extras/PathwayResultsAssemblyNotes.md

In ohdsi-studies/EhdenRaDrugUtilization: Rheumatoid arthritis (RA) Drug Utilization Study (EHDEN Study-a-thon Barcelona 2020)

Gathering Pathways Results

• Import pathway design from /inst/characterization/Pathways-Analysis.json into ATLAS
• Generate the pathway results using ATLAS
• Export the results from ATLAS (WebAPI) using extras/ExportPathwaysResults.R
• The exported results will consist of 2 files: ra-pathway-design.json, ra-pathway-result.json which respectively contain the design & results of the execution.
• The exported results are centrally stored in E:\EhdenPathwaysResults\results with a subfolder per data source.
• The code in extras/pathwayResultsViewer.html was used to transform the ATLAS results into a CSV. The resulting CSV was then saved to the results folder with the ATLAS exported results. The code for the webapp was hosted on a local web server and the JavaScript dependencies were taken from ATLAS. Specifically, the JavaScript subfolders: js\*, node_modules\file-saver
• The code in extras\MakeBigCSV.R is used to assemble all of the individual set of result CSVs into a single, big CSV with all of the results pulled together: E:\EhdenPathwaysResults\results\EhdenRaDrugUtilization_1yr_pathways_results.csv
• The data from EhdenRaDrugUtilization_1yr_pathways_results.csv was loaded into a PostgreSQL DB to analyze the data.

Data Preparation

• The data loaded into the PostgreSQL DB (described above) is then transformed using the script found in inst/sql/postgresql/Pull-EHDEN-DUS-Results.sql. Additionally, a database table was created to hold the various attributes for each data source that supplied results for th study.
• The data was then exported for use in the Shiny results viewer in the inst/shiny/ResultsExplorer/data folder.

ohdsi-studies/EhdenRaDrugUtilization documentation built on July 19, 2021, 6:24 p.m.