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Background
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Conventions
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< h1 class = "title toc-ignore" > Oncology Extension< / h1 >
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< 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 >
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< 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 >
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< div id = "episode" class = "section level3 tabset tabset-pills" >
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< h3 class = "tabset tabset-pills" > EPISODE< / h3 >
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< p > < strong > Table Description< / strong > < / p >
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< 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 ‘ ’ < / p >
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< / div >
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< h3 class = "tabset tabset-pills" > EPISODE_EVENT< / h3 >
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< p > < strong > Table Description< / strong > < / p >
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< 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 >
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< 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 >
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< h3 class = "tabset tabset-pills" > MEASUREMENT< / h3 >
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< p > < strong > Table Description< / strong > < / p >
< p > The MEASUREMENT table contains records of Measurement, i.e. ’ < / p >
< p > < strong > User Guide< / strong > < / p >
< p > Measurements differ from Observations in that they require a standardized test or some other activity to generate a quantitative or qualitative result.< / p >
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$('.unlisted.unnumbered').addClass('toc-ignore')
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// 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,h4,h5",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
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return text.replace(/[.\\/?& !#< >]/g, '').replace(/\s/g, '_');
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},
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 >
