Output visualization

Once running the pipeline is completed, the generated files are displayed in the Output folder. These files can be viewed in two different formats (.xmi , .txt):
Clicking on a file with the .xmi extension allows you to view its original content annotated with recognized clinical concepts. Different types of clinical concepts will be highlighted with different colors.

Clicking on a file with the .txt extension will display a view of tab delimited, detailed output information in a new window. As shown in the figure below, each line in the file illustrates the detailed information of one recognized clinical concept. The following information is included in a tab delimited output:

1. Start Index: Starting position of the recognized concept.
2. End Index: Ending position of the recognized concept.
3. Semantic Type: Semantic type of the recognized concept.
4. CUI: The Concept Unique Identifier of the concept in Unified Medical Language System (UMLS). If the pipeline does not include the model of UMLS encoder, the value of this column will be "null".
5. Assertion: If the pipeline does not include the model of Assertion identifier, the value of this column will be "null".
6. Concept Mention: Referring to a concept, i.e., named entity in the text