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Go to the myNLP2HPO_GenDis_pipeline directory.
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Replace test notes in the clinicalnotes folder with the desired clinical notes to analyze.
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Run the meta shell script
runanalysis.sh. The pipeline requires a stable internet connection! -
Version 2 can be tested with the meta shell script
runanalysis_v2.sh, which also requires internet connection. The folders created with the second version have the prefix "v2_". This version has an improved mapping process of the HPO term's synonyms to the clinical note. -
Version 3 can be tested with the meta shell script
runanalysis_v3.sh, which also requires internet connection. The folders created with the third version have the prefix "v3_". This version uses a more aggressive lemmatization method as well as an extended negation process.
/sources: contains three .tsv files, HPO_Terms.tsv with all HPO terms including synonyms and parent ids, HPO2Genes.tsv with genes linked to each HPO term and HPO2Diseases.tsv with diseases linked to each HPO term.- Following folders are related to the first version of the pipeline. Second and third version folders have gained the prefix "v2_" and "v3_", respectively.
/out_extracted_HPO: contains extracted HPO terms for each clinical note in the clinicalnotes folder as .txt files./out_annotated_genes: contains annotated genes for every extracted HPO term from the clinical notes as .txt files./out_prioritized_genes: contains genes prioritized and ranked by their frequency for each clinical note as .txt files./out_annotated_diseases: contains annotated diseases for every extracted HPO term from the clinical notes as .txt files./out_prioritized_diseases: contains diseases prioritized and ranked by their frequency for each clinical note as .txt files.