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Annotation Project Creation and Management

MedCATtrainer supports two management surfaces:

  • Project Admin UI (/project-admin) for most project operations.
  • Django Admin (/admin) for advanced actions and low-level data management.

Create a project (Project Admin UI)

  1. Open /project-admin.
  2. Go to the Projects tab and select Create New Project.
  3. Fill in:
    • Basic information (name, dataset, description, guideline link)
    • Model configuration
    • Annotation settings
    • Concept filter (optional)
    • Members
  4. Save.

Model configuration options

Pick exactly one of:

  1. Model Pack (recommended), or
  2. Concept DB + Vocabulary pair.

You may also enable:

  • Remote model service (use_model_service) and provide model_service_url.

Notes:

  • Remote model service projects do not support interim train-on-submit updates.
  • You cannot set Model Pack and CDB/Vocab at the same time.

Key project settings

Setting Description
require_entity_validation If enabled, model suggestions must be explicitly reviewed before submit.
train_model_on_submit If enabled, validated annotations are used for incremental training on submit.
add_new_entities Allows users to add brand-new concepts.
restrict_concept_lookup Restricts concept search to project CUI filters.
terminate_available Shows terminate action in annotation toolbar.
irrelevant_available Shows irrelevant action in annotation toolbar.
enable_entity_annotation_comments Enables free-text comments per annotation.
tasks Meta annotation tasks available in the annotator UI.
relations Relation labels available for relation annotation.
project_locked Locks project from further annotation edits.
project_status Annotating / Complete / Discontinued.

Dataset format

Upload CSV or XLSX with at least:

name text
unique-doc-id document text to annotate

name should be unique per dataset.

Project list operations

From the home Projects table:

  • Open and annotate a project.
  • Run document preparation in the background.
  • View model-loaded state and clear model cache.
  • Save current model state.
  • Select compatible projects and submit a metrics report.

Concept lookup index (Solr import)

Concept picker search requires CDB concepts to be imported into Solr.

  1. Open /admin.
  2. Go to Concept Dbs.
  3. Select one or more CDBs.
  4. Run Import concepts action.

After import, project list shows whether concepts are indexed for the selected cdb_search_filter.

Clone, reset, and delete

In Project Admin UI

  • Clone: duplicate project configuration under a new name.
  • Reset: remove annotations and clear prepared/validated document state.
  • Delete: permanently remove the project.

In Django Admin

Equivalent bulk actions are available under Project annotate entities.

Downloading annotations

From Django admin (/admin -> Project annotate entities), use bulk actions to export annotations:

  • with source text
  • without source text
  • without source text but with document names

Notebook examples for downstream processing are in:

  • notebook_docs/Processing_Annotations.ipynb

Saving and downloading model artifacts

For online-learning projects, admins can save current model state from the project list. In general, offline retraining from exported annotations is still recommended for production model releases.