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Add legends to show Disease and Chemical as Annotation #54

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@Leolty Leolty commented Jul 21, 2022

This PR fixes #53.

Description of changes

This PR makes the following 4 main changes:

  1. add new ontology Disease and Chemical ( as annotation)
  2. add a new processor to label Disease and Chemical NER
  3. add the test file to test the processor
  4. add a example where you can use streamlit as search engine to link to Stave, and show Disease and Chemical annotations

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codecov bot commented Jul 22, 2022

Codecov Report

Merging #54 (a8494cf) into master (867b854) will increase coverage by 0.87%.
The diff coverage is 90.10%.

@@            Coverage Diff             @@
##           master      #54      +/-   ##
==========================================
+ Coverage   84.17%   85.04%   +0.87%     
==========================================
  Files           9       10       +1     
  Lines         512      602      +90     
==========================================
+ Hits          431      512      +81     
- Misses         81       90       +9     
Impacted Files Coverage Δ
fortex/health/processors/ner_label_processor.py 83.63% <83.63%> (ø)
ftx/medical/clinical_ontology.py 69.06% <100.00%> (+1.08%) ⬆️
...rtex/health/processors/ner_label_processor_test.py 100.00% <100.00%> (ø)

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fortex/health/processors/ner_label_processor.py Outdated Show resolved Hide resolved
fortex/health/processors/ner_label_processor.py Outdated Show resolved Hide resolved
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examples/label_example/search_utils.py Outdated Show resolved Hide resolved
@@ -0,0 +1,57 @@
'''
this file defines search functions for searching data in elasticsearch.
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Any specific reason why we aren't using LastUtteranceSearcher processor to search through elastic search and return the links for documents?

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Here is what I think:

We create a search engine by streamlit, and I think it is a simple and easy way to wrap the search into method and when the user clicks "Query", this method is called directly to query and then displayed the results on the interface

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I feel its just redundant if we already have this functionality implemented in our processors and we still write another method to achieve the same thing, but it could be simpler and hence could be used for just the demo. You should confirm this with hector once. @hunterhector

examples/label_example/search_engine.py Outdated Show resolved Hide resolved
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Update the legends in Stave to show Disease, Medical, etc.
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