Documentation updates to support CDM v5.4
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Clair Blacketer
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README.md
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README.md
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---
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title: "Readme"
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output:
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pdf_document:
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toc: yes
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html_document:
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toc: TRUE
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toc_float: TRUE
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toc: yes
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toc_float: yes
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---
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# How to Update the CDM
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# How to Use this Repository
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**NOTE** This information is for the maintainers of the CDM as it is best for all information to be in one place. If you want to suggest an update or addition to the OMOP CDM please visit the [CommonDataModel repo](https://github.com/OHDSI/CommonDataModel/issues). The instructions contained herein are meant to describe the process by which new versions of the CDM are produced, should it need to be replicated in the future. These steps are also enumerated in `extras/codeToRun.R`.
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## Generating the DDLs
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*By John and Sam Gresh*
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Typically, new CDM versions and updates are decided by the CDM working group (details to join meetings on [homepage](https://ohdsi.github.io/CommonDataModel/)). These changes are tracked as issues in the [github repo](https://github.com/OHDSI/CommonDataModel/issues). Once the working group decides which changes make up a version, all the corresponding issues should be tagged with a version number e.g. v6.1.
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If you prefer to generate the DDLs on your own without downloading them from the github tags, these instructions will guide you on how to do so.
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### Introduction
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This module will demonstrate how to individually create the DDL scripts for DDL, foreign keys, primary keys, and indexed for a single database instance at a time. This module is intended for end users that wish to generate these scripts from R without the need to clone or download the source code from github. The scripts that are created through this process are available as zip files here (TODO: NEED LINK).
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#### Dependencies and prerequisites
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This process required R-Studio to be installed as well as [DatabaseConnector](https://github.com/ohdsi/DatabaseConnector) and [SqlRender](https://github.com/ohdsi/SqlRender).
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#### Create DDL, Foreign Keys, Primary Keys, and Indexes from R
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Launch R-Studio and create a new project: File -> New Project -> New Directory -> New Project
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After completing this step you should see something like the following:
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For the next step, you can either open a new R script (File -> New File -> R Script), paste the text in the console, or open an R notebook (File -> New File -> New R Notebook). Whatever you choose, paste the following, replacing "output" with the name of the output file where you want the DDLs to appear and "YOUR_CDM_SCHEMA" with the name of your CDM schema. In this example we are generating the postgresql DDLs by specifying the dialect in the function calls. To determine which dialects are supported, run the `CommonDataModel::listSupportedDialects()` function.
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```{r}
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if (!require("devtools")) install.packages("devtools")
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devtools::install_github("OHDSI/CommonDataModel", "v5.4")
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CommonDataModel::writeDdl("postgresql", "5.4", "output", "YOUR_CDM_SCHEMA")
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CommonDataModel::writeForeignKeys("postgresql", "5.4", "output", "YOUR_CDM_SCHEMA")
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CommonDataModel::writePrimaryKeys("postgresql", "5.4", "output", "YOUR_CDM_SCHEMA")
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CommonDataModel::writeIndex("postgresql", "5.4", "output", "YOUR_CDM_SCHEMA")
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```
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You will then see something like the below, with your output directory created and the DDLs available in the folder you specified.
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## Bug Fixes/Model Updates
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**NOTE** This information is for the maintainers of the CDM as well as anyone looking to submit a pull request. If you want to suggest an update or addition to the OMOP Common Data Model itself please open an [issue](https://github.com/OHDSI/CommonDataModel/issues) using the proposal template. The instructions contained herein are meant to describe the process by which bugs in the DDL code should be addressed and/or new versions of the CDM are produced.
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*Just looking for the latest version of the CDM and you don't care about the R package? Please visit the [releases tab](https://github.com/OHDSI/CommonDataModel/tags) and download the latest. It will include the DDLs for all currently supported versions of the CDM for all supported SQL dialects.*
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Typically, new CDM versions and updates are decided by the CDM working group (details to join meetings on [homepage](https://ohdsi.github.io/CommonDataModel/)). These changes are tracked as issues in the [github repo](https://github.com/OHDSI/CommonDataModel/issues). Once the working group decides which changes make up a version, all the corresponding issues should be tagged with a version number, e.g. v5.4, and added to a project board.
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## Step 0
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All the issues and additions that are incorporated into the new CDM version will be handled in the [CommonDataModel repository](https://github.com/OHDSI/CommonDataModel). Changes should be made in the representative csv files and it is the job of the CdmDdlBase repo to take those files and convert them to DDLs and documentation. This README will walk through how to update and create all the relevant DDLs, constraints, indices, and documentation for the CDM utilizing both the CommonDataModel repo and the CdmDdlBase repo.
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**Changes to the model structure** should be made in the representative csv files by adding, subtracting, or renaming fields or tables. ETL conventions are not currently tracked by CDM version unless they are conventions specific to new fields (for example CONDITION_STATUS was added in v5.3 which specifies the way in which primary condition designations should be captured).
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**Bug fixes** are made much the same way using the csv files, but they should be limited to typos, primary/foreign key relationships, and formatting (like datetime vs datetime2).
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## Step 1
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Create a branch in the CommonDataModel repository for the new version of the CDM you are creating.
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If you are making **changes to the model structure** request a new branch in the CommonDataModel repository for the new version of the CDM you are creating. Then, fork the repository and clone the newly made branch. If you are **squashing bugs** fork the repository and clone the master branch.
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### Step 1.1
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Rename the csv files from the current released version to the new version. For example, if the new version you are creating is v6.0 and the most recent released version is v5.3.1, rename the csv files named "OMOP_CDMv5.3.1_Field_Level.csv" and "OMOP_CDMv5.3.1_Table_Level.csv" to "OMOP_CDMv6.0_Field_Level.csv" and "OMOP_CDMv6.0_Table_Level.csv". These files serve multiple functions; they serve as the basis for the CDM DDL, CDM documentation, and Data Quality Dashboard (DQD). You can read more about the DQD [here](https://ohdsi.github.io/DataQualityDashboard/index.html).
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For **changes to the model structure**, rename the table level and field level inst/csv files from the current released version to the new version. For example, if the new version you are creating is v5.4 and the most recent released version is v5.3, rename the csv files named "OMOP_CDMv5.3_Field_Level.csv" and "OMOP_CDMv5.3_Table_Level.csv" to "OMOP_CDMv5.4_Field_Level.csv" and "OMOP_CDMv5.4_Table_Level.csv". These files serve multiple functions; they serve as the basis for the CDM DDL, CDM documentation, and Data Quality Dashboard (DQD). You can read more about the DQD [here](https://ohdsi.github.io/DataQualityDashboard/index.html).
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For **squashing bugs** make the necessary changes in the csv file corresponding to the major.minor version you are fixing. For example, if you are working on fixes to v5.3.3 you would make changes in the v5.3 files. (skip to step 2)
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### Step 1.2
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The csv files can now be updated with the changes and additions for the new CDM version. If a new table should be added, add a line to the *Table_Level.csv* with the table name and description and list it as part of the CDM schema. The remaining columns are quality checks that can be run. Details [here](https://ohdsi.github.io/DataQualityDashboard/index.html) on what those are. After adding any tables, make any changes or additions to CDM fields in the *Field_Level.csv*. The columns are meant to mimic how a DDL is structured, which is how it will eventually be generated. A yes in the field *isRequired* indicates a NOT NULL constraint and the datatype field should be filled in exactly how it would look in the DDL. Any additions or changes should also be reflected in the userGuidance and etlConventions fields, which are the basis for the documentation. **DO NOT MAKE ANY CHANGES IN THE DDL ITSELF**. The structure is set up in such a way that the csv files are the ground truth. If changes are made in the DDL instead of the csv files then the DDL will be out of sync with the documentation and the DQD.
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## Step 2
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Push the csv files up to the branch for the new CDM version and then switch to the CdmDdlBase repository. Get the zip url for the CDM branch (on the github page for the branch, click on the green download button and then right click on download zip to get the url) in progress and use the file `packageMaintenance.R` and the instructions therein to copy the csv files over to the inst/csv folder of the CdmDdlBase package. For each CDM version represented in CdmDdlBase there should be two csv files. For example, CDM v5.3.1 has csv files "OMOP_CDMv5.3.1_Field_Level" and "OMOP_CDMv5.3.1_Table_Level" in the inst/csv folder.
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Once all changes are made the csvs, rebuild the package and then open `extras/codeToRun.R`. To make sure that your new version is recognized by the package run the function `listSupportedVersions()`. If you do not see it, make sure your new csv files are in inst/csv and that you have rebuilt the package. Once you have confirmed that the package recognizes your new version, run the function `buildRelease()`. You should now see a file in inst/ddl for your new version.
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## Step 3
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Once all changes are made the csvs, open `extras/codeToRun.R` and run the `createDdlFromFile` function, setting the parameters `cdmTableCsvLoc` and `cdmFieldCsvLoc` to the locations of the csv files created in step 3. For example, the `cdmTableCsvLoc` for cdm v5.3.1 is "inst/csv/OMOP_CDMv5.3.1_Table_Level.csv". This will create a sql file in *inst/sql/sql_server* with the ddl for the current cdm version. Once the DDL is created, run the `createPkFromFile` and `createFkFromFile` functions to create the primary key and foreign key scripts.
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**NOTE ABOUT CDM v6.0**
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====================
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## Step 4
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Use the`writeDDL` function to tranlate the sql script created in the step above into oracle, postgres, and sql server dialects.
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**NOTE** This documentation is a work in progress and will continue to be updated.
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Please be aware that v6.0 of the OMOP CDM is **not** fully supported by the OHDSI suite of tools and methods. The major difference in CDM v5.3 and CDM v6.0 involves switching the \*_datetime fields to mandatory rather than optional. This switch radically changes the assumptions related to exposure and outcome timing. Rather than move forward with v6.0, please transform your data to [CDM v5.4](https://github.com/OHDSI/CommonDataModel/releases/tag/v5.4) until such time that we as a community have fully defined the role of dates vs datetimes both when it comes to the model and the evidence we generate.
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<li>
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<a href="background.html">Model Background</a>
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</li>
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<li>
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<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
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</li>
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<li>
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<a href="vocabulary.html">How the Vocabulary is Built</a>
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</li>
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</ul>
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</li>
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<li>
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<a href="dataModelConventions.html">
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<span class="fas fa-list-alt"></span>
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Conventions
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<span class="caret"></span>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="dataModelConventions.html">General Conventions</a>
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</li>
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<li>
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<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
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</li>
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<li>
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<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
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</li>
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</ul>
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</li>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<a href="cdm30.html">CDM v3.0</a>
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</li>
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<li>
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<a href="cdm531.html">CDM v5.3.1</a>
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<a href="cdm60.html">CDM v6.0</a>
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</li>
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<li>
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<a href="cdm60.html">CDM v6.0</a>
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<a href="cdm53.html">CDM v5.3</a>
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</li>
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<li class="dropdown-submenu">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="cdm54.html">CDM v5.4</a>
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</li>
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<li>
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<a href="cdm54Changes.html">Changes from CDM v5.3</a>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="reviewProposals.html">Under Review</a>
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<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
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</li>
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<li class="dropdown-submenu">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="oncology.html">Oncology CDM Proposal</a>
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<li>
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<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
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</li>
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<li>
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<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
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</li>
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</ul>
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</li>
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</ul>
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<span class="fas fa-question"></span>
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Help
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How to
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="download.html">Download the DDL</a>
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</li>
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<li>
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<a href="cdmRPackage.html">Use the CDM R Package</a>
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</li>
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<li>
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<a href="drug_dose.html">Calculate Drug Dose</a>
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</li>
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</ul>
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<li>
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<a href="faq.html">FAQ</a>
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<a href="contribute.html">Ask a Question</a>
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<a href="sqlScripts.html">SQL Scripts</a>
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<a href="download.html">Download the DDL</a>
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</li>
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<li>
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<a href="drug_dose.html">Calculate Drug Dose</a>
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<a href="contribute.html">Ask a Question</a>
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</li>
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</ul>
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</li>
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<ul class="nav navbar-nav navbar-right">
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<a href="https://github.com/OHDSI/CommonDataModel">
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<span class="fas fa-github fa-lg"></span>
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<span class="fas fa-github"></span>
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<li>Develop tools and capabilities for transforming, characterizing, and analysing disparate data sources across the health care delivery spectrum</li>
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<li>Establish a shared resource so that the broader research community can collaboratively advance the science</li>
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</ul>
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<p>The results of OMOP’s research has been widely published and presented at scientific conferences, including <a href="https://www.ohdsi.org/events/2019-ohdsi-symposium/">annual symposia</a>.</p>
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<p>The results of OMOP’s research has been widely published and presented at scientific conferences, including <a href="https://www.ohdsi.org/2021-ohdsi-global-symposium-info/">annual symposia</a>.</p>
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<p>The OMOP Legacy continues…</p>
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<p>The community is actively using the OMOP Common Data Model for their various research purposes. Those tools will continue to be maintained and supported, and information about this work is available in the <a href="http://www.github.com/ohdsi">public domain</a>.</p>
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<p>The OMOP Common Data Model will continue to be an open-source community standard for observational healthcare data. The model specifications and associated work products will be placed in the public domain, and the entire research community is encouraged to use these tools to support everybody’s own research activities.</p>
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@ -380,17 +380,33 @@ div.tocify {
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<li>
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<a href="background.html">Model Background</a>
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</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
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||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="dataModelConventions.html">
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<span class="fas fa-list-alt"></span>
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||||
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||||
Conventions
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||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
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||||
<a href="dataModelConventions.html">General Conventions</a>
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||||
</li>
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||||
<li>
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<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
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||||
</li>
|
||||
<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
||||
</li>
|
||||
</ul>
|
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</li>
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<li class="dropdown">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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|
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@ -405,10 +421,21 @@ div.tocify {
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<a href="cdm30.html">CDM v3.0</a>
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||||
</li>
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||||
<li>
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||||
<a href="cdm531.html">CDM v5.3.1</a>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
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<a href="cdm53.html">CDM v5.3</a>
|
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</li>
|
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<li class="dropdown-submenu">
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
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<ul class="dropdown-menu" role="menu">
|
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<li>
|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
</ul>
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</li>
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||||
</ul>
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</li>
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</a>
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<ul class="dropdown-menu" role="menu">
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<li>
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<a href="reviewProposals.html">Under Review</a>
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<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
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|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -444,7 +465,27 @@ div.tocify {
|
|||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-question"></span>
|
||||
|
||||
Help
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-life-ring"></span>
|
||||
|
||||
Support
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
|
|
@ -452,28 +493,11 @@ div.tocify {
|
|||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -481,7 +505,7 @@ div.tocify {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fas fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@
|
|||
|
||||
|
||||
|
||||
<title>cdm531.utf8</title>
|
||||
<title>cdm53.utf8</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.6/header-attrs.js"></script>
|
||||
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
|
||||
|
|
@ -380,17 +380,33 @@ div.tocify {
|
|||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="dataModelConventions.html">
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-list-alt"></span>
|
||||
|
||||
Conventions
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="dataModelConventions.html">General Conventions</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
|
|
@ -405,10 +421,21 @@ div.tocify {
|
|||
<a href="cdm30.html">CDM v3.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm531.html">CDM v5.3.1</a>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -422,20 +449,14 @@ div.tocify {
|
|||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="reviewProposals.html">Under Review</a>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -444,7 +465,27 @@ div.tocify {
|
|||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-question"></span>
|
||||
|
||||
Help
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-life-ring"></span>
|
||||
|
||||
Support
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
|
|
@ -452,28 +493,11 @@ div.tocify {
|
|||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -481,7 +505,7 @@ div.tocify {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fas fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
@ -498,9 +522,10 @@ div.tocify {
|
|||
</div>
|
||||
|
||||
|
||||
<div id="omop-cdm-v5.3.1" class="section level1">
|
||||
<h1><strong>OMOP CDM v5.3.1</strong></h1>
|
||||
<p>Below is the specification document for the OMOP Common Data Model, v5.3.1. Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the <a href="https://forums.ohdsi.org/">forums</a> or the <a href="https://github.com/ohdsi/CommonDataModel/issues">github issue</a> page.</p>
|
||||
<div id="omop-cdm-v5.3" class="section level1">
|
||||
<h1><strong>OMOP CDM v5.3</strong></h1>
|
||||
<p>Below is the specification document for the OMOP Common Data Model, v5.3 (previously v5.3.1). Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the <a href="https://forums.ohdsi.org/">forums</a> or the <a href="https://github.com/ohdsi/CommonDataModel/issues">github issue</a> page.</p>
|
||||
<p><em><strong>Special Note</strong> This documentation previously referenced v5.3.1. During the OHDSI/CommonDataModel Hack-A-Thon that occurred on August 18, 2021 the decision was made to align documentation with the minor releases. Hot fixes and minor.minor release can be found through the searching of tags.</em></p>
|
||||
<p>–after regeneration of DDLs link to csv of cdm link to pdf of cdm documentation link to forum on doc page</p>
|
||||
<div id="clinical-data-tables" class="section level2">
|
||||
<h2><strong>Clinical Data Tables</strong></h2>
|
||||
|
|
@ -12203,7 +12228,7 @@ No
|
|||
valid_start_date
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The date when the Concept was first recorded. The default value is 1-Jan-1970.
|
||||
The date when the Concept was first recorded. The default value is <<<<<<< HEAD:inst/csv/OMOP_CDMv5.3_Field_Level.csv 1-Jan-1970.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
BIN
docs/cdm531.pdf
BIN
docs/cdm531.pdf
Binary file not shown.
File diff suppressed because it is too large
Load Diff
|
|
@ -0,0 +1,941 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>cdm54Changes.utf8</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.6/header-attrs.js"></script>
|
||||
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
|
||||
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
|
||||
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
|
||||
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
|
||||
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
|
||||
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
|
||||
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
|
||||
<script src="site_libs/navigation-1.1/tabsets.js"></script>
|
||||
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
|
||||
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
|
||||
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
|
||||
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
|
||||
<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
|
||||
|
||||
<style type="text/css">
|
||||
code{white-space: pre-wrap;}
|
||||
span.smallcaps{font-variant: small-caps;}
|
||||
span.underline{text-decoration: underline;}
|
||||
div.column{display: inline-block; vertical-align: top; width: 50%;}
|
||||
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
|
||||
ul.task-list{list-style: none;}
|
||||
</style>
|
||||
|
||||
<style type="text/css">code{white-space: pre;}</style>
|
||||
<style type="text/css">
|
||||
pre:not([class]) {
|
||||
background-color: white;
|
||||
}
|
||||
</style>
|
||||
<script type="text/javascript">
|
||||
if (window.hljs) {
|
||||
hljs.configure({languages: []});
|
||||
hljs.initHighlightingOnLoad();
|
||||
if (document.readyState && document.readyState === "complete") {
|
||||
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
|
||||
}
|
||||
}
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
h1 {
|
||||
font-size: 34px;
|
||||
}
|
||||
h1.title {
|
||||
font-size: 38px;
|
||||
}
|
||||
h2 {
|
||||
font-size: 30px;
|
||||
}
|
||||
h3 {
|
||||
font-size: 24px;
|
||||
}
|
||||
h4 {
|
||||
font-size: 18px;
|
||||
}
|
||||
h5 {
|
||||
font-size: 16px;
|
||||
}
|
||||
h6 {
|
||||
font-size: 12px;
|
||||
}
|
||||
.table th:not([align]) {
|
||||
text-align: left;
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
||||
<style type = "text/css">
|
||||
.main-container {
|
||||
max-width: 940px;
|
||||
margin-left: auto;
|
||||
margin-right: auto;
|
||||
}
|
||||
code {
|
||||
color: inherit;
|
||||
background-color: rgba(0, 0, 0, 0.04);
|
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}
|
||||
img {
|
||||
max-width:100%;
|
||||
}
|
||||
.tabbed-pane {
|
||||
padding-top: 12px;
|
||||
}
|
||||
.html-widget {
|
||||
margin-bottom: 20px;
|
||||
}
|
||||
button.code-folding-btn:focus {
|
||||
outline: none;
|
||||
}
|
||||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
/* padding for bootstrap navbar */
|
||||
body {
|
||||
padding-top: 51px;
|
||||
padding-bottom: 40px;
|
||||
}
|
||||
/* offset scroll position for anchor links (for fixed navbar) */
|
||||
.section h1 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h2 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h3 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h4 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h5 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h6 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.dropdown-submenu {
|
||||
position: relative;
|
||||
}
|
||||
.dropdown-submenu>.dropdown-menu {
|
||||
top: 0;
|
||||
left: 100%;
|
||||
margin-top: -6px;
|
||||
margin-left: -1px;
|
||||
border-radius: 0 6px 6px 6px;
|
||||
}
|
||||
.dropdown-submenu:hover>.dropdown-menu {
|
||||
display: block;
|
||||
}
|
||||
.dropdown-submenu>a:after {
|
||||
display: block;
|
||||
content: " ";
|
||||
float: right;
|
||||
width: 0;
|
||||
height: 0;
|
||||
border-color: transparent;
|
||||
border-style: solid;
|
||||
border-width: 5px 0 5px 5px;
|
||||
border-left-color: #cccccc;
|
||||
margin-top: 5px;
|
||||
margin-right: -10px;
|
||||
}
|
||||
.dropdown-submenu:hover>a:after {
|
||||
border-left-color: #ffffff;
|
||||
}
|
||||
.dropdown-submenu.pull-left {
|
||||
float: none;
|
||||
}
|
||||
.dropdown-submenu.pull-left>.dropdown-menu {
|
||||
left: -100%;
|
||||
margin-left: 10px;
|
||||
border-radius: 6px 0 6px 6px;
|
||||
}
|
||||
</style>
|
||||
|
||||
<script>
|
||||
// manage active state of menu based on current page
|
||||
$(document).ready(function () {
|
||||
// active menu anchor
|
||||
href = window.location.pathname
|
||||
href = href.substr(href.lastIndexOf('/') + 1)
|
||||
if (href === "")
|
||||
href = "index.html";
|
||||
var menuAnchor = $('a[href="' + href + '"]');
|
||||
|
||||
// mark it active
|
||||
menuAnchor.parent().addClass('active');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.dropdown').addClass('active');
|
||||
});
|
||||
</script>
|
||||
|
||||
<!-- tabsets -->
|
||||
|
||||
<style type="text/css">
|
||||
.tabset-dropdown > .nav-tabs {
|
||||
display: inline-table;
|
||||
max-height: 500px;
|
||||
min-height: 44px;
|
||||
overflow-y: auto;
|
||||
background: white;
|
||||
border: 1px solid #ddd;
|
||||
border-radius: 4px;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li.active:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
|
||||
content: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li.active {
|
||||
display: block;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li > a,
|
||||
.tabset-dropdown > .nav-tabs > li > a:focus,
|
||||
.tabset-dropdown > .nav-tabs > li > a:hover {
|
||||
border: none;
|
||||
display: inline-block;
|
||||
border-radius: 4px;
|
||||
background-color: transparent;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
|
||||
display: block;
|
||||
float: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li {
|
||||
display: none;
|
||||
}
|
||||
</style>
|
||||
|
||||
<!-- code folding -->
|
||||
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
|
||||
#TOC {
|
||||
margin: 25px 0px 20px 0px;
|
||||
}
|
||||
@media (max-width: 768px) {
|
||||
#TOC {
|
||||
position: relative;
|
||||
width: 100%;
|
||||
}
|
||||
}
|
||||
|
||||
@media print {
|
||||
.toc-content {
|
||||
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
|
||||
float: right;
|
||||
}
|
||||
}
|
||||
|
||||
.toc-content {
|
||||
padding-left: 30px;
|
||||
padding-right: 40px;
|
||||
}
|
||||
|
||||
div.main-container {
|
||||
max-width: 1200px;
|
||||
}
|
||||
|
||||
div.tocify {
|
||||
width: 20%;
|
||||
max-width: 260px;
|
||||
max-height: 85%;
|
||||
}
|
||||
|
||||
@media (min-width: 768px) and (max-width: 991px) {
|
||||
div.tocify {
|
||||
width: 25%;
|
||||
}
|
||||
}
|
||||
|
||||
@media (max-width: 767px) {
|
||||
div.tocify {
|
||||
width: 100%;
|
||||
max-width: none;
|
||||
}
|
||||
}
|
||||
|
||||
.tocify ul, .tocify li {
|
||||
line-height: 20px;
|
||||
}
|
||||
|
||||
.tocify-subheader .tocify-item {
|
||||
font-size: 0.90em;
|
||||
}
|
||||
|
||||
.tocify .list-group-item {
|
||||
border-radius: 0px;
|
||||
}
|
||||
|
||||
|
||||
</style>
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
<!-- setup 3col/9col grid for toc_float and main content -->
|
||||
<div class="row-fluid">
|
||||
<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">
|
||||
|
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|
||||
|
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|
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<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
<div class="container">
|
||||
<div class="navbar-header">
|
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<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
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<span class="icon-bar"></span>
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<span class="icon-bar"></span>
|
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<span class="icon-bar"></span>
|
||||
</button>
|
||||
<a class="navbar-brand" href="index.html"><div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div></a>
|
||||
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|
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|
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<ul class="nav navbar-nav">
|
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<li>
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<span class="fas fa-landmark"></span>
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|
||||
|
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<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
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|
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|
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|
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|
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|
||||
|
||||
<span class="caret"></span>
|
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</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="dataModelConventions.html">General Conventions</a>
|
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|
||||
<li>
|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
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</li>
|
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<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
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|
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|
||||
|
||||
<span class="caret"></span>
|
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</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
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|
||||
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|
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|
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|
||||
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|
||||
</li>
|
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|
||||
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|
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</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
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|
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|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
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|
||||
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|
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</ul>
|
||||
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|
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<li class="dropdown">
|
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
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<span class="fas fa-plus-square"></span>
|
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||||
Proposals
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
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<li class="dropdown">
|
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<span class="fas fa-question"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
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<span class="fas fa-life-ring"></span>
|
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|
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|
||||
|
||||
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|
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</a>
|
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<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
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<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
</ul>
|
||||
</div><!--/.nav-collapse -->
|
||||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
||||
<div class="fluid-row" id="header">
|
||||
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<div id="changes-by-table" class="section level1">
|
||||
<h1><strong>Changes by Table</strong></h1>
|
||||
<p><em>from CDM v5.3 -> CDM v5.4</em></p>
|
||||
<p>For a full description of each table and field listed here, please see the <a href="http://ohdsi.github.io/CommonDataModel/cdm54.html">CDM specification</a>.</p>
|
||||
<p>Notation:</p>
|
||||
<ul>
|
||||
<li>a <strong>+</strong> indicates an addition to the model, either a table or field</li>
|
||||
<li>a <strong>-></strong> indicates an alteration either in naming or specification</li>
|
||||
<li>a <strong>-</strong> indicates a subtraction from the model, either a table or field</li>
|
||||
</ul>
|
||||
<div id="person" class="section level2">
|
||||
<h2>PERSON</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="observation_period" class="section level2">
|
||||
<h2>OBSERVATION_PERIOD</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="visit_occurrence" class="section level2">
|
||||
<h2>VISIT_OCCURRENCE</h2>
|
||||
<ul>
|
||||
<li>Admitting_source_concept_id -> <strong>Admitted_from_concept_id</strong></li>
|
||||
<li>Admitting_source_value -> <strong>Admitted_from_source_value</strong></li>
|
||||
<li>Discharge_to_concept_id -> <strong>Discharged_to_concept_id</strong></li>
|
||||
<li>Discharge_to_source_value -> <strong>Discharged_to_concept_id</strong></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="visit_detail" class="section level2">
|
||||
<h2>VISIT_DETAIL</h2>
|
||||
<ul>
|
||||
<li>Admitting_source_concept_id -> <strong>Admitted_from_concept_id</strong></li>
|
||||
<li>Admitting_source_value -> <strong>Admitted_from_source_value</strong></li>
|
||||
<li>Discharge_to_concept_id -> <strong>Discharged_to_concept_id</strong></li>
|
||||
<li>Discharge_to_source_value -> <strong>Discharged_to_concept_id</strong></li>
|
||||
<li>Visit_detail_parent_id -> <strong>Parent_visit_detail_id</strong></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="condition_occurrence" class="section level2">
|
||||
<h2>CONDITION_OCCURRENCE</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="drug_exposure" class="section level2">
|
||||
<h2>DRUG_EXPOSURE</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="procedure_occurrence" class="section level2">
|
||||
<h2>PROCEDURE_OCCURRENCE</h2>
|
||||
<ul>
|
||||
<li>+ <strong>Procedure_end_date</strong></li>
|
||||
<li>+ <strong>Procedure_end_datetime</strong></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="device_exposure" class="section level2">
|
||||
<h2>DEVICE_EXPOSURE</h2>
|
||||
<ul>
|
||||
<li>Unique_device_id -> <strong>Changed to varchar(255)</strong></li>
|
||||
<li>+ <strong>Production_id</strong></li>
|
||||
<li>+ <strong>Unit_concept_id</strong></li>
|
||||
<li>+ <strong>Unit_source_value</strong></li>
|
||||
<li>+ <strong>Unit_source_concept_id</strong></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="measurement" class="section level2">
|
||||
<h2>MEASUREMENT</h2>
|
||||
<ul>
|
||||
<li>+ <strong>Unit_source_concept_id</strong></li>
|
||||
<li>+ <strong>Measurement_event_id</strong></li>
|
||||
<li>+ <strong>Meas_event_field_concept_id</strong></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="observation" class="section level2">
|
||||
<h2>OBSERVATION</h2>
|
||||
<ul>
|
||||
<li>+ <strong>Value_source_value</strong></li>
|
||||
<li>+ <strong>Observation_event_id</strong></li>
|
||||
<li>+ <strong>Obs_event_field_concept_id</strong></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="death" class="section level2">
|
||||
<h2>DEATH</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="note" class="section level2">
|
||||
<h2>NOTE</h2>
|
||||
<ul>
|
||||
<li>+ <strong>Note_event_id</strong></li>
|
||||
<li>+ <strong>Note_event_field_concept_id</strong></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="note_nlp" class="section level2">
|
||||
<h2>NOTE_NLP</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="specimen" class="section level2">
|
||||
<h2>SPECIMEN</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="fact_relationship" class="section level2">
|
||||
<h2>FACT_RELATIONSHIP</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="location" class="section level2">
|
||||
<h2>LOCATION</h2>
|
||||
<ul>
|
||||
<li>+ <strong>Country_concept_id</strong></li>
|
||||
<li>+ <strong>Country_source_value</strong></li>
|
||||
<li>+ <strong>Latitude</strong></li>
|
||||
<li>+ <strong>Longitude</strong></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="care_site" class="section level2">
|
||||
<h2>CARE_SITE</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="payer_plan_period" class="section level2">
|
||||
<h2>PAYER_PLAN_PERIOD</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="cost" class="section level2">
|
||||
<h2>COST</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="drug_era" class="section level2">
|
||||
<h2>DRUG_ERA</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="dose_era" class="section level2">
|
||||
<h2>DOSE_ERA</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="condition_era" class="section level2">
|
||||
<h2>CONDITION_ERA</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="episode" class="section level2">
|
||||
<h2>+ <strong>EPISODE</strong></h2>
|
||||
<table>
|
||||
<thead>
|
||||
<tr class="header">
|
||||
<th>EPISODE</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td>episode_id</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>person_id</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>episode_concept_id</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>episode_start_date</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>episode_start_datetime</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>episode_end_date</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>episode_end_datetime</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>episode_parent_id</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>episode_number</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>episode_object_concept_id</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>episode_type_concept_id</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>episode_source_value</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>episode_source_concept_id</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div id="episode_event" class="section level2">
|
||||
<h2>+ <strong>EPISODE_EVENT</strong></h2>
|
||||
<table>
|
||||
<thead>
|
||||
<tr class="header">
|
||||
<th>EPISODE_EVENT</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td>episode_id</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>event_id</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>episode_event_field_concept_id</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div id="metadata" class="section level2">
|
||||
<h2>METADATA</h2>
|
||||
<ul>
|
||||
<li>+ <strong>Metadata_id</strong></li>
|
||||
<li>+ <strong>Value_as_number</strong></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="cdm_source" class="section level2">
|
||||
<h2>CDM_SOURCE</h2>
|
||||
<ul>
|
||||
<li>Cdm_source_name -> <strong>Mandatory field</strong></li>
|
||||
<li>Cdm_source_abbreviation -> <strong>Mandatory field</strong></li>
|
||||
<li>Cdm_holder -> <strong>Mandatory field</strong></li>
|
||||
<li>Source_release_date -> <strong>Mandatory field</strong></li>
|
||||
<li>Cdm_release_date -> <strong>Mandatory field</strong></li>
|
||||
<li>+ <strong>Cdm_version_concept_id</strong></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="concept" class="section level2">
|
||||
<h2>CONCEPT</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="vocabulary" class="section level2">
|
||||
<h2>VOCABULARY</h2>
|
||||
<ul>
|
||||
<li>Vocabulary_reference -> <strong>Non-mandatory field</strong></li>
|
||||
<li>Vocabulary_version -> <strong>Non-mandatory field</strong></li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="domain" class="section level2">
|
||||
<h2>DOMAIN</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="concept_class" class="section level2">
|
||||
<h2>CONCEPT_CLASS</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="concept_relationship" class="section level2">
|
||||
<h2>CONCEPT_RELATIONSHIP</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="relationship" class="section level2">
|
||||
<h2>RELATIONSHIP</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="concept_synonym" class="section level2">
|
||||
<h2>CONCEPT_SYNONYM</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="concept_ancestor" class="section level2">
|
||||
<h2>CONCEPT_ANCESTOR</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="source_to_concept_map" class="section level2">
|
||||
<h2>SOURCE_TO_CONCEPT_MAP</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="drug_strength" class="section level2">
|
||||
<h2>DRUG_STRENGTH</h2>
|
||||
<ul>
|
||||
<li>No change</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="attribute_definition" class="section level2">
|
||||
<h2>- <strong>ATTRIBUTE_DEFINITION</strong></h2>
|
||||
</div>
|
||||
<div id="cohort" class="section level2">
|
||||
<h2>+ <strong>COHORT</strong></h2>
|
||||
<table>
|
||||
<thead>
|
||||
<tr class="header">
|
||||
<th>COHORT</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td>cohort_definition_id</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>subject_id</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>cohort_start_date</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>cohort_end_date</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
|
||||
</div>
|
||||
|
||||
<script>
|
||||
|
||||
// add bootstrap table styles to pandoc tables
|
||||
function bootstrapStylePandocTables() {
|
||||
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
|
||||
}
|
||||
$(document).ready(function () {
|
||||
bootstrapStylePandocTables();
|
||||
});
|
||||
|
||||
|
||||
</script>
|
||||
|
||||
<!-- tabsets -->
|
||||
|
||||
<script>
|
||||
$(document).ready(function () {
|
||||
window.buildTabsets("TOC");
|
||||
});
|
||||
|
||||
$(document).ready(function () {
|
||||
$('.tabset-dropdown > .nav-tabs > li').click(function () {
|
||||
$(this).parent().toggleClass('nav-tabs-open')
|
||||
});
|
||||
});
|
||||
</script>
|
||||
|
||||
<!-- code folding -->
|
||||
|
||||
<script>
|
||||
$(document).ready(function () {
|
||||
|
||||
// move toc-ignore selectors from section div to header
|
||||
$('div.section.toc-ignore')
|
||||
.removeClass('toc-ignore')
|
||||
.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
|
||||
|
||||
// establish options
|
||||
var options = {
|
||||
selectors: "h1,h2,h3",
|
||||
theme: "bootstrap3",
|
||||
context: '.toc-content',
|
||||
hashGenerator: function (text) {
|
||||
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
|
||||
},
|
||||
ignoreSelector: ".toc-ignore",
|
||||
scrollTo: 0
|
||||
};
|
||||
options.showAndHide = true;
|
||||
options.smoothScroll = true;
|
||||
|
||||
// tocify
|
||||
var toc = $("#TOC").tocify(options).data("toc-tocify");
|
||||
});
|
||||
</script>
|
||||
|
||||
<!-- dynamically load mathjax for compatibility with self-contained -->
|
||||
<script>
|
||||
(function () {
|
||||
var script = document.createElement("script");
|
||||
script.type = "text/javascript";
|
||||
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
|
||||
document.getElementsByTagName("head")[0].appendChild(script);
|
||||
})();
|
||||
</script>
|
||||
|
||||
</body>
|
||||
</html>
|
||||
564
docs/cdm60.html
564
docs/cdm60.html
|
|
@ -380,17 +380,33 @@ div.tocify {
|
|||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="dataModelConventions.html">
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-list-alt"></span>
|
||||
|
||||
Conventions
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="dataModelConventions.html">General Conventions</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
|
|
@ -405,10 +421,21 @@ div.tocify {
|
|||
<a href="cdm30.html">CDM v3.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm531.html">CDM v5.3.1</a>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -422,20 +449,14 @@ div.tocify {
|
|||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="reviewProposals.html">Under Review</a>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -444,7 +465,27 @@ div.tocify {
|
|||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-question"></span>
|
||||
|
||||
Help
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-life-ring"></span>
|
||||
|
||||
Support
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
|
|
@ -452,28 +493,11 @@ div.tocify {
|
|||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -481,7 +505,7 @@ div.tocify {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fas fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
@ -3722,7 +3746,7 @@ It is up to the ETL to choose how to map modifiers if they exist in source data.
|
|||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
|
|
@ -6218,7 +6242,7 @@ No
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
offset
|
||||
"offset"
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
Character offset of the extracted term in the input note
|
||||
|
|
@ -9525,11 +9549,12 @@ FK Domain
|
|||
cost_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A unique identifier for each COST record.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
INTEGER
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
|
|
@ -9547,11 +9572,38 @@ No
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
person_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
cost_event_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
If the Cost record is related to another record in the database, this field is the primary key of the linked record.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the primary key of the linked record, if applicable, here.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
|
|
@ -9572,14 +9624,16 @@ No
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
cost_domain_id
|
||||
cost_event_field_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
If the Cost record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the CONCEPT_ID that identifies which table and field the COST_EVENT_ID came from.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
VARCHAR(20)
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
|
|
@ -9591,7 +9645,34 @@ No
|
|||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
DOMAIN
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
cost_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key that refers to a Standard Cost Concept identifier in the Standardized Vocabularies belonging to the ‘Cost’ vocabulary.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
|
|
@ -9601,6 +9682,7 @@ DOMAIN
|
|||
cost_type_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key identifier to a concept in the CONCEPT table for the provenance or the source of the COST data and belonging to the ‘Type Concept’ vocabulary
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
|
|
@ -9608,7 +9690,7 @@ cost_type_concept_id
|
|||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
|
|
@ -9620,6 +9702,60 @@ Yes
|
|||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Type Concept
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
cost_source_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key to a Cost Concept that refers to the code used in the source.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
cost_source_value
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The source value for the cost as it appears in the source data
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
varchar(50)
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
|
|
@ -9627,6 +9763,7 @@ CONCEPT
|
|||
currency_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key identifier to the concept representing the 3-letter code used to delineate international currencies, such as USD for US Dollar. These belong to the ‘Currency’ vocabulary
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
|
|
@ -9640,7 +9777,7 @@ No
|
|||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
|
|
@ -9650,14 +9787,15 @@ CONCEPT
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
total_charge
|
||||
cost
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The actual financial cost amount
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
float
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
|
|
@ -9675,14 +9813,15 @@ No
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
total_cost
|
||||
incurred_date
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The first date of service of the clinical event corresponding to the cost as in table capturing the information (e.g. date of visit, date of procedure, date of condition, date of drug etc).
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
date
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
|
|
@ -9700,14 +9839,15 @@ No
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
total_paid
|
||||
billed_date
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The date a bill was generated for a service or encounter
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
date
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
|
|
@ -9725,239 +9865,15 @@ No
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
paid_by_payer
|
||||
paid_date
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The date payment was received for a service or encounter
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
paid_by_patient
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
paid_patient_copay
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
paid_patient_coinsurance
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
paid_patient_deductible
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
paid_by_primary
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
paid_ingredient_cost
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
paid_dispensing_fee
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
payer_plan_period_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
amount_allowed
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
FLOAT
|
||||
date
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
|
|
@ -9978,6 +9894,34 @@ No
|
|||
revenue_code_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key referring to a Standard Concept ID in the Standardized Vocabularies for Revenue codes belonging to the ‘Revenue Code’ vocabulary.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
drg_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key referring to a Standard Concept ID in the Standardized Vocabularies for DRG codes belonging to the ‘DRG’ vocabulary.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
|
|
@ -10004,12 +9948,12 @@ CONCEPT
|
|||
revenue_code_source_value
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
Revenue codes are a method to charge for a class of procedures and conditions in the U.S. hospital system.
|
||||
The source value for the Revenue code as it appears in the source data, stored here for reference.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
VARCHAR(50)
|
||||
varchar(50)
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
|
|
@ -10027,41 +9971,41 @@ No
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
drg_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
drg_source_value
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
Diagnosis Related Groups are US codes used to classify hospital cases into one of approximately 500 groups.
|
||||
The source value for the 3-digit DRG source code as it appears in the source data, stored here for reference.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
VARCHAR(3)
|
||||
varchar(50)
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
payer_plan_period_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key to the PAYER_PLAN_PERIOD table, where the details of the Payer, Plan and Family are stored. Record the payer_plan_id that relates to the payer who contributed to the paid_by_payer field.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
|
|
@ -10203,7 +10147,7 @@ Drug
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
drug_era_start_date
|
||||
drug_era_start_datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
|
|
@ -10229,7 +10173,7 @@ No
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
drug_era_end_date
|
||||
drug_era_end_datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
|
|
@ -10481,7 +10425,7 @@ No
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
dose_era_start_date
|
||||
dose_era_start_datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The date the Person started on the specific dosage, with at least 31 days since any prior exposure.
|
||||
|
|
@ -10507,7 +10451,7 @@ No
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
dose_era_end_date
|
||||
dose_era_end_datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
</td>
|
||||
|
|
@ -10586,7 +10530,7 @@ condition_era_id
|
|||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
|
|
@ -10658,7 +10602,7 @@ Condition
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
condition_era_start_date
|
||||
condition_era_start_datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The start date for the Condition Era constructed from the individual instances of Condition Occurrences. It is the start date of the very first chronologically recorded instance of the condition with at least 31 days since any prior record of the same Condition.
|
||||
|
|
@ -10684,7 +10628,7 @@ No
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
condition_era_end_date
|
||||
condition_era_end_datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The end date for the Condition Era constructed from the individual instances of Condition Occurrences. It is the end date of the final continuously recorded instance of the Condition.
|
||||
|
|
@ -13307,7 +13251,7 @@ This is the identifier given to the cohort, usually by the ATLAS application
|
|||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
bigint
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
|
|
|
|||
|
|
@ -0,0 +1,715 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>Preserving Privacy in an OMOP CDM Implementation</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.6/header-attrs.js"></script>
|
||||
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
|
||||
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
|
||||
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
|
||||
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
|
||||
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
|
||||
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
|
||||
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
|
||||
<script src="site_libs/navigation-1.1/tabsets.js"></script>
|
||||
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
|
||||
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
|
||||
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
|
||||
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
|
||||
<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
|
||||
|
||||
<style type="text/css">
|
||||
code{white-space: pre-wrap;}
|
||||
span.smallcaps{font-variant: small-caps;}
|
||||
span.underline{text-decoration: underline;}
|
||||
div.column{display: inline-block; vertical-align: top; width: 50%;}
|
||||
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
|
||||
ul.task-list{list-style: none;}
|
||||
</style>
|
||||
|
||||
<style type="text/css">code{white-space: pre;}</style>
|
||||
<style type="text/css">
|
||||
pre:not([class]) {
|
||||
background-color: white;
|
||||
}
|
||||
</style>
|
||||
<script type="text/javascript">
|
||||
if (window.hljs) {
|
||||
hljs.configure({languages: []});
|
||||
hljs.initHighlightingOnLoad();
|
||||
if (document.readyState && document.readyState === "complete") {
|
||||
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
|
||||
}
|
||||
}
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
h1 {
|
||||
font-size: 34px;
|
||||
}
|
||||
h1.title {
|
||||
font-size: 38px;
|
||||
}
|
||||
h2 {
|
||||
font-size: 30px;
|
||||
}
|
||||
h3 {
|
||||
font-size: 24px;
|
||||
}
|
||||
h4 {
|
||||
font-size: 18px;
|
||||
}
|
||||
h5 {
|
||||
font-size: 16px;
|
||||
}
|
||||
h6 {
|
||||
font-size: 12px;
|
||||
}
|
||||
.table th:not([align]) {
|
||||
text-align: left;
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
||||
<style type = "text/css">
|
||||
.main-container {
|
||||
max-width: 940px;
|
||||
margin-left: auto;
|
||||
margin-right: auto;
|
||||
}
|
||||
code {
|
||||
color: inherit;
|
||||
background-color: rgba(0, 0, 0, 0.04);
|
||||
}
|
||||
img {
|
||||
max-width:100%;
|
||||
}
|
||||
.tabbed-pane {
|
||||
padding-top: 12px;
|
||||
}
|
||||
.html-widget {
|
||||
margin-bottom: 20px;
|
||||
}
|
||||
button.code-folding-btn:focus {
|
||||
outline: none;
|
||||
}
|
||||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
/* padding for bootstrap navbar */
|
||||
body {
|
||||
padding-top: 51px;
|
||||
padding-bottom: 40px;
|
||||
}
|
||||
/* offset scroll position for anchor links (for fixed navbar) */
|
||||
.section h1 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h2 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h3 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h4 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h5 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h6 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.dropdown-submenu {
|
||||
position: relative;
|
||||
}
|
||||
.dropdown-submenu>.dropdown-menu {
|
||||
top: 0;
|
||||
left: 100%;
|
||||
margin-top: -6px;
|
||||
margin-left: -1px;
|
||||
border-radius: 0 6px 6px 6px;
|
||||
}
|
||||
.dropdown-submenu:hover>.dropdown-menu {
|
||||
display: block;
|
||||
}
|
||||
.dropdown-submenu>a:after {
|
||||
display: block;
|
||||
content: " ";
|
||||
float: right;
|
||||
width: 0;
|
||||
height: 0;
|
||||
border-color: transparent;
|
||||
border-style: solid;
|
||||
border-width: 5px 0 5px 5px;
|
||||
border-left-color: #cccccc;
|
||||
margin-top: 5px;
|
||||
margin-right: -10px;
|
||||
}
|
||||
.dropdown-submenu:hover>a:after {
|
||||
border-left-color: #ffffff;
|
||||
}
|
||||
.dropdown-submenu.pull-left {
|
||||
float: none;
|
||||
}
|
||||
.dropdown-submenu.pull-left>.dropdown-menu {
|
||||
left: -100%;
|
||||
margin-left: 10px;
|
||||
border-radius: 6px 0 6px 6px;
|
||||
}
|
||||
</style>
|
||||
|
||||
<script>
|
||||
// manage active state of menu based on current page
|
||||
$(document).ready(function () {
|
||||
// active menu anchor
|
||||
href = window.location.pathname
|
||||
href = href.substr(href.lastIndexOf('/') + 1)
|
||||
if (href === "")
|
||||
href = "index.html";
|
||||
var menuAnchor = $('a[href="' + href + '"]');
|
||||
|
||||
// mark it active
|
||||
menuAnchor.parent().addClass('active');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.dropdown').addClass('active');
|
||||
});
|
||||
</script>
|
||||
|
||||
<!-- tabsets -->
|
||||
|
||||
<style type="text/css">
|
||||
.tabset-dropdown > .nav-tabs {
|
||||
display: inline-table;
|
||||
max-height: 500px;
|
||||
min-height: 44px;
|
||||
overflow-y: auto;
|
||||
background: white;
|
||||
border: 1px solid #ddd;
|
||||
border-radius: 4px;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li.active:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
|
||||
content: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li.active {
|
||||
display: block;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li > a,
|
||||
.tabset-dropdown > .nav-tabs > li > a:focus,
|
||||
.tabset-dropdown > .nav-tabs > li > a:hover {
|
||||
border: none;
|
||||
display: inline-block;
|
||||
border-radius: 4px;
|
||||
background-color: transparent;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
|
||||
display: block;
|
||||
float: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li {
|
||||
display: none;
|
||||
}
|
||||
</style>
|
||||
|
||||
<!-- code folding -->
|
||||
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
|
||||
#TOC {
|
||||
margin: 25px 0px 20px 0px;
|
||||
}
|
||||
@media (max-width: 768px) {
|
||||
#TOC {
|
||||
position: relative;
|
||||
width: 100%;
|
||||
}
|
||||
}
|
||||
|
||||
@media print {
|
||||
.toc-content {
|
||||
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
|
||||
float: right;
|
||||
}
|
||||
}
|
||||
|
||||
.toc-content {
|
||||
padding-left: 30px;
|
||||
padding-right: 40px;
|
||||
}
|
||||
|
||||
div.main-container {
|
||||
max-width: 1200px;
|
||||
}
|
||||
|
||||
div.tocify {
|
||||
width: 20%;
|
||||
max-width: 260px;
|
||||
max-height: 85%;
|
||||
}
|
||||
|
||||
@media (min-width: 768px) and (max-width: 991px) {
|
||||
div.tocify {
|
||||
width: 25%;
|
||||
}
|
||||
}
|
||||
|
||||
@media (max-width: 767px) {
|
||||
div.tocify {
|
||||
width: 100%;
|
||||
max-width: none;
|
||||
}
|
||||
}
|
||||
|
||||
.tocify ul, .tocify li {
|
||||
line-height: 20px;
|
||||
}
|
||||
|
||||
.tocify-subheader .tocify-item {
|
||||
font-size: 0.90em;
|
||||
}
|
||||
|
||||
.tocify .list-group-item {
|
||||
border-radius: 0px;
|
||||
}
|
||||
|
||||
|
||||
</style>
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
<!-- setup 3col/9col grid for toc_float and main content -->
|
||||
<div class="row-fluid">
|
||||
<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">
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<h1 class="title toc-ignore">Preserving Privacy in an OMOP CDM Implementation</h1>
|
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</div>
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|
||||
<p><em>By Kristin Kostka</em></p>
|
||||
<div id="background" class="section level1">
|
||||
<h1>Background</h1>
|
||||
<p>The OMOP CDM is a person-centric model. Being person-centric means the model can retain attributes that may be considered personal identified information (PII) or protected health information (PHI). There are many different ways a site may treat their OMOP CDM to uphold their privacy protocols. In this article we provide guidance on overall process and the potential fields that should be monitored to adhere to these various privacy preserving protocols.</p>
|
||||
<div id="defining-pii-and-phi" class="section level3">
|
||||
<h3>Defining PII and PHI</h3>
|
||||
<ul>
|
||||
<li>PII is defined as any representation of information that permits the identity of an individual to whom the information applies to be reasonably inferred to either direct or indirect means [1].</li>
|
||||
<li>The United States Department of Health & Human Services´ Office for Civil Rights has defined PHI as any Personal Identifying Information (PII) that – individually or combined – could potentially identify a specific individual, their past, present or future healthcare, or the method of payment. There are eighteen unique identifiers considered to be PHI: 1) names, 2) geographic data, 3) all elements of dates, 4) telephone numbers, 5) FAX numbers, 6) email addresses, 7) Social Security numbers (SSN), 8) medical record numbers (MRN), 9) health plan beneficiary numbers, 10) account numbers, 11) certificate/license numbers, 12) vehicle identifiers and serial numbers including license places, 13) device identifiers and serial numbers, 14) web URLs, 15) internet protocol addresses, 16) biometric identifiers (i.e. retinal scan, fingerprints), 17) full face photos and comparable images, and 18) any unique identifying number, characteristic or code. PHI is no longer considered PHI when it de-identified of these unique attributes. PHI is commonly referred to in relation to the Health Insurance Portability and Accountability Act (HIPAA) and associated legislation such as the Health Information Technology for Economic and Clinical Health Act (HITECH) [2].</li>
|
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|
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</div>
|
||||
<div id="the-data-holders-responsibility" class="section level1">
|
||||
<h1>The Data Holder’s Responsibility</h1>
|
||||
<p>In OHDSI, it is the responsibility of each data holder to know, understand and follow local data governance processes related to use of the OMOP CDM. In the United States, these processes will follow your organization’s local interpretation for maintaining compliance to PII and PHI protection. In OMOP CDM implementations containing European Union citizen data, local governance processes will include measures to comply with General Data Protection Regulation (GDPR) [3]. As a community, the OHDSI data network covers more than 330 databases from 34 countries. There is extensive community knowledge on the interpretation of rule sets and exemplar IRB and local governance workflows that can be made available to institutions navigating these processes for the first time. If your organization does not have an established data governance process, please reach out on the <a href="forums.ohdsi.org">OHDSI Forums</a> under “Implementers” and the community can respond with shared guidance from their own deployments. As a community, we aim to conduct research that keeps patient-level data local and share only aggregate results.</p>
|
||||
</div>
|
||||
<div id="complying-with-privacy-preservation" class="section level1">
|
||||
<h1>Complying with Privacy Preservation</h1>
|
||||
<p>Complying with local governance processes depends on the rule set being used. There may be allowable times when data use agreements and data transfer agreements exist between collaborating institutions to facilitate sharing of PII and PHI. In this section we will discuss common rule sets that organizations adhere to.</p>
|
||||
<div id="limited-data-sets" class="section level2">
|
||||
<h2>Limited Data Sets</h2>
|
||||
<p>A limited data set (LDS) is defined as protected health information that excludes certain direct identifiers of an individual or of relatives, employers or household members of the individual — but may include city, state, ZIP code and elements of dates. A LDS can be disclosed only for purposes of research, public health or health care operations. LDS requirements are dictated by the HIPAA Privacy Rule.</p>
|
||||
</div>
|
||||
<div id="de-identified-data-sets" class="section level2">
|
||||
<h2>De-identified Data Sets</h2>
|
||||
<p>A de-identified data, as defined by Section 164.514(a) of the HIPAA Privacy rule, is health information that does not identify an individual and with respect to which there is no reasonable basis to believe that the information can be used to identify an individual is not individually identifiable health information. There are two methods for achieving de-identification in accordance with HIPAA [4].</p>
|
||||
<ol style="list-style-type: decimal">
|
||||
<li>Expert Determination (§164.514(a))- Implementation specifications: requirements for de-identification of protected health information. A covered entity may determine that health information is not individually identifiable health information only if:</li>
|
||||
</ol>
|
||||
<ol style="list-style-type: decimal">
|
||||
<li>A person with appropriate knowledge of and experience with generally accepted statistical and scientific principles and methods for rendering information not individually identifiable:</li>
|
||||
</ol>
|
||||
<ol style="list-style-type: lower-roman">
|
||||
<li>Applying such principles and methods, determines that the risk is very small that the information could be used, alone or in combination with other reasonably available information, by an anticipated recipient to identify an individual who is a subject of the information; and</li>
|
||||
<li>Documents the methods and results of the analysis that justify such determination.</li>
|
||||
</ol>
|
||||
<ol start="2" style="list-style-type: decimal">
|
||||
<li>Safe Harbor (§164.514(b)) The eighteen unique identifiers are obfuscated. This includes processes such as:</li>
|
||||
</ol>
|
||||
<ol style="list-style-type: upper-alpha">
|
||||
<li>Dates of service are algorithmically shifted to protect patient privacy.</li>
|
||||
<li>Patient ZIP codes are truncated to the first three digits or removed entirely if the ZIP code represents fewer than 20,000 individuals.</li>
|
||||
<li>Removing and, when necessary, replacing unique identifiers AND The entity does not have actual knowledge that the information could be used alone or in combination with other information to identify an individual who is a subject of the information.</li>
|
||||
</ol>
|
||||
</div>
|
||||
<div id="field-level-implications-of-de-identification-processes" class="section level2">
|
||||
<h2>Field-level Implications of De-identification Processes</h2>
|
||||
<div id="person-table-attributes" class="section level3">
|
||||
<h3>PERSON Table Attributes</h3>
|
||||
<p>In the OMOP CDM, the PERSON table serves as the central identity management for all Persons in the database. It contains records that uniquely identify each person or patient, and some demographic information. It is a table that has a number of field-level implications for privacy preserving protocols.</p>
|
||||
<p>Considerations include: - PERSON.person_id should never contain Medical Record Number, Social Security Number or similar uniquely identifiable number. This should be a number that is essentially meaningless but has the ability to be a primary key across tables. - PERSON.year_of_birth, PERSON.month_of_birth and PERSON.date_of_birth, PERSON.birth_datetime may require some redaction or modification depending on interpretation of rule set. Consult local guidance on the need to modify these fields when creating compliant views of de-identified data. - PERSON.person_source_value may contain sensitive information used to generate the person_id field. It is advised to practice caution when creating views of these data. It would be wise to obfuscate or redact this field if you are not sure what is contained in the raw information being extracted, transformed and loaded into the CDM.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div id="date-fields-across-domains" class="section level2">
|
||||
<h2>Date Fields Across Domains</h2>
|
||||
<p>Date fields are used across many OMOP domains including: OBSERVATION_PERIOD, VISIT_OCCURRENCE, VISIT_DETAIL, CONDITION_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE, MEASUREMENT, OBSERVATION, DEATH, NOTE, NOTE_NLP, SPECIMEN, PAYER_PLAN_PERIOD, DRUG_ERA, DOSE_ERA, and CONDITION_ERA.</p>
|
||||
<p>As discussed previously, some rule sets may require algorithmically shifting dates. It is advised that when date shifting is applied, it is done holistically. This means that when shifting dates, you should not treat each record independently. Instead, a robust date shifting algorithm will link off the <em>.person_id (where </em> is the domain name such as CONDITION_OCCURRENCE, etc) and apply the same offset to all events. This allows researchers to have the ability to understand the sequence of events while preserving patient privacy.</p>
|
||||
<p>The implications of not holistically shifting all events together by the same offset means that information may be out of sequence or illogical. An example would be a death record that happens prior to other event records (conditions, drugs, procedures, etc). When applying an algorithmic shift of dates, it is important to educate your OMOP CDM user group of the known offset. This is especially important in temporal studies which may be looking to make statements about disease history relative to the time when an event is observed.</p>
|
||||
<p>Some rule sets do not require algorithmic shifting of dates, such as Limited Data Sets. In these situations, a user of a LDS OMOP CDM would not be expecting dates to the shifted. If a shift is applied, it should be disclosed and the offset amount (e.g. +/- 7 days, +/- 30 days, etc) should be made available to those who have received permission to use a LDS dataset. Otherwise, these data are not upholding the assumptions of the rule set applied.</p>
|
||||
</div>
|
||||
<div id="location-table-attributes" class="section level2">
|
||||
<h2>LOCATION Table Attributes</h2>
|
||||
<p>The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites. When applying privacy preserving procedures, this table should be reviewed and scrubbed relative to the rule set. The LOCATION.zip field should be redacted relative to the type of process applied (e.g. 3-digit zip for de-identified data). The LOCATION.location_source_value should be reviewed for potential PII/PHI. It would be wise to obfuscate or redact this field if you are not sure what is contained in the raw information being extracted, transformed and loaded into the CDM.</p>
|
||||
</div>
|
||||
<div id="provider-table-attributes" class="section level2">
|
||||
<h2>PROVIDER Table Attributes</h2>
|
||||
<p>The PROVIDER table contains a list of uniquely identified healthcare providers. These are individuals providing hands-on healthcare to patients, such as physicians, nurses, midwives, physical therapists etc. In some privacy preserving processes, the PROVIDER.npi and PROVIDER.dea fields may be redacted. Please review this field and confirm that you are adhering to privacy rule sets. The PROVIDER.year_of_birth field is an optional field that may also require treatment in certain rule sets.</p>
|
||||
</div>
|
||||
<div id="observation-table-attributes" class="section level2">
|
||||
<h2>OBSERVATION Table Attributes</h2>
|
||||
<p>The OBSERVATION table captures clinical facts about a Person obtained in the context of examination, questioning or a procedure. Any data that cannot be represented by any other domains, such as social and lifestyle facts, medical history, family history, etc. are recorded here.</p>
|
||||
<p>We strongly caution ETL teams to review the OBSERVATION table for potential PII/PHI. In some source systems, there can be information coming in these vocabularies that are not laboratory or clinical observations but instead are patient identifiers. If you search in ATHENA, you will find there are a number of standard terms in the SNOMED and LOINC vocabularies that can represent phone numbers, emails, and other PII information.</p>
|
||||
<p>It is difficult to create an exhaustive list of terms because these ontologies do not maintain or publish lists of terms that may contain patient identifiers. It is, therefore, up to data holders to perform a review of this domain with an eye for these potential privacy issues. The National COVID Cohort Collaborative, a NIH consortium which uses the OMOP CDM, has published a resource for sites needing assistance with identifying these potentially problematic records. A “live” version of this table that will track updates over time is hosted at <a href="https://github.com/data2health/next-gen-data-sharing/blob/master/CodesWithPPIPotential.csv" class="uri">https://github.com/data2health/next-gen-data-sharing/blob/master/CodesWithPPIPotential.csv</a>. We welcome additions to this list from the community.</p>
|
||||
</div>
|
||||
<div id="scrutinizing-_source_value" class="section level2">
|
||||
<h2>Scrutinizing *_source_value</h2>
|
||||
<p>The *_source_value (where * is the domain name such as CONDITION_OCCURRENCE, etc) fields present an opportunity for sites to carry forward potential PII/PHI in ETL processes. Because the convention of the OMOP CDM has minimal boundaries on what are retained in these fields, it is important to treat all source_value fields as potentially containing PII/PHI. We highly advise all data holders to scrutinize these fields when applying privacy preserving processes. It is not uncommon for fields to be overloaded and contain potential patient identifiers. Please use caution when transmitting or making views of these fields available to users.</p>
|
||||
</div>
|
||||
<div id="scrutinizing-string-fields" class="section level2">
|
||||
<h2>Scrutinizing String Fields</h2>
|
||||
<p>Across OMOP Domains, there are many fields which permit the use of strings (e.g. DRUG_EXPOSURE.sig, MEASUREMENT.value_as_string, OBSERVATION.value_as_string, We’ve discussed some of these in prior sections. It is advised that fields with strings often have the potential to contain unintentional PII/PHI. Targeted regular expressions can be built into ETL processes in order to “sniff” out any additional PII (or potential PII)–such as any data in the format of a phone number, or a person or place name. (E.g., the regular expression “Mr.|Mrs.|Dr.|, M.?D.?” will find any string with an English name prefix.) Depending on risk tolerance, the expressions could err toward sensitivity or specificity, and could be tweaked over time to meet different rule sets.</p>
|
||||
<p>Extensive regular expression matching during ETL may add significant processing time and should therefore not be relied upon as a sole solution, but rather an extra protection against edge cases. Other algorithmic rules may also prove useful, such as automatically quarantining records with lengthy string values (which could signal the presence of free text). If these approaches are implemented, records that match the regular expressions or rules can be quarantined in a separate table or staging area to be manually reviewed by a data broker. Thus, in addition to adding another layer of PII protection, another advantage of these approaches is the potential to uncover ways that underlying vocabularies may be contributing to unintentional sharing of PII and create awareness for future privacy preserving processes shared across the community.</p>
|
||||
</div>
|
||||
<div id="note-and-note_nlp-table-attributes" class="section level2">
|
||||
<h2>NOTE and NOTE_NLP Table Attributes</h2>
|
||||
<p>The NOTE table captures unstructured information that was recorded by a provider about a patient in free text (in ASCII, or preferably in UTF8 format) notes on a given date. The NOTE_NLP table encodes all output of NLP on clinical notes. Each row represents a single extracted term from a note. There is a high potential these tables may retain information that is considered PII/PHI. In addition to overall string searching, these tables are likely to be dropped altogether to adhere to the most stringent rule sets.</p>
|
||||
<p>It is highly advised that if you are conducting a study with NOTE and NOTE_NLP table information, please consult with your local governance and privacy officers to ensure compliance with local rule sets.</p>
|
||||
</div>
|
||||
<div id="conclusion" class="section level2">
|
||||
<h2>Conclusion</h2>
|
||||
<p>Privacy preserving processes are not one-size fits all. There are many different rule sets that can be applied to datasets. Data holders are recommended to consult with their local privacy officer(s) to ensure all processes applied to a database are compliant with local interpretation of the selected rule set.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div id="references" class="section level1">
|
||||
<h1>References</h1>
|
||||
<ol style="list-style-type: decimal">
|
||||
<li>BibText version: <span class="citation">@MISC</span>{noauthor_undated-mg, title = “Guidance on the Protection of Personal Identifiable Information”, abstract = “Personal Identifiable Information (PII) is defined as:”, howpublished = “”, note = “Accessed: 2021-8-18” }</li>
|
||||
</ol>
|
||||
<p>Regular citation: Guidance on the Protection of Personal Identifiable Information. [cited 18 Aug 2021]. Available: <a href="https://www.dol.gov/general/ppii" class="uri">https://www.dol.gov/general/ppii</a></p>
|
||||
<ol start="2" style="list-style-type: decimal">
|
||||
<li>BibText version: <span class="citation">@MISC</span>{HIPAA_Journal2017-yo, title = “What Does {PHI} Stand For?”, author = “{HIPAA Journal}”, abstract = “PHI is a term used in connection with health data, but what does PHI stand for? What information is included in the definition of PHI.”, month = dec, year = 2017, howpublished = “”, note = “Accessed: 2021-8-18”, language = “en” }</li>
|
||||
</ol>
|
||||
<p>Regular citation: HIPAA Journal. What Does PHI Stand For? 23 Dec 2017 [cited 18 Aug 2021]. Available: <a href="https://www.hipaajournal.com/what-does-phi-stand-for/" class="uri">https://www.hipaajournal.com/what-does-phi-stand-for/</a></p>
|
||||
<ol start="3" style="list-style-type: decimal">
|
||||
<li>BibText version:</li>
|
||||
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|
||||
<p><span class="citation">@MISC</span>{noauthor_2018-mt, title = “General Data Protection Regulation ({GDPR}) Compliance Guidelines”, abstract = “The EU General Data Protection Regulation went into effect on May 25, 2018, replacing the Data Protection Directive 95/46/EC. Designed to increase data privacy for EU citizens, the regulation levies steep fines on organizations that don’t follow the law.”, month = jun, year = 2018, howpublished = “”, note = “Accessed: 2021-8-18”, language = “en” }</p>
|
||||
<p>Regular citation: General Data Protection Regulation (GDPR) Compliance Guidelines. 18 Jun 2018 [cited 18 Aug 2021]. Available: <a href="https://gdpr.eu/" class="uri">https://gdpr.eu/</a></p>
|
||||
<ol start="4" style="list-style-type: decimal">
|
||||
<li>BibText version:</li>
|
||||
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|
||||
<p><span class="citation">@MISC</span>{Office_for_Civil_Rights_OCR_undated-zy, title = “Methods for De-identification of {PHI}”, author = “{Office for Civil Rights (OCR)}”, abstract = “Guidance about methods and approaches to achieve de-identification in accordance with the Health Insurance Portability and Accountability Act of 1996.”, howpublished = “”, note = “Accessed: 2021-8-19” }</p>
|
||||
<p>Regular citation: Office for Civil Rights (OCR). Methods for De-identification of PHI. [cited 19 Aug 2021]. Available: <a href="https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html" class="uri">https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html</a></p>
|
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|
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|
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|
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|
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|
||||
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|
||||
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|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
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|
||||
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|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
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|
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||||
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Proposals
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||||
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||||
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|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
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|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
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|
||||
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How to
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|
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</a>
|
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|
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<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
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|
||||
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|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
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|
||||
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|
||||
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||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
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|
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</div>
|
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|
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|
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|
||||
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
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|
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</div>
|
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|
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<script>
|
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|
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// add bootstrap table styles to pandoc tables
|
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|
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|
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|
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bootstrapStylePandocTables();
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<script>
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|
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|
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<!-- code folding -->
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|
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|
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|
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|
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|
@ -0,0 +1,644 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
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<img src="ohdsi40x40.png"></img> CDM Refresh Process
|
||||
</div></h1>
|
||||
|
||||
</div>
|
||||
|
||||
|
||||
<p>The OMOP Common Data Model is managed by the OHDSI CDM Working Group. The formal remit of the CDM Working Group (WG) is to hear proposals for change, ratifying only those with valid use cases and data to support them. Then, once ratified, these proposals are incorporated into the next version of the CDM. In the past, this was done by the WG alone. The group would invite others from around the community to present use cases for change and suggestions for improvement. The WG would then vote on the proposals and a new CDM version would be released after a certain period of time or if enough proposals were voted in. This approach worked when the community was smaller but as it is growing rapidly the CDM WG needed to adapt the refresh cycle such that everyone has an opportunity to weigh in on the proposed changes.</p>
|
||||
<div id="cdm-refresh-cycle" class="section level2">
|
||||
<h2>CDM Refresh Cycle</h2>
|
||||
<p><img src="images/CDM_refresh_cycle.png" /></p>
|
||||
<div id="define-new-version-completed-for-v5.4" class="section level3">
|
||||
<h3>1. Define New Version [Completed for v5.4]</h3>
|
||||
<p>The image above describes the new CDM refresh cycle. It begins with <strong>defining a new version</strong>. This has been completed for the current cycle. Issues and proposals on the github were considered during a 4-hour workshop where it was decided the next CDM version will be CDM v5.4, building off of CDM v5.3. The group then participated in a rapid-fire voting activity to identify which changes should be incorporated into CDM v5.4. Any items that were not unanimously agreed upon were then discussed in small groups to hone the proposal and suggestions were presented back to the group. The final roadmap for CDM v5.4 can be found <a href="https://github.com/OHDSI/CommonDataModel/projects/3">here</a>.</p>
|
||||
<p>Looking to open a proposal to change or augment the CDM? Please open an <a href="https://github.com/OHDSI/CommonDataModel/issues">issue</a> and use the <strong>proposal template</strong>.</p>
|
||||
</div>
|
||||
<div id="sign-off-from-work-groups-completed-for-v5.4" class="section level3">
|
||||
<h3>2. Sign off from Work Groups [Completed for v5.4]</h3>
|
||||
<p>Each member of the CDM WG is a liaison for another workgroup in the community. They are responsible for presenting the proposed changes to the CDM and collecting the feedback. This has resulted in very helpful suggestions from the EHR, Data Quality, Device, HADES, and ACHILLES groups. This outreach has proven to be very effective and should result in a very stable version.</p>
|
||||
</div>
|
||||
<div id="release-ddls" class="section level3">
|
||||
<h3>3. Release DDLs</h3>
|
||||
<p>After all changes and suggestions are agreed upon by the community and work groups the next step is to generate the DDLs. The CDM WG hosted a hackathon on August 18-19, 2021. During this time the group created an R package to automatically generate the DDLs and the code to instantiate an empty CDM instance. Changes were made to v5.3 to generate v5.4 and the repository was refactored.</p>
|
||||
</div>
|
||||
<div id="software-update" class="section level3">
|
||||
<h3>4. Software Update</h3>
|
||||
<p>There will be period of time once the DDLs are ready to allow the software and methods developers to prepare for the official release of the CDM. This is meant to serve as a buffer so that once the community starts adopting the new model, the tools and methods will be ready to support it.</p>
|
||||
</div>
|
||||
<div id="community-support" class="section level3">
|
||||
<h3>5. Community Support</h3>
|
||||
<p>This is the final stage of the CDM refresh cycle. Once the DDLs are ready and the software and tools supports the new version, the CDM WG will work to help the community convert their data to the new model.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div id="cdm-wg-meeting-information" class="section level1">
|
||||
<h1>CDM WG Meeting Information</h1>
|
||||
<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 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> These were recently changed from a Skype meeting to a Microsoft Teams meeting. If you do you have access to the OHDSI Teams Tenet, please contact Clair Blacketer at <a href="mailto:mblacke@its.jnj.com" class="email">mblacke@its.jnj.com</a>.</p>
|
||||
<div id="cdm-wg-important-links" class="section level3">
|
||||
<h3>CDM WG Important Links</h3>
|
||||
<ul>
|
||||
<li><a href="https://drive.google.com/open?id=1DaNKe6ivIAZPJeI31VJ-pzNB9wS9hDqu">Google Drive Location</a></li>
|
||||
<li><a href="https://docs.google.com/document/d/1WgKePjrI_cGdqn2XQCe1JdGaTzdMqU4p5ihkMt8fcAc/edit?usp=sharing">Running Agenda</a></li>
|
||||
<li><a href="https://github.com/OHDSI/CommonDataModel">CDM Github</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
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<a href="background.html">Model Background</a>
|
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|
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<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
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|
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|
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<a href="vocabulary.html">How the Vocabulary is Built</a>
|
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|
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|
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|
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|
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<a href="cdm54.html">CDM v5.4</a>
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<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
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<a href="oncology.html">Oncology CDM Proposal</a>
|
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|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
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</li>
|
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</ul>
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@ -444,7 +465,27 @@ div.tocify {
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</a>
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<ul class="dropdown-menu" role="menu">
|
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<li>
|
||||
<a href="download.html">Download the DDL</a>
|
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|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
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|
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<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
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|
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||||
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||||
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|
||||
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|
||||
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|
||||
<a href="download.html">Download the DDL</a>
|
||||
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|
||||
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|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
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|
||||
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|
||||
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|
||||
|
|
@ -481,7 +505,7 @@ div.tocify {
|
|||
<ul class="nav navbar-nav navbar-right">
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||||
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|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
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||||
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|
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|
|||
|
|
@ -380,17 +380,33 @@ div.tocify {
|
|||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
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|
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|
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<a href="vocabulary.html">How the Vocabulary is Built</a>
|
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|
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@ -405,10 +421,21 @@ div.tocify {
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<a href="cdm30.html">CDM v3.0</a>
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</li>
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<li>
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<a href="cdm531.html">CDM v5.3.1</a>
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@ -422,20 +449,14 @@ div.tocify {
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<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
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<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
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@ -444,7 +465,27 @@ div.tocify {
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<a href="cdmRPackage.html">Use the CDM R Package</a>
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</li>
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||||
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||||
<a href="drug_dose.html">Calculate Drug Dose</a>
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@ -452,28 +493,11 @@ div.tocify {
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||||
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||||
<a href="drug_dose.html">Calculate Drug Dose</a>
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<a href="contribute.html">Ask a Question</a>
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|
||||
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||||
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|
@ -481,7 +505,7 @@ div.tocify {
|
|||
<ul class="nav navbar-nav navbar-right">
|
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<li>
|
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<a href="https://github.com/OHDSI/CommonDataModel">
|
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<span class="fas fa-github fa-lg"></span>
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<span class="fas fa-github"></span>
|
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||||
</a>
|
||||
</li>
|
||||
|
|
@ -562,7 +586,6 @@ div.tocify {
|
|||
<li>Concept Class attributes should not be confused with Classification Concepts. These are separate Concepts that have a hierarchical relationship to Standard Concepts or each other, while Concept Classes are unique Vocabulary-specific attributes for each Concept.</li>
|
||||
<li>For Concepts inherited from published terminologies, the source code is retained in the concept_code field and can be used to reference the source vocabulary.</li>
|
||||
<li>Standard Concepts (designated as ‘S’ in the standard_concept field) may appear in CDM tables in all *_concept_id fields, whereas Classification Concepts (‘C’) should not appear in the CDM data, but participate in the construction of the CONCEPT_ANCESTOR table and can be used to identify Descendants that may appear in the data. See CONCEPT_ANCESTOR table. Non-standard Concepts can only appear in *_source_concept_id fields and are not used in <a href="https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor">CONCEPT_ANCESTOR</a> table. Please refer to the Standardized Vocabularies specifications for details of the Standard Concept designation.</li>
|
||||
<li>All logical data elements associated with the various CDM tables (usually in the _type_concept_id field) are called Type Concepts, including defining characteristics, qualifying attributes etc. They are also stored as Concepts in the CONCEPT table. Since they are generated by OMOP, their is no meaningful concept_code.</li>
|
||||
<li>The lifespan of a Concept is recorded through its valid_start_date, valid_end_date and the invalid_ reason fields. This allows Concepts to correctly reflect at which point in time were defined. Usually, Concepts get deprecated if their meaning was deemed ambiguous, a duplication of another Concept, or needed revision for scientific reason. For example, drug ingredients get updated when different salt or isomer variants enter the market. Usually, drugs taken off the market do not cause a deprecation by the terminology vendor. Since observational data are valid with respect to the time they are recorded, it is key for the Standardized Vocabularies to provide even obsolete codes and maintain their relationships to other current Concepts .</li>
|
||||
<li>Concepts without a known instantiated date are assigned valid_start_date of ‘1-Jan-1970’.</li>
|
||||
<li>Concepts that are not invalid are assigned valid_end_date of ‘31-Dec-2099’.</li>
|
||||
|
|
@ -693,9 +716,97 @@ div.tocify {
|
|||
</ul>
|
||||
<p>Source Values are only provided for convenience and quality assurance (QA) purposes. Source Values and Source Concepts are optional, while Standard Concepts are mandatory. Source Values may contain information that is only meaningful in the context of a specific data source.</p>
|
||||
</div>
|
||||
<div id="general-concepts-and-type-concepts" class="section level3">
|
||||
<h3>General Concepts and Type Concepts</h3>
|
||||
<p>Type Concepts (ending in _TYPE_CONCEPT_ID) and general Concepts (ending in _CONCEPT_ID) are part of many tables. The former are special Concepts with the purpose of indicating where the data are derived from in the source. For example, the Type Concept field can be used to distinguish a DRUG_EXPOSURE record that is derived from a pharmacy-dispensing claim from one indicative of a prescription written in an electronic health record (EHR).</p>
|
||||
<div id="type-concepts" class="section level3">
|
||||
<h3>Type Concepts</h3>
|
||||
<p><em>By Mik Kallfelz and Dmitry Dymshyts</em></p>
|
||||
<p>Type Concepts (ending in _TYPE_CONCEPT_ID) are present in many tables. They are special Concepts with the purpose of indicating from where the data are derived in the source. For example, the Type Concept field can be used to distinguish a DRUG_EXPOSURE record that is derived from a pharmacy-dispensing claim from one indicative of a prescription written in an electronic health record (EHR).</p>
|
||||
<ul>
|
||||
<li>Type concepts help determining the provenance of a record in the OMOP CDM. Many tables hold a specific _type_concept_id field for which <a href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=">valid concepts</a> can be used to indicate a particular source of that record. For a condition it can be helpful to know, if it was derived from an EHR system or insurance claims. For a drug exposure it should be very useful to distinguish between prescriptions and actual administrations.</li>
|
||||
<li>In respect to the target table, matching type concepts should be chosen during the ETL step while processing sources. There are various representations in the list of type concepts of which some are quite specific for one table and others can be applied for many tables / domains, as they are quite generic. There is however no plausibility check or dependency between type concepts and tables which means they have to be chosen correctly.</li>
|
||||
<li>There is now one specific <a href="https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT">vocabulary</a> for type concepts which replaced a number of previously existing tables. For example, where previously there was a dedicated vocabulary for Drug Type Concepts, now we would choose the respective ones from the overall vocabulary (and ignore some of the old ones):</li>
|
||||
</ul>
|
||||
<table>
|
||||
<colgroup>
|
||||
<col width="64%" />
|
||||
<col width="35%" />
|
||||
</colgroup>
|
||||
<thead>
|
||||
<tr class="header">
|
||||
<th>Drug Type</th>
|
||||
<th>Type Concept</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr class="odd">
|
||||
<td>Inpatient administration</td>
|
||||
<td>EHR administration record</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>Physician administered drug (identified from EHR problem list)</td>
|
||||
<td>EHR administration record</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>Physician administered drug (identified from referral record)</td>
|
||||
<td>EHR administration record</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>Physician administered drug (identified from EHR observation)</td>
|
||||
<td>EHR administration record</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>Physician administered drug (identified from EHR order)</td>
|
||||
<td>EHR administration record</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>Prescription dispensed in pharmacy</td>
|
||||
<td>EHR dispensing record</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>Dispensed in Outpatient office</td>
|
||||
<td>EHR dispensing record</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>Medication list entry</td>
|
||||
<td>EHR medication list</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>Prescription written</td>
|
||||
<td>EHR prescription</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td></td>
|
||||
<td>EHR prescription issue record</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>Prescription dispensed through mail order</td>
|
||||
<td>Mail order record</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>NLP derived</td>
|
||||
<td>NLP</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>Patient Self-Reported Medication</td>
|
||||
<td>Patient self-report</td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>Physician administered drug (identified as procedure)</td>
|
||||
<td>Pharmacy claim</td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>Drug era - 0 days persistence window</td>
|
||||
<td></td>
|
||||
</tr>
|
||||
<tr class="even">
|
||||
<td>Drug era - 30 days persistence window</td>
|
||||
<td></td>
|
||||
</tr>
|
||||
<tr class="odd">
|
||||
<td>Randomized Drug</td>
|
||||
<td></td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div id="time-span-of-available-data" class="section level3">
|
||||
<h3>Time span of available data</h3>
|
||||
|
|
|
|||
|
|
@ -380,17 +380,33 @@ div.tocify {
|
|||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
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|
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|
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<a href="dataModelConventions.html">
|
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|
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|
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|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
||||
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|
||||
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|
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<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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|
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@ -405,10 +421,21 @@ div.tocify {
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<a href="cdm30.html">CDM v3.0</a>
|
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</li>
|
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<li>
|
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<a href="cdm531.html">CDM v5.3.1</a>
|
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<a href="cdm60.html">CDM v6.0</a>
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|
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<a href="cdm60.html">CDM v6.0</a>
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|
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|
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@ -422,20 +449,14 @@ div.tocify {
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|
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|
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<a href="reviewProposals.html">Under Review</a>
|
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<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
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|
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||||
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||||
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|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
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|
||||
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|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
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|
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|
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@ -444,7 +465,27 @@ div.tocify {
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<ul class="dropdown-menu" role="menu">
|
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|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
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|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
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|
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|
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Support
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|
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<li>
|
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<a href="faq.html">FAQ</a>
|
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|
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|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -481,7 +505,7 @@ div.tocify {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fas fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
|
|||
|
|
@ -306,17 +306,33 @@ $(document).ready(function () {
|
|||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="dataModelConventions.html">
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-list-alt"></span>
|
||||
|
||||
Conventions
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="dataModelConventions.html">General Conventions</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
|
|
@ -331,10 +347,21 @@ $(document).ready(function () {
|
|||
<a href="cdm30.html">CDM v3.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm531.html">CDM v5.3.1</a>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -348,20 +375,14 @@ $(document).ready(function () {
|
|||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="reviewProposals.html">Under Review</a>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -370,7 +391,27 @@ $(document).ready(function () {
|
|||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-question"></span>
|
||||
|
||||
Help
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-life-ring"></span>
|
||||
|
||||
Support
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
|
|
@ -378,28 +419,11 @@ $(document).ready(function () {
|
|||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -407,7 +431,7 @@ $(document).ready(function () {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fas fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
|
|||
|
|
@ -0,0 +1,559 @@
|
|||
<!DOCTYPE html>
|
||||
|
||||
<html>
|
||||
|
||||
<head>
|
||||
|
||||
<meta charset="utf-8" />
|
||||
<meta name="generator" content="pandoc" />
|
||||
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
|
||||
|
||||
|
||||
|
||||
|
||||
<title>Observation Period Considerations for EHR Data</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.6/header-attrs.js"></script>
|
||||
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
|
||||
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
|
||||
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
|
||||
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
|
||||
<script src="site_libs/navigation-1.1/tabsets.js"></script>
|
||||
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
|
||||
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
|
||||
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
|
||||
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
|
||||
<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
|
||||
|
||||
<style type="text/css">
|
||||
code{white-space: pre-wrap;}
|
||||
span.smallcaps{font-variant: small-caps;}
|
||||
span.underline{text-decoration: underline;}
|
||||
div.column{display: inline-block; vertical-align: top; width: 50%;}
|
||||
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
|
||||
ul.task-list{list-style: none;}
|
||||
</style>
|
||||
|
||||
<style type="text/css">code{white-space: pre;}</style>
|
||||
<style type="text/css">
|
||||
pre:not([class]) {
|
||||
background-color: white;
|
||||
}
|
||||
</style>
|
||||
<script type="text/javascript">
|
||||
if (window.hljs) {
|
||||
hljs.configure({languages: []});
|
||||
hljs.initHighlightingOnLoad();
|
||||
if (document.readyState && document.readyState === "complete") {
|
||||
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
|
||||
}
|
||||
}
|
||||
</script>
|
||||
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
h1 {
|
||||
font-size: 34px;
|
||||
}
|
||||
h1.title {
|
||||
font-size: 38px;
|
||||
}
|
||||
h2 {
|
||||
font-size: 30px;
|
||||
}
|
||||
h3 {
|
||||
font-size: 24px;
|
||||
}
|
||||
h4 {
|
||||
font-size: 18px;
|
||||
}
|
||||
h5 {
|
||||
font-size: 16px;
|
||||
}
|
||||
h6 {
|
||||
font-size: 12px;
|
||||
}
|
||||
.table th:not([align]) {
|
||||
text-align: left;
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
||||
<style type = "text/css">
|
||||
.main-container {
|
||||
max-width: 940px;
|
||||
margin-left: auto;
|
||||
margin-right: auto;
|
||||
}
|
||||
code {
|
||||
color: inherit;
|
||||
background-color: rgba(0, 0, 0, 0.04);
|
||||
}
|
||||
img {
|
||||
max-width:100%;
|
||||
}
|
||||
.tabbed-pane {
|
||||
padding-top: 12px;
|
||||
}
|
||||
.html-widget {
|
||||
margin-bottom: 20px;
|
||||
}
|
||||
button.code-folding-btn:focus {
|
||||
outline: none;
|
||||
}
|
||||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
/* padding for bootstrap navbar */
|
||||
body {
|
||||
padding-top: 51px;
|
||||
padding-bottom: 40px;
|
||||
}
|
||||
/* offset scroll position for anchor links (for fixed navbar) */
|
||||
.section h1 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h2 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h3 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h4 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h5 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h6 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.dropdown-submenu {
|
||||
position: relative;
|
||||
}
|
||||
.dropdown-submenu>.dropdown-menu {
|
||||
top: 0;
|
||||
left: 100%;
|
||||
margin-top: -6px;
|
||||
margin-left: -1px;
|
||||
border-radius: 0 6px 6px 6px;
|
||||
}
|
||||
.dropdown-submenu:hover>.dropdown-menu {
|
||||
display: block;
|
||||
}
|
||||
.dropdown-submenu>a:after {
|
||||
display: block;
|
||||
content: " ";
|
||||
float: right;
|
||||
width: 0;
|
||||
height: 0;
|
||||
border-color: transparent;
|
||||
border-style: solid;
|
||||
border-width: 5px 0 5px 5px;
|
||||
border-left-color: #cccccc;
|
||||
margin-top: 5px;
|
||||
margin-right: -10px;
|
||||
}
|
||||
.dropdown-submenu:hover>a:after {
|
||||
border-left-color: #ffffff;
|
||||
}
|
||||
.dropdown-submenu.pull-left {
|
||||
float: none;
|
||||
}
|
||||
.dropdown-submenu.pull-left>.dropdown-menu {
|
||||
left: -100%;
|
||||
margin-left: 10px;
|
||||
border-radius: 6px 0 6px 6px;
|
||||
}
|
||||
</style>
|
||||
|
||||
<script>
|
||||
// manage active state of menu based on current page
|
||||
$(document).ready(function () {
|
||||
// active menu anchor
|
||||
href = window.location.pathname
|
||||
href = href.substr(href.lastIndexOf('/') + 1)
|
||||
if (href === "")
|
||||
href = "index.html";
|
||||
var menuAnchor = $('a[href="' + href + '"]');
|
||||
|
||||
// mark it active
|
||||
menuAnchor.parent().addClass('active');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.dropdown').addClass('active');
|
||||
});
|
||||
</script>
|
||||
|
||||
<!-- tabsets -->
|
||||
|
||||
<style type="text/css">
|
||||
.tabset-dropdown > .nav-tabs {
|
||||
display: inline-table;
|
||||
max-height: 500px;
|
||||
min-height: 44px;
|
||||
overflow-y: auto;
|
||||
background: white;
|
||||
border: 1px solid #ddd;
|
||||
border-radius: 4px;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li.active:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
|
||||
content: "";
|
||||
border: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
|
||||
content: "";
|
||||
font-family: 'Glyphicons Halflings';
|
||||
display: inline-block;
|
||||
padding: 10px;
|
||||
border-right: 1px solid #ddd;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li.active {
|
||||
display: block;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li > a,
|
||||
.tabset-dropdown > .nav-tabs > li > a:focus,
|
||||
.tabset-dropdown > .nav-tabs > li > a:hover {
|
||||
border: none;
|
||||
display: inline-block;
|
||||
border-radius: 4px;
|
||||
background-color: transparent;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
|
||||
display: block;
|
||||
float: none;
|
||||
}
|
||||
|
||||
.tabset-dropdown > .nav-tabs > li {
|
||||
display: none;
|
||||
}
|
||||
</style>
|
||||
|
||||
<!-- code folding -->
|
||||
|
||||
|
||||
|
||||
|
||||
</head>
|
||||
|
||||
<body>
|
||||
|
||||
|
||||
<div class="container-fluid main-container">
|
||||
|
||||
|
||||
|
||||
|
||||
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
|
||||
<div class="container">
|
||||
<div class="navbar-header">
|
||||
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
|
||||
<span class="icon-bar"></span>
|
||||
<span class="icon-bar"></span>
|
||||
<span class="icon-bar"></span>
|
||||
</button>
|
||||
<a class="navbar-brand" href="index.html"><div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div></a>
|
||||
</div>
|
||||
<div id="navbar" class="navbar-collapse collapse">
|
||||
<ul class="nav navbar-nav">
|
||||
<li>
|
||||
<a href="index.html">
|
||||
<span class="fas fa-home"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
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<h1 class="title toc-ignore">Observation Period Considerations for EHR Data</h1>
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<p><em>By Melanie Philofsky and the EHR Working Group</em></p>
|
||||
<p>The EHR WG convened on July 24, August 7, and August 21, 2020 to discuss the creation of an Observation Period from EHR data. The current and future conventions are not prescriptive enough and leave room for various ways of interpretation. The goals of our discussions were to increase the standardization for the implementation of the OBSERVATION_PERIOD table by providing some general guidelines for determining the start, end, and gaps in Observation Periods. The suggestions we came up with are only “suggestions” at this point. More research should be done to understand how these choices might impact evidence generated using these data. All of these decisions should be tempered by local understanding of patients in the EHR you are ETLing.</p>
|
||||
<ul>
|
||||
<li><em>Note - These suggestions are not intended for HMO EHR sites since HMO EHR Observation Periods more closely resemble claims data Observation Periods.</em></li>
|
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</ul>
|
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<div id="observation-period-start-date" class="section level2">
|
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<h2>Observation Period Start Date</h2>
|
||||
<ul>
|
||||
<li>Generally an Observation Period does NOT begin before birth, however, it might begin before birth IF the pregnant mother receives care recorded in your EHR. The child’s record is then split from the mother’s record at birth but may retain care given during pregnancy. For these children in your dataset, the field <strong>observation_period_start_date should be the birth date minus 9 months</strong></li>
|
||||
<li>An <strong>Observation Period does NOT begin before the implementation of the EHR at your site</strong>. Any records prior to implementation are probably “history of” record types and not a complete EHR record of clinical events.</li>
|
||||
<li>Special consideration should be given to migration from previous EHR, implementation at different sites within your healthcare system, implementation of different modules, etc.</li>
|
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</ul>
|
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</div>
|
||||
<div id="observation-period-end-date" class="section level2">
|
||||
<h2>Observation Period end date</h2>
|
||||
<p>Set the <strong>observation_period_end_date</strong> as the first date from the following:</p>
|
||||
<ul>
|
||||
<li><strong>Date of death + 60 days</strong>
|
||||
<ul>
|
||||
<li>This is a CDM convention to allow events after death (autopsy, final notes, etc).</li>
|
||||
</ul></li>
|
||||
<li><strong>Last clinical event + 60 days</strong>
|
||||
<ul>
|
||||
<li>The assumption is that person will return to the same health provider if an adverse reaction/complication/unresolved condition occurs.</li>
|
||||
</ul></li>
|
||||
<li><strong>Date of the data pull from the system</strong></li>
|
||||
</ul>
|
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</div>
|
||||
<div id="observation-period-gaps-and-persistence-windows" class="section level2">
|
||||
<h2>Observation Period Gaps and Persistence Windows</h2>
|
||||
<div id="observation-period-gaps" class="section level3">
|
||||
<h3>Observation Period Gaps</h3>
|
||||
<p>Periods of time when a Person does not receive care from your institution and therefore is not observed and should not have an Observation Period. These gaps are usually hard to determine because most Persons don’t announce their departure from an EHR/healthcare institution. Therefore, a heuristic will need to be instituted to determine Observation Period Gaps where the information is not explicit.</p>
|
||||
</div>
|
||||
<div id="observation-period-persistence-window" class="section level3">
|
||||
<h3>Observation Period Persistence Window</h3>
|
||||
<p>Defined as the maximum time allowed between two clinical events under the assumption a Person would have a clinical event recorded, if they are not healthy and seek care.</p>
|
||||
<p><strong>Example:</strong> Person 1 has a series of clinical events recorded from <strong>Jan. 1, 2010 to June 15, 2012</strong>, where the time between clinical events does not exceed 60 days. The next clinical event for Person 1 is on <strong>Oct. 1, 2018</strong>. Starting Oct. 1, 2018 Person 1 has clinical events occurring at least every 90 days up to the present date.</p>
|
||||
<p>There is a 6+ year gap between groups of clinical events recorded in the CDM. After discussion in the EHR WG, we believe this 6+ year gap is indicative of a Person not being seen within our EHR/healthcare institution. Per convention #4 for Observation Period table, “As a general assumption, during an Observation Period any clinical event that happens to the patient is expected to be recorded. Conversely, the absence of data indicates that no clinical events occurred to the patient.” Person 1 has two Observation Periods.</p>
|
||||
<p><strong>1st Observation Period</strong></p>
|
||||
<ul>
|
||||
<li>observation_period_start_date = <strong>01/01/2010</strong></li>
|
||||
<li>observation_period_end_date = <strong>08/15/2012</strong> (Per the end_date guideline above)</li>
|
||||
</ul>
|
||||
<p><strong>2nd Observation Period</strong></p>
|
||||
<ul>
|
||||
<li>observation_period_start_date = <strong>10/01/2018</strong></li>
|
||||
<li>observation_period_end_date = <strong>09/01/2020</strong> (Date of the data pull, per the end_date guideline above)</li>
|
||||
</ul>
|
||||
<p>Now, there are cases where a Person only receives care within you EHR system when absolutely necessary. And if your EHR doesn’t offer primary care services, the majority of Persons who lack healthcare insurance or any other reason why Persons are only seen in urgent or emergent situations, the above heuristic might be too restrictive. This is a guideline. A question the EHR WG debated was how long between clinical events should we assume any clinical event that happens to the Person is expected to be recorded? When should we end one Observation Period and begin another? What should be the time between events for an Observation Period Persistence Window? Wellness checkups/Visits happen approximately every 12-18 months depending on a multitude of factors.</p>
|
||||
<p><strong>Our recommendation: If Observation Period Gaps are 548 days or more, then the previous Observation Period should end and another Observation Period should begin on the date of the next clinical event as per the Person 1 example above.</strong></p>
|
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<div id="additional-etl-considerations" class="section level2">
|
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<h2>Additional ETL considerations</h2>
|
||||
<ul>
|
||||
<li>Implementation of your EHR, migration from previous EHR, implementation at different sites within your healthcare system, implementation of different modules</li>
|
||||
<li>Coverage of your healthcare system within your area, population served by the healthcare system</li>
|
||||
<li>All decisions should be tempered by local understanding of patients in the EHR you are ETLing.</li>
|
||||
</ul>
|
||||
<p>The Observation Period can be created by only one clinical event. However, the clinical event must NOT be from the Death table. If a Death date does not have any other clinical records 18 months before AND 18 months after the death date, then an Observation Period will not be created. We believe this logic is needed because if a Person only has a death death_date without other clinical event records, a Person is most likely not being “observed” when the death occurred. If a Person was being observed at their time of death, then other records (visit, condition, measurement, etc.) would be created. This rule is most relevant for those with death registry data since a Person who dies in the hospital has many clinical event records.</p>
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|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-list-alt"></span>
|
||||
|
||||
Conventions
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="dataModelConventions.html">General Conventions</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
|
|
@ -329,10 +345,21 @@ $(document).ready(function () {
|
|||
<a href="cdm30.html">CDM v3.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm531.html">CDM v5.3.1</a>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -346,20 +373,14 @@ $(document).ready(function () {
|
|||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="reviewProposals.html">Under Review</a>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -368,7 +389,27 @@ $(document).ready(function () {
|
|||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-question"></span>
|
||||
|
||||
Help
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-life-ring"></span>
|
||||
|
||||
Support
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
|
|
@ -376,28 +417,11 @@ $(document).ready(function () {
|
|||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -405,7 +429,7 @@ $(document).ready(function () {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fas fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
@ -425,45 +449,29 @@ $(document).ready(function () {
|
|||
</div>
|
||||
|
||||
|
||||
<p>The OMOP Common Data Model is managed by the <a href="https://www.ohdsi.org/web/wiki/doku.php?id=projects:workgroups:cdm-wg">OHDSI CDM Working Group</a>. Through the end of 2019 and into 2020 our goal was to fully update the documentation in an effort to facilitate greater understanding of the model. Almost every <a href="https://www.forums.ohdsi.org">forum post</a> relating to a question on how to map data into the CDM inevitably referenced the (now outdated) technical and difficult-to-understand explanations of the tables and fields currently on the wiki. To remedy we focused on one or two tables each month, diving fully into the user guidance and ETL specifications. The results of our efforts can be seen on the pages detailing <a href="https://ohdsi.github.io/CommonDataModel/cdm531.html">v5.3</a> and <a href="https://ohdsi.github.io/CommonDataModel/cdm60.html">v6.0</a>.</p>
|
||||
<p>In addition to documentation the formal remit of the CDM Working Group (WG) is to hear proposals for change, ratifying only those with valid use cases and data to support them. In the past, this was done by the WG alone. The group would invite others from around the community to present use cases for change and suggestions for improvement. The WG would then vote on the proposals and a new CDM version would be released after a certain period of time or if enough proposals were voted in. This approach worked when the community was smaller but as it is growing rapidly the CDM WG needed to adapt the refresh cycle such that everyone has an opportunity to weigh in on the proposed changes.</p>
|
||||
<div id="cdm-refresh-cycle" class="section level2">
|
||||
<h2>CDM Refresh Cycle</h2>
|
||||
<p><img src="images/CDM_refresh_cycle.png" /></p>
|
||||
<div id="define-new-version" class="section level3">
|
||||
<h3>1. Define New Version</h3>
|
||||
<p>The image above describes the new CDM refresh cycle. It begins with <strong>defining a new version</strong>. This has been completed for the current cycle. Issues and proposals on the github were considered during a 4-hour workshop where it was decided the next CDM version will be CDM v5.4, building off of CDM v5.3. The group then participated in a rapid-fire voting activity to identify which changes should be incorporated into CDM v5.4. Any items that were not unanimously agreed upon were then discussed in small groups to hone the proposal and suggestions were presented back to the group. The final roadmap for CDM v5.4 can be found <a href="https://github.com/OHDSI/CommonDataModel/projects/3">here</a>.</p>
|
||||
<p>The OMOP Common Data Model is managed by the OHDSI CDM Working Group. If you would like to join our group please fill out <a href="https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu">this form</a> and check “Common Data Model” to be added to our Microsoft Teams environment. This working group endeavors to maintain the OMOP CDM as a living model by soliciting and responding to requests from the community based on use cases and research purposes. For more information on the CDM refresh process please see the description <a href="http://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html">here</a>. You will find information on our meetings and links to join at the end of this page.</p>
|
||||
<div id="current-cdm-version" class="section level2">
|
||||
<h2>Current CDM Version</h2>
|
||||
<p>The current CDM version is <a href="http://ohdsi.github.io/CommonDataModel/cdm54.html">CDM v5.4</a>, depicted below. This CDM version was developed over the course of a year by considering requests that were sent via our <a href="https://github.com/OHDSI/CommonDataModel/issues">issues page</a>. The list of proposed changes was then shared with the community in multiple ways: through discussions at the weekly OHDSI Community calls, discussions with the OHDSI Steering Committee, and discussions with all potentially affected workgroups. The <a href="http://ohdsi.github.io/CommonDataModel/cdm54Changes.html">final changes</a> were then delivered to the Community through a new R package designed to dynamically generate the DDLs and documentation for all supported SQL dialects.</p>
|
||||
<ul>
|
||||
<li><a href="https://github.com/OHDSI/CommonDataModel/tree/v5.4.0">Link to DDLs for CDM v5.4</a></li>
|
||||
<li><a href="https://github.com/OHDSI/CommonDataModel/tree/master#readme">Link to ReadMe for instructions on how to use the R package</a></li>
|
||||
</ul>
|
||||
<p><img src="images/cdm54.png" /></p>
|
||||
</div>
|
||||
<div id="sign-off-from-work-groups" class="section level3">
|
||||
<h3>2. Sign off from Work Groups</h3>
|
||||
<p>This is the current stage of the refresh cycle for CDM v5.4. Each member of the CDM WG is a liaison for another workgroup in the community. They are responsible for presenting the proposed changes to the CDM and collecting the feedback. This has resulted in very helpful suggestions from the EHR, Data Quality, Device, HADES, and ACHILLES groups. This outreach has proven to be very effective and should result in a very stable version.</p>
|
||||
</div>
|
||||
<div id="release-ddls" class="section level3">
|
||||
<h3>3. Release DDLs</h3>
|
||||
<p>After all changes and suggestions are agreed upon by the community and work groups the next step is to generate the DDLs this will be done by the CDM Development group.</p>
|
||||
</div>
|
||||
<div id="software-update" class="section level3">
|
||||
<h3>4. Software Update</h3>
|
||||
<p>There will be period of time once the DDLs are ready to allow the software and methods developers to prepare for the official release of the CDM. This is meant to serve as a buffer so that once the community starts adopting the new model, the tools and methods will be ready to support it.</p>
|
||||
</div>
|
||||
<div id="community-support" class="section level3">
|
||||
<h3>5. Community Support</h3>
|
||||
<p>This is the final stage of the CDM refresh cycle. Once the DDLs are ready and the software and tools supports the new version, the CDM WG will work to help the community convert their data to the new model.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div id="cdm-wg-meeting-information" class="section level1">
|
||||
<h1>CDM WG Meeting Information</h1>
|
||||
<div id="cdm-wg-meeting-information" class="section level2">
|
||||
<h2>CDM WG Meeting Information</h2>
|
||||
<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 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> These were recently changed from a Skype meeting to a Microsoft Teams meeting. If you do you have access to the OHDSI Teams Tenet, please contact Clair Blacketer at <a href="mailto:mblacke@its.jnj.com" class="email">mblacke@its.jnj.com</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>
|
||||
<div id="cdm-wg-important-links" class="section level3">
|
||||
<h3>CDM WG Important Links</h3>
|
||||
<ul>
|
||||
<li><a href="https://drive.google.com/open?id=1DaNKe6ivIAZPJeI31VJ-pzNB9wS9hDqu">Google Drive Location</a></li>
|
||||
<li><a href="https://docs.google.com/document/d/1WgKePjrI_cGdqn2XQCe1JdGaTzdMqU4p5ihkMt8fcAc/edit?usp=sharing">Running Agenda</a></li>
|
||||
<li><a href="https://github.com/OHDSI/CommonDataModel">CDM Github</a></li>
|
||||
<li><a href="https://www.ohdsi.org/web/wiki/doku.php?id=documentation:next_cdm:cdm_process">Process for adopting CDM and Vocabulary changes</a></li>
|
||||
<li><a href="http://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html">Process for adopting CDM and Vocabulary changes</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
|
|
|||
|
|
@ -13,21 +13,13 @@
|
|||
|
||||
<title>Indices, Primary Keys and Foreign Key Constraints</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.6/header-attrs.js"></script>
|
||||
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
|
||||
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
|
||||
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
|
||||
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
|
||||
<style>h1 {font-size: 34px;}
|
||||
h1.title {font-size: 38px;}
|
||||
h2 {font-size: 30px;}
|
||||
h3 {font-size: 24px;}
|
||||
h4 {font-size: 18px;}
|
||||
h5 {font-size: 16px;}
|
||||
h6 {font-size: 12px;}
|
||||
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
|
||||
pre:not([class]) { background-color: white }</style>
|
||||
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
|
||||
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
|
||||
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
|
||||
|
|
@ -48,6 +40,11 @@
|
|||
</style>
|
||||
|
||||
<style type="text/css">code{white-space: pre;}</style>
|
||||
<style type="text/css">
|
||||
pre:not([class]) {
|
||||
background-color: white;
|
||||
}
|
||||
</style>
|
||||
<script type="text/javascript">
|
||||
if (window.hljs) {
|
||||
hljs.configure({languages: []});
|
||||
|
|
@ -60,6 +57,32 @@ if (window.hljs) {
|
|||
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
h1 {
|
||||
font-size: 34px;
|
||||
}
|
||||
h1.title {
|
||||
font-size: 38px;
|
||||
}
|
||||
h2 {
|
||||
font-size: 30px;
|
||||
}
|
||||
h3 {
|
||||
font-size: 24px;
|
||||
}
|
||||
h4 {
|
||||
font-size: 18px;
|
||||
}
|
||||
h5 {
|
||||
font-size: 16px;
|
||||
}
|
||||
h6 {
|
||||
font-size: 12px;
|
||||
}
|
||||
.table th:not([align]) {
|
||||
text-align: left;
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
|
@ -72,6 +95,10 @@ if (window.hljs) {
|
|||
margin-left: auto;
|
||||
margin-right: auto;
|
||||
}
|
||||
code {
|
||||
color: inherit;
|
||||
background-color: rgba(0, 0, 0, 0.04);
|
||||
}
|
||||
img {
|
||||
max-width:100%;
|
||||
}
|
||||
|
|
@ -87,13 +114,40 @@ button.code-folding-btn:focus {
|
|||
summary {
|
||||
display: list-item;
|
||||
}
|
||||
pre code {
|
||||
padding: 0;
|
||||
}
|
||||
</style>
|
||||
|
||||
|
||||
<style type="text/css">
|
||||
/* padding for bootstrap navbar */
|
||||
body {
|
||||
padding-top: 51px;
|
||||
padding-bottom: 40px;
|
||||
}
|
||||
/* offset scroll position for anchor links (for fixed navbar) */
|
||||
.section h1 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h2 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h3 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h4 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h5 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.section h6 {
|
||||
padding-top: 56px;
|
||||
margin-top: -56px;
|
||||
}
|
||||
.dropdown-submenu {
|
||||
position: relative;
|
||||
}
|
||||
|
|
@ -121,7 +175,7 @@ pre code {
|
|||
margin-right: -10px;
|
||||
}
|
||||
.dropdown-submenu:hover>a:after {
|
||||
border-left-color: #adb5bd;
|
||||
border-left-color: #ffffff;
|
||||
}
|
||||
.dropdown-submenu.pull-left {
|
||||
float: none;
|
||||
|
|
@ -133,7 +187,7 @@ pre code {
|
|||
}
|
||||
</style>
|
||||
|
||||
<script type="text/javascript">
|
||||
<script>
|
||||
// manage active state of menu based on current page
|
||||
$(document).ready(function () {
|
||||
// active menu anchor
|
||||
|
|
@ -144,23 +198,10 @@ $(document).ready(function () {
|
|||
var menuAnchor = $('a[href="' + href + '"]');
|
||||
|
||||
// mark it active
|
||||
menuAnchor.tab('show');
|
||||
menuAnchor.parent().addClass('active');
|
||||
|
||||
// if it's got a parent navbar menu mark it active as well
|
||||
menuAnchor.closest('li.dropdown').addClass('active');
|
||||
|
||||
// Navbar adjustments
|
||||
var navHeight = $(".navbar").first().height() + 15;
|
||||
var style = document.createElement('style');
|
||||
var pt = "padding-top: " + navHeight + "px; ";
|
||||
var mt = "margin-top: -" + navHeight + "px; ";
|
||||
var css = "";
|
||||
// offset scroll position for anchor links (for fixed navbar)
|
||||
for (var i = 1; i <= 6; i++) {
|
||||
css += ".section h" + i + "{ " + pt + mt + "}\n";
|
||||
}
|
||||
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
|
||||
document.head.appendChild(style);
|
||||
});
|
||||
</script>
|
||||
|
||||
|
|
@ -172,6 +213,7 @@ $(document).ready(function () {
|
|||
max-height: 500px;
|
||||
min-height: 44px;
|
||||
overflow-y: auto;
|
||||
background: white;
|
||||
border: 1px solid #ddd;
|
||||
border-radius: 4px;
|
||||
}
|
||||
|
|
@ -297,7 +339,7 @@ div.tocify {
|
|||
|
||||
|
||||
<!-- setup 3col/9col grid for toc_float and main content -->
|
||||
<div class="row">
|
||||
<div class="row-fluid">
|
||||
<div class="col-xs-12 col-sm-4 col-md-3">
|
||||
<div id="TOC" class="tocify">
|
||||
</div>
|
||||
|
|
@ -322,13 +364,13 @@ div.tocify {
|
|||
<ul class="nav navbar-nav">
|
||||
<li>
|
||||
<a href="index.html">
|
||||
<span class="fa fa-home"></span>
|
||||
<span class="fas fa-home"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fa fa-landmark"></span>
|
||||
<span class="fas fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
||||
|
|
@ -338,21 +380,37 @@ div.tocify {
|
|||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="dataModelConventions.html">
|
||||
<span class="fa fa-list-alt"></span>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-list-alt"></span>
|
||||
|
||||
Conventions
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="dataModelConventions.html">General Conventions</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fa fa-history"></span>
|
||||
<span class="fas fa-history"></span>
|
||||
|
||||
CDM Versions
|
||||
|
||||
|
|
@ -362,20 +420,28 @@ div.tocify {
|
|||
<li>
|
||||
<a href="cdm30.html">CDM v3.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm531.html">CDM v5.3.1</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm531.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
<span class="fas fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
|
||||
|
|
@ -383,29 +449,43 @@ div.tocify {
|
|||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="reviewProposals.html">Under Review</a>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fa fa-question"></span>
|
||||
<span class="fas fa-question"></span>
|
||||
|
||||
Help
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-life-ring"></span>
|
||||
|
||||
Support
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
|
|
@ -413,28 +493,11 @@ div.tocify {
|
|||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fa fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -442,7 +505,7 @@ div.tocify {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fa fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
@ -451,7 +514,7 @@ div.tocify {
|
|||
</div><!--/.container -->
|
||||
</div><!--/.navbar -->
|
||||
|
||||
<div id="header">
|
||||
<div class="fluid-row" id="header">
|
||||
|
||||
|
||||
|
||||
|
|
@ -460,13 +523,6 @@ div.tocify {
|
|||
</div>
|
||||
|
||||
|
||||
<div id="to-do" class="section level3">
|
||||
<h3>To Do</h3>
|
||||
<ul>
|
||||
<li>Need something for hashing</li>
|
||||
<li>What about constraints that aren’t foreign keys</li>
|
||||
</ul>
|
||||
</div>
|
||||
<div id="overview" class="section level2">
|
||||
<h2>Overview</h2>
|
||||
<p>Database indices improve the performance of queries against a database by organizing the data in a way that increase query execution.</p>
|
||||
|
|
@ -479,7 +535,7 @@ div.tocify {
|
|||
<li>Indexing on all columns containing an "_id" (e.g. condition_occurrence_id, drug_exposure_id, measurement_id, procedure_occurrence_id, etc.)</li>
|
||||
<li>Indexing on primary and foreign keys</li>
|
||||
</ul>
|
||||
<p>For all databases, regardless of custom indice support, primary and foreign keys should be set. This is a step towards ensuring data integrity.</p>
|
||||
<p>For all databases, regardless of custom indice support, primary and foreign keys should be set. This is a step towards ensuring data integrity. Information on what table level attributes should be set as primary and foreign keys can be found within the *_Field_Level.csv file(s) located in the <a href="https://github.com/OHDSI/CommonDataModel/tree/v5.4/inst/csv">INST/CSV directory</a></p>
|
||||
</div>
|
||||
<div id="database-support" class="section level2">
|
||||
<h2>Database support</h2>
|
||||
|
|
@ -552,7 +608,7 @@ $(document).ready(function () {
|
|||
|
||||
$(document).ready(function () {
|
||||
$('.tabset-dropdown > .nav-tabs > li').click(function () {
|
||||
$(this).parent().toggleClass('nav-tabs-open');
|
||||
$(this).parent().toggleClass('nav-tabs-open')
|
||||
});
|
||||
});
|
||||
</script>
|
||||
|
|
@ -562,9 +618,6 @@ $(document).ready(function () {
|
|||
<script>
|
||||
$(document).ready(function () {
|
||||
|
||||
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
|
||||
$('.unlisted.unnumbered').addClass('toc-ignore')
|
||||
|
||||
// move toc-ignore selectors from section div to header
|
||||
$('div.section.toc-ignore')
|
||||
.removeClass('toc-ignore')
|
||||
|
|
|
|||
|
|
@ -380,17 +380,33 @@ div.tocify {
|
|||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="dataModelConventions.html">
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-list-alt"></span>
|
||||
|
||||
Conventions
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="dataModelConventions.html">General Conventions</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
|
|
@ -405,10 +421,21 @@ div.tocify {
|
|||
<a href="cdm30.html">CDM v3.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm531.html">CDM v5.3.1</a>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -422,20 +449,14 @@ div.tocify {
|
|||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="reviewProposals.html">Under Review</a>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -444,7 +465,27 @@ div.tocify {
|
|||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-question"></span>
|
||||
|
||||
Help
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-life-ring"></span>
|
||||
|
||||
Support
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
|
|
@ -452,28 +493,11 @@ div.tocify {
|
|||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -481,7 +505,7 @@ div.tocify {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fas fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
@ -503,12 +527,14 @@ div.tocify {
|
|||
<h2>OMOP Common Data Model Oncology Extension Documentation</h2>
|
||||
<p>This documentation details the ratified proposal of adding an oncology extension to the OMOP CDM. These tables and fields will become part of the next release (v6.1) of the Common Data Model. Below are their descriptions; showing <em>additions</em> to the model only. For example, two fields were added to the MEASUREMENT table as part of this extension so only those two fields are listed below for MEASUREMENT instead of the entire table. For more information, please see the <a href="https://github.com/OHDSI/OncologyWG/wiki">OMOP Oncology wiki site</a>.</p>
|
||||
<p>The DDLs for these tables are located on the Oncology github, as detailed in the <a href="https://github.com/OHDSI/OncologyWG/wiki/Oncology-CDM-Extension-Installation">installation instructions</a>.</p>
|
||||
<pre><code>## Warning in read.table(file = file, header = header, sep = sep, quote = quote, : incomplete final line found by readTableHeader on '../inst/csv/
|
||||
## OMOP_CDM_Oncology_Ex_Table_Level.csv'</code></pre>
|
||||
<div id="episode" class="section level3 tabset tabset-pills">
|
||||
<h3 class="tabset tabset-pills">EPISODE</h3>
|
||||
<p><strong>Table Description</strong></p>
|
||||
<p>The EPISODE table aggregates lower-level clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) into a higher-level abstraction representing clinically and analytically relevant disease phases/outcomes and treatments. The EPISODE_EVENT table connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry.</p>
|
||||
<p><strong>ETL Conventions</strong></p>
|
||||
<p>Valid Episode Concepts belong to the ‘Episode’ domain.<br><br> Standard Episode Concepts are categorized by concept class:<br> Disease Episode<br> 32528 “Disease First Occurrence”<br> 32529 “Disease Recurrence”<br> 32530 “Disease Remission”<br> 32677 “Disease Progression”<br> Treatment Episode 32531 “Treatment Regimen”<br> 32532 “Treatment Cycle”<br> Episode of Care 32533 “Episode of Care”<br><br> The relationship between a disease episode and treatment episodes can be represented by the self-referencing foreign key column EPISODE.episode_parent_id.<br><br> A treatment EPISODE can be delivered at regular intervals, cycles or fractions. The parent-child relationship between a treatment episode and its constituent treatment cycles can be represented by the self-referencing foreign key column EPISODE.episode_parent_id. 5 Some episodes may not have links to any underlying clinical events. For such episodes, the EPISODE_EVENT table is not populated.</p>
|
||||
<p>The EPISODE table aggregates lower-level clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) into a higher-level abstraction representing clinically and analytically relevant disease phases,outcomes and treatments. The EPISODE_EVENT table connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry. For example cancers including their development over time, their treatment, and final resolution.</p>
|
||||
<p><strong>User Guide</strong></p>
|
||||
<p>Valid Episode Concepts belong to the ‘Episode’ domain. For cancer episodes please see [article], for non-cancer episodes please see [article]. If your source data does not have all episodes that are relevant to the therapeutic area, write only those you can easily derive from the data. It is understood that that table is not currently expected to be comprehensive.</p>
|
||||
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
|
||||
<thead>
|
||||
<tr>
|
||||
|
|
@ -550,7 +576,7 @@ FK Class
|
|||
episode_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A unique identifier for each Episode event.
|
||||
A unique identifier for each Episode.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
|
|
@ -578,7 +604,7 @@ No
|
|||
person_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key identifier to the Person who is experiencing the episdoe. The demographic details of that Person are stored in the PERSON table.
|
||||
The PERSON_ID of the PERSON for whom the episode is recorded.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
|
|
@ -607,9 +633,10 @@ PERSON
|
|||
episode_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key that refers to a Standard Concept identifier in the Standardized Vocabularies belonging to the ‘Episode’ domain.
|
||||
The EPISODE_CONCEPT_ID represents the kind abstraction related to the disease phase, outcome or treatment.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Choose a concept in the Episode domain that best represents the ongoing disease phase, outcome, or treatment. Please see [article] for cancers and [article] for non-cancers describing how these are defined. <a href="https://athena.ohdsi.org/search-terms/terms?domain=Episode&page=1&pageSize=15&query=">Accepted Concepts</a>
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
|
|
@ -633,6 +660,35 @@ Episode
|
|||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_start_date
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The date when the Episode beings.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Please see [article] for how to define an Episode start date.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
date
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_start_datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
|
|
@ -644,12 +700,35 @@ The date and time when the Episode begins.
|
|||
datetime
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
episode_end_date
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The date when the instance of the Episode is considered to have ended.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Please see [article] for how to define an Episode end date.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
date
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
|
|
@ -658,6 +737,10 @@ No
|
|||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
|
|
@ -692,9 +775,10 @@ No
|
|||
episode_parent_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key that refers to a parent Episode entry representing an entire episode if the episode spans multiple cycles.
|
||||
Use this field to find the Episode that subsumes the given Episode record. This is used in the case that an Episode are nested into each other.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
If there are multiple nested levels to how Episodes are represented, the EPISODE_PARENT_ID can be used to record this relationship.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
|
|
@ -720,9 +804,10 @@ No
|
|||
episode_number
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
An ordinal count for an Episode that spans multiple times.
|
||||
For sequences of episodes, this is used to indicate the order the episodes occurred. For example, lines of treatment could be indicated here.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Please see [article] for the details of how to count episodes.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
|
|
@ -748,9 +833,10 @@ No
|
|||
episode_object_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key that refers to a concept identifier in the Standardized Vocabularies describing the disease, treatment, or other abstraction that the episode describes. Episode entries from the ‘Disease Episode’ concept class should have an episode_object_concept_id that comes from the Condition domain. Episode entries from the ‘Treatment Episode’ concept class should have an episode_object_concept_id that scome from the ‘Procedure’ or ‘Regimen’ domain.
|
||||
A Standard Concept representing the disease phase, outcome, or other abstraction of which the episode consists. For example, if the EPISODE_CONCEPT_ID is <a href="https://athena.ohdsi.org/search-terms/terms/32531">treatment regimen</a> then the EPISODE_OBJECT_CONCEPT_ID should contain the chemotherapy regimen concept, like <a href="https://athena.ohdsi.org/search-terms/terms/35804392">Afatinib monotherapy</a>.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Episode entries from the ‘Disease Episode’ concept class should have an episode_object_concept_id that comes from the Condition domain. Episode entries from the ‘Treatment Episode’ concept class should have an episode_object_concept_id that scome from the ‘Procedure’ domain or ‘Regimen’ concept class.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
|
|
@ -778,9 +864,10 @@ Procedure, Regimen
|
|||
episode_type_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key to the predefined Concept identifier in the Standardized Vocabularies reflecting the source data from which the Episode was recorded, the level of standardization, and the type of occurrence. These belong to the ‘Episode Type’ vocabulary
|
||||
This field can be used to determine the provenance of the Episode record, as in whether the episode was from an EHR system, insurance claim, registry, or other sources.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Choose the EPISODE_TYPE_CONCEPT_ID that best represents the provenance of the record. <a href="https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=">Accepted Concepts</a>.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
|
|
@ -836,9 +923,10 @@ No
|
|||
episode_source_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key to a Episdoe Concept that refers to the code used in the source.
|
||||
A foreign key to a Episode Concept that refers to the code used in the source.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Given that the Episodes are user-defined it is unlikely that there will be a Source Concept available. If that is the case then set this field to zero.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
|
|
@ -866,7 +954,9 @@ CONCEPT
|
|||
<div id="episode_event" class="section level3 tabset tabset-pills">
|
||||
<h3 class="tabset tabset-pills">EPISODE_EVENT</h3>
|
||||
<p><strong>Table Description</strong></p>
|
||||
<p>The EPISODE_EVENT table connects qualifying clinical events (VISIT_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE) to the appropriate EPISODE entry. The EPISODE_EVENT table supports the linkage of an EPISODE abstraction to the low-level clinical events that implement the EPISODE abstraction.</p>
|
||||
<p>The EPISODE_EVENT table connects qualifying clinical events (such as CONDITION_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, MEASUREMENT) to the appropriate EPISODE entry. For example, linking the precise location of the metastasis (cancer modifier in MEASUREMENT) to the disease episode.</p>
|
||||
<p><strong>User Guide</strong></p>
|
||||
<p>This connecting table is used instead of the FACT_RELATIONSHIP table for linking low-level events to abstracted Episodes.</p>
|
||||
<p><strong>ETL Conventions</strong></p>
|
||||
<p>Some episodes may not have links to any underlying clinical events. For such episodes, the EPISODE_EVENT table is not populated.</p>
|
||||
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
|
||||
|
|
@ -910,9 +1000,10 @@ FK Class
|
|||
episode_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key identifier to the Episode that the Episode Event belongs to.
|
||||
Use this field to link the EPISODE_EVENT record to its EPISODE.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the EPISODE_ID that subsumes the EPISODE_EVENT record here.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
|
|
@ -930,7 +1021,6 @@ Yes
|
|||
EPISODE
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Episode
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
|
|
@ -940,9 +1030,10 @@ Episode
|
|||
event_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key identifier to the underlying event (condition, procedure, measurement, etc.) record in a respective table for which an episode is recorded.
|
||||
This field is the primary key of the linked record in the database. For example, if the Episode Event is a Condition Occurrence, then the CONDITION_OCCURRENCE_ID of the linked record goes in this field.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the primary key of the linked record here.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
|
|
@ -968,9 +1059,10 @@ No
|
|||
episode_event_field_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key identifier to the standardized concept corresponding to the table primary key column (condition_occurrence.condition_occurrence_id, procedure_occurrence.procedure_occurrence_id, measurment.measurment_id etc.) where the underlying event is stored.
|
||||
This field is the CONCEPT_ID that identifies which table the primary key of the linked record came from.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the CONCEPT_ID that identifies which table and field the EVENT_ID came from. <a href="https://athena.ohdsi.org/search-terms/terms?vocabulary=CDM&conceptClass=Field&page=1&pageSize=15&query=">Accepted Concepts</a>
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
|
|
@ -1043,9 +1135,10 @@ FK Class
|
|||
modifier_of_event_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key identifier to the event (e.g. condition, procedure, episode) record for which the modifier is recorded.
|
||||
If the Measurement record is related to another record in the database, this field is the primary key of the linked record.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the primary key of the linked record, if applicable, here.
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
bigint
|
||||
|
|
@ -1071,9 +1164,10 @@ No
|
|||
modifier_of_field_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
The concept representing the table field concept that contains the value of the event id for which the modifier is recorded (e.g. CONDITION_OCCURRENCE.condition_occurre nce_id).
|
||||
If the Measurement record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
Put the CONCEPT_ID that identifies which table and field the MODIFIER_OF_EVENT_ID came from. <a href="https://athena.ohdsi.org/search-terms/terms?vocabulary=CDM&conceptClass=Field&page=1&pageSize=15&query=">Accepted Concepts</a>
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
|
|
@ -1099,164 +1193,6 @@ Metadata
|
|||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
<div id="concept_numeric" class="section level3 tabset tabset-pills">
|
||||
<h3 class="tabset tabset-pills">CONCEPT_NUMERIC</h3>
|
||||
<p><strong>Table Description</strong></p>
|
||||
<p>In this table, numeric values, units and math operators indicating range limits (less than) corresponding to “numeric” concepts will be stored. It is an extension of the OMOP CDM and vocabulary that supports formal representation of concepts containing numeric values or ranges. This proposal has not yet been ratified by a larger CDM Workgroup. However, it plays a critical role in supporting ETL from tumor registries. NAACCR vocabulary includes concepts representing numeric values or numeric ranges. Often, these concepts also contain measurement units. For example, “Described as less than 1 centimeter (cm)”. In OMOP CDM, these concepts are normally used in Measurement and Observation tables to store value_as_concept_id. Analysis of these data is currently possible only if the user knows exactly which concepts are used to represent range or value, including their respective units. It is not possible to perform analysis on numeric values of these data, nor is it possible to differentiate numeric values by units.</p>
|
||||
<table class="table table-condensed table-hover" style="font-size: 13px; margin-left: auto; margin-right: auto;">
|
||||
<thead>
|
||||
<tr>
|
||||
<th style="text-align:left;">
|
||||
CDM Field
|
||||
</th>
|
||||
<th style="text-align:left;width: 3in; ">
|
||||
User Guide
|
||||
</th>
|
||||
<th style="text-align:left;width: 4in; ">
|
||||
ETL Conventions
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Datatype
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Required
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Primary Key
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
Foreign Key
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Table
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Domain
|
||||
</th>
|
||||
<th style="text-align:left;width: 1in; ">
|
||||
FK Class
|
||||
</th>
|
||||
</tr>
|
||||
</thead>
|
||||
<tbody>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key that refers to a respective concept in the Standardized Vocabularies.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
value_as_number
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A value of the concept expressed as a numeric value.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
float
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
unit_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key to a Standard Concept ID of the concept units in the Standardized Vocabularies that belong to the ‘Unit’ domain.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
integer
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
<tr>
|
||||
<td style="text-align:left;font-weight: bold;">
|
||||
operator_concept_id
|
||||
</td>
|
||||
<td style="text-align:left;width: 3in; ">
|
||||
A foreign key identifier to the predefined Concept in the Standardized Vocabularies reflecting the mathematical operator that is applied to the value_as_number. Operators are <, <=, =, >=, > and these concepts belong to the ‘Meas Value Operator’ domain.
|
||||
</td>
|
||||
<td style="text-align:left;width: 4in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
float
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
No
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
Yes
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
CONCEPT
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
<td style="text-align:left;width: 1in; ">
|
||||
</td>
|
||||
</tr>
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -306,17 +306,33 @@ $(document).ready(function () {
|
|||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="dataModelConventions.html">
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-list-alt"></span>
|
||||
|
||||
Conventions
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="dataModelConventions.html">General Conventions</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
|
|
@ -331,10 +347,21 @@ $(document).ready(function () {
|
|||
<a href="cdm30.html">CDM v3.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm531.html">CDM v5.3.1</a>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -348,20 +375,14 @@ $(document).ready(function () {
|
|||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="reviewProposals.html">Under Review</a>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -370,7 +391,27 @@ $(document).ready(function () {
|
|||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-question"></span>
|
||||
|
||||
Help
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-life-ring"></span>
|
||||
|
||||
Support
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
|
|
@ -378,28 +419,11 @@ $(document).ready(function () {
|
|||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -407,7 +431,7 @@ $(document).ready(function () {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fas fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
|
|||
|
|
@ -304,17 +304,33 @@ $(document).ready(function () {
|
|||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="dataModelConventions.html">
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-list-alt"></span>
|
||||
|
||||
Conventions
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="dataModelConventions.html">General Conventions</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
|
|
@ -329,10 +345,21 @@ $(document).ready(function () {
|
|||
<a href="cdm30.html">CDM v3.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm531.html">CDM v5.3.1</a>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -346,20 +373,14 @@ $(document).ready(function () {
|
|||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="reviewProposals.html">Under Review</a>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -368,7 +389,27 @@ $(document).ready(function () {
|
|||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-question"></span>
|
||||
|
||||
Help
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-life-ring"></span>
|
||||
|
||||
Support
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
|
|
@ -376,28 +417,11 @@ $(document).ready(function () {
|
|||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -405,7 +429,7 @@ $(document).ready(function () {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fas fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
|
|||
|
|
@ -23,6 +23,7 @@ window.initializeCodeFolding = function(show) {
|
|||
// create a collapsable div to wrap the code in
|
||||
var div = $('<div class="collapse r-code-collapse"></div>');
|
||||
var showThis = (show || $(this).hasClass('fold-show')) && !$(this).hasClass('fold-hide');
|
||||
if (showThis) div.addClass('in');
|
||||
var id = 'rcode-643E0F36' + currentIndex++;
|
||||
div.attr('id', id);
|
||||
$(this).before(div);
|
||||
|
|
@ -30,7 +31,7 @@ window.initializeCodeFolding = function(show) {
|
|||
|
||||
// add a show code button right above
|
||||
var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Code') + '</span>');
|
||||
var showCodeButton = $('<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm code-folding-btn pull-right float-right"></button>');
|
||||
var showCodeButton = $('<button type="button" class="btn btn-default btn-xs code-folding-btn pull-right"></button>');
|
||||
showCodeButton.append(showCodeText);
|
||||
showCodeButton
|
||||
.attr('data-toggle', 'collapse')
|
||||
|
|
@ -46,27 +47,13 @@ window.initializeCodeFolding = function(show) {
|
|||
|
||||
div.before(buttonRow);
|
||||
|
||||
// show the div if necessary
|
||||
if (showThis) div.collapse('show');
|
||||
|
||||
// update state of button on show/hide
|
||||
// * Change text
|
||||
// * add a class for intermediate states styling
|
||||
div.on('hide.bs.collapse', function () {
|
||||
showCodeText.text('Code');
|
||||
showCodeButton.addClass('btn-collapsing');
|
||||
});
|
||||
div.on('hidden.bs.collapse', function () {
|
||||
showCodeButton.removeClass('btn-collapsing');
|
||||
showCodeText.text('Code');
|
||||
});
|
||||
div.on('show.bs.collapse', function () {
|
||||
showCodeText.text('Hide');
|
||||
showCodeButton.addClass('btn-expanding');
|
||||
});
|
||||
div.on('shown.bs.collapse', function () {
|
||||
showCodeButton.removeClass('btn-expanding');
|
||||
});
|
||||
|
||||
});
|
||||
|
||||
}
|
||||
|
|
|
|||
|
|
@ -176,7 +176,7 @@
|
|||
self._setEventHandlers();
|
||||
|
||||
// Binding to the Window load event to make sure the correct scrollTop is calculated
|
||||
$(window).on("load", function() {
|
||||
$(window).load(function() {
|
||||
|
||||
// Sets the active TOC item
|
||||
self._setActiveElement(true);
|
||||
|
|
|
|||
|
|
@ -380,17 +380,33 @@ div.tocify {
|
|||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
||||
<a href="dataModelConventions.html">
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-list-alt"></span>
|
||||
|
||||
Conventions
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="dataModelConventions.html">General Conventions</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
|
|
@ -405,10 +421,21 @@ div.tocify {
|
|||
<a href="cdm30.html">CDM v3.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm531.html">CDM v5.3.1</a>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -422,20 +449,14 @@ div.tocify {
|
|||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="reviewProposals.html">Under Review</a>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
|
|
@ -444,7 +465,27 @@ div.tocify {
|
|||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-question"></span>
|
||||
|
||||
Help
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
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<span class="fas fa-life-ring"></span>
|
||||
|
||||
Support
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
|
|
@ -452,28 +493,11 @@ div.tocify {
|
|||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
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</li>
|
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</ul>
|
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</li>
|
||||
<li class="dropdown">
|
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -481,7 +505,7 @@ div.tocify {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fas fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@
|
|||
|
||||
<title>How the Vocabulary is Built</title>
|
||||
|
||||
<script src="site_libs/header-attrs-2.6/header-attrs.js"></script>
|
||||
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
|
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<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<link href="site_libs/bootstrap-3.3.5/css/cosmo.min.css" rel="stylesheet" />
|
||||
|
|
@ -25,8 +26,6 @@
|
|||
<script src="site_libs/navigation-1.1/tabsets.js"></script>
|
||||
<link href="site_libs/highlightjs-9.12.0/default.css" rel="stylesheet" />
|
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<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
|
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<link href="site_libs/anchor-sections-1.0/anchor-sections.css" rel="stylesheet" />
|
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<script src="site_libs/anchor-sections-1.0/anchor-sections.js"></script>
|
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<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet" />
|
||||
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet" />
|
||||
<link rel='shortcut icon' type='image/x-icon' href='favicon.ico' />
|
||||
|
|
@ -85,6 +84,7 @@ h6 {
|
|||
}
|
||||
</style>
|
||||
|
||||
|
||||
<link rel="stylesheet" href="style.css" type="text/css" />
|
||||
|
||||
|
||||
|
|
@ -364,13 +364,13 @@ div.tocify {
|
|||
<ul class="nav navbar-nav">
|
||||
<li>
|
||||
<a href="index.html">
|
||||
<span class="fa fa-home"></span>
|
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<span class="fas fa-home"></span>
|
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|
||||
</a>
|
||||
</li>
|
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<li class="dropdown">
|
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
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<span class="fa fa-landmark"></span>
|
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<span class="fas fa-landmark"></span>
|
||||
|
||||
Background
|
||||
|
||||
|
|
@ -380,21 +380,37 @@ div.tocify {
|
|||
<li>
|
||||
<a href="background.html">Model Background</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRefreshProcess.html">CDM Refresh Process</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="vocabulary.html">How the Vocabulary is Built</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li>
|
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<a href="dataModelConventions.html">
|
||||
<span class="fa fa-list-alt"></span>
|
||||
<li class="dropdown">
|
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<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
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<span class="fas fa-list-alt"></span>
|
||||
|
||||
Conventions
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="dataModelConventions.html">General Conventions</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="ehrObsPeriods.html">Observation Periods for EHR Data</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmPrivacy.html">Patient Privacy and OMOP</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fa fa-history"></span>
|
||||
<span class="fas fa-history"></span>
|
||||
|
||||
CDM Versions
|
||||
|
||||
|
|
@ -404,20 +420,28 @@ div.tocify {
|
|||
<li>
|
||||
<a href="cdm30.html">CDM v3.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm53.html">CDM v5.3</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">NEW CDM v5.4</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="cdm54.html">CDM v5.4</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdm60.html">CDM v6.0</a>
|
||||
<a href="cdm54Changes.html">Changes from CDM v5.3</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fa fa-plus-square"></span>
|
||||
<span class="fas fa-plus-square"></span>
|
||||
|
||||
Proposals
|
||||
|
||||
|
|
@ -425,29 +449,43 @@ div.tocify {
|
|||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="reviewProposals.html">Under Review</a>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal">Under Review</a>
|
||||
</li>
|
||||
<li class="dropdown-submenu">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">Accepted</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="oncology.html">Oncology CDM Proposal</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/252">Region_concept_id</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel/issues/264">Units in Device Table</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fa fa-question"></span>
|
||||
<span class="fas fa-question"></span>
|
||||
|
||||
Help
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="cdmRPackage.html">Use the CDM R Package</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fas fa-life-ring"></span>
|
||||
|
||||
Support
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
|
|
@ -455,28 +493,11 @@ div.tocify {
|
|||
<li>
|
||||
<a href="faq.html">FAQ</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
<li class="dropdown">
|
||||
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
|
||||
<span class="fa fa-wrench"></span>
|
||||
|
||||
How to
|
||||
|
||||
<span class="caret"></span>
|
||||
</a>
|
||||
<ul class="dropdown-menu" role="menu">
|
||||
<li>
|
||||
<a href="sqlScripts.html">SQL Scripts</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="download.html">Download the DDL</a>
|
||||
</li>
|
||||
<li>
|
||||
<a href="drug_dose.html">Calculate Drug Dose</a>
|
||||
<a href="contribute.html">Ask a Question</a>
|
||||
</li>
|
||||
</ul>
|
||||
</li>
|
||||
|
|
@ -484,7 +505,7 @@ div.tocify {
|
|||
<ul class="nav navbar-nav navbar-right">
|
||||
<li>
|
||||
<a href="https://github.com/OHDSI/CommonDataModel">
|
||||
<span class="fa fa-github fa-lg"></span>
|
||||
<span class="fas fa-github"></span>
|
||||
|
||||
</a>
|
||||
</li>
|
||||
|
|
|
|||
|
|
@ -3,6 +3,6 @@
|
|||
# Run this in standalone R session. Runs orders of magnitude faster compared
|
||||
# to running in RStudio:
|
||||
|
||||
setwd("C:/Git/Github/CdmDdlBase/rmd")
|
||||
setwd("/Users/clairblacketer/Documents/Github/CommonDataModel/rmd")
|
||||
rmarkdown::render_site()
|
||||
|
||||
|
|
|
|||
|
|
@ -514,4 +514,3 @@ ATTRIBUTE_DEFINITION,attribute_name,Yes,varchar(255),,,No,No,,,,,
|
|||
ATTRIBUTE_DEFINITION,attribute_description,No,varchar(MAX),,,No,No,,,,,
|
||||
ATTRIBUTE_DEFINITION,attribute_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
ATTRIBUTE_DEFINITION,attribute_syntax,No,varchar(MAX),,,No,No,,,,,
|
||||
|
||||
|
|
|
|||
|
|
|
@ -27,22 +27,22 @@ VISIT_OCCURRENCE,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
|
|||
VISIT_OCCURRENCE,visit_concept_id,Yes,integer,"This field contains a concept id representing the kind of visit, like inpatient or outpatient. All concepts in this field should be standard and belong to the Visit domain.","Populate this field based on the kind of visit that took place for the person. For example this could be ""Inpatient Visit"", ""Outpatient Visit"", ""Ambulatory Visit"", etc. This table will contain standard concepts in the Visit domain. These concepts are arranged in a hierarchical structure to facilitate cohort definitions by rolling up to generally familiar Visits adopted in most healthcare systems worldwide. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,,
|
||||
VISIT_OCCURRENCE,visit_start_date,Yes,date,"For inpatient visits, the start date is typically the admission date. For outpatient visits the start date and end date will be the same.","When populating VISIT_START_DATE, you should think about the patient experience to make decisions on how to define visits. In the case of an inpatient visit this should be the date the patient was admitted to the hospital or institution. In all other cases this should be the date of the patient-provider interaction.",No,No,,,,,
|
||||
VISIT_OCCURRENCE,visit_start_datetime,No,datetime,,"If no time is given for the start date of a visit, set it to midnight (00:00:0000).",No,No,,,,,
|
||||
VISIT_OCCURRENCE,visit_end_date,Yes,date,For inpatient visits the end date is typically the discharge date.,"Visit end dates are mandatory. If end dates are not provided in the source there are three ways in which to derive them:
|
||||
VISIT_OCCURRENCE,visit_end_date,Yes,date,"For inpatient visits the end date is typically the discharge date. If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_date, then set the visit_end_date to the date of the data pull.","Visit end dates are mandatory. If end dates are not provided in the source there are three ways in which to derive them:
|
||||
- Outpatient Visit: visit_end_datetime = visit_start_datetime
|
||||
- Emergency Room Visit: visit_end_datetime = visit_start_datetime
|
||||
- Inpatient Visit: Usually there is information about discharge. If not, you should be able to derive the end date from the sudden decline of activity or from the absence of inpatient procedures/drugs.
|
||||
- Non-hospital institution Visits: Particularly for claims data, if end dates are not provided assume the visit is for the duration of month that it occurs.
|
||||
For Inpatient Visits ongoing at the date of ETL, put date of processing the data into visit_end_datetime and visit_type_concept_id with 32220 ""Still patient"" to identify the visit as incomplete.
|
||||
- All other Visits: visit_end_datetime = visit_start_datetime. If this is a one-day visit the end date should match the start date.",No,No,,,,,
|
||||
VISIT_OCCURRENCE,visit_end_datetime,No,datetime,,"If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,,,,,
|
||||
VISIT_OCCURRENCE,visit_end_datetime,No,datetime,"If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_datetime, then set the visit_end_datetime to the datetime of the data pull.","If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,,,,,
|
||||
VISIT_OCCURRENCE,visit_type_concept_id,Yes,Integer,"Use this field to understand the provenance of the visit record, or where the record comes from.","Populate this field based on the provenance of the visit record, as in whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
|
||||
VISIT_OCCURRENCE,provider_id,No,integer,"There will only be one provider per visit record and the ETL document should clearly state how they were chosen (attending, admitting, etc.). If there are multiple providers associated with a visit in the source, this can be reflected in the event tables (CONDITION_OCCURRENCE, PROCEDURE_OCCURRENCE, etc.) or in the VISIT_DETAIL table.","If there are multiple providers associated with a visit, you will need to choose which one to put here. The additional providers can be stored in the [VISIT_DETAIL](https://ohdsi.github.io/CommonDataModel/cdm531.html#visit_detail) table.",No,Yes,PROVIDER,PROVIDER_ID,,,
|
||||
VISIT_OCCURRENCE,care_site_id,No,integer,This field provides information about the Care Site where the Visit took place.,There should only be one Care Site associated with a Visit.,No,Yes,CARE_SITE,CARE_SITE_ID,,,
|
||||
VISIT_OCCURRENCE,visit_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the kind of visit that took place (inpatient, outpatient, emergency, etc.)","If there is information about the kind of visit in the source data that value should be stored here. If a visit is an amalgamation of visits from the source then use a hierarchy to choose the visit source value, such as IP -> ER-> OP. This should line up with the logic chosen to determine how visits are created.",No,No,,,,,
|
||||
VISIT_OCCURRENCE,visit_source_concept_id,No,integer,,If the visit source value is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
VISIT_OCCURRENCE,admitted_from_concept_id,No,integer,"Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example.","If available, map the admitted_from_source_value to a standard concept in the visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,,
|
||||
VISIT_OCCURRENCE,admitted_from_concept_id,No,integer,"Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example.","If available, map the admitted_from_source_value to a standard concept in the visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=). If a person was admitted from home, set this to 0.",No,Yes,CONCEPT,CONCEPT_ID,Visit,,
|
||||
VISIT_OCCURRENCE,admitted_from_source_value,No,varchar(50),,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was admitted from. Typically this applies only to visits that have a length of stay, like inpatient visits or long-term care visits.",No,No,,,,,
|
||||
VISIT_OCCURRENCE,discharged_to_concept_id,No,integer,"Use this field to determine where the patient was discharged to after a visit. This concept is part of the visit domain and can indicate if a patient was discharged to home or sent to a long-term care facility, for example.","If available, map the discharge_to_source_value to a standard concept in the visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,,
|
||||
VISIT_OCCURRENCE,discharged_to_concept_id,No,integer,"Use this field to determine where the patient was discharged to after a visit. This concept is part of the visit domain and can indicate if a patient was transferred to another hospital or sent to a long-term care facility, for example. It is assumed that a person is discharged to home therefore there is not a standard concept id for ""home"". Use concept id = 0 when a person is discharged to home.","If available, map the discharged_to_source_value to a standard concept in the visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,,
|
||||
VISIT_OCCURRENCE,discharged_to_source_value,No,varchar(50),,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was discharged to after a visit, as in they went home or were moved to long-term care. Typically this applies only to visits that have a length of stay of a day or more.",No,No,,,,,
|
||||
VISIT_OCCURRENCE,preceding_visit_occurrence_id,No,integer,Use this field to find the visit that occurred for the person prior to the given visit. There could be a few days or a few years in between.,"This field can be used to link a visit immediately preceding the current visit. Note this is not symmetrical, and there is no such thing as a ""following_visit_id"".",No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,
|
||||
VISIT_DETAIL,visit_detail_id,Yes,integer,Use this to identify unique interactions between a person and the health care system. This identifier links across the other CDM event tables to associate events with a visit detail.,This should be populated by creating a unique identifier for each unique interaction between a person and the healthcare system where the person receives a medical good or service over a span of time.,Yes,No,,,,,
|
||||
|
|
@ -50,23 +50,23 @@ VISIT_DETAIL,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
|
|||
VISIT_DETAIL,visit_detail_concept_id,Yes,integer,"This field contains a concept id representing the kind of visit detail, like inpatient or outpatient. All concepts in this field should be standard and belong to the Visit domain.","Populate this field based on the kind of visit that took place for the person. For example this could be ""Inpatient Visit"", ""Outpatient Visit"", ""Ambulatory Visit"", etc. This table will contain standard concepts in the Visit domain. These concepts are arranged in a hierarchical structure to facilitate cohort definitions by rolling up to generally familiar Visits adopted in most healthcare systems worldwide. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,,
|
||||
VISIT_DETAIL,visit_detail_start_date,Yes,date,This is the date of the start of the encounter. This may or may not be equal to the date of the Visit the Visit Detail is associated with.,"When populating VISIT_DETAIL_START_DATE, you should think about the patient experience to make decisions on how to define visits. Most likely this should be the date of the patient-provider interaction.",No,No,,,,,
|
||||
VISIT_DETAIL,visit_detail_start_datetime,No,datetime,,"If no time is given for the start date of a visit, set it to midnight (00:00:0000).",No,No,,,,,
|
||||
VISIT_DETAIL,visit_detail_end_date,Yes,date,This the end date of the patient-provider interaction.,"Visit Detail end dates are mandatory. If end dates are not provided in the source there are three ways in which to derive them:<br>
|
||||
VISIT_DETAIL,visit_detail_end_date,Yes,date,"This the end date of the patient-provider interaction. If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_date, then set the visit_end_date to the date of the data pull.","Visit Detail end dates are mandatory. If end dates are not provided in the source there are three ways in which to derive them:<br>
|
||||
- Outpatient Visit Detail: visit_detail_end_datetime = visit_detail_start_datetime
|
||||
- Emergency Room Visit Detail: visit_detail_end_datetime = visit_detail_start_datetime
|
||||
- Inpatient Visit Detail: Usually there is information about discharge. If not, you should be able to derive the end date from the sudden decline of activity or from the absence of inpatient procedures/drugs.
|
||||
- Non-hospital institution Visit Details: Particularly for claims data, if end dates are not provided assume the visit is for the duration of month that it occurs.<br>
|
||||
For Inpatient Visit Details ongoing at the date of ETL, put date of processing the data into visit_detai_end_datetime and visit_detail_type_concept_id with 32220 ""Still patient"" to identify the visit as incomplete.
|
||||
All other Visits Details: visit_detail_end_datetime = visit_detail_start_datetime. ",No,No,,,,,
|
||||
VISIT_DETAIL,visit_detail_end_datetime,No,datetime,,"If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,,,,,
|
||||
VISIT_DETAIL,visit_detail_end_datetime,No,datetime,"If a Person is still an inpatient in the hospital at the time of the data extract and does not have a visit_end_datetime, then set the visit_end_datetime to the datetime of the data pull.","If no time is given for the end date of a visit, set it to midnight (00:00:0000).",No,No,,,,,
|
||||
VISIT_DETAIL,visit_detail_type_concept_id,Yes,integer,"Use this field to understand the provenance of the visit detail record, or where the record comes from.","Populate this field based on the provenance of the visit detail record, as in whether it came from an EHR record or billing claim. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
|
||||
VISIT_DETAIL,provider_id,No,integer,"There will only be one provider per **visit** record and the ETL document should clearly state how they were chosen (attending, admitting, etc.). This is a typical reason for leveraging the VISIT_DETAIL table as even though each VISIT_DETAIL record can only have one provider, there is no limit to the number of VISIT_DETAIL records that can be associated to a VISIT_OCCURRENCE record.",The additional providers associated to a Visit can be stored in this table where each VISIT_DETAIL record represents a different provider.,No,Yes,PROVIDER,PROVIDER_ID,,,
|
||||
VISIT_DETAIL,care_site_id,No,integer,This field provides information about the Care Site where the Visit Detail took place.,There should only be one Care Site associated with a Visit Detail.,No,Yes,CARE_SITE,CARE_SITE_ID,,,
|
||||
VISIT_DETAIL,visit_detail_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the kind of visit detail that took place (inpatient, outpatient, emergency, etc.)","If there is information about the kind of visit detail in the source data that value should be stored here. If a visit is an amalgamation of visits from the source then use a hierarchy to choose the VISIT_DETAIL_SOURCE_VALUE, such as IP -> ER-> OP. This should line up with the logic chosen to determine how visits are created.",No,No,,,,,
|
||||
VISIT_DETAIL,visit_detail_source_concept_id,No,Integer,,If the VISIT_DETAIL_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
VISIT_DETAIL,admitted_from_concept_id,No,Integer,"Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example.","If available, map the admitted_from_source_value to a standard concept in the visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,,
|
||||
VISIT_DETAIL,admitted_from_source_value,No,Varchar(50),,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was admitted from. Typically this applies only to visits that have a length of stay, like inpatient visits or long-term care visits.",No,No,,,,,
|
||||
VISIT_DETAIL,discharged_to_source_value,No,Varchar(50),,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was discharged to after a visit, as in they went home or were moved to long-term care. Typically this applies only to visits that have a length of stay of a day or more.",No,No,,,,,
|
||||
VISIT_DETAIL,discharged_to_concept_id,No,integer,"Use this field to determine where the patient was discharged to after a visit detail record. This concept is part of the visit domain and can indicate if a patient was discharged to home or sent to a long-term care facility, for example.","If available, map the DISCHARGE_TO_SOURCE_VALUE to a Standard Concept in the Visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,,
|
||||
VISIT_DETAIL,admitted_from_concept_id,No,Integer,"Use this field to determine where the patient was admitted from. This concept is part of the visit domain and can indicate if a patient was admitted to the hospital from a long-term care facility, for example.","If available, map the admitted_from_source_value to a standard concept in the visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=). If the person was admitted from home, set this to 0.",No,Yes,CONCEPT,CONCEPT_ID,Visit,,
|
||||
VISIT_DETAIL,admitted_from_source_value,No,varchar(50),,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was admitted from. Typically this applies only to visits that have a length of stay, like inpatient visits or long-term care visits.",No,No,,,,,
|
||||
VISIT_DETAIL,discharged_to_source_value,No,varchar(50),,"This information may be called something different in the source data but the field is meant to contain a value indicating where a person was discharged to after a visit, as in they went home or were moved to long-term care. Typically this applies only to visits that have a length of stay of a day or more.",No,No,,,,,
|
||||
VISIT_DETAIL,discharged_to_concept_id,No,integer,"Use this field to determine where the patient was discharged to after a visit. This concept is part of the visit domain and can indicate if a patient was transferred to another hospital or sent to a long-term care facility, for example. It is assumed that a person is discharged to home therefore there is not a standard concept id for ""home"". Use concept id = 0 when a person is discharged to home.","If available, map the DISCHARGE_TO_SOURCE_VALUE to a Standard Concept in the Visit domain. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Visit,,
|
||||
VISIT_DETAIL,preceding_visit_detail_id,No,integer,Use this field to find the visit detail that occurred for the person prior to the given visit detail record. There could be a few days or a few years in between.,"The PRECEDING_VISIT_DETAIL_ID can be used to link a visit immediately preceding the current Visit Detail. Note this is not symmetrical, and there is no such thing as a ""following_visit_id"".",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,,
|
||||
VISIT_DETAIL,parent_visit_detail_id,No,integer,Use this field to find the visit detail that subsumes the given visit detail record. This is used in the case that a visit detail record needs to be nested beyond the VISIT_OCCURRENCE/VISIT_DETAIL relationship.,"If there are multiple nested levels to how Visits are represented in the source, the VISIT_DETAIL_PARENT_ID can be used to record this relationship. ",No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,,
|
||||
VISIT_DETAIL,visit_occurrence_id,Yes,integer,Use this field to link the VISIT_DETAIL record to its VISIT_OCCURRENCE.,Put the VISIT_OCCURRENCE_ID that subsumes the VISIT_DETAIL record here.,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,
|
||||
|
|
@ -110,23 +110,23 @@ DRUG_EXPOSURE,visit_detail_id,No,integer,"The VISIT_DETAIL record during which t
|
|||
DRUG_EXPOSURE,drug_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the drug exposure that occurred. For example, this could be an NDC or Gemscript code.",This code is mapped to a Standard Drug Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,No,,,,,
|
||||
DRUG_EXPOSURE,drug_source_concept_id,No,integer,"This is the concept representing the drug source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Drug necessary for a given analytic use case. Consider using DRUG_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the DRUG_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
DRUG_EXPOSURE,route_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the drug route.,This information may be called something different in the source data but the field is meant to contain a value indicating when and how a drug was given to a patient. This source value is mapped to a standard concept which is stored in the ROUTE_CONCEPT_ID field.,No,No,,,,,
|
||||
DRUG_EXPOSURE,dose_unit_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the dose unit of the drug given.,This information may be called something different in the source data but the field is meant to contain a value indicating the unit of dosage of drug given to the patient. This is an older column and will be deprecated in an upcoming version.,No,No,,,,,
|
||||
DRUG_EXPOSURE,dose_unit_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the dose unit of the drug given.,This information may be called something different in the source data but the field is meant to contain a value indicating the unit of dosage of drug given to the patient. **This is an older column and will be deprecated in an upcoming version.**,No,No,,,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_occurrence_id,Yes,integer,The unique key given to a procedure record for a person. Refer to the ETL for how duplicate procedures during the same visit were handled.,"Each instance of a procedure occurrence in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same procedure within the same visit. It is valid to keep these duplicates and assign them individual, unique, PROCEDURE_OCCURRENCE_IDs, though it is up to the ETL how they should be handled.",Yes,No,,,,,
|
||||
PROCEDURE_OCCURRENCE,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the procedure is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_concept_id,Yes,integer,"The PROCEDURE_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source value which represents a procedure","The CONCEPT_ID that the PROCEDURE_SOURCE_VALUE maps to. Only records whose source values map to standard concepts with a domain of ""Procedure"" should go in this table. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Procedure&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Procedure,,
|
||||
PROCEDURE_OCCURRENCE,procedure_date,Yes,date,Use this date to determine the date the procedure occurred.,"If a procedure lasts more than a day, then it should be recorded as a separate record for each day the procedure occurred, this logic is in lieu of the procedure_end_date, which will be added in a future version of the CDM.",No,No,,,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_datetime,No,datetime,,"This is not required, though it is in v6. If a source does not specify datetime the convention is to set the time to midnight (00:00:0000)",No,No,,,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_date,Yes,date,Use this date to determine the date the procedure started.,This is meant to be the **start date** of the procedure. It will be renamed in a future version to **PROCEDURE_START_DATE**. ,No,No,,,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_datetime,No,datetime,,"If the procedure has a start time in the native date, use this field to house that information. This will be renamed in a future version to **PROCEDURE_START_DATETIME**.",No,No,,,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_end_date,No,date,Use this field to house the date that the procedure ended. ,This is meant to be the end date of the procedure. It is not required and for most cases will be the same as the PROCEDURE_START_DATE.,No,No,,,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_end_datetime,No,datetime,Use this field to house the datetime that the procedure ended. ,This is meant to house the end datetime of the procedure and will most often be used in conjunction with the procedure_start_datetime to determine the length of the procedure.,No,No,,,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Procedure record, as in whether the procedure was from an EHR system, insurance claim, registry, or other sources.","Choose the PROCEDURE_TYPE_CONCEPT_ID that best represents the provenance of the record, for example whether it came from an EHR record or billing claim. If a procedure is recorded as an EHR encounter, the PROCEDURE_TYPE_CONCEPT would be 'EHR encounter record'. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
|
||||
PROCEDURE_OCCURRENCE,modifier_concept_id,No,integer,The modifiers are intended to give additional information about the procedure but as of now the vocabulary is under review.,"It is up to the ETL to choose how to map modifiers if they exist in source data. These concepts are typically distinguished by 'Modifier' concept classes (e.g., 'CPT4 Modifier' as part of the 'CPT4' vocabulary). If there is more than one modifier on a record, one should be chosen that pertains to the procedure rather than provider. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?conceptClass=CPT4+Modifier&conceptClass=HCPCS+Modifier&vocabulary=CPT4&vocabulary=HCPCS&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
PROCEDURE_OCCURRENCE,quantity,No,integer,"If the quantity value is omitted, a single procedure is assumed.","If a Procedure has a quantity of '0' in the source, this should default to '1' in the ETL. If there is a record in the source it can be assumed the exposure occurred at least once",No,No,,,,,
|
||||
PROCEDURE_OCCURRENCE,provider_id,No,integer,"The provider associated with the procedure record, e.g. the provider who performed the Procedure.","The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record, for example the admitting vs attending physician on an EHR record.",No,No,PROVIDER,PROVIDER_ID,,,
|
||||
PROCEDURE_OCCURRENCE,visit_occurrence_id,No,integer,The visit during which the procedure occurred.,"Depending on the structure of the source data, this may have to be determined based on dates. If a PROCEDURE_DATE occurs within the start and end date of a Visit it is a valid ETL choice to choose the VISIT_OCCURRENCE_ID from the Visit that subsumes it, even if not explicitly stated in the data. While not required, an attempt should be made to locate the VISIT_OCCURRENCE_ID of the PROCEDURE_OCCURRENCE record.",No,No,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,
|
||||
PROCEDURE_OCCURRENCE,visit_detail_id,No,integer,"The VISIT_DETAIL record during which the Procedure occurred. For example, if the Person was in the ICU at the time of the Procedure the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit.",Same rules apply as for the VISIT_OCCURRENCE_ID.,No,No,VISIT_DETAIL,VISIT_DETAIL_ID,,,
|
||||
PROCEDURE_OCCURRENCE,provider_id,No,integer,"The provider associated with the procedure record, e.g. the provider who performed the Procedure.","The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record, for example the admitting vs attending physician on an EHR record.",No,Yes,PROVIDER,PROVIDER_ID,,,
|
||||
PROCEDURE_OCCURRENCE,visit_occurrence_id,No,integer,The visit during which the procedure occurred.,"Depending on the structure of the source data, this may have to be determined based on dates. If a PROCEDURE_DATE occurs within the start and end date of a Visit it is a valid ETL choice to choose the VISIT_OCCURRENCE_ID from the Visit that subsumes it, even if not explicitly stated in the data. While not required, an attempt should be made to locate the VISIT_OCCURRENCE_ID of the PROCEDURE_OCCURRENCE record.",No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,
|
||||
PROCEDURE_OCCURRENCE,visit_detail_id,No,integer,"The VISIT_DETAIL record during which the Procedure occurred. For example, if the Person was in the ICU at the time of the Procedure the VISIT_OCCURRENCE record would reflect the overall hospital stay and the VISIT_DETAIL record would reflect the ICU stay during the hospital visit.",Same rules apply as for the VISIT_OCCURRENCE_ID.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the procedure that occurred. For example, this could be an CPT4 or OPCS4 code.",Use this value to look up the source concept id and then map the source concept id to a standard concept id.,No,No,,,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_source_concept_id,No,integer,"This is the concept representing the procedure source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Procedure necessary for a given analytic use case. Consider using PROCEDURE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the PROCEDURE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,No,CONCEPT,CONCEPT_ID,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_source_concept_id,No,integer,"This is the concept representing the procedure source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Procedure necessary for a given analytic use case. Consider using PROCEDURE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the PROCEDURE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
PROCEDURE_OCCURRENCE,modifier_source_value,No,varchar(50),,The original modifier code from the source is stored here for reference.,No,No,,,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_status_source_value,No,varchar(50),This field houses the verbatim value from the source data representing the procedure status (primary or secondary).,"This information may be called something different in the source data but the field is meant to contain a value indicating whether the procedure was the primary reason for performing a surgical operation, infusion, etc. This source value is mapped to a standard concept which is stored in the PROCEDURE_STATUS_CONCEPT_ID field.",,,,,,,
|
||||
PROCEDURE_OCCURRENCE,procedure_status_concept_id,Yes,integer,"This concept represents if the procedure was the primary reason for the surgical operation, infusion, etc . ",Choose the Concept in the Procedure Status domain that best represents the status ( [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Condition+Status&standardConcept=Standard&page=1&pageSize=15&query=).,,,,,,,
|
||||
DEVICE_EXPOSURE,device_exposure_id,Yes,integer,The unique key given to records a person's exposure to a foreign physical object or instrument.,Each instance of an exposure to a foreign object or device present in the source data should be assigned this unique key. ,Yes,No,,,,,
|
||||
DEVICE_EXPOSURE,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
|
||||
DEVICE_EXPOSURE,device_concept_id,Yes,integer,"The DEVICE_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies. This is the standard concept mapped from the source concept id which represents a foreign object or instrument the person was exposed to. ",The CONCEPT_ID that the DEVICE_SOURCE_VALUE maps to. ,No,Yes,CONCEPT,CONCEPT_ID,Device,,
|
||||
|
|
@ -136,16 +136,16 @@ DEVICE_EXPOSURE,device_exposure_end_date,No,date,"The DEVICE_EXPOSURE_END_DATE d
|
|||
DEVICE_EXPOSURE,device_exposure_end_datetime,No,datetime,,If a source does not specify datetime the convention is to set the time to midnight (00:00:0000),No,No,,,,,
|
||||
DEVICE_EXPOSURE,device_type_concept_id,Yes,integer,"You can use the TYPE_CONCEPT_ID to denote the provenance of the record, as in whether the record is from administrative claims or EHR. ","Choose the drug_type_concept_id that best represents the provenance of the record, for example whether it came from a record of a prescription written or physician administered drug. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
|
||||
DEVICE_EXPOSURE,unique_device_id,No,varchar(255),"This is the Unique Device Identification (UDI-DI) number for devices regulated by the FDA, if given. ","For medical devices that are regulated by the FDA, a Unique Device Identification (UDI) is provided if available in the data source and is recorded in the UNIQUE_DEVICE_ID field.",No,No,,,,,
|
||||
DEVICE_EXPOSURE,production_id,No,varchar(255),This is the Production Identifier (UDI-PI) portion of the Unique Device Identification.,,,,,,,,
|
||||
DEVICE_EXPOSURE,production_id,No,varchar(255),This is the Production Identifier (UDI-PI) portion of the Unique Device Identification.,,No,No,,,,,
|
||||
DEVICE_EXPOSURE,quantity,No,integer,,,No,No,,,,,
|
||||
DEVICE_EXPOSURE,provider_id,No,integer,"The Provider associated with device record, e.g. the provider who wrote the prescription or the provider who implanted the device.",The ETL may need to make a choice as to which PROVIDER_ID to put here. Based on what is available this may or may not be different than the provider associated with the overall VISIT_OCCURRENCE record.,No,Yes,PROVIDER,PROVIDER_ID,,,
|
||||
DEVICE_EXPOSURE,visit_occurrence_id,No,integer,The Visit during which the device was prescribed or given.,To populate this field device exposures must be explicitly initiated in the visit.,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,
|
||||
DEVICE_EXPOSURE,visit_detail_id,No,integer,The Visit Detail during which the device was prescribed or given.,To populate this field device exposures must be explicitly initiated in the visit detail record.,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,,
|
||||
DEVICE_EXPOSURE,device_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the device exposure that occurred. For example, this could be an NDC or Gemscript code.",This code is mapped to a Standard Device Concept in the Standardized Vocabularies and the original code is stored here for reference.,No,No,,,,,
|
||||
DEVICE_EXPOSURE,device_source_concept_id,No,integer,"This is the concept representing the device source value and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Device necessary for a given analytic use case. Consider using DEVICE_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the DEVICE_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here.,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
DEVICE_EXPOSURE,unit_concept_id,No,integer,UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data. ,"There is no standardization requirement for units associated with DEVICE_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. If there is no unit associated with a Device record, set to NULL.",,,,,,,
|
||||
DEVICE_EXPOSURE,unit_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the unit of the Device. For example, blood transfusions are considered devices and can be given in mL quantities. ","This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. Using the blood transfusion example, blood transfusion is represented by the DEVICE_CONCEPT_ID and the unit (mL) would be housed in the UNIT_SOURCE_VALUE and mapped to a standard concept in the unit domain. ",,,,,,,
|
||||
DEVICE_EXPOSURE,unit_source_concept_id,No,integer,"This is the concept representing the UNIT_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Unit necessary for a given analytic use case. Consider using UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. ,,,,,,,
|
||||
DEVICE_EXPOSURE,unit_concept_id,No,integer,UNIT_SOURCE_VALUES should be mapped to a Standard Concept in the Unit domain that best represents the unit as given in the source data. ,"There is no standardization requirement for units associated with DEVICE_CONCEPT_IDs, however, it is the responsibility of the ETL to choose the most plausible unit. If there is no unit associated with a Device record, set to NULL.",No,Yes,CONCEPT,CONCEPT_ID,Unit,,
|
||||
DEVICE_EXPOSURE,unit_source_value,No,varchar(50),"This field houses the verbatim value from the source data representing the unit of the Device. For example, blood transfusions are considered devices and can be given in mL quantities. ","This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference. Using the blood transfusion example, blood transfusion is represented by the DEVICE_CONCEPT_ID and the unit (mL) would be housed in the UNIT_SOURCE_VALUE and mapped to a standard concept in the unit domain. ",No,No,,,,,
|
||||
DEVICE_EXPOSURE,unit_source_concept_id,No,integer,"This is the concept representing the UNIT_SOURCE_VALUE and may not necessarily be standard. This field is discouraged from use in analysis because it is not required to contain Standard Concepts that are used across the OHDSI community, and should only be used when Standard Concepts do not adequately represent the source detail for the Unit necessary for a given analytic use case. Consider using UNIT_CONCEPT_ID instead to enable standardized analytics that can be consistent across the network.",If the UNIT_SOURCE_VALUE is coded in the source data using an OMOP supported vocabulary put the concept id representing the source value here. ,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
MEASUREMENT,measurement_id,Yes,integer,The unique key given to a Measurement record for a Person. Refer to the ETL for how duplicate Measurements during the same Visit were handled.,"Each instance of a measurement present in the source data should be assigned this unique key. In some cases, a person can have multiple records of the same measurement within the same visit. It is valid to keep these duplicates and assign them individual, unique, MEASUREMENT_IDs, though it is up to the ETL how they should be handled.",Yes,No,,,,,
|
||||
MEASUREMENT,person_id,Yes,integer,The PERSON_ID of the Person for whom the Measurement is recorded. This may be a system generated code.,,No,Yes,PERSON,PERSON_ID,,,
|
||||
MEASUREMENT,measurement_concept_id,Yes,integer,"The MEASUREMENT_CONCEPT_ID field is recommended for primary use in analyses, and must be used for network studies.","The CONCEPT_ID that the MEASUREMENT_SOURCE_CONCEPT_ID maps to. Only records whose SOURCE_CONCEPT_IDs map to Standard Concepts with a domain of ""Measurement"" should go in this table.",No,Yes,CONCEPT,CONCEPT_ID,Measurement,,
|
||||
|
|
@ -199,8 +199,6 @@ DEATH,cause_source_value,No,varchar(50),,"If available, put the source code repr
|
|||
DEATH,cause_source_concept_id,No,integer,,If the cause of death was coded using a Vocabulary present in the OMOP Vocabularies put the CONCEPT_ID representing the cause of death here.,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
NOTE,note_id,Yes,integer,A unique identifier for each note.,,Yes,No,,,,,
|
||||
NOTE,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
|
||||
NOTE,note_event_id,No,bigint,"If the Note record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here.",No,No,,,,,
|
||||
NOTE,note_event_field_concept_id,No,integer,"If the Note record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. ",Put the CONCEPT_ID that identifies which table and field the NOTE_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
NOTE,note_date,Yes,date,The date the note was recorded.,,No,No,,,,,
|
||||
NOTE,note_datetime,No,datetime,,If time is not given set the time to midnight.,No,No,,,,,
|
||||
NOTE,note_type_concept_id,Yes,integer,The provenance of the note. Most likely this will be EHR. ,"Put the source system of the note, as in EHR record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?standardConcept=Standard&domain=Type+Concept&page=1&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
|
||||
|
|
@ -214,11 +212,13 @@ NOTE,provider_id,No,integer,The Provider who wrote the note.,The ETL may need to
|
|||
NOTE,visit_occurrence_id,No,integer,The Visit during which the note was written. ,,No,Yes,VISIT_OCCURRENCE,VISIT_OCCURRENCE_ID,,,
|
||||
NOTE,visit_detail_id,No,integer,The Visit Detail during which the note was written.,,No,Yes,VISIT_DETAIL,VISIT_DETAIL_ID,,,
|
||||
NOTE,note_source_value,No,varchar(50),,The source value mapped to the NOTE_CLASS_CONCEPT_ID.,No,No,,,,,
|
||||
NOTE,note_event_id,No,bigint,"If the Note record is related to another record in the database, this field is the primary key of the linked record. ","Put the primary key of the linked record, if applicable, here.",No,No,,,,,
|
||||
NOTE,note_event_field_concept_id,No,integer,"If the Note record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. ",Put the CONCEPT_ID that identifies which table and field the NOTE_EVENT_ID came from.,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
NOTE_NLP,note_nlp_id,Yes,integer,A unique identifier for the NLP record.,,Yes,No,,,,,
|
||||
NOTE_NLP,note_id,Yes,integer,This is the NOTE_ID for the NOTE record the NLP record is associated to.,,No,No,,,,,
|
||||
NOTE_NLP,section_concept_id,No,integer,,"The SECTION_CONCEPT_ID should be used to represent the note section contained in the NOTE_NLP record. These concepts can be found as parts of document panels and are based on the type of note written, i.e. a discharge summary. These panels can be found as concepts with the relationship 'Subsumes' to CONCEPT_ID [45875957](https://athena.ohdsi.org/search-terms/terms/45875957).",No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
NOTE_NLP,snippet,No,varchar(250),A small window of text surrounding the term,,No,No,,,,,
|
||||
NOTE_NLP,offset,No,varchar(50),Character offset of the extracted term in the input note,,No,No,,,,,
|
||||
NOTE_NLP,"""offset""",No,varchar(50),Character offset of the extracted term in the input note,,No,No,,,,,
|
||||
NOTE_NLP,lexical_variant,Yes,varchar(250),Raw text extracted from the NLP tool.,,No,No,,,,,
|
||||
NOTE_NLP,note_nlp_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
NOTE_NLP,note_nlp_source_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
|
|
@ -266,14 +266,14 @@ LOCATION,location_id,Yes,integer,The unique key given to a unique Location.,Each
|
|||
LOCATION,address_1,No,varchar(50),This is the first line of the address.,,No,No,,,,,
|
||||
LOCATION,address_2,No,varchar(50),This is the second line of the address,,No,No,,,,,
|
||||
LOCATION,city,No,varchar(50),,,No,No,,,,,
|
||||
LOCATION,state,No,varchar(2),Please see the user guide for the location table for clarification on what this field represents in locations outside of the US.,,No,No,,,,,
|
||||
LOCATION,state,No,varchar(2),,,No,No,,,,,
|
||||
LOCATION,zip,No,varchar(9),,"Zip codes are handled as strings of up to 9 characters length. For US addresses, these represent either a 3-digit abbreviated Zip code as provided by many sources for patient protection reasons, the full 5-digit Zip or the 9-digit (ZIP + 4) codes. Unless for specific reasons analytical methods should expect and utilize only the first 3 digits. For international addresses, different rules apply.",No,No,,,,,
|
||||
LOCATION,county,No,varchar(20),,,No,No,,,,,
|
||||
LOCATION,location_source_value,No,varchar(50),,"Put the verbatim value for the location here, as it shows up in the source. ",No,No,,,,,
|
||||
LOCATION,country_concept_id,No,integer,The Concept Id representing the country. Values should conform to the [Geography](https://athena.ohdsi.org/search-terms/terms?domain=Geography&standardConcept=Standard&page=1&pageSize=15&query=&boosts) domain. ,,,,,,,,
|
||||
LOCATION,country_source_value,No,varchar(80),The name of the country.,,,,,,,,
|
||||
LOCATION,latitude,No,float,,Must be between -90 and 90.,,,,,,,
|
||||
LOCATION,longitude,No,float,,Must be between -180 and 180.,,,,,,,
|
||||
LOCATION,country_concept_id,No,integer,The Concept Id representing the country. Values should conform to the [Geography](https://athena.ohdsi.org/search-terms/terms?domain=Geography&standardConcept=Standard&page=1&pageSize=15&query=&boosts) domain. ,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
LOCATION,country_source_value,No,varchar(80),The name of the country.,,No,No,,,,,
|
||||
LOCATION,latitude,No,float,,Must be between -90 and 90.,No,No,,,,,
|
||||
LOCATION,longitude,No,float,,Must be between -180 and 180.,No,No,,,,,
|
||||
CARE_SITE,care_site_id,Yes,integer,,Assign an id to each unique combination of location_id and place_of_service_source_value,Yes,No,,,,,
|
||||
CARE_SITE,care_site_name,No,varchar(255),The name of the care_site as it appears in the source data,,No,No,,,,,
|
||||
CARE_SITE,place_of_service_concept_id,No,integer,"This is a high-level way of characterizing a Care Site. Typically, however, Care Sites can provide care in multiple settings (inpatient, outpatient, etc.) and this granularity should be reflected in the visit.","Choose the concept in the visit domain that best represents the setting in which healthcare is provided in the Care Site. If most visits in a Care Site are Inpatient, then the place_of_service_concept_id should represent Inpatient. If information is present about a unique Care Site (e.g. Pharmacy) then a Care Site record should be created. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Visit&standardConcept=Standard&page=2&pageSize=15&query=).",No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
|
|
@ -350,7 +350,7 @@ DOSE_ERA,dose_value,Yes,float,The numeric value of the dosage of the drug_ingred
|
|||
DOSE_ERA,dose_era_start_date,Yes,datetime,"The date the Person started on the specific dosage, with at least 31 days since any prior exposure.",,No,No,,,,,
|
||||
DOSE_ERA,dose_era_end_date,Yes,datetime,,The date the Person was no longer exposed to the dosage of the specific drug ingredient. An era is ended if there are 31 days or more between dosage records.,No,No,,,,,
|
||||
CONDITION_ERA,condition_era_id,Yes,integer,,,Yes,No,,,,,
|
||||
CONDITION_ERA,person_id,Yes,integer,,,No,No,PERSON,PERSON_ID,,,
|
||||
CONDITION_ERA,person_id,Yes,integer,,,No,Yes,PERSON,PERSON_ID,,,
|
||||
CONDITION_ERA,condition_concept_id,Yes,integer,The Concept Id representing the Condition.,,No,Yes,CONCEPT,CONCEPT_ID,Condition,,
|
||||
CONDITION_ERA,condition_era_start_date,Yes,datetime,"The start date for the Condition Era
|
||||
constructed from the individual
|
||||
|
|
@ -367,21 +367,21 @@ Condition.",,No,No,,,,,
|
|||
CONDITION_ERA,condition_occurrence_count,No,integer,"The number of individual Condition
|
||||
Occurrences used to construct the
|
||||
condition era.",,No,No,,,,,
|
||||
EPISODE,episode_id,Yes,integer,A unique identifier for each Episode.,,Yes,No,,,,,
|
||||
EPISODE,person_id,Yes,integer,The PERSON_ID of the PERSON for whom the episode is recorded.,,No,Yes,PERSON,PERSON_ID,,,
|
||||
EPISODE,episode_concept_id,Yes,integer,"The EPISODE_CONCEPT_ID represents the kind abstraction related to the disease phase, outcome or treatment.","Choose a concept in the Episode domain that best represents the ongoing disease phase, outcome, or treatment. Please see [article] for cancers and [article] for non-cancers describing how these are defined. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Episode&page=1&pageSize=15&query=)",No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
EPISODE,episode_id,Yes,bigint,A unique identifier for each Episode.,,Yes,No,,,,,
|
||||
EPISODE,person_id,Yes,bigint,The PERSON_ID of the PERSON for whom the episode is recorded.,,No,Yes,PERSON,PERSON_ID,,,
|
||||
EPISODE,episode_concept_id,Yes,integer,"The EPISODE_CONCEPT_ID represents the kind abstraction related to the disease phase, outcome or treatment.","Choose a concept in the Episode domain that best represents the ongoing disease phase, outcome, or treatment. Please see [article] for cancers and [article] for non-cancers describing how these are defined. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Episode&page=1&pageSize=15&query=)",No,Yes,CONCEPT,CONCEPT_ID,Episode,,
|
||||
EPISODE,episode_start_date,Yes,date,The date when the Episode beings. ,Please see [article] for how to define an Episode start date.,No,No,,,,,
|
||||
EPISODE,episode_start_datetime,No,datetime,The date and time when the Episode begins.,,No,No,,,,,
|
||||
EPISODE,episode_end_date,No,date,The date when the instance of the Episode is considered to have ended.,Please see [article] for how to define an Episode end date.,,,,,,,
|
||||
EPISODE,episode_end_date,No,date,The date when the instance of the Episode is considered to have ended.,Please see [article] for how to define an Episode end date.,No,No,,,,,
|
||||
EPISODE,episode_end_datetime,No,datetime,The date when the instance of the Episode is considered to have ended.,,No,No,,,,,
|
||||
EPISODE,episode_parent_id,No,integer,Use this field to find the Episode that subsumes the given Episode record. This is used in the case that an Episode are nested into each other.,"If there are multiple nested levels to how Episodes are represented, the EPISODE_PARENT_ID can be used to record this relationship. ",No,No,,,,,
|
||||
EPISODE,episode_parent_id,No,bigint,Use this field to find the Episode that subsumes the given Episode record. This is used in the case that an Episode are nested into each other.,"If there are multiple nested levels to how Episodes are represented, the EPISODE_PARENT_ID can be used to record this relationship. ",No,No,,,,,
|
||||
EPISODE,episode_number,No,integer,"For sequences of episodes, this is used to indicate the order the episodes occurred. For example, lines of treatment could be indicated here. ",Please see [article] for the details of how to count episodes.,No,No,,,,,
|
||||
EPISODE,episode_object_concept_id,Yes,integer,"A Standard Concept representing the disease phase, outcome, or other abstraction of which the episode consists. For example, if the EPISODE_CONCEPT_ID is [treatment regimen](https://athena.ohdsi.org/search-terms/terms/32531) then the EPISODE_OBJECT_CONCEPT_ID should contain the chemotherapy regimen concept, like [Afatinib monotherapy](https://athena.ohdsi.org/search-terms/terms/35804392). ",Episode entries from the 'Disease Episode' concept class should have an episode_object_concept_id that comes from the Condition domain. Episode entries from the 'Treatment Episode' concept class should have an episode_object_concept_id that scome from the 'Procedure' domain or 'Regimen' concept class.,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
EPISODE,episode_object_concept_id,Yes,integer,"A Standard Concept representing the disease phase, outcome, or other abstraction of which the episode consists. For example, if the EPISODE_CONCEPT_ID is [treatment regimen](https://athena.ohdsi.org/search-terms/terms/32531) then the EPISODE_OBJECT_CONCEPT_ID should contain the chemotherapy regimen concept, like [Afatinib monotherapy](https://athena.ohdsi.org/search-terms/terms/35804392). ",Episode entries from the 'Disease Episode' concept class should have an episode_object_concept_id that comes from the Condition domain. Episode entries from the 'Treatment Episode' concept class should have an episode_object_concept_id that scome from the 'Procedure' domain or 'Regimen' concept class.,No,Yes,CONCEPT,CONCEPT_ID,"Procedure, Regimen",,
|
||||
EPISODE,episode_type_concept_id,Yes,integer,"This field can be used to determine the provenance of the Episode record, as in whether the episode was from an EHR system, insurance claim, registry, or other sources.",Choose the EPISODE_TYPE_CONCEPT_ID that best represents the provenance of the record. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=).,No,Yes,CONCEPT,CONCEPT_ID,Type Concept,,
|
||||
EPISODE,episode_source_value,No,varchar(50),The source code for the Episdoe as it appears in the source data. This code is mapped to a Standard Condition Concept in the Standardized Vocabularies and the original code is stored here for reference.,,No,No,,,,,
|
||||
EPISODE,episode_source_concept_id,No,integer,A foreign key to a Episode Concept that refers to the code used in the source.,Given that the Episodes are user-defined it is unlikely that there will be a Source Concept available. If that is the case then set this field to zero. ,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
EPISODE_EVENT,episode_id,Yes,integer,Use this field to link the EPISODE_EVENT record to its EPISODE.,Put the EPISODE_ID that subsumes the EPISODE_EVENT record here.,No,Yes,EPISODE,EPISODE_ID,,,
|
||||
EPISODE_EVENT,event_id,Yes,integer,"This field is the primary key of the linked record in the database. For example, if the Episode Event is a Condition Occurrence, then the CONDITION_OCCURRENCE_ID of the linked record goes in this field. ",Put the primary key of the linked record here. ,No,No,,,,,
|
||||
EPISODE_EVENT,episode_id,Yes,bigint,Use this field to link the EPISODE_EVENT record to its EPISODE.,Put the EPISODE_ID that subsumes the EPISODE_EVENT record here.,No,Yes,EPISODE,EPISODE_ID,,,
|
||||
EPISODE_EVENT,event_id,Yes,bigint,"This field is the primary key of the linked record in the database. For example, if the Episode Event is a Condition Occurrence, then the CONDITION_OCCURRENCE_ID of the linked record goes in this field. ",Put the primary key of the linked record here. ,No,No,,,,,
|
||||
EPISODE_EVENT,episode_event_field_concept_id,Yes,integer,This field is the CONCEPT_ID that identifies which table the primary key of the linked record came from. ,Put the CONCEPT_ID that identifies which table and field the EVENT_ID came from. [Accepted Concepts](https://athena.ohdsi.org/search-terms/terms?vocabulary=CDM&conceptClass=Field&page=1&pageSize=15&query=),No,Yes,CONCEPT,CONCEPT_ID,Metadata,,
|
||||
METADATA,metadata_id,Yes,integer,The unique key given to a Metadata record.,Attribute value is auto-generated,Yes,No,,,,,
|
||||
METADATA,metadata_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
|
|
@ -389,7 +389,7 @@ METADATA,metadata_type_concept_id,Yes,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
|||
METADATA,name,Yes,varchar(250),,,No,No,,,,,
|
||||
METADATA,value_as_string,No,varchar(250),,,No,No,,,,,
|
||||
METADATA,value_as_concept_id,No,integer,,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
METADATA,value_as_number,No,float,"This is the numerical value of the Result of the Metadata, if applicable and available. It is not expected that all Metadata will have numeric results, rather, this field is here to house values should they exist. ",,No,No,,,,,
|
||||
METADATA,value_as_number,No,float,"This is the numerical value of the result of the Metadata, if applicable and available. It is not expected that all Metadata will have numeric results, rather, this field is here to house values should they exist. ",,No,No,,,,,
|
||||
METADATA,metadata_date,No,date,,,No,No,,,,,
|
||||
METADATA,metadata_datetime,No,datetime,,,No,No,,,,,
|
||||
CDM_SOURCE,cdm_source_name,Yes,varchar(255),The name of the CDM instance.,,No,No,,,,,
|
||||
|
|
@ -401,7 +401,7 @@ CDM_SOURCE,cdm_etl_reference,No,varchar(255),,Put the link to the CDM version us
|
|||
CDM_SOURCE,source_release_date,Yes,date,The release date of the source data.,,No,No,,,,,
|
||||
CDM_SOURCE,cdm_release_date,Yes,date,The release data of the CDM instance.,,No,No,,,,,
|
||||
CDM_SOURCE,cdm_version,No,varchar(10),,,No,No,,,,,
|
||||
CDM_SOURCE,cdm_version_concept_id,Yes,integer,The Concept Id representing the version of the CDM.,,,,,,,,
|
||||
CDM_SOURCE,cdm_version_concept_id,Yes,integer,The Concept Id representing the version of the CDM.,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
CDM_SOURCE,vocabulary_version,Yes,varchar(20),,,No,No,,,,,
|
||||
CONCEPT,concept_id,Yes,integer,A unique identifier for each Concept across all domains.,,Yes,No,,,,,
|
||||
CONCEPT,concept_name,Yes,varchar(255),"An unambiguous, meaningful and descriptive name for the Concept.",,No,No,,,,,
|
||||
|
|
@ -444,7 +444,7 @@ VOCABULARY,vocabulary_name,Yes,varchar(255),"The name describing the vocabulary,
|
|||
example, International Classification of
|
||||
Diseases, Ninth Revision, Clinical
|
||||
Modification, Volume 1 and 2 (NCHS) etc.",,No,No,,,,,
|
||||
VOCABULARY,vocabulary_reference,Yes,varchar(255),"External reference to documentation or
|
||||
VOCABULARY,vocabulary_reference,No,varchar(255),"External reference to documentation or
|
||||
available download of the about the
|
||||
vocabulary.",,No,No,,,,,
|
||||
VOCABULARY,vocabulary_version,No,varchar(255),"Version of the Vocabulary as indicated in
|
||||
|
|
@ -542,7 +542,7 @@ COHORT,cohort_definition_id,Yes,integer,,,No,No,,,,,
|
|||
COHORT,subject_id,Yes,integer,,,No,No,,,,,
|
||||
COHORT,cohort_start_date,Yes,date,,,No,No,,,,,
|
||||
COHORT,cohort_end_date,Yes,date,,,No,No,,,,,
|
||||
COHORT_DEFINITION,cohort_definition_id,Yes,integer,"This is the identifier given to the cohort, usually by the ATLAS application",,No,No,COHORT,COHORT_DEFINITION_ID,,,
|
||||
COHORT_DEFINITION,cohort_definition_id,Yes,integer,"This is the identifier given to the cohort, usually by the ATLAS application",,No,Yes,COHORT,COHORT_DEFINITION_ID,,,
|
||||
COHORT_DEFINITION,cohort_definition_name,Yes,varchar(255),A short description of the cohort,,No,No,,,,,
|
||||
COHORT_DEFINITION,cohort_definition_description,No,varchar(MAX),A complete description of the cohort.,,No,No,,,,,
|
||||
COHORT_DEFINITION,definition_type_concept_id,Yes,integer,Type defining what kind of Cohort Definition the record represents and how the syntax may be executed.,,No,Yes,CONCEPT,CONCEPT_ID,,,
|
||||
|
|
|
|||
|
|
|
@ -40,7 +40,7 @@ SPECIMEN,CDM,No,SPECIMEN_,Yes,0,,The specimen domain contains the records identi
|
|||
FACT_RELATIONSHIP,CDM,No,,No,,,"The FACT_RELATIONSHIP table contains records about the relationships between facts stored as records in any table of the CDM. Relationships can be defined between facts from the same domain, or different domains. Examples of Fact Relationships include: [Person relationships](https://athena.ohdsi.org/search-terms/terms?domain=Relationship&standardConcept=Standard&page=2&pageSize=15&query=) (parent-child), care site relationships (hierarchical organizational structure of facilities within a health system), indication relationship (between drug exposures and associated conditions), usage relationships (of devices during the course of an associated procedure), or facts derived from one another (measurements derived from an associated specimen).",,"All relationships are directional, and each relationship is represented twice symmetrically within the FACT_RELATIONSHIP table. For example, two persons if person_id = 1 is the mother of person_id = 2 two records are in the FACT_RELATIONSHIP table (all strings in fact concept_id records in the Concept table:
|
||||
- Person, 1, Person, 2, parent of
|
||||
- Person, 2, Person, 1, child of"
|
||||
LOCATION,CDM,No,,No,,,The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites.,"The current iteration of the LOCATION table is US centric. Until a major release to correct this, certain fields can be used to represent different international values. <br><br> - STATE can also be used for province or district<br>- ZIP is also the postal code or postcode","Each address or Location is unique and is present only once in the table. Locations do not contain names, such as the name of a hospital. In order to construct a full address that can be used in the postal service, the address information from the Location needs to be combined with information from the Care Site."
|
||||
LOCATION,CDM,No,,No,,,The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites.,"The current iteration of the LOCATION table is US centric. Until a major release to correct this, certain fields can be used to represent different international values. <br><br> - STATE can also be used for province or district<br>- ZIP is also the postal code or postcode <br>- COUNTY can also be used to represent region","Each address or Location is unique and is present only once in the table. Locations do not contain names, such as the name of a hospital. In order to construct a full address that can be used in the postal service, the address information from the Location needs to be combined with information from the Care Site."
|
||||
CARE_SITE,CDM,No,,No,,,"The CARE_SITE table contains a list of uniquely identified institutional (physical or organizational) units where healthcare delivery is practiced (offices, wards, hospitals, clinics, etc.).",,"Care site is a unique combination of location_id and place_of_service_source_value. Care site does not take into account the provider (human) information such a specialty. Many source data do not make a distinction between individual and institutional providers. The CARE_SITE table contains the institutional providers. If the source, instead of uniquely identifying individual Care Sites, only provides limited information such as Place of Service, generic or ""pooled"" Care Site records are listed in the CARE_SITE table. There can be hierarchical and business relationships between Care Sites. For example, wards can belong to clinics or departments, which can in turn belong to hospitals, which in turn can belong to hospital systems, which in turn can belong to HMOs.The relationships between Care Sites are defined in the FACT_RELATIONSHIP table."
|
||||
PROVIDER,CDM,No,,No,,,"The PROVIDER table contains a list of uniquely identified healthcare providers. These are individuals providing hands-on healthcare to patients, such as physicians, nurses, midwives, physical therapists etc.","Many sources do not make a distinction between individual and institutional providers. The PROVIDER table contains the individual providers. If the source, instead of uniquely identifying individual providers, only provides limited information such as specialty, generic or 'pooled' Provider records are listed in the PROVIDER table.",
|
||||
PAYER_PLAN_PERIOD,CDM,No,,Yes,0,,"The PAYER_PLAN_PERIOD table captures details of the period of time that a Person is continuously enrolled under a specific health Plan benefit structure from a given Payer. Each Person receiving healthcare is typically covered by a health benefit plan, which pays for (fully or partially), or directly provides, the care. These benefit plans are provided by payers, such as health insurances or state or government agencies. In each plan the details of the health benefits are defined for the Person or her family, and the health benefit Plan might change over time typically with increasing utilization (reaching certain cost thresholds such as deductibles), plan availability and purchasing choices of the Person. The unique combinations of Payer organizations, health benefit Plans and time periods in which they are valid for a Person are recorded in this table.","A Person can have multiple, overlapping, Payer_Plan_Periods in this table. For example, medical and drug coverage in the US can be represented by two Payer_Plan_Periods. The details of the benefit structure of the Plan is rarely known, the idea is just to identify that the Plans are different.",
|
||||
|
|
|
|||
|
|
|
@ -1,2 +1,2 @@
|
|||
setwd("/Users/clairblacketer/Documents/GitHub/CdmDdlBase/rmd")#
|
||||
setwd("/Users/clairblacketer/Documents/Github/CommonDataModel/rmd")#
|
||||
rmarkdown::render_site()
|
||||
|
|
|
|||
|
|
@ -9,6 +9,9 @@ output:
|
|||
exclude: ["extras"]
|
||||
navbar:
|
||||
title: '<div><img src="ohdsi16x16.png"></img> OMOP Common Data Model </div>'
|
||||
right:
|
||||
- icon: fa-github
|
||||
href: https://github.com/OHDSI/CommonDataModel
|
||||
left:
|
||||
- icon: fa-home
|
||||
href: index.html
|
||||
|
|
@ -17,52 +20,58 @@ navbar:
|
|||
menu:
|
||||
- text: "Model Background"
|
||||
href: background.html
|
||||
- text: "CDM Refresh Process"
|
||||
href: cdmRefreshProcess.html
|
||||
- text: "How the Vocabulary is Built"
|
||||
href: vocabulary.html
|
||||
- text: "Conventions"
|
||||
icon: fa-list-alt
|
||||
menu:
|
||||
- text: "General Conventions"
|
||||
href: dataModelConventions.html
|
||||
- text: "Observation Periods for EHR Data"
|
||||
href: ehrObsPeriods.html
|
||||
- text: "Patient Privacy and OMOP"
|
||||
href: cdmPrivacy.html
|
||||
- text: "CDM Versions"
|
||||
icon: fa-history
|
||||
menu:
|
||||
- text: "CDM v3.0"
|
||||
href: cdm30.html
|
||||
- text: "CDM v5.3"
|
||||
href: cdm53.html
|
||||
- text: "CDM v5.4"
|
||||
href: cdm54.html
|
||||
- text: "CDM v6.0"
|
||||
href: cdm60.html
|
||||
- text: "CDM v5.3"
|
||||
href: cdm53.html
|
||||
- text: "NEW CDM v5.4"
|
||||
menu:
|
||||
- text: "CDM v5.4"
|
||||
href: cdm54.html
|
||||
- text: "Changes from CDM v5.3"
|
||||
href: cdm54Changes.html
|
||||
- text: "Proposals"
|
||||
icon: fa-plus-square
|
||||
menu:
|
||||
- text: "Under Review"
|
||||
href: reviewProposals.html
|
||||
href: https://github.com/OHDSI/CommonDataModel/issues?q=is%3Aopen+is%3Aissue+label%3AProposal
|
||||
- text: "Accepted"
|
||||
menu:
|
||||
- text: "Oncology CDM Proposal"
|
||||
href: oncology.html
|
||||
- text: "Region_concept_id"
|
||||
href: https://github.com/OHDSI/CommonDataModel/issues/252
|
||||
- text: "Units in Device Table"
|
||||
href: https://github.com/OHDSI/CommonDataModel/issues/264
|
||||
- text: "Help"
|
||||
- text: "How to"
|
||||
icon: fa-question
|
||||
menu:
|
||||
- text: "Download the DDL"
|
||||
href: download.html
|
||||
- text: "Use the CDM R Package"
|
||||
href: cdmRPackage.html
|
||||
- text: "Calculate Drug Dose"
|
||||
href: drug_dose.html
|
||||
- text: "Support"
|
||||
icon: fa-life-ring
|
||||
menu:
|
||||
- text: "FAQ"
|
||||
href: faq.html
|
||||
- text: "Ask a Question"
|
||||
href: contribute.html
|
||||
- text: "How to"
|
||||
icon: fa-wrench
|
||||
menu:
|
||||
- text: "SQL Scripts"
|
||||
href: sqlScripts.html
|
||||
- text: "Download the DDL"
|
||||
href: download.html
|
||||
- text: "Calculate Drug Dose"
|
||||
href: drug_dose.html
|
||||
|
||||
right:
|
||||
- icon: fa-github fa-lg
|
||||
href: https://github.com/OHDSI/CommonDataModel
|
||||
- text: "Ask a Question"
|
||||
href: contribute.html
|
||||
|
|
|
|||
|
|
@ -13,7 +13,7 @@ The Observational Medical Outcomes Partnership (OMOP) was a public-private partn
|
|||
- Develop tools and capabilities for transforming, characterizing, and analysing disparate data sources across the health care delivery spectrum
|
||||
- Establish a shared resource so that the broader research community can collaboratively advance the science
|
||||
|
||||
The results of OMOP's research has been widely published and presented at scientific conferences, including [annual symposia](https://www.ohdsi.org/events/2019-ohdsi-symposium/).
|
||||
The results of OMOP's research has been widely published and presented at scientific conferences, including [annual symposia](https://www.ohdsi.org/2021-ohdsi-global-symposium-info/).
|
||||
|
||||
The OMOP Legacy continues...
|
||||
|
||||
|
|
|
|||
|
|
@ -1,8 +1,5 @@
|
|||
---
|
||||
output:
|
||||
# pdf_document:
|
||||
# toc: yes
|
||||
# toc_depth: '5'
|
||||
html_document:
|
||||
toc: yes
|
||||
toc_depth: 5
|
||||
|
|
|
|||
BIN
rmd/cdm531.pdf
BIN
rmd/cdm531.pdf
Binary file not shown.
|
|
@ -1,8 +1,5 @@
|
|||
---
|
||||
output:
|
||||
# pdf_document:
|
||||
# toc: yes
|
||||
# toc_depth: '5'
|
||||
html_document:
|
||||
toc: yes
|
||||
toc_depth: 5
|
||||
|
|
@ -23,14 +20,11 @@ library(stringr)
|
|||
|
||||
# **OMOP CDM v5.4**
|
||||
|
||||
Below is the specification document for the OMOP Common Data Model, v5.4. Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the [forums](https://forums.ohdsi.org/) or the [github issue](https://github.com/ohdsi/CommonDataModel/issues) page.
|
||||
Below is the specification document for the OMOP Common Data Model, v5.4. **This is the latest version of the OMOP CDM.** Each table is represented with a high-level description and ETL conventions that should be followed. This is continued with a discussion of each field in each table, any conventions related to the field, and constraints that should be followed (like primary key, foreign key, etc). Should you have questions please feel free to visit the [forums](https://forums.ohdsi.org/) or the [github issue](https://github.com/ohdsi/CommonDataModel/issues) page.
|
||||
|
||||
--after regeneration of DDLs
|
||||
link to csv of cdm
|
||||
link to pdf of cdm documentation
|
||||
link to forum on doc page
|
||||
Looking to send us a pull request for a bug fix? Please see the [readme](https://github.com/OHDSI/CommonDataModel#readme) on the main github page.
|
||||
|
||||
```{r docLoop53, echo=FALSE, results='asis'}
|
||||
```{r docLoop54, echo=FALSE, results='asis'}
|
||||
tableSpecs <- read.csv("../inst/csv/OMOP_CDMv5.4_Table_Level.csv", stringsAsFactors = FALSE)
|
||||
cdmSpecs <- read.csv("../inst/csv/OMOP_CDMv5.4_Field_Level.csv", stringsAsFactors = FALSE)
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,184 @@
|
|||
---
|
||||
output:
|
||||
html_document:
|
||||
toc: TRUE
|
||||
toc_float: TRUE
|
||||
---
|
||||
|
||||
# **Changes by Table**
|
||||
*from CDM v5.3 -> CDM v5.4*
|
||||
|
||||
For a full description of each table and field listed here, please see the [CDM specification](http://ohdsi.github.io/CommonDataModel/cdm54.html).
|
||||
|
||||
Notation:
|
||||
|
||||
- a **\+** indicates an addition to the model, either a table or field
|
||||
- a **->** indicates an alteration either in naming or specification
|
||||
- a **-** indicates a subtraction from the model, either a table or field
|
||||
|
||||
## PERSON
|
||||
- No change
|
||||
|
||||
## OBSERVATION_PERIOD
|
||||
- No change
|
||||
|
||||
## VISIT_OCCURRENCE
|
||||
- Admitting_source_concept_id -> **Admitted_from_concept_id**
|
||||
- Admitting_source_value -> **Admitted_from_source_value**
|
||||
- Discharge_to_concept_id -> **Discharged_to_concept_id**
|
||||
- Discharge_to_source_value -> **Discharged_to_concept_id**
|
||||
|
||||
## VISIT_DETAIL
|
||||
- Admitting_source_concept_id -> **Admitted_from_concept_id**
|
||||
- Admitting_source_value -> **Admitted_from_source_value**
|
||||
- Discharge_to_concept_id -> **Discharged_to_concept_id**
|
||||
- Discharge_to_source_value -> **Discharged_to_concept_id**
|
||||
- Visit_detail_parent_id -> **Parent_visit_detail_id**
|
||||
|
||||
## CONDITION_OCCURRENCE
|
||||
- No change
|
||||
|
||||
## DRUG_EXPOSURE
|
||||
- No change
|
||||
|
||||
## PROCEDURE_OCCURRENCE
|
||||
- \+ **Procedure_end_date**
|
||||
- \+ **Procedure_end_datetime**
|
||||
|
||||
## DEVICE_EXPOSURE
|
||||
- Unique_device_id -> **Changed to varchar(255)**
|
||||
- \+ **Production_id**
|
||||
- \+ **Unit_concept_id**
|
||||
- \+ **Unit_source_value**
|
||||
- \+ **Unit_source_concept_id**
|
||||
|
||||
## MEASUREMENT
|
||||
- \+ **Unit_source_concept_id**
|
||||
- \+ **Measurement_event_id**
|
||||
- \+ **Meas_event_field_concept_id**
|
||||
|
||||
## OBSERVATION
|
||||
- \+ **Value_source_value**
|
||||
- \+ **Observation_event_id**
|
||||
- \+ **Obs_event_field_concept_id**
|
||||
|
||||
## DEATH
|
||||
- No change
|
||||
|
||||
## NOTE
|
||||
- \+ **Note_event_id**
|
||||
- \+ **Note_event_field_concept_id**
|
||||
|
||||
## NOTE_NLP
|
||||
- No change
|
||||
|
||||
## SPECIMEN
|
||||
- No change
|
||||
|
||||
## FACT_RELATIONSHIP
|
||||
- No change
|
||||
|
||||
## LOCATION
|
||||
- \+ **Country_concept_id**
|
||||
- \+ **Country_source_value**
|
||||
- \+ **Latitude**
|
||||
- \+ **Longitude**
|
||||
|
||||
## CARE_SITE
|
||||
- No change
|
||||
|
||||
## PAYER_PLAN_PERIOD
|
||||
- No change
|
||||
|
||||
## COST
|
||||
- No change
|
||||
|
||||
## DRUG_ERA
|
||||
- No change
|
||||
|
||||
## DOSE_ERA
|
||||
- No change
|
||||
|
||||
## CONDITION_ERA
|
||||
- No change
|
||||
|
||||
## \+ **EPISODE**
|
||||
|
||||
| EPISODE |
|
||||
|----------------------------------|
|
||||
| episode_id |
|
||||
| person_id |
|
||||
| episode_concept_id |
|
||||
| episode_start_date |
|
||||
| episode_start_datetime |
|
||||
| episode_end_date |
|
||||
| episode_end_datetime |
|
||||
| episode_parent_id |
|
||||
| episode_number |
|
||||
| episode_object_concept_id |
|
||||
| episode_type_concept_id |
|
||||
| episode_source_value |
|
||||
| episode_source_concept_id |
|
||||
|
||||
## \+ **EPISODE_EVENT**
|
||||
|
||||
| EPISODE_EVENT |
|
||||
|------------------------------------|
|
||||
| episode_id |
|
||||
| event_id |
|
||||
| episode_event_field_concept_id |
|
||||
|
||||
## METADATA
|
||||
- \+ **Metadata_id**
|
||||
- \+ **Value_as_number**
|
||||
|
||||
## CDM_SOURCE
|
||||
- Cdm_source_name -> **Mandatory field**
|
||||
- Cdm_source_abbreviation -> **Mandatory field**
|
||||
- Cdm_holder -> **Mandatory field**
|
||||
- Source_release_date -> **Mandatory field**
|
||||
- Cdm_release_date -> **Mandatory field**
|
||||
- \+ **Cdm_version_concept_id**
|
||||
|
||||
## CONCEPT
|
||||
- No change
|
||||
|
||||
## VOCABULARY
|
||||
- Vocabulary_reference -> **Non-mandatory field**
|
||||
- Vocabulary_version -> **Non-mandatory field**
|
||||
|
||||
## DOMAIN
|
||||
- No change
|
||||
|
||||
## CONCEPT_CLASS
|
||||
- No change
|
||||
|
||||
## CONCEPT_RELATIONSHIP
|
||||
- No change
|
||||
|
||||
## RELATIONSHIP
|
||||
- No change
|
||||
|
||||
## CONCEPT_SYNONYM
|
||||
- No change
|
||||
|
||||
## CONCEPT_ANCESTOR
|
||||
- No change
|
||||
|
||||
## SOURCE_TO_CONCEPT_MAP
|
||||
- No change
|
||||
|
||||
## DRUG_STRENGTH
|
||||
- No change
|
||||
|
||||
## - **ATTRIBUTE_DEFINITION**
|
||||
|
||||
## \+ **COHORT**
|
||||
|
||||
| COHORT |
|
||||
|------------------------------------|
|
||||
| cohort_definition_id |
|
||||
| subject_id |
|
||||
| cohort_start_date |
|
||||
| cohort_end_date |
|
||||
|
||||
|
|
@ -0,0 +1,157 @@
|
|||
---
|
||||
title: "Preserving Privacy in an OMOP CDM Implementation"
|
||||
output:
|
||||
html_document:
|
||||
toc: TRUE
|
||||
toc_float: TRUE
|
||||
---
|
||||
*By Kristin Kostka*
|
||||
|
||||
# Background
|
||||
The OMOP CDM is a person-centric model. Being person-centric means the model can retain attributes that may be considered personal identified information (PII) or protected health information (PHI). There are many different ways a site may treat their OMOP CDM to uphold their privacy protocols. In this article we provide guidance on overall process and the potential fields that should be monitored to adhere to these various privacy preserving protocols.
|
||||
|
||||
### Defining PII and PHI
|
||||
- PII is defined as any representation of information that permits the identity of an individual to whom the information applies to be reasonably inferred to either direct or indirect means [1].
|
||||
- The United States Department of Health & Human Services´ Office for Civil Rights has defined PHI as any Personal Identifying Information (PII) that – individually or combined – could potentially identify a specific individual, their past, present or future healthcare, or the method of payment. There are eighteen unique identifiers considered to be PHI: 1) names, 2) geographic data, 3) all elements of dates, 4) telephone numbers, 5) FAX numbers, 6) email addresses, 7) Social Security numbers (SSN), 8) medical record numbers (MRN), 9) health plan beneficiary numbers, 10) account numbers, 11) certificate/license numbers, 12) vehicle identifiers and serial numbers including license places, 13) device identifiers and serial numbers, 14) web URLs, 15) internet protocol addresses, 16) biometric identifiers (i.e. retinal scan, fingerprints), 17) full face photos and comparable images, and 18) any unique identifying number, characteristic or code. PHI is no longer considered PHI when it de-identified of these unique attributes. PHI is commonly referred to in relation to the Health Insurance Portability and Accountability Act (HIPAA) and associated legislation such as the Health Information Technology for Economic and Clinical Health Act (HITECH) [2].
|
||||
|
||||
# The Data Holder's Responsibility
|
||||
In OHDSI, it is the responsibility of each data holder to know, understand and follow local data governance processes related to use of the OMOP CDM. In the United States, these processes will follow your organization's local interpretation for maintaining compliance to PII and PHI protection. In OMOP CDM implementations containing European Union citizen data, local governance processes will include measures to comply with General Data Protection Regulation (GDPR) [3]. As a community, the OHDSI data network covers more than 330 databases from 34 countries. There is extensive community knowledge on the interpretation of rule sets and exemplar IRB and local governance workflows that can be made available to institutions navigating these processes for the first time. If your organization does not have an established data governance process, please reach out on the [OHDSI Forums](forums.ohdsi.org) under "Implementers" and the community can respond with shared guidance from their own deployments. As a community, we aim to conduct research that keeps patient-level data local and share only aggregate results.
|
||||
|
||||
# Complying with Privacy Preservation
|
||||
Complying with local governance processes depends on the rule set being used. There may be allowable times when data use agreements and data transfer agreements exist between collaborating institutions to facilitate sharing of PII and PHI. In this section we will discuss common rule sets that organizations adhere to.
|
||||
|
||||
## Limited Data Sets
|
||||
A limited data set (LDS) is defined as protected health information that excludes certain direct identifiers of an individual or of relatives, employers or household members of the individual — but may include city, state, ZIP code and elements of dates. A LDS can be disclosed only for purposes of research, public health or health care operations. LDS requirements are dictated by the HIPAA Privacy Rule.
|
||||
|
||||
## De-identified Data Sets
|
||||
A de-identified data, as defined by Section 164.514(a) of the HIPAA Privacy rule, is health information that does not identify an individual and with respect to which there is no reasonable basis to believe that the information can be used to identify an individual is not individually identifiable health information. There are two methods for achieving de-identification in accordance with HIPAA [4].
|
||||
|
||||
1) Expert Determination (§164.514(a))- Implementation specifications: requirements for de-identification of protected health information. A covered entity may determine that health information is not individually identifiable health information only if:
|
||||
(1) A person with appropriate knowledge of and experience with generally accepted statistical and scientific principles and methods for rendering information not individually identifiable:
|
||||
(i) Applying such principles and methods, determines that the risk is very small that the information could be used, alone or in combination with other reasonably available information, by an anticipated recipient to identify an individual who is a subject of the information; and
|
||||
(ii) Documents the methods and results of the analysis that justify such determination.
|
||||
|
||||
2) Safe Harbor (§164.514(b)) The eighteen unique identifiers are obfuscated. This includes processes such as:
|
||||
A) Dates of service are algorithmically shifted to protect patient privacy.
|
||||
B) Patient ZIP codes are truncated to the first three digits or removed entirely if the ZIP code represents fewer than 20,000 individuals.
|
||||
C) Removing and, when necessary, replacing unique identifiers
|
||||
AND
|
||||
The entity does not have actual knowledge that the information could be used alone or in combination with other information to identify an individual who is a subject of the information.
|
||||
|
||||
## Field-level Implications of De-identification Processes
|
||||
|
||||
### PERSON Table Attributes
|
||||
In the OMOP CDM, the PERSON table serves as the central identity management for all Persons in the database. It contains records that uniquely identify each person or patient, and some demographic information. It is a table that has a number of field-level implications for privacy preserving protocols.
|
||||
|
||||
Considerations include:
|
||||
- PERSON.person_id should never contain Medical Record Number, Social Security Number or similar uniquely identifiable number. This should be a number that is essentially meaningless but has the ability to be a primary key across tables.
|
||||
- PERSON.year_of_birth, PERSON.month_of_birth and PERSON.date_of_birth, PERSON.birth_datetime may require some redaction or modification depending on interpretation of rule set. Consult local guidance on the need to modify these fields when creating compliant views of de-identified data.
|
||||
- PERSON.person_source_value may contain sensitive information used to generate the person_id field. It is advised to practice caution when creating views of these data. It would be wise to obfuscate or redact this field if you are not sure what is contained in the raw information being extracted, transformed and loaded into the CDM.
|
||||
|
||||
## Date Fields Across Domains
|
||||
Date fields are used across many OMOP domains including: OBSERVATION_PERIOD, VISIT_OCCURRENCE, VISIT_DETAIL, CONDITION_OCCURRENCE, DRUG_EXPOSURE, PROCEDURE_OCCURRENCE, DEVICE_EXPOSURE, MEASUREMENT, OBSERVATION, DEATH, NOTE, NOTE_NLP, SPECIMEN, PAYER_PLAN_PERIOD, DRUG_ERA, DOSE_ERA, and CONDITION_ERA.
|
||||
|
||||
As discussed previously, some rule sets may require algorithmically shifting dates. It is advised that when date shifting is applied, it is done holistically. This means that when shifting dates, you should not treat each record independently. Instead, a robust date shifting algorithm will link off the *.person_id (where * is the domain name such as CONDITION_OCCURRENCE, etc) and apply the same offset to all events. This allows researchers to have the ability to understand the sequence of events while preserving patient privacy.
|
||||
|
||||
The implications of not holistically shifting all events together by the same offset means that information may be out of sequence or illogical. An example would be a death record that happens prior to other event records (conditions, drugs, procedures, etc). When applying an algorithmic shift of dates, it is important to educate your OMOP CDM user group of the known offset. This is especially important in temporal studies which may be looking to make statements about disease history relative to the time when an event is observed.
|
||||
|
||||
Some rule sets do not require algorithmic shifting of dates, such as Limited Data Sets. In these situations, a user of a LDS OMOP CDM would not be expecting dates to the shifted. If a shift is applied, it should be disclosed and the offset amount (e.g. +/- 7 days, +/- 30 days, etc) should be made available to those who have received permission to use a LDS dataset. Otherwise, these data are not upholding the assumptions of the rule set applied.
|
||||
|
||||
## LOCATION Table Attributes
|
||||
The LOCATION table represents a generic way to capture physical location or address information of Persons and Care Sites. When applying privacy preserving procedures, this table should be reviewed and scrubbed relative to the rule set. The LOCATION.zip field should be redacted relative to the type of process applied (e.g. 3-digit zip for de-identified data). The LOCATION.location_source_value should be reviewed for potential PII/PHI. It would be wise to obfuscate or redact this field if you are not sure what is contained in the raw information being extracted, transformed and loaded into the CDM.
|
||||
|
||||
## PROVIDER Table Attributes
|
||||
The PROVIDER table contains a list of uniquely identified healthcare providers. These are individuals providing hands-on healthcare to patients, such as physicians, nurses, midwives, physical therapists etc. In some privacy preserving processes, the PROVIDER.npi and PROVIDER.dea fields may be redacted. Please review this field and confirm that you are adhering to privacy rule sets. The PROVIDER.year_of_birth field is an optional field that may also require treatment in certain rule sets.
|
||||
|
||||
## OBSERVATION Table Attributes
|
||||
The OBSERVATION table captures clinical facts about a Person obtained in the context of examination, questioning or a procedure. Any data that cannot be represented by any other domains, such as social and lifestyle facts, medical history, family history, etc. are recorded here.
|
||||
|
||||
We strongly caution ETL teams to review the OBSERVATION table for potential PII/PHI. In some source systems, there can be information coming in these vocabularies that are not laboratory or clinical observations but instead are patient identifiers. If you search in ATHENA, you will find there are a number of standard terms in the SNOMED and LOINC vocabularies that can represent phone numbers, emails, and other PII information.
|
||||
|
||||
It is difficult to create an exhaustive list of terms because these ontologies do not maintain or publish lists of terms that may contain patient identifiers. It is, therefore, up to data holders to perform a review of this domain with an eye for these potential privacy issues. The National COVID Cohort Collaborative, a NIH consortium which uses the OMOP CDM, has published a resource for sites needing assistance with identifying these potentially problematic records. A “live” version of this table that will track updates over time is hosted at https://github.com/data2health/next-gen-data-sharing/blob/master/CodesWithPPIPotential.csv. We welcome additions to this list from the community.
|
||||
|
||||
## Scrutinizing *_source_value
|
||||
The *_source_value (where * is the domain name such as CONDITION_OCCURRENCE, etc) fields present an opportunity for sites to carry forward potential PII/PHI in ETL processes. Because the convention of the OMOP CDM has minimal boundaries on what are retained in these fields, it is important to treat all source_value fields as potentially containing PII/PHI. We highly advise all data holders to scrutinize these fields when applying privacy preserving processes. It is not uncommon for fields to be overloaded and contain potential patient identifiers. Please use caution when transmitting or making views of these fields available to users.
|
||||
|
||||
## Scrutinizing String Fields
|
||||
Across OMOP Domains, there are many fields which permit the use of strings (e.g. DRUG_EXPOSURE.sig, MEASUREMENT.value_as_string, OBSERVATION.value_as_string, We've discussed some of these in prior sections. It is advised that fields with strings often have the potential to contain unintentional PII/PHI. Targeted regular expressions can be built into ETL processes in order to “sniff” out any additional PII (or potential PII)--such as any data in the format of a phone number, or a person or place name. (E.g., the regular expression "Mr\.|Mrs\.|\bMiss\b|Dr\.|, M\.?D\.?" will find any string with an English name prefix.) Depending on risk tolerance, the expressions could err toward sensitivity or specificity, and could be tweaked over time to meet different rule sets.
|
||||
|
||||
Extensive regular expression matching during ETL may add significant processing time and should therefore not be relied upon as a sole solution, but rather an extra protection against edge cases. Other algorithmic rules may also prove useful, such as automatically quarantining records with lengthy string values (which could signal the presence of free text). If these approaches are implemented, records that match the regular expressions or rules can be quarantined in a separate table or staging area to be manually reviewed by a data broker. Thus, in addition to adding another layer of PII protection, another advantage of these approaches is the potential to uncover ways that underlying vocabularies may be contributing to unintentional sharing of PII and create awareness for future privacy preserving processes shared across the community.
|
||||
|
||||
## NOTE and NOTE_NLP Table Attributes
|
||||
The NOTE table captures unstructured information that was recorded by a provider about a patient in free text (in ASCII, or preferably in UTF8 format) notes on a given date. The NOTE_NLP table encodes all output of NLP on clinical notes. Each row represents a single extracted term from a note. There is a high potential these tables may retain information that is considered PII/PHI. In addition to overall string searching, these tables are likely to be dropped altogether to adhere to the most stringent rule sets.
|
||||
|
||||
It is highly advised that if you are conducting a study with NOTE and NOTE_NLP table information, please consult with your local governance and privacy officers to ensure compliance with local rule sets.
|
||||
|
||||
## Conclusion
|
||||
Privacy preserving processes are not one-size fits all. There are many different rule sets that can be applied to datasets. Data holders are recommended to consult with their local privacy officer(s) to ensure all processes applied to a database are compliant with local interpretation of the selected rule set.
|
||||
|
||||
# References
|
||||
1.
|
||||
BibText version:
|
||||
@MISC{noauthor_undated-mg,
|
||||
title = "Guidance on the Protection of Personal Identifiable
|
||||
Information",
|
||||
abstract = "Personal Identifiable Information (PII) is defined as:",
|
||||
howpublished = "\url{https://www.dol.gov/general/ppii}",
|
||||
note = "Accessed: 2021-8-18"
|
||||
}
|
||||
|
||||
Regular citation:
|
||||
Guidance on the Protection of Personal Identifiable Information. [cited 18 Aug 2021]. Available: https://www.dol.gov/general/ppii
|
||||
|
||||
2.
|
||||
BibText version:
|
||||
@MISC{HIPAA_Journal2017-yo,
|
||||
title = "What Does {PHI} Stand For?",
|
||||
author = "{HIPAA Journal}",
|
||||
abstract = "PHI is a term used in connection with health data, but what
|
||||
does PHI stand for? What information is included in the
|
||||
definition of PHI.",
|
||||
month = dec,
|
||||
year = 2017,
|
||||
howpublished = "\url{https://www.hipaajournal.com/what-does-phi-stand-for/}",
|
||||
note = "Accessed: 2021-8-18",
|
||||
language = "en"
|
||||
}
|
||||
|
||||
Regular citation:
|
||||
HIPAA Journal. What Does PHI Stand For? 23 Dec 2017 [cited 18 Aug 2021]. Available: https://www.hipaajournal.com/what-does-phi-stand-for/
|
||||
|
||||
3.
|
||||
BibText version:
|
||||
|
||||
@MISC{noauthor_2018-mt,
|
||||
title = "General Data Protection Regulation ({GDPR}) Compliance
|
||||
Guidelines",
|
||||
abstract = "The EU General Data Protection Regulation went into effect on
|
||||
May 25, 2018, replacing the Data Protection Directive
|
||||
95/46/EC. Designed to increase data privacy for EU citizens,
|
||||
the regulation levies steep fines on organizations that don't
|
||||
follow the law.",
|
||||
month = jun,
|
||||
year = 2018,
|
||||
howpublished = "\url{https://gdpr.eu/}",
|
||||
note = "Accessed: 2021-8-18",
|
||||
language = "en"
|
||||
}
|
||||
|
||||
|
||||
Regular citation:
|
||||
General Data Protection Regulation (GDPR) Compliance Guidelines. 18 Jun 2018 [cited 18 Aug 2021]. Available: https://gdpr.eu/
|
||||
|
||||
4.
|
||||
BibText version:
|
||||
|
||||
@MISC{Office_for_Civil_Rights_OCR_undated-zy,
|
||||
title = "Methods for De-identification of {PHI}",
|
||||
author = "{Office for Civil Rights (OCR)}",
|
||||
abstract = "Guidance about methods and approaches to achieve
|
||||
de-identification in accordance with the Health Insurance
|
||||
Portability and Accountability Act of 1996.",
|
||||
howpublished = "\url{https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html}",
|
||||
note = "Accessed: 2021-8-19"
|
||||
}
|
||||
|
||||
Regular citation:
|
||||
Office for Civil Rights (OCR). Methods for De-identification of PHI. [cited 19 Aug 2021]. Available: https://www.hhs.gov/hipaa/for-professionals/privacy/special-topics/de-identification/index.html
|
||||
|
|
@ -0,0 +1,7 @@
|
|||
---
|
||||
output:
|
||||
html_document:
|
||||
toc: TRUE
|
||||
toc_float: TRUE
|
||||
---
|
||||
|
||||
|
|
@ -0,0 +1,55 @@
|
|||
---
|
||||
title: '<div><img src="ohdsi40x40.png"></img> CDM Refresh Process </div>'
|
||||
output:
|
||||
html_document:
|
||||
toc: TRUE
|
||||
toc_float: TRUE
|
||||
---
|
||||
|
||||
The OMOP Common Data Model is managed by the OHDSI CDM Working Group. The formal remit of the CDM Working Group (WG) is to hear proposals for change, ratifying only those with valid use cases and data to support them. Then, once ratified, these proposals are incorporated into the next version of the CDM. In the past, this was done by the WG alone. The group would invite others from around the community to present use cases for change and suggestions for improvement. The WG would then vote on the proposals and a new CDM version would be released after a certain period of time or if enough proposals were voted in. This approach worked when the community was smaller but as it is growing rapidly the CDM WG needed to adapt the refresh cycle such that everyone has an opportunity to weigh in on the proposed changes.
|
||||
|
||||
## CDM Refresh Cycle
|
||||
|
||||
|
||||
|
||||
### 1. Define New Version [Completed for v5.4]
|
||||
|
||||
The image above describes the new CDM refresh cycle. It begins with **defining a new version**. This has been completed for the current cycle. Issues and proposals on the github were considered during a 4-hour workshop where it was decided the next CDM version will be CDM v5.4, building off of CDM v5.3. The group then participated in a rapid-fire voting activity to identify which changes should be incorporated into CDM v5.4. Any items that were not unanimously agreed upon were then discussed in small groups to hone the proposal and suggestions were presented back to the group. The final roadmap for CDM v5.4 can be found [here](https://github.com/OHDSI/CommonDataModel/projects/3).
|
||||
|
||||
Looking to open a proposal to change or augment the CDM? Please open an [issue](https://github.com/OHDSI/CommonDataModel/issues) and use the **proposal template**.
|
||||
|
||||
### 2. Sign off from Work Groups [Completed for v5.4]
|
||||
|
||||
Each member of the CDM WG is a liaison for another workgroup in the community. They are responsible for presenting the proposed changes to the CDM and collecting the feedback. This has resulted in very helpful suggestions from the EHR, Data Quality, Device, HADES, and ACHILLES groups. This outreach has proven to be very effective and should result in a very stable version.
|
||||
|
||||
### 3. Release DDLs
|
||||
|
||||
After all changes and suggestions are agreed upon by the community and work groups the next step is to generate the DDLs. The CDM WG hosted a hackathon on August 18-19, 2021. During this time the group created an R package to automatically generate the DDLs and the code to instantiate an empty CDM instance. Changes were made to v5.3 to generate v5.4 and the repository was refactored.
|
||||
|
||||
### 4. Software Update
|
||||
|
||||
There will be period of time once the DDLs are ready to allow the software and methods developers to prepare for the official release of the CDM. This is meant to serve as a buffer so that once the community starts adopting the new model, the tools and methods will be ready to support it.
|
||||
|
||||
### 5. Community Support
|
||||
|
||||
This is the final stage of the CDM refresh cycle. Once the DDLs are ready and the software and tools supports the new version, the CDM WG will work to help the community convert their data to the new model.
|
||||
|
||||
|
||||
# CDM WG Meeting Information
|
||||
|
||||
The CDM working group meets the first and third Tuesday of the month. See below for links to the meetings.
|
||||
|
||||
**Every first Tuesday of the month at 1pm est** [Teams Meeting](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)
|
||||
|
||||
**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** These were recently changed from a Skype meeting to a Microsoft Teams meeting. If you do you have access to the OHDSI Teams Tenet, please contact Clair Blacketer at mblacke@its.jnj.com.
|
||||
|
||||
|
||||
### CDM WG Important Links
|
||||
|
||||
- [Google Drive Location](https://drive.google.com/open?id=1DaNKe6ivIAZPJeI31VJ-pzNB9wS9hDqu)
|
||||
- [Running Agenda](https://docs.google.com/document/d/1WgKePjrI_cGdqn2XQCe1JdGaTzdMqU4p5ihkMt8fcAc/edit?usp=sharing)
|
||||
- [CDM Github](https://github.com/OHDSI/CommonDataModel)
|
||||
|
||||
|
|
@ -64,10 +64,6 @@ identify Descendants that may appear in the data. See CONCEPT_ANCESTOR table. No
|
|||
Concepts can only appear in *_source_concept_id fields and are not used in [CONCEPT_ANCESTOR](https://ohdsi.github.io/CommonDataModel/cdm531.html#concept_ancestor)
|
||||
table. Please refer to the Standardized Vocabularies specifications for details of the Standard Concept
|
||||
designation.
|
||||
- All logical data elements associated with the various CDM tables (usually in the _type_concept_id
|
||||
field) are called Type Concepts, including defining characteristics, qualifying attributes etc. They are
|
||||
also stored as Concepts in the CONCEPT table. Since they are generated by OMOP, their is no
|
||||
meaningful concept_code.
|
||||
- The lifespan of a Concept is recorded through its valid_start_date, valid_end_date and the invalid_
|
||||
reason fields. This allows Concepts to correctly reflect at which point in time were defined.
|
||||
Usually, Concepts get deprecated if their meaning was deemed ambiguous, a duplication of another
|
||||
|
|
@ -268,9 +264,34 @@ Many tables contain equivalent information multiple times: As a Source Value, a
|
|||
|
||||
Source Values are only provided for convenience and quality assurance (QA) purposes. Source Values and Source Concepts are optional, while Standard Concepts are mandatory. Source Values may contain information that is only meaningful in the context of a specific data source.
|
||||
|
||||
### General Concepts and Type Concepts
|
||||
### Type Concepts
|
||||
*By Mik Kallfelz and Dmitry Dymshyts*
|
||||
|
||||
Type Concepts (ending in _TYPE_CONCEPT_ID) and general Concepts (ending in _CONCEPT_ID) are part of many tables. The former are special Concepts with the purpose of indicating where the data are derived from in the source. For example, the Type Concept field can be used to distinguish a DRUG_EXPOSURE record that is derived from a pharmacy-dispensing claim from one indicative of a prescription written in an electronic health record (EHR).
|
||||
Type Concepts (ending in _TYPE_CONCEPT_ID) are present in many tables. They are special Concepts with the purpose of indicating from where the data are derived in the source. For example, the Type Concept field can be used to distinguish a DRUG_EXPOSURE record that is derived from a pharmacy-dispensing claim from one indicative of a prescription written in an electronic health record (EHR).
|
||||
|
||||
- Type concepts help determining the provenance of a record in the OMOP CDM. Many tables hold a specific _type_concept_id field for which [valid concepts](https://athena.ohdsi.org/search-terms/terms?domain=Type+Concept&standardConcept=Standard&page=1&pageSize=15&query=) can be used to indicate a particular source of that record. For a condition it can be helpful to know, if it was derived from an EHR system or insurance claims. For a drug exposure it should be very useful to distinguish between prescriptions and actual administrations.
|
||||
- In respect to the target table, matching type concepts should be chosen during the ETL step while processing sources. There are various representations in the list of type concepts of which some are quite specific for one table and others can be applied for many tables / domains, as they are quite generic. There is however no plausibility check or dependency between type concepts and tables which means they have to be chosen correctly.
|
||||
- There is now one specific [vocabulary](https://github.com/OHDSI/Vocabulary-v5.0/wiki/Vocab.-TYPE_CONCEPT) for type concepts which replaced a number of previously existing tables. For example, where previously there was a dedicated vocabulary for Drug Type Concepts, now we would choose the respective ones from the overall vocabulary (and ignore some of the old ones):
|
||||
|
||||
| Drug Type | Type Concept |
|
||||
|-------------------------------------------------------------------------|----------------------------------------|
|
||||
| Inpatient administration | EHR administration record |
|
||||
| Physician administered drug (identified from EHR problem list) | EHR administration record |
|
||||
| Physician administered drug (identified from referral record) | EHR administration record |
|
||||
| Physician administered drug (identified from EHR observation) | EHR administration record |
|
||||
| Physician administered drug (identified from EHR order) | EHR administration record |
|
||||
| Prescription dispensed in pharmacy | EHR dispensing record |
|
||||
| Dispensed in Outpatient office | EHR dispensing record |
|
||||
| Medication list entry | EHR medication list |
|
||||
| Prescription written | EHR prescription |
|
||||
| | EHR prescription issue record |
|
||||
| Prescription dispensed through mail order | Mail order record |
|
||||
| NLP derived | NLP |
|
||||
| Patient Self-Reported Medication | Patient self-report |
|
||||
| Physician administered drug (identified as procedure) | Pharmacy claim |
|
||||
| Drug era - 0 days persistence window | |
|
||||
| Drug era - 30 days persistence window | |
|
||||
| Randomized Drug | |
|
||||
|
||||
### Time span of available data
|
||||
|
||||
|
|
|
|||
|
|
@ -0,0 +1,63 @@
|
|||
---
|
||||
title: "Observation Period Considerations for EHR Data"
|
||||
output: html_document
|
||||
---
|
||||
|
||||
*By Melanie Philofsky and the EHR Working Group*
|
||||
|
||||
The EHR WG convened on July 24, August 7, and August 21, 2020 to discuss the creation of an Observation Period from EHR data. The current and future conventions are not prescriptive enough and leave room for various ways of interpretation. The goals of our discussions were to increase the standardization for the implementation of the OBSERVATION_PERIOD table by providing some general guidelines for determining the start, end, and gaps in Observation Periods. The suggestions we came up with are only “suggestions” at this point. More research should be done to understand how these choices might impact evidence generated using these data. All of these decisions should be tempered by local understanding of patients in the EHR you are ETLing.
|
||||
|
||||
* *Note - These suggestions are not intended for HMO EHR sites since HMO EHR Observation Periods more closely resemble claims data Observation Periods.*
|
||||
|
||||
## Observation Period Start Date
|
||||
|
||||
- Generally an Observation Period does NOT begin before birth, however, it might begin before birth IF the pregnant mother receives care recorded in your EHR. The child’s record is then split from the mother’s record at birth but may retain care given during pregnancy. For these children in your dataset, the field **observation_period_start_date should be the birth date minus 9 months**
|
||||
- An **Observation Period does NOT begin before the implementation of the EHR at your site**. Any records prior to implementation are probably “history of” record types and not a complete EHR record of clinical events.
|
||||
- Special consideration should be given to migration from previous EHR, implementation at different sites within your healthcare system, implementation of different modules, etc.
|
||||
|
||||
## Observation Period end date
|
||||
|
||||
Set the **observation_period_end_date** as the first date from the following:
|
||||
|
||||
- **Date of death + 60 days**
|
||||
- This is a CDM convention to allow events after death (autopsy, final notes, etc).
|
||||
- **Last clinical event + 60 days**
|
||||
- The assumption is that person will return to the same health provider if an adverse reaction/complication/unresolved condition occurs.
|
||||
- **Date of the data pull from the system**
|
||||
|
||||
## Observation Period Gaps and Persistence Windows
|
||||
|
||||
### Observation Period Gaps
|
||||
|
||||
Periods of time when a Person does not receive care from your institution and therefore is not observed and should not have an Observation Period. These gaps are usually hard to determine because most Persons don’t announce their departure from an EHR/healthcare institution. Therefore, a heuristic will need to be instituted to determine Observation Period Gaps where the information is not explicit.
|
||||
|
||||
### Observation Period Persistence Window
|
||||
|
||||
Defined as the maximum time allowed between two clinical events under the assumption a Person would have a clinical event recorded, if they are not healthy and seek care.
|
||||
|
||||
**Example:** Person 1 has a series of clinical events recorded from **Jan. 1, 2010 to June 15, 2012**, where the time between clinical events does not exceed 60 days. The next clinical event for Person 1 is on **Oct. 1, 2018**. Starting Oct. 1, 2018 Person 1 has clinical events occurring at least every 90 days up to the present date.
|
||||
|
||||
There is a 6+ year gap between groups of clinical events recorded in the CDM. After discussion in the EHR WG, we believe this 6+ year gap is indicative of a Person not being seen within our EHR/healthcare institution. Per convention #4 for Observation Period table, “As a general assumption, during an Observation Period any clinical event that happens to the patient is expected to be recorded. Conversely, the absence of data indicates that no clinical events occurred to the patient." Person 1 has two Observation Periods.
|
||||
|
||||
**1st Observation Period**
|
||||
|
||||
- observation_period_start_date = **01/01/2010**
|
||||
- observation_period_end_date = **08/15/2012** (Per the end_date guideline above)
|
||||
|
||||
**2nd Observation Period**
|
||||
|
||||
- observation_period_start_date = **10/01/2018**
|
||||
- observation_period_end_date = **09/01/2020** (Date of the data pull, per the end_date guideline above)
|
||||
|
||||
|
||||
Now, there are cases where a Person only receives care within you EHR system when absolutely necessary. And if your EHR doesn’t offer primary care services, the majority of Persons who lack healthcare insurance or any other reason why Persons are only seen in urgent or emergent situations, the above heuristic might be too restrictive. This is a guideline. A question the EHR WG debated was how long between clinical events should we assume any clinical event that happens to the Person is expected to be recorded? When should we end one Observation Period and begin another? What should be the time between events for an Observation Period Persistence Window? Wellness checkups/Visits happen approximately every 12-18 months depending on a multitude of factors.
|
||||
|
||||
**Our recommendation: If Observation Period Gaps are 548 days or more, then the previous Observation Period should end and another Observation Period should begin on the date of the next clinical event as per the Person 1 example above.**
|
||||
|
||||
## Additional ETL considerations
|
||||
|
||||
- Implementation of your EHR, migration from previous EHR, implementation at different sites within your healthcare system, implementation of different modules
|
||||
- Coverage of your healthcare system within your area, population served by the healthcare system
|
||||
- All decisions should be tempered by local understanding of patients in the EHR you are ETLing.
|
||||
|
||||
The Observation Period can be created by only one clinical event. However, the clinical event must NOT be from the Death table. If a Death date does not have any other clinical records 18 months before AND 18 months after the death date, then an Observation Period will not be created. We believe this logic is needed because if a Person only has a death death_date without other clinical event records, a Person is most likely not being “observed” when the death occurred. If a Person was being observed at their time of death, then other records (visit, condition, measurement, etc.) would be created. This rule is most relevant for those with death registry data since a Person who dies in the hospital has many clinical event records.
|
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|
@ -3,37 +3,19 @@ title: '<div><img src="ohdsi40x40.png"></img> OMOP Common Data Model</div>'
|
|||
output: html_document
|
||||
---
|
||||
|
||||
The OMOP Common Data Model is managed by the [OHDSI CDM Working Group](https://www.ohdsi.org/web/wiki/doku.php?id=projects:workgroups:cdm-wg). Through the end of 2019 and into 2020 our goal was to fully update the documentation in an effort to facilitate greater understanding of the model. Almost every [forum post](https://www.forums.ohdsi.org) relating to a question on how to map data into the CDM inevitably referenced the (now outdated) technical and difficult-to-understand explanations of the tables and fields currently on the wiki. To remedy we focused on one or two tables each month, diving fully into the user guidance and ETL specifications. The results of our efforts can be seen on the pages detailing [v5.3](https://ohdsi.github.io/CommonDataModel/cdm531.html) and [v6.0](https://ohdsi.github.io/CommonDataModel/cdm60.html).
|
||||
The OMOP Common Data Model is managed by the OHDSI CDM Working Group. If you would like to join our group please fill out [this form](https://forms.office.com/Pages/ResponsePage.aspx?id=lAAPoyCRq0q6TOVQkCOy1ZyG6Ud_r2tKuS0HcGnqiQZUOVJFUzBFWE1aSVlLN0ozR01MUVQ4T0RGNyQlQCN0PWcu) and check "Common Data Model" to be added to our Microsoft Teams environment. This working group endeavors to maintain the OMOP CDM as a living model by soliciting and responding to requests from the community based on use cases and research purposes. For more information on the CDM refresh process please see the description [here](http://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html). You will find information on our meetings and links to join at the end of this page.
|
||||
|
||||
In addition to documentation the formal remit of the CDM Working Group (WG) is to hear proposals for change, ratifying only those with valid use cases and data to support them. In the past, this was done by the WG alone. The group would invite others from around the community to present use cases for change and suggestions for improvement. The WG would then vote on the proposals and a new CDM version would be released after a certain period of time or if enough proposals were voted in. This approach worked when the community was smaller but as it is growing rapidly the CDM WG needed to adapt the refresh cycle such that everyone has an opportunity to weigh in on the proposed changes.
|
||||
## Current CDM Version
|
||||
|
||||
## CDM Refresh Cycle
|
||||
The current CDM version is [CDM v5.4](http://ohdsi.github.io/CommonDataModel/cdm54.html), depicted below. This CDM version was developed over the course of a year by considering requests that were sent via our [issues page](https://github.com/OHDSI/CommonDataModel/issues). The list of proposed changes was then shared with the community in multiple ways: through discussions at the weekly OHDSI Community calls, discussions with the OHDSI Steering Committee, and discussions with all potentially affected workgroups. The [final changes](http://ohdsi.github.io/CommonDataModel/cdm54Changes.html) were then delivered to the Community through a new R package designed to dynamically generate the DDLs and documentation for all supported SQL dialects.
|
||||
|
||||
|
||||
- [Link to DDLs for CDM v5.4](https://github.com/OHDSI/CommonDataModel/tree/v5.4.0)
|
||||
- [Link to ReadMe for instructions on how to use the R package](https://github.com/OHDSI/CommonDataModel/tree/master#readme)
|
||||
|
||||
### 1. Define New Version
|
||||
|
||||
The image above describes the new CDM refresh cycle. It begins with **defining a new version**. This has been completed for the current cycle. Issues and proposals on the github were considered during a 4-hour workshop where it was decided the next CDM version will be CDM v5.4, building off of CDM v5.3. The group then participated in a rapid-fire voting activity to identify which changes should be incorporated into CDM v5.4. Any items that were not unanimously agreed upon were then discussed in small groups to hone the proposal and suggestions were presented back to the group. The final roadmap for CDM v5.4 can be found [here](https://github.com/OHDSI/CommonDataModel/projects/3).
|
||||
|
||||
### 2. Sign off from Work Groups
|
||||
|
||||
This is the current stage of the refresh cycle for CDM v5.4. Each member of the CDM WG is a liaison for another workgroup in the community. They are responsible for presenting the proposed changes to the CDM and collecting the feedback. This has resulted in very helpful suggestions from the EHR, Data Quality, Device, HADES, and ACHILLES groups. This outreach has proven to be very effective and should result in a very stable version.
|
||||
|
||||
### 3. Release DDLs
|
||||
|
||||
After all changes and suggestions are agreed upon by the community and work groups the next step is to generate the DDLs this will be done by the CDM Development group.
|
||||
|
||||
### 4. Software Update
|
||||
|
||||
There will be period of time once the DDLs are ready to allow the software and methods developers to prepare for the official release of the CDM. This is meant to serve as a buffer so that once the community starts adopting the new model, the tools and methods will be ready to support it.
|
||||
|
||||
### 5. Community Support
|
||||
|
||||
This is the final stage of the CDM refresh cycle. Once the DDLs are ready and the software and tools supports the new version, the CDM WG will work to help the community convert their data to the new model.
|
||||
|
||||
|
||||
|
||||
|
||||
# CDM WG Meeting Information
|
||||
## CDM WG Meeting Information
|
||||
|
||||
The CDM working group meets the first and third Tuesday of the month. See below for links to the meetings.
|
||||
|
||||
|
|
@ -42,12 +24,12 @@ 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)
|
||||
|
||||
|
||||
**Note** These were recently changed from a Skype meeting to a Microsoft Teams meeting. If you do you have access to the OHDSI Teams Tenet, please contact Clair Blacketer at mblacke@its.jnj.com.
|
||||
|
||||
**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"
|
||||
|
||||
### CDM WG Important Links
|
||||
|
||||
- [Google Drive Location](https://drive.google.com/open?id=1DaNKe6ivIAZPJeI31VJ-pzNB9wS9hDqu)
|
||||
- [Running Agenda](https://docs.google.com/document/d/1WgKePjrI_cGdqn2XQCe1JdGaTzdMqU4p5ihkMt8fcAc/edit?usp=sharing)
|
||||
- [CDM Github](https://github.com/OHDSI/CommonDataModel)
|
||||
- [Process for adopting CDM and Vocabulary changes](https://www.ohdsi.org/web/wiki/doku.php?id=documentation:next_cdm:cdm_process)
|
||||
- [Process for adopting CDM and Vocabulary changes](http://ohdsi.github.io/CommonDataModel/cdmRefreshProcess.html)
|
||||
|
|
|
|||
Loading…
Reference in New Issue