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Update tools.md - prettier and added a link
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howff authored Feb 15, 2024
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## Anonymise a directory of text documents

This is optional for the example because there's nothing to anonymise in these documents, but
```
export SMI_LOGS_ROOT=.
export PYTHONPATH=/path/to/Smi_Common_Python # if SmiServices is not yet in your virtualenv
./semehr_anon.py -i input_dir -o anon_dir --xml
```

## Run SemEHR on the sample document to get the semehr_results

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Note: all tables, indexes and functions reside in the `semehr` schema of the `semehr` database.

For full details see the [annotation database document](annotation_database.md)

## Table: cui_count

The `cui_count` table contains a record of the frequency of each CUI,
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