Knowtator XML Files
-------------------

Some examples of how knowtator represents relations and entity categories in XML files will be shown below. 
Looking at these examples can be useful for understanding the code of the collection reader.

********** Entity and Entity Types **********

<annotations textSource="2290848406_2">

  ...

  <annotation>
    <mention id="Relations_Sept21_Schema_Instance_30340" />
    <annotator id="annotationSchemaMarch4_Instance_0">james masanz, mayo clinic</annotator>
    <span start="86" end="97" />
    <spannedText>sore throat</spannedText>
    <creationDate>Thu Oct 14 22:39:26 MDT 2010</creationDate>
  </annotation>
  <annotation>

  ...

  <classMention id="Relations_Sept21_Schema_Instance_30340">
    <mentionClass id="Sign_Symptom">Sign_Symptom</mentionClass>
    <hasSlotMention id="Relations_Sept21_Schema_Instance_30341" />
  </classMention>

  <stringSlotMention id="Relations_Sept21_Schema_Instance_30341">
    <mentionSlot id="cui" />
    <stringSlotMentionValue value="C0242429" />
  </stringSlotMention>

</annotations>


********** Relations **********

E.g. "soar throat" co_occurs_with "headache"

To find relations and their argument, need to find classMention(s)
that have two hasSlotMention(s), which in turn lead to the actual arguments.

  <annotation>
    <mention id="Relations_Sept21_Schema_Instance_30340" />
    <annotator id="annotationSchemaMarch4_Instance_0">james masanz, mayo clinic</annotator>
    <span start="86" end="97" />
    <spannedText>sore throat</spannedText>
    <creationDate>Thu Oct 14 22:39:26 MDT 2010</creationDate>
  </annotation>

  <annotation>
    <mention id="Relations_Sept21_Schema_Instance_30350" />
    <annotator id="annotationSchemaMarch4_Instance_0">james masanz, mayo clinic</annotator>
    <span start="102" end="110" />
    <spannedText>headache</spannedText>
    <creationDate>Thu Oct 14 22:39:28 MDT 2010</creationDate>
  </annotation>

  ...

  <annotation>
    <mention id="Relations_Sept21_Schema_Set02_Instance_70014" />
    <annotator id="Relations_Aug18_Schema_Instance_2">CU annotator ,</annotator>
    <creationDate>Wed Oct 27 21:45:39 MDT 2010</creationDate>
  </annotation>

  ...

  <classMention id="Relations_Sept21_Schema_Set02_Instance_70014">
    <mentionClass id="co_occurs_with">co_occurs_with</mentionClass>
    <hasSlotMention id="Relations_Sept21_Schema_Set02_Instance_90018" />
    <hasSlotMention id="Relations_Sept21_Schema_Set02_Instance_90020" />
  </classMention>  

  ...

  <complexSlotMention id="Relations_Sept21_Schema_Set02_Instance_90018">
    <mentionSlot id="Related_to" />
    <complexSlotMentionValue value="Relations_Sept21_Schema_Instance_30350" />
  </complexSlotMention>

  <complexSlotMention id="Relations_Sept21_Schema_Set02_Instance_90020">
    <mentionSlot id="Argument" />
    <complexSlotMentionValue value="Relations_Sept21_Schema_Instance_30340" />
  </complexSlotMention>


*******************************

In the example above, Relations_Sept21_Schema_Instance_30350 and
Relations_Sept21_Schema_Instance_30340 become relation arguments
 and the key of the relation index hash table (kid1-kid2).