Overview of Updated Instructions

  1. Use negation to indicate the opposite of something or failure.
  2. Label all IV or oral medicine names present.
  3. For hospital names, use "Geographic data (geografiske data)" from the Sensitive category (Sensitv).
  4. The following subcategories have been corrected:
  5. Missing subcategories are in red below.
    Click for update summary
    • Sign category (Tegn)
      • Itchy (Kløende)
      • Headache (Hodepine)
      • Dizziness (Svimmel)
      • Cognitive function (Kognitiv funksjon)
        • Confusion (Forvirring)
        • Psychosis (Psykose)
        • Emotional state (Følelsesmessige tilstand)
      • Trauma (Traume)
        • Bleeding (Blødning)
        • Injury (Skade)
      • Mobility impairment (Bevegelseshemming)
    • Procedure category (Prosedyre)
      • Catheter care (Kateter stell)
        • Insertion (Innleggelse)
        • Observation (Observasjon)
        • Rinse (Skylle)
        • Replace (Bytt)
        • Removal (Fjerning)
        • Discontinue (Seponert)
        • Self removal (Selvseponert)
  6. The entity attribute "Not related to catheters (Ikke relatert til kateter)" has been added to identify device parts not related to catheters.

Background

Of the 30 million patients who develop sepsis annually worldwide, over 5 million die. Sepsis a complex disease that can lead to tissue damage, organ failure, and death caused by a dysregulated host response to infection spread through the bloodstream. Bloodstream infections (BSIs) can enter the body through peripheral venous catheters (PVKs), which are the most commonly used invasive devices worldwide in hospitals. 80% of patients admitted to hospitals receive one or more PVKs.

Annotation is identifying and marking up text with labels to categorize different concepts. In addition to categorizing concepts, it is possible to link categories based on relationships. The annotated adverse event text samples from this study will be used to automatically identify risk factors and signs of PVK-related BSI to assist in preventing, identifying and treating sepsis.

Instructions

  1. Log on to BRAT with your provided username and password in a Chrome browser.

    Click for example

  2. Annotate Norwegian anonymous synthetic adverse event notes:

How to Annotate with BRAT

Using the Brat rapid annotation tool (BRAT) it is possible to:

  • Add and delete annotations for categories.
    Click for example
  • Provide additional attribute information in the "entity attributes" section if applicable.
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  • Add and delete relationships (Add relationships by clicking 1 label and dragging the arrow to another label; Delete by double clicking the relationship).
    Click for example
  • Include notes in annotations.
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General Annotation Rules

  1. Label all notes, even ones that seem irrelevant to PVK or sepsis.
    • We need to give the machine learning model good examples and bad examples so it can learn "what is pvk and sepsis relevant" vs "what is not relevant".
  2. Only annotate what is explicitly in the text, do not annotate inferences or speculations.
  3. Label each word or phrase with only 1 label.
    Click for example
    • Incorrect
    • Correct
  4. Include nearby words that describe the labels and add 'entity attributes' to give additional label information whenever possible.
    Click for example
  5. Annotate a category or subcategory each time it is mentioned.
  6. If a subcategory cannot be specified, chose the most general category level that describes the term or phrase.
  7. Provide additional category information from the drop-down selection when possible.
  8. Add "negation" to "entity attribute" if "it is not" a sign, location, device, or procedure.
    Click for example
  9. Link relationships between categories when possible to assist the machine in learning what the label is referring to: