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Welcome to the SemEHR wiki!

Run SemEHR pipeline

A typical SemEHR process contains the following steps:

• query a database to get the documents for processing
• NLP processing (e.g., using bio-yodie to annotate umls concepts)
• index contextualised concepts into an elaticsearch instance
• do patient centric indexing to integrate all patient docs and annotations

To do the process, the easiest way is to 0. (only do this ONCE) initialise SemEHR index using the mapping file.

1. setup the database view from which SemEHR will pull documents from.
2. edit the process configuration file using this template.
3. run the script python semehr_processor.py PATH_TO_YOUR_CONFIGURATION

Useful Links

• sql server connection setup on linux

troubleshooting

• when you see no concepts indexed for patients, please double check the index mapping to make sure the mappings are correct as defined in the script.