Update README.md

module/PJI_NLP/README.md

@@ -5,24 +5,15 @@ Process consultation notes, operative notes, pathology reports, and microbiology
 @author Fu S, Wyles CC, Osmon DR, Carvour ML, Sagheb E, Ramazanian T, Kremers WK, Lewallen DG, Berry DJ, Sohn S, Maradit Kremers H.
 
 ## CONFIGURATION:
-INPUT_DIR: full directory path of input folder
-OUTPUT_DIR: full directory path of output folder
-OUTPUT_SUMMARY_DIR: full directory path of output summary folder
-RULES_DIR: full directory path of 'TJA' folder
+
 
 ## INPUT:
- Input folder: the input folder contains a list of surgical reports 
- Input file: document level .txt file. The naming convention of each report would be unique identifier + surgery date. P.S. one patient may have multiple surgeries. 
- Input file preprocessing: replace all '/n' to '. '
+
 
 ## RUN:
- command line:
- ```
- ./runMedTagger-fit-tja.sh
-```
+
 ## OUTPUT:
- raw folder: concept level finding
- summary folder: document level finding
+
 
 ## REFERENCE: 
 Fu S, Wyles CC, Osmon DR, Carvour ML, Sagheb E, Ramazanian T, Kremers WK, Lewallen DG, Berry DJ, Sohn S, Maradit Kremers H. Automated Detection of Periprosthetic Joint Infections and Data Elements Using Natural Language Processing. J Arthroplasty. 2021 Feb;36(2):688-692. doi: 10.1016/j.arth.2020.07.076. Epub 2020 Aug 5. PMID: 32854996; PMCID: PMC7855617.