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Customize the data explorer app

In this tutorial, we are going to expose different ways to customize the Data Explorer app (demoed with the Quaero dataset in the previous tutorial:

  • Add new fields to the data model and display them in the UI.
  • Pre-annotate entities using EDS-NLP.
  • Annotate higher-level structures such as patients the notes are attached to

Prerequisites

Reuse the same environment you prepared in the Run Quaero Explorer tutorial and run the app in a notebook or as a standalone app.

Adding new fields

You control which attributes appear in the UI by editing the data you import and by listing those attributes in the table views. Check out the Table component documentation for more details about the types of attributes you can add.

Load the data

For example, add a note_type to notes and a negation field to entities.

notes = [
    {
        "note_id": doc._.note_id,
        "note_text": doc.text,
        # This is an example. Make sure that your data actually has this attribute
+       "note_type": doc._.note_type, #(1)!
    }
    for doc in data
]

entities = [
    {
        "id": f"#-{doc._.note_id}-{e.start_char}-{e.end_char}-{e.label_}",
        "note_id": doc._.note_id,
        "text": str(e),
        "begin": e.start_char,
        "end": e.end_char,
        "label": e.label_,
        "concept": e._.cui,
        # This is an example. Make sure that your data actually has this attribute
+       "negation": e._.negation, #(1)!
    }
    for doc in data
    for e in sorted(doc.spans["entities"])
]

Show these fields

Update the table/text renderers in the Build the views section to include the new attributes. Metanno will automatically detect that the negation attribute is boolean and will display it as a checkbox.

- first_columns=["note_id", "seen", "note_text"],
+ first_columns=["note_id", "seen", "note_type", "note_text"],
...
- editable_columns=["seen"],
+ editable_columns=["seen", "review_status"],

- first_columns=["id", "note_id", "text", "label", "concept", "begin", "end"],
+ first_columns=["id", "note_id", "text", "label", "concept", "begin", "end", "negation"],
...
- editable_columns=["label", "concept"],
+ editable_columns=["label", "concept", "source"],

Dropdown input

Add any new columns to categorical_columns if they should show a dropdown filter like the concept column.

Pre-annotation

TBD

Annotate higher-level structures

TBD