= Medical text analysis =
== Annotation manual ==

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[[Image(bratann.png,width=20%,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 (quite nonintuitive) [BratManual logging in] with the 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.

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 ===

{{{#!html
<style>
pre.wiki span { background-color: lightblue }
span.ent { 
    background-color: lightgreen;
    border: 1px solid;
    border-radius: 5px;
    padding: 0px 1px 1px 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. v
{{{#!html 
<pre class="wiki">našla v <span>pravém</span> prsu bulku</pre>
}}}
* [[span(!DiseaseDisorder, class=ent)]]
  * names of diseases and disorders, e.g. 
{{{#!html 
<pre class="wiki">léčena xareltem <span>inf mononukleoza</span> v 15 letech</pre>
}}}
* [[span(!SignSymptom, class=ent)]]
  * medical occurrences which are not names of diseases and disorders but can indicate their presence or absence, e.g. 
{{{#!html 
<pre class="wiki">při <span>bolestech svalů</span>, <span>teplotě</span></pre>
}}}
    If unsure whether it is an official ''disorder name'' or only a ''symptom'', annotate as [[span(!SignSymptom, class=ent)]].
* [[span(Procedure, class=ent)]] 
  * name of a procedure or process (diagnostic or therapeutic) carried out by medical personnel, e.g. 
{{{#!html 
<pre class="wiki">benefit <span>adjuvantní chemoterapie</span> minimální</pre>
}}}
* Medication
  * name of a drug or substance
  * every Medication annotation is either
    * [[span(Medication_name, class=ent)]]: the name of the product, e.g. 
{{{#!html 
<pre class="wiki">adjuv HT - <span>Tamoxifen</span> od 6/2018 s ef</pre>
}}}
    * [[span(Medication_strength, class=ent)]]: the strength of the product, e.g. 
{{{#!html 
<pre class="wiki">večer: Lexaurin <span>1,5 mg</span> p.o. dle potřeby</pre>
}}}
    * [[span(Medication_dosage, class=ent)]]: an expression of recommended dosage, e.g. 
{{{#!html 
<pre class="wiki">METAMIZOL STADA [TBL NOB] 500 mg / p.o. [<span>při bolesti 1 tbl</span>]</pre>
}}}
* 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.
{{{#!html 
<pre class="wiki"><span>S_Estradiol</span>: 18 pmol/l, <span>S_FSH</span>: 3.8 IU/l</pre>
}}} 
    * [[span(Lab_value, class=ent)]]: the value, mostly numeric, measured, e.g. 
{{{#!html 
<pre class="wiki">S_Estradiol: <span>18</span> pmol/l, S_FSH: <span>3.8</span> IU/l</pre>
}}}
    * [[span(Lab_unit, class=ent)]]: the unit of measurement, e.g. 
{{{#!html 
<pre class="wiki">S_Estradiol: 18 <span>pmol/l</span>, S_FSH: 3.8 <span>IU/l</span></pre>
}}}
* [[span(!DateTime, class=ent)]]
  * any date or time-related information, e.g. 
{{{#!html 
<pre class="wiki">HER2 negat, premenopauza, dg. <span>9/2020</span></pre>
}}}
* [[span(Negation, class=ent)]]
  * words marking negation, e.g. something was not found, not proven, negative etc., e.g. 
{{{#!html 
<pre class="wiki">adjuvantní radioterapie <span>není</span> indikována</pre>
}}}
* [[span(Abbreviation, class=ent)]]
  * Acronym or shortened word, e.g. 
{{{#!html 
<pre class="wiki">adjuvantní <span>RT</span> není <span>indik.</span></pre>
}}}
   If you know the full form of the abbreviation, enter it into the Notes field.

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