wiki:AnotacniManualEhr

Version 30 (modified by Ales Horak, 13 months ago) (diff)

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Medical text analysis

Annotation manual

The goal is to mark the occurrence of known medical entities or other important information in the text of health records. Please keep in mind that all health records you will be working with are confidential and must be used only within the annotation system.

You will familiarize yourself with the BRAT annotation tool. After (quite nonintuitive) logging in with the credentials assigned to you, you will be able to read through the assigned medical texts for annotation. Read the text and highlight the entities to be annotated, after which a pop-up will appear, letting you choose the category of the entity you highlighted. Some of the entities are automatically pre-annotated - check them and, if needed, update or delete them.

Within the pop-up, you will choose the category of the annotation and in the Notes field you will be able to enter or correct additional content relevant to the annotation (in the case of Abbreviations, you may correct the meaning of it).

You do not have to specify Confidence but if you are unsure if your annotation is correct, you can select the option "Confidence: Low".

Entities to be annotated

You can view a sample annotation here.

  • AnatomicalSite
    • names of body parts and locations on the body
    • every AnatomicalSite annotation is either of these two:
      • AnatomicalSite_name: the name itself, e.g.
        našla v pravém prsu bulku
      • AnatomicalSite_laterality: further specification of location, e.g. v
        našla v pravém prsu bulku
  • DiseaseDisorder
    • names of diseases and disorders, e.g.
      léčena xareltem inf mononukleoza v 15 letech
  • SignSymptom
    • medical occurrences which are not names of diseases and disorders but can indicate their presence or absence, e.g.
      při bolestech svalů, teplotě
      If unsure whether it is an official disorder name or only a symptom, annotate as SignSymptom.
  • Procedure
    • name of a procedure or process (diagnostic or therapeutic) carried out by medical personnel, e.g.
      benefit adjuvantní chemoterapie minimální
  • Medication
    • name of a drug or substance
    • every Medication annotation is either
      • Medication_name: the name of the product, e.g.
        adjuv HT - Tamoxifen od 6/2018 s ef
      • Medication_strength: the strength of the product, e.g.
        večer: Lexaurin 1,5 mg p.o. dle potřeby
      • Medication_dosage: an expression of recommended dosage, e.g.
        METAMIZOL STADA [TBL NOB] 500 mg / p.o. [při bolesti 1 tbl]
  • Lab
    • measurements related to the body, e.g. blood test values
    • every Lab annotation is either
      • Lab_name: the name of the measured aspect, e.g.
        S_Estradiol: 18 pmol/l, S_FSH: 3.8 IU/l
      • Lab_value: the value, mostly numeric, measured, e.g.
        S_Estradiol: 18 pmol/l, S_FSH: 3.8 IU/l
      • Lab_unit: the unit of measurement, e.g.
        S_Estradiol: 18 pmol/l, S_FSH: 3.8 IU/l
  • DateTime
    • any date or time-related information, e.g.
      HER2 negat, premenopauza, dg. 9/2020
  • Negation
    • words marking negation, e.g. something was not found, not proven, negative etc., e.g.
      adjuvantní radioterapie není indikována
  • Abbreviation
    • Acronym or shortened word, e.g.
      adjuvantní RT není indik.
      If you know the full form of the abbreviation, enter it into the Notes field. Do not annotate units (e.g. "cm") or "cca" as abbreviations.

You may consult our list of Czech medical abbreviations.

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