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backbone-demo-config.json
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backbone-demo-config.json
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{
"id": "nlp_ohdsi_to_ohdsi",
"description": "A pipeline configuration that extracts clinical narratives from OHDSI CDM, runs a MedTagger NLP rulesets, and outputs back to OHDSI CDM.",
"pipeline": [
{
"clazz": "org.ohnlp.backbone.io.jdbc.JDBCExtract",
"config": {
"_desc": "An example configuration to extract notes from mssql OHDSI CDM instance, replace values as appropriate",
"url": "jdbc:mysql://db-mysql-sfo2-26313-do-user-512513-0.b.db.ondigitalocean.com:25060/defaultdb?ssl-mode=REQUIRED",
"driver": "com.mysql.jdbc.Driver",
"user": "backbonedemo",
"password": "backbonedemo",
"query": "SELECT note_id, note_text FROM DEMO.note"
}
},
{
"clazz": "org.ohnlp.medtagger.backbone.MedTaggerBackboneTransform",
"config": {
"_desc": "Runs NLP. In this case, we use COVID-19 ruleset that is bundled by default as an example",
"_desc_ctd": "Note: you will need to install the MedTagger Backbone Component found at https://www.github.com/OHNLP/MedTagger",
"input": "note_text",
"ruleset": "covid19",
"mode": "standalone"
}
},
{
"clazz": "org.ohnlp.medtagger.backbone.MedTaggerOutputToOHDSIFormatTransform",
"config": {
"_desc": "Converts MedTagger output to OHDSI format",
"_desc_ctd": "Note: you will need to install the MedTagger Backbone Component found at https://www.github.com/OHNLP/MedTagger",
"ruleset": "covid19"
}
},
{
"clazz": "org.ohnlp.backbone.io.local.FileSystemLoad",
"config": {
"_desc": "An example configuration to load NLP artifacts into OHDSI CDM, replace values as appropriate",
"fileSystemPath": "out"
}
}
]
}