231 lines
6.9 KiB
Plaintext
231 lines
6.9 KiB
Plaintext
---
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title: "OMOP Common Data Model Specifications"
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author: Christian Reich, Patrick Ryan, Rimma Belenkaya, Karthik Natarajan and Clair
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Blacketer
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date: "`r Sys.Date()`"
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output:
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html_document:
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df_print: paged
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toc: yes
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pdf_document:
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latex_engine: xelatex
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number_sections: yes
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toc: yes
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linkcolor: blue
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params:
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mdFilesLocation: S:/Git/GitHub/CommonDataModel.wiki
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keep-tex: yes
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---
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```{r, echo=FALSE}
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mdFilesLocation <- params$mdFilesLocation
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```
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# License
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```{r child = paste0(mdFilesLocation,'/License.md')}
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```
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# Background
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```{r child = paste0(mdFilesLocation,'/Background/Background.md')}
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```
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## The Role of the Common Data Model
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```{r child = paste0(mdFilesLocation,'/Background/The-Role-of-the-Common-Data-Model.md')}
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```
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## Design Principles
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```{r child = paste0(mdFilesLocation,'/Background/Design-Principles.md')}
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```
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## Data Model Conventions
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```{r child = paste0(mdFilesLocation,'/Background/Data-Model-Conventions.md')}
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```
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# Glossary of Terms
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```{r child = paste0(mdFilesLocation,'/Glossary-of-Terms.md')}
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```
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# Standardized Vocabularies
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```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/Standardized-Vocabularies.md')}
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```
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## CONCEPT
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```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/CONCEPT.md')}
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```
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## VOCABULARY
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```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/VOCABULARY.md')}
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```
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## DOMAIN
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```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/DOMAIN.md')}
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```
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## CONCEPT_CLASS
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```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/CONCEPT_CLASS.md')}
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```
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## CONCEPT_RELATIONSHIP
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```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/CONCEPT_RELATIONSHIP.md')}
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```
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## RELATIONSHIP
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```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/RELATIONSHIP.md')}
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```
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## CONCEPT_SYNONYM
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```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/CONCEPT_SYNONYM.md')}
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```
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## CONCEPT_ANCESTOR
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```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/CONCEPT_ANCESTOR.md')}
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```
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## SOURCE_TO_CONCEPT_MAP
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```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/SOURCE_TO_CONCEPT_MAP.md')}
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```
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## DRUG_STRENGTH
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```{r child = paste0(mdFilesLocation,'/StandardizedVocabularies/DRUG_STRENGTH.md')}
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```
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# Standardized Metadata
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```{r child = paste0(mdFilesLocation,'/StandardizedMetadata/Standardized-Metadata.md')}
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```
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## CDM_SOURCE
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```{r child = paste0(mdFilesLocation,'/StandardizedMetadata/CDM_SOURCE.md')}
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```
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## METADATA
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```{r child = paste0(mdFilesLocation,'/StandardizedMetadata/METADATA.md')}
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```
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# Standardized Clinical Data Tables
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```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/Standardized-clinical-Data-Tables.md')}
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```
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## PERSON
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```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/PERSON.md')}
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```
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<!-- ## OBSERVATION_PERIOD -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/OBSERVATION_PERIOD.md')} -->
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<!-- ``` -->
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<!-- ## VISIT_OCCURRENCE -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/VISIT_OCCURRENCE.md')} -->
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<!-- ``` -->
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<!-- ## VISIT_DETAIL -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/VISIT_DETAIL.md')} -->
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<!-- ``` -->
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<!-- ## CONDITION_OCCURRENCE -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/CONDITION_OCCURRENCE.md')} -->
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<!-- ``` -->
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<!-- ## DEATH -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/DEATH.md')} -->
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<!-- ``` -->
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<!-- ## DRUG_EXPOSURE -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/DRUG_EXPOSURE.md')} -->
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<!-- ``` -->
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<!-- ## PROCEDURE_OCCURRENCE -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/PROCEDURE_OCCURRENCE.md')} -->
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<!-- ``` -->
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<!-- ## DEVICE_EXPOSURE -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/DEVICE_EXPOSURE.md')} -->
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<!-- ``` -->
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<!-- ## MEASUREMENT -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/MEASUREMENT.md')} -->
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<!-- ``` -->
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<!-- ## NOTE -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/NOTE.md')} -->
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<!-- ``` -->
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<!-- ## NOTE_NLP -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/NOTE_NLP.md')} -->
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<!-- ``` -->
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<!-- ## SURVEY_CONDUCT -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/SURVEY_CONDUCT.md')} -->
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<!-- ``` -->
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<!-- ## OBSERVATION -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/OBSERVATION.md')} -->
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<!-- ``` -->
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<!-- ## SPECIMEN -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/SPECIMEN.md')} -->
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<!-- ``` -->
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<!-- ## FACT_RELATIONSHIP -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedclinicalDataTables/FACT_RELATIONSHIP.md')} -->
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<!-- ``` -->
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<!-- # Standardized Health System Data Tables -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedHealthSystemDataTables/Standardized-Health-System-Data-Tables.md')} -->
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<!-- ``` -->
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<!-- ## LOCATION -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedHealthSystemDataTables/LOCATION.md')} -->
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<!-- ``` -->
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<!-- ## LOCATION_HISTORY -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedHealthSystemDataTables/LOCATION_HISTORY.md')} -->
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<!-- ``` -->
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<!-- ## CARE_SITE -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedHealthSystemDataTables/CARE_SITE.md')} -->
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<!-- ``` -->
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<!-- ## PROVIDER -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedHealthSystemDataTables/PROVIDER.md')} -->
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<!-- ``` -->
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<!-- # Standardized Health Economics Data Tables -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedHealthEconomicsDataTables/Standardized-Health-Economics-Data-Tables.md')} -->
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<!-- ``` -->
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<!-- ## PAYER_PLAN_PERIOD -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedHealthEconomicsDataTables/PAYER_PLAN_PERIOD.md')} -->
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<!-- ``` -->
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<!-- ## COST -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedHealthEconomicsDataTables/COST.md')} -->
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<!-- ``` -->
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<!-- # Standardized Derived Elements -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedDerivedElements/Standardized-Derived-Elements.md')} -->
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<!-- ``` -->
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<!-- ## DRUG_ERA -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedDerivedElements/DRUG_ERA.md')} -->
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<!-- ``` -->
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<!-- ## DOSE_ERA -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedDerivedElements/DOSE_ERA.md')} -->
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<!-- ``` -->
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<!-- ## CONDITION_ERA -->
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<!-- ```{r child = paste0(mdFilesLocation,'/StandardizedDerivedElements/CONDITION_ERA.md')} -->
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<!-- ``` -->
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<!-- # Results Schema -->
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<!-- ```{r child = paste0(mdFilesLocation,'/ResultsSchema/Results-Schema.md')} -->
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<!-- ``` -->
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<!-- ## COHORT -->
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<!-- ```{r child = paste0(mdFilesLocation,'/ResultsSchema/COHORT.md')} -->
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<!-- ``` -->
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<!-- ## COHORT_DEFINITION -->
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<!-- ```{r child = paste0(mdFilesLocation,'/ResultsSchema/COHORT_DEFINITION.md')} -->
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<!-- ``` -->
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