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Adding system requirements to FAQ 

fixes #492
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Clair Blacketer 2022-04-22 15:12:19 -04:00
parent 800dca15e2
commit fb07ebe7f9
6 changed files with 187 additions and 26 deletions
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156
docs/faq.html
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@ -13,7 +13,7 @@
<title>OMOP CDM Frequently Asked Questions</title> <title>OMOP CDM Frequently Asked Questions</title>
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<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
@ -29,6 +29,9 @@
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<link rel="stylesheet" href="style.css" type="text/css" /> <link rel="stylesheet" href="style.css" type="text/css" />
@ -85,6 +89,9 @@ button.code-folding-btn:focus {
summary { summary {
display: list-item; display: list-item;
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details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
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@ -222,6 +229,69 @@ $(document).ready(function () {
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}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
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padding-right: 40px;
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}
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width: 25%;
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.tocify ul, .tocify li {
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.tocify-subheader .tocify-item {
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</style>
</head> </head>
@ -231,12 +301,22 @@ $(document).ready(function () {
<div class="container-fluid main-container"> <div class="container-fluid main-container">
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
<div class="navbar-header"> <div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
<span class="icon-bar"></span> <span class="icon-bar"></span>
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@ -252,7 +332,7 @@ $(document).ready(function () {
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<span class="fa fa-landmark"></span> <span class="fa fa-landmark"></span>
Background Background
@ -272,7 +352,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-list-alt"></span> <span class="fa fa-list-alt"></span>
Conventions Conventions
@ -292,7 +372,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-history"></span> <span class="fa fa-history"></span>
CDM Versions CDM Versions
@ -310,7 +390,7 @@ $(document).ready(function () {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">NEW CDM v5.4</a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -323,7 +403,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-plus-square"></span> <span class="fa fa-plus-square"></span>
Proposals Proposals
@ -335,7 +415,7 @@ $(document).ready(function () {
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Accepted</a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -345,7 +425,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-question"></span> <span class="fa fa-question"></span>
How to How to
@ -365,7 +445,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-life-ring"></span> <span class="fa fa-life-ring"></span>
Support Support
@ -504,9 +584,36 @@ $(document).ready(function () {
<p>OHDSI runs as a distributed data network. All analyses are publicly available and can be downloaded to run at each site. The packages can be run locally and, at the data partner’s discretion, aggregate results can be shared with the study coordinator.</p> <p>OHDSI runs as a distributed data network. All analyses are publicly available and can be downloaded to run at each site. The packages can be run locally and, at the data partner’s discretion, aggregate results can be shared with the study coordinator.</p>
<p>Data partners can also make use of one of OHDSI’s open-source tools called <a href="https://github.com/OHDSI/arachne">ARACHNE</a>, a tool to facilitate distributed network analytics against the OMOP CDM.</p> <p>Data partners can also make use of one of OHDSI’s open-source tools called <a href="https://github.com/OHDSI/arachne">ARACHNE</a>, a tool to facilitate distributed network analytics against the OMOP CDM.</p>
</div> </div>
<div id="recommended-system-requirements" class="section level2">
<h2>Recommended System Requirements</h2>
<p>It is difficult to recommend what technical capabilities a site needs to set up an ETL because it is heavily dependent on the amount of data they have and how they plan to use it. Here are some examples of options that have worked well for small to medium organizations and large organizations:</p>
<p><strong>Small-to-Medium Organization</strong></p>
<ul>
<li>CDM size is 100MB to several GBs</li>
<li>Vocab ~20GB</li>
<li>Results &lt; 500 MB</li>
<li>Recommend
<ul>
<li>Server class machine disk &gt;= 250GB (SSD preferred), &gt;= 4 cores, &gt;= 32GB RAM</li>
</ul></li>
</ul>
<p><strong>Large Organization</strong></p>
<ul>
<li>CDM size is 12GB to several TBs</li>
<li>Vocab ~20GB</li>
<li>Results &lt; 500 MB</li>
<li>Recommend
<ul>
<li>Cloud-based infrastructure like multiple AWS Redshift clusters, for example:</li>
<li><img src="images/AWS_clusters.png" /></li>
</ul></li>
</ul>
</div>
</div>
</div>
</div> </div>
@ -539,6 +646,35 @@ $(document).ready(function () {
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@ -13,7 +13,7 @@
<title>index.knit</title> <title>index.knit</title>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script> <script src="site_libs/header-attrs-2.13/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script> <script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" /> <link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
@ -60,6 +60,7 @@ if (window.hljs) {
<link rel="stylesheet" href="style.css" type="text/css" /> <link rel="stylesheet" href="style.css" type="text/css" />
@ -85,6 +86,9 @@ button.code-folding-btn:focus {
summary { summary {
display: list-item; display: list-item;
} }
details > summary > p:only-child {
display: inline;
}
pre code { pre code {
padding: 0; padding: 0;
} }
@ -236,7 +240,7 @@ $(document).ready(function () {
<div class="navbar navbar-default navbar-fixed-top" role="navigation"> <div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container"> <div class="container">
<div class="navbar-header"> <div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"> <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-bs-toggle="collapse" data-target="#navbar" data-bs-target="#navbar">
<span class="icon-bar"></span> <span class="icon-bar"></span>
<span class="icon-bar"></span> <span class="icon-bar"></span>
<span class="icon-bar"></span> <span class="icon-bar"></span>
@ -252,7 +256,7 @@ $(document).ready(function () {
</a> </a>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-landmark"></span> <span class="fa fa-landmark"></span>
Background Background
@ -272,7 +276,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-list-alt"></span> <span class="fa fa-list-alt"></span>
Conventions Conventions
@ -292,7 +296,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-history"></span> <span class="fa fa-history"></span>
CDM Versions CDM Versions
@ -310,7 +314,7 @@ $(document).ready(function () {
<a href="cdm53.html">CDM v5.3</a> <a href="cdm53.html">CDM v5.3</a>
</li> </li>
<li class="dropdown-submenu"> <li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">NEW CDM v5.4</a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="cdm54.html">CDM v5.4</a> <a href="cdm54.html">CDM v5.4</a>
@ -323,7 +327,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-plus-square"></span> <span class="fa fa-plus-square"></span>
Proposals Proposals
@ -335,7 +339,7 @@ $(document).ready(function () {
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a> <a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
</li> </li>
<li class="dropdown-submenu"> <li class="dropdown-submenu">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">Accepted</a>
<ul class="dropdown-menu" role="menu"> <ul class="dropdown-menu" role="menu">
<li> <li>
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a> <a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
@ -345,7 +349,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-question"></span> <span class="fa fa-question"></span>
How to How to
@ -365,7 +369,7 @@ $(document).ready(function () {
</ul> </ul>
</li> </li>
<li class="dropdown"> <li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false"> <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-life-ring"></span> <span class="fa fa-life-ring"></span>
Support Support
@ -499,7 +503,7 @@ $(document).ready(function () {
<p>The CDM working group meets the first and third Tuesday of the month. See below for links to the meetings.</p> <p>The CDM working group meets the first and third Tuesday of the month. See below for links to the meetings.</p>
<p><strong>Every first Tuesday of the month at 1pm est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1601910741972?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%2281c21b6d-448d-4634-abbc-6b0962d1138a%22%7d">Teams Meeting</a></p> <p><strong>Every first Tuesday of the month at 1pm est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1601910741972?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%2281c21b6d-448d-4634-abbc-6b0962d1138a%22%7d">Teams Meeting</a></p>
<p><strong>Every third Tuesday of the month at 1pm est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1611000164347?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%223c193b7f-c2ab-4bcf-b88c-f89a6b1fba38%22%7d">Teams Meeting</a></p> <p><strong>Every third Tuesday of the month at 1pm est</strong> <a href="https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1611000164347?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%223c193b7f-c2ab-4bcf-b88c-f89a6b1fba38%22%7d">Teams Meeting</a></p>
<p><strong>Note</strong> If you do you have access to the OHDSI Teams Tenet, either contact Clair Blacketer at <a href="mailto:mblacke@its.jnj.com" class="email">mblacke@its.jnj.com</a> or fill out [this form] (<a href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu" class="uri">https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu</a>) and check “Common Data Model”</p> <p><strong>Note</strong> If you do you have access to the OHDSI Teams Tenet, either contact Clair Blacketer at <a href="mailto:mblacke@its.jnj.com" class="email">mblacke@its.jnj.com</a> or fill out <a href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu">this form</a> and check “Common Data Model”</p>
</div> </div>
<div id="cdm-wg-important-links" class="section level3"> <div id="cdm-wg-important-links" class="section level3">
<h3>CDM WG Important Links</h3> <h3>CDM WG Important Links</h3>

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@ -1,11 +1,12 @@
--- ---
title: "OMOP CDM Frequently Asked Questions" title: "OMOP CDM Frequently Asked Questions"
output: output:
html_document html_document:
toc: yes
toc_depth: 5
toc_float: yes
--- ---
**1. I understand that the common data model (CDM) is a way of organizing disparate data sources into the same relational database design, but how can it be effective since many databases use different coding schemes?** **1. I understand that the common data model (CDM) is a way of organizing disparate data sources into the same relational database design, but how can it be effective since many databases use different coding schemes?**
During the extract, transform, load (ETL) process of converting a data source into the OMOP common data model, we standardize the structure (e.g. tables, fields, data types), conventions (e.g. rules that govern how source data should be represented), and content (e.g. what common vocabularies are used to speak the same language across clinical domains). The common data model preserves all source data, including the original source vocabulary codes, but adds the standardized vocabularies to allow for network research across the entire OHDSI research community. During the extract, transform, load (ETL) process of converting a data source into the OMOP common data model, we standardize the structure (e.g. tables, fields, data types), conventions (e.g. rules that govern how source data should be represented), and content (e.g. what common vocabularies are used to speak the same language across clinical domains). The common data model preserves all source data, including the original source vocabulary codes, but adds the standardized vocabularies to allow for network research across the entire OHDSI research community.
@ -171,3 +172,24 @@ Queries are written in R and SQL. The [SqlRender](https://github.com/OHDSI/sqlre
OHDSI runs as a distributed data network. All analyses are publicly available and can be downloaded to run at each site. The packages can be run locally and, at the data partner’s discretion, aggregate results can be shared with the study coordinator. OHDSI runs as a distributed data network. All analyses are publicly available and can be downloaded to run at each site. The packages can be run locally and, at the data partner’s discretion, aggregate results can be shared with the study coordinator.
Data partners can also make use of one of OHDSI's open-source tools called [ARACHNE](https://github.com/OHDSI/arachne), a tool to facilitate distributed network analytics against the OMOP CDM. Data partners can also make use of one of OHDSI's open-source tools called [ARACHNE](https://github.com/OHDSI/arachne), a tool to facilitate distributed network analytics against the OMOP CDM.
## Recommended System Requirements
It is difficult to recommend what technical capabilities a site needs to set up an ETL because it is heavily dependent on the amount of data they have and how they plan to use it. Here are some examples of options that have worked well for small to medium organizations and large organizations:
**Small-to-Medium Organization**
- CDM size is 100MB to several GBs
- Vocab ~20GB
- Results < 500 MB
- Recommend
- Server class machine disk >= 250GB (SSD preferred), >= 4 cores, >= 32GB RAM
**Large Organization**
- CDM size is 12GB to several TBs
- Vocab ~20GB
- Results < 500 MB
- Recommend
- Cloud-based infrastructure like multiple AWS Redshift clusters, for example:
- ![](images/AWS_clusters.png)

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@ -51,8 +51,7 @@ The CDM working group meets the first and third Tuesday of the month. See below
**Every third Tuesday of the month at 1pm est** [Teams Meeting](https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1611000164347?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%223c193b7f-c2ab-4bcf-b88c-f89a6b1fba38%22%7d) **Every third Tuesday of the month at 1pm est** [Teams Meeting](https://teams.microsoft.com/l/meetup-join/19%3a133f2b94b86a41a884d4a4d160610148%40thread.tacv2/1611000164347?context=%7b%22Tid%22%3a%22a30f0094-9120-4aab-ba4c-e5509023b2d5%22%2c%22Oid%22%3a%223c193b7f-c2ab-4bcf-b88c-f89a6b1fba38%22%7d)
**Note** If you do you have access to the OHDSI Teams Tenet, either contact Clair Blacketer at mblacke@its.jnj.com or fill out [this form] **Note** If you do you have access to the OHDSI Teams Tenet, either contact Clair Blacketer at mblacke@its.jnj.com or fill out [this form](https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu) and check "Common Data Model"
(https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu) and check "Common Data Model"
### CDM WG Important Links ### CDM WG Important Links