= Medical text analysis =
== Annotation manual ==

[[Image(ehr-image.png,width=35%,right)]]

The goal is to mark the occurrence of known medical entities or other important information in the text of health records.

You will familiarize yourself with the BRAT annotation tool. After logging in with credentials assigned to you, you will be able to highlight the entities to be annotated, after which a pop-up will appear, letting you choose the category of the entity you highlighted.

=== Entities to be annotated ===

{{{#!html
<style>
pre.wiki span { background-color: lightgreen }
span.ent { 
    background-color: lightgreen;
    border: 1px solid;
    border-radius: 5px;
    padding: 1px;
    display: inline;
}
</style>
}}}

* !AnatomicalSite
  * names of body parts and locations on the body
  * every !AnatomicalSite annotation is either of these two: 
    * [[span(AnatomicalSite_name, class=ent)]]: the name itself, e.g. 
{{{#!html 
<pre class="wiki">našla v pravém <span>prsu</span> bulku</pre>
}}}
    * [[span(AnatomicalSite_laterality, class=ent)]]: further specification of location, e.g. "našla v **pravém** prsu bulku"
* [[span(!DiseaseDisorder, class=ent)]]
  * names of diseases and disorders, e.g. "léčena xareltem **inf mononukleoza** v 15 letech"
* [[span(!SignSymptom, class=ent)]]
  * 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 symptom.
* [[span(Procedure, class=ent)]] 
  * name of a procedure or process (diagnostic or therapeutic) carried out by medical personnel, e.g. "benefit **adjuvantní chemoterapie** minimální" [[Image(typesystem.png,width=35%,right)]]
* Medication
  * name of a drug or substance
  * every Medication annotation is either
    * [[span(Medication_name, class=ent)]]: the name of the product, e.g. "adjuv HT - **Tamoxifen** od 6/2018 s ef"
    * [[span(Medication_strength, class=ent)]]: the strength of the product, e.g. "večer: Lexaurin **1,5 mg** p.o. dle potřeby"
    * [[span(Medication_dosage, class=ent)]]: 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
    * [[span(Lab_name, class=ent)]]: the name of the measured aspect, e.g. "**S_Estradiol**: 18 pmol/l, **S_FSH**: 3.8 IU/l" 
    * [[span(Lab_value, class=ent)]]: the value, mostly numeric, measured, e.g. " S_Estradiol: **18** pmol/l, S_FSH: **3.8** IU/l"
    * [[span(Lab_unit, class=ent)]]: the unit of measurement, e.g. " S_Estradiol: 18 **pmol/l**, S_FSH: 3.8 **IU/l**"
* [[span(!DateTime, class=ent)]]
  * any date or time-related information, e.g. "HER2 negat, premenopauza, dg. **9/2020**"
* [[span(Negation, class=ent)]]
  * words marking negation, e.g. something was not found, not proven, negative etc., e.g. "adjuvantní radioterapie **není** indikována"