for the Evaluation and Improvement of Screening Diagnosis and Treatment of Inherited Metabolic Disorders - External Quality Assessment Schemes, ERNDIM EQAS", "External Quality Assessment for Molecular Genetic Testing for Phenylketonuria, EQA-PKU", "Human Genetic Society of Australasia, HGSA", "Institute for Standardization and Documentation in the Medical Laboratory, INSTAND", "Pacific Northwest Regional Genetics Group, PacNoRGG", "Society for Inherited Metabolic Disorders, SIMD"</code></div>
|
|
</div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>researchPerformedAfterClinicalTestingIsComplete</code></span>
|
|
<span class="propertyAttr">string, optional</span></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>sampleRequirement</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Instructions for proper processing of the sample, including collection, sample container, volume, storage, temperature, causes for rejection, days that samples may or may not be received.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>searchTerms</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Keywords by which users can search for the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>specimen</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">Specimen sample allowed for the test.</div><div class="property">
|
|
<span class="propertyName"><code>otherSource</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if specimen source is not in the provider enum list</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>sources</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Specimen sample source, from enum list</div><div class="property_enum"><b>Allowed values</b>: <code>"Amniotic fluid", "Bone marrow", "Bronchoalveolar lavage", "Buccal swab", "Buffy coat", "Cell culture", "Cerebrospinal fluid", "Chorionic villi", "Cord blood", "Fetal blood", "Fresh tissue", "Frozen tissue", "Nasal aspirates", "Nasal swab", "Nasopharyngeal (NP) swab", "Nasopharyngeal washes", "Oropharyngeal swab", "Paraffin block", "Peripheral (whole) blood", "Plasma", "Product of conception (POC)", "Saliva", "Serum", "Skin", "Sputum", "Throat swab", "Urine", "White blood cell prep"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>url</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The URL at lab's website that describes specimen requirements and/or collection protocol.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>targetPopulation</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Segment(s) of the population that should be tested for the condition or phenotype and why.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testCodeURL</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The URL for information on codes (e.g. CPT, ICD-9, ICD-10).</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testComment</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Optional textual description of the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testContactPersons</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Lab person name in the format: first-name last-name. The lab person should be in the lab personnel list.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testContactPolicies</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Laboratory policy regarding who may contact lab (e.g., patients and/or health care providers) and when during the testing process the laboratory will discuss tests with patients.</div><div class="property_enum"><b>Allowed values</b>: <code>"Laboratory can only accept contact from health care providers. Patients/families are encouraged to discuss testing options with their health care provider.", "Post-test email/phone consultation regarding test results and interpretation is provided to patients/families.", "Pre-test email/phone consultation regarding test results and interpretation is provided to patients/families."</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testDevelopment</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_description">Information about how the test is developed.</div><div class="property_enum"><b>Allowed values</b>: <code>"FDA-reviewed (has FDA test name)", "Manufactured (research use only; not FDA-reviewed)", "Modified FDA (has FDA-reviewed entry, but with lab modifications/field changes)", "Test developed by laboratory (no manufacturer test name)"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testingStrategy</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Description of the clinical testing strategy, not the test procedure; can include prior testing requirements</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testOrderCode</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The test order code, commonly found on the laboratory's requisition form, test menu or test catalog.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testPerformanceLocations</code></span>
|
|
<span class="propertyAttr">array, required, 1 or more items</span><div class="property_description">Locations for test performance.</div><div class="property_enum"><b>Allowed values</b>: <code>"Entire test performed in-house", "Interpretation performed at an outside lab", "Interpretation performed both in-house and at an outside lab", "Interpretation performed in-house", "Report generated at an outside lab", "Report generated both in-house and at an outside lab", "Report generated in-house", "Specimen preparation performed at an outside lab", "Specimen preparation performed both in-house and at an outside lab", "Specimen preparation performed in-house", "Wet lab work performed at an outside lab", "Wet lab work performed both in-house and at an outside lab", "Wet lab work performed in-house"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testProcedureOrProtocol</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Summary of the methodology, including specific steps for each method used in the assay.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testPurposes</code></span>
|
|
<span class="propertyAttr">array, required, 1 or more items</span><div class="property_description">Purpose of the test.</div><div class="property_enum"><b>Allowed values</b>: <code>"Diagnosis", "Drug Response", "Microbe identification", "Monitoring", "Predictive", "Recurrence", "Screening", "Therapeutic management", "Viral load"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testResultsConfirmation</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Information about whether results are confirmed and if so, how.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testServices</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Laboratory service that is offered in conjunction with the test, from enum list</div><div class="property">
|
|
<span class="propertyName"><code>comment</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Helpful information regarding the test service, e.g., how to request the service.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>orderCode</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Order code for test service</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>otherService</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Value if test service is not in the enum list</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testService</code></span>
|
|
<span class="propertyAttr">string, optional, enumeration</span><div class="property_enum"><b>Allowed values</b>: <code>"Data Storage and Backup", "Result interpretation"</code></div>
|
|
</div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testTargets</code></span>
|
|
<span class="propertyAttr">array, required, 0 or more items</span><div class="property_description">The microorganism(s) and their genes, variants, proteins, analytes, and/or extrachromosomal or nucleic acid sequences that are measured in the test.</div><div class="property">
|
|
<span class="propertyName"><code>analytes</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Microbial analyte(s) measured in the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>chromosomalRegionOrMitochondrions</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Microbial chromosomal region, mitochondrion, extrachromosomal elements, and/or nucleic acid sequences measured in the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>genes</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Microbial gene(s) measured in the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>microbeType</code></span>
|
|
<span class="propertyAttr">string, required, enumeration</span><div class="property_description">Type of microorganism, from the enum list.</div><div class="property_enum"><b>Allowed values</b>: <code>"bacterium", "fungus", "microbe", "protozoan", "virus"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>organism</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">Name of the microorganism.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>proteins</code></span>
|
|
<span class="propertyAttr">array, optional, 1 or more items</span><div class="property_description">Microbial protein(s) measured in the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>variants</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Microbial gene variant(s) measured in the test.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testURL</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The URL for the test.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>turnaroundTime</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The usual number of hours or days between the time a specimen is received and a result is released. Specify the time unit (e.g. 2-3 days).</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>whoCanOrder</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">One or more types of individuals who are able to order the test.</div><div class="property_enum"><b>Allowed values</b>: <code>"Genetic Counselor", "Health Care Provider", "In-State Patients", "Licensed Dentist", "Licensed Physician", "Nurse Practitioner", "Out-of-State Patients", "Physician Assistant", "Public Health Mandate", "Registered Nurse"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>zCode</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Z-Code Identifier for this test. 5-character alpha-numeric code associated with certain molecular diagnostics (MDx) tests used in addition to the CPT code, to help payers and providers clearly understand which test is being ordered, performed, and billed.</div></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>testDeletion</code></span>
|
|
<span class="propertyAttr">object, optional</span><div class="property_description">Delete a previously registered human clinical test or clinical microbe test.</div><div class="property">
|
|
<span class="propertyName"><code>gtrAccession</code></span>
|
|
<span class="propertyAttr">None, required</span><div class="property_description">The GTR test accession number to be deleted.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>reason</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Reason for deleting the test.</div></div>
|
|
</div>
|
|
</div>
|
|
<h2 id="h2_summary_raw">Status response schema</h2>
|
|
<div class="api_scroll"><pre>
|
|
{
|
|
<span class="quotedn">"$schema"</span>: <span class="quotedv">"http://json-schema.org/draft-07/schema#"</span>,
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"title"</span>: <span class="quotedv">"GTR test submission status"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"GTR API submission status schema"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"submissionID",
|
|
"submissionDate",
|
|
"processingStatus"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"errors"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"A detailed description of each error when 'processingStatus' is 'Error'"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"input",
|
|
"userMessage"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"input"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The field names and values that are erroneous"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"field",
|
|
"value"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"field"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The json path of the item with the error"</span>
|
|
},
|
|
<span class="quotedn">"value"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The submitted value"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
}
|
|
},
|
|
<span class="quotedn">"userMessage"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The error message related to input"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"User friendly error message"</span>
|
|
}
|
|
}
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"gtrAccession"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The test accession assigned by NCBI."</span>
|
|
},
|
|
<span class="quotedn">"processingStatus"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"enum"</span>: [
|
|
"In processing",
|
|
"Success",
|
|
"Error"
|
|
]
|
|
},
|
|
<span class="quotedn">"releaseDate"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The date the record was released publicly in GTR; it is only reported after release."</span>
|
|
},
|
|
<span class="quotedn">"releaseStatus"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Indicates whether the record is released publicly in GTR and is only reported after release."</span>
|
|
},
|
|
<span class="quotedn">"submissionDate"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The date this submission was uploaded to NCBI."</span>
|
|
},
|
|
<span class="quotedn">"submissionID"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The submission identifier for the request."</span>
|
|
},
|
|
<span class="quotedn">"warnings"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"Detailed warning messages if any"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"input",
|
|
"userMessage"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"input"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The field names and values that are related to the warning"</span>,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"object"</span>,
|
|
<span class="quotedn">"required"</span>: [
|
|
"field",
|
|
"value"
|
|
],
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"field"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The json path of the item with the warning"</span>
|
|
},
|
|
<span class="quotedn">"value"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The submitted value"</span>
|
|
}
|
|
},
|
|
<span class="quotedn">"additionalProperties"</span>: false
|
|
}
|
|
},
|
|
<span class="quotedn">"userMessage"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"array"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"The warning message related to input"</span>,
|
|
<span class="quotedn">"minItems"</span>: 1,
|
|
<span class="quotedn">"items"</span>: {
|
|
<span class="quotedn">"type"</span>: <span class="quotedv">"string"</span>,
|
|
<span class="quotedn">"description"</span>: <span class="quotedv">"User friendly warning message"</span>
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"$id"</span>: <span class="quotedv">"https://submit.ncbi.nlm.nih.gov/gtr/v0.0.1/status.schema.json"</span>,
|
|
<span class="quotedn">"additionalProperties"</span>: false,
|
|
<span class="quotedn">"if"</span>: {
|
|
<span class="quotedn">"properties"</span>: {
|
|
<span class="quotedn">"processingStatus"</span>: {
|
|
<span class="quotedn">"const"</span>: <span class="quotedv">"Success"</span>
|
|
}
|
|
}
|
|
},
|
|
<span class="quotedn">"then"</span>: {
|
|
<span class="quotedn">"required"</span>: [
|
|
"gtrAccession"
|
|
]
|
|
}
|
|
}
|
|
</pre></div>
|
|
<h2 id="h2_summary_desc">Status response description</h2>
|
|
<span class="propertyOpenAll">Expand all</span>
|
|
<span class="propertyCloseAll">Collapse all</span>
|
|
<div class="json_schema">
|
|
<div class="property_description">GTR API submission status schema</div><div class="property">
|
|
<span class="propertyName"><code>errors</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">A detailed description of each error when 'processingStatus' is 'Error'</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>gtrAccession</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The test accession assigned by NCBI.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>processingStatus</code></span>
|
|
<span class="propertyAttr">string, required, enumeration</span><div class="property_enum"><b>Allowed values</b>: <code>"In processing", "Success", "Error"</code></div>
|
|
</div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>releaseDate</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">The date the record was released publicly in GTR; it is only reported after release.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>releaseStatus</code></span>
|
|
<span class="propertyAttr">string, optional</span><div class="property_description">Indicates whether the record is released publicly in GTR and is only reported after release.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>submissionDate</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">The date this submission was uploaded to NCBI.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>submissionID</code></span>
|
|
<span class="propertyAttr">string, required</span><div class="property_description">The submission identifier for the request.</div></div>
|
|
<div class="property">
|
|
<span class="propertyName"><code>warnings</code></span>
|
|
<span class="propertyAttr">array, optional, 0 or more items</span><div class="property_description">Detailed warning messages if any</div></div>
|
|
</div>
|
|
<h2 id="h2_sample">Sample Submission Script</h2>
|
|
<div id="sample_submission_script">
|
|
<p>To jumpstart your API submissions, a sample submission Python script has been provided.</p>
|
|
<div class="indent3lr">
|
|
<p>The script is available here: <a target="_blank" href="https://github.com/ncbi/gtr/blob/master/api/gtr_api.py">https://github.com/ncbi/gtr/blob/master/api/gtr_api.py</a></p>
|
|
</div>
|
|
<p>In a text or code editor, replace "YOUR-API-KEY-HERE" with the new API key.</p>
|
|
|
|
<h3 id="h3_usage">Usage</h3>
|
|
<div class="indent3lr">
|
|
<pre>
|
|
$ ./gtr_api.py -h
|
|
usage: gtr_api.py [-h]
|
|
[{gtr_sub_api,gtr_get_action,multi_subs,multi_deletes,dry_run}] [{api,apitest}]
|
|
[additional_data]
|
|
|
|
Script to call GTR api endpoints
|
|
|
|
positional arguments:
|
|
{gtr_sub_api,gtr_get_action,multi_subs,multi_deletes,dry_run}
|
|
action to perform
|
|
{api,apitest} submission mode
|
|
additional_data additional data to perform the action. For gtr_sub_api or dry_run, this is the
|
|
json file. For gtr_get_action, this is the submission ID. For multi_subs, this
|
|
is the text file of json file name list. For multi_deletes, this is the text
|
|
file of GTR accession list.
|
|
|
|
optional arguments:
|
|
-h, --help show this help message and exit
|
|
</pre>
|
|
</div>
|
|
|
|
<h3 id="h3_usage_samples">Script Usage Examples</h3>
|
|
<h4 id="h4_single_file">Submitting a Single File</h4>
|
|
<pre>
|
|
./gtr_api.py gtr_sub_api api FILE_PATH/FILE.json
|
|
</pre>
|
|
<p>Script returns:</p>
|
|
<pre>
|
|
{"file": "FILE_PATH/FILE.json", "status": 201, "id": "SUB######"}
|
|
</pre>
|
|
<h4 id="h4_multi_files">Submitting Multiple Files</h4>
|
|
<p>You can submit multiple files using the 'multi_subs' argument. 'FILE_LIST.txt' includes a list of JSON file names.</p>
|
|
<pre>
|
|
./gtr_api.py multi_subs api FILE_PATH/FILE_LIST.txt
|
|
</pre>
|
|
<h4 id="h4_delete_files">Deleting Multiple Files</h4>
|
|
<p>You can delete multiple files using the 'multi_deletes' argument. 'FILE_LIST.txt' includes a list of GTR test accessions (GTR000######).</p>
|
|
<pre>
|
|
./gtr_api.py multi_deletes api FILE_PATH/FILE_LIST.txt
|
|
</pre>
|
|
<h4 id="h4_dryrun">Performing a Dry Run</h4>
|
|
<p>Use the argument 'dry_run'.</p>
|
|
<pre>
|
|
./gtr_api.py dry_run api FILE_PATH/FILE.json
|
|
</pre>
|
|
<p>Script returns:</p>
|
|
<pre>
|
|
{"file": "FILE_PATH/FILE.json", "dry_run": true, "status": 204}
|
|
</pre>
|
|
</div>
|
|
<h2 id="h2_check_status">Checking the Submission Status</h2>
|
|
<div id="check_status">
|
|
<p>You can check on the status of your submission using the 'gtr_get_action' argument.</p>
|
|
<pre>$ gtr_api.py gtr_get_action api SUB782626</pre>
|
|
<p>The script returns the status in the following format:</p>
|
|
<pre>
|
|
{"actions":[{"id":"SUB782626-1","targetDb":"GTRTesting","status":"error","updated":"2022-07-26T12:37:19.088845Z","responses":[{"status":"error","message":{"severity":"info","errorCode":null,"text":"Your GTR submission processing status is \"Error\". Please find the details in the file referenced by actions[0].responses[0].files[0].url."},"files":[{"url":"https://dsubmit.ncbi.nlm.nih.gov/api/2.0/files/3ckxmwv0/sub782626-report.json/?format=attachment"}],"objects":[]}]}]}
|
|
</pre>
|
|
<h3 id="h3_view_json">Download and View the JSON File with Submission Status</h3>
|
|
<pre class="example">
|
|
{
|
|
"submissionID": "SUB782626",
|
|
"submissionDate": "2022-07-26",
|
|
"processingStatus": "Error",
|
|
"errors": [
|
|
{
|
|
"input": [
|
|
{
|
|
"field": "fdaReviews.reviewCategoryDesignation",
|
|
"value": null
|
|
}
|
|
],
|
|
"userMessage": [
|
|
"The value is not in the allowed list."
|
|
]
|
|
}
|
|
]
|
|
}
|
|
</pre>
|
|
</div>
|
|
<h2 id="h2_sample_submission_files">Sample Submission Files</h2>
|
|
<p>Download sample submission files here: <a target="_blank" href="https://github.com/ncbi/gtr/tree/master/api/sample_json">https://github.com/ncbi/gtr/tree/master/api/sample_json</a></p>
|
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</div>
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<script src="/core/assets/gtr/js/api.js" type="text/javascript"></script>
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