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<!DOCTYPE html>
<html>
<meta charset="UTF-8"></meta>

<meta
  name="viewport"
  content="width=device-width, initial-scale=1.0">
</meta>

<style>table, th, td {   border: 1px solid black; }</style>

<title>PEDSnet Codeset Library</title>

<link
  href="style.css"
  rel="stylesheet"
  type="text/css"
  title="Cool stylesheet">
</link>

<h1>Introduction</h1>

<p>
  This site links researchers with the various codesets developed by the PEDSnet team for
  identifying patient cohorts, treatments or outcomes in our database.  We are making them available
  here for both potential collaborators and outside researchers whose work can benefit from what we
  have already done.
</p>

<p>
  The codesets are based on the

  <i>Common Data Model</i>

  as described

  <a href="https://github.com/PEDSnet/data_science_training/blob/master/reading_materials/session_1/ETL Conventions for use with PEDSnet CDM v3.2 OMOP V5.2.pdf">
    here
  </a>

  . The exception is the “Query Logic” group which contains R files that draw on the codesets   and
  implement other logic and   calculations.
</p>

<p>
  Usually codesets will be of the “

  <i>iccc</i>

  ” form,

  <i>integer concept_id</i>

  and three text fields:

  <i>concept_code</i>

  ,

  <i>concept_name</i>

  , and

  <i>vocabulary_id</i>

  .  Note that for labs done, the performance of the lab may be listed as a Procedure, but the
  results of the lab may be listed as a Measurement.
</p>

<p>Please contact us at [Email goes here] if you wish to:</p>

<ul>
  <li>Ask about a codeset you can’t find or understand</li>

  <li>Suggest revisions of a codeset</li>

  <li>Send us a proposed new codeset</li>

  <li>Collaborate in some other way with PEDSnet research</li>
</ul>

<p></p>

<h1>Codeset Groupings</h1>

<div id="root"></div>

<table style="width:100%">
  <tbody>
    <tr><th>Group</th><th>Brief Description</th><th>Vocabularies Typically Used</th></tr>

    <tr>
      <td><a href="conditions_list.html">Conditions</a></td>

      <td>Diagnoses of interest in the<i>condition_occurrence</i>table</td>

      <td>
        SNOMED for searching on

        <i>condition_concept_id</i>

        , ICD 9 and ICD10 for searching on

        <i>condition_source_concept_id</i>

        . The Nebraska Lexicon is not used.
      </td>
    </tr>

    <tr>
      <td>Drugs</td>

      <td>Diagnoses of interest in the<i>drug_exposure</i>table</td>

      <td>
        RxNorm for searching on

        <i>drug_concept_id</i>

        or, if necessary, on

        <i>drug_source_concept_id</i>
      </td>
    </tr>

    <tr>
      <td>Procedures, including labs performed</td>

      <td>
        Specific procedures, including diagnostic tests, performed on a patient as described in the

        <i>procedure_occurrence</i>

        table
      </td>

      <td>CPT4, HCPCS, ICD9Proc, ICD10Proc</td>
    </tr>

    <tr>
      <td>Measurements, including lab results</td>

      <td>
        Specific measurements of interest as described in the

        <i>measurements</i>

        table.  Querying measurments should also check units.
      </td>

      <td>LOINC for lab results</td>
    </tr>

    <tr>
      <td><a href="r_code_list.html">Query code</a></td>

      <td>R or SQL code developed and tested to extract specific estimates (such as Z-scores or estimated Glomerular Flow Rate) or phenotypes (such as Glomerular Disease)</td>
      <td>Not applicable</td>


    <script
      src="main.js"
      type="text/javascript">
    </script>
  </tbody>
</table>
</html>