First draft of dietician notes extraction schema

[caufieldjh]

No description provided.

[caufieldjh]

Running this:

$ ontogpt pubmed-annotate -t dietician_notes -m gpt-4-1106-preview -o diet_notes_test.yaml -O yaml --limit 1 "37736457"

has this output:

---
input_text: |-
  Title: Exploring Celiac Disease: A Case Analysis of Multi-Systemic Symptoms and Effective Dietary Intervention in a Young Female.
  Keywords: celiac disease (cd); dermatitis herpetiformis; intraepithelial lymphocytes; iron deficiency anemia (ida); ttg-iga antibodies
  PMID: 37736457
  Abstract: This study presents the case of a 23-year-old woman diagnosed with celiac disease (CD), a condition triggered by an immune response to gluten, leading to inflammation in the small intestine. The patient manifested typical gastrointestinal symptoms, including diarrhea, abdominal pain, and vomiting, complemented by extra-intestinal signs such as fatigue and skin rashes. Diagnosis was corroborated through the presence of tTG-IgA antibodies and distinct histological changes in the duodenum. A notable finding was the patient's iron deficiency anemia, directly linked to the duodenal damage caused by CD. Effective management, encompassing a strict gluten-free diet and iron supplementation, resulted in marked improvement in her condition. This case accentuates the significance of early CD detection, especially in patients exhibiting a combination of gastrointestinal and extra-intestinal symptoms. Emphasis is placed on the pivotal role of timely diagnosis, adherence to a gluten-free regimen, and sustained monitoring to ensure patient well-being and prevent complications.Copyright © 2023, Ahmed et al.
raw_completion_output: 'observations: celiac disease; dermatitis herpetiformis; intraepithelial
  lymphocytes; iron deficiency anemia; ttg-iga antibodies'
prompt: |+
  From the text below, extract the following entities in the following format:

  observations: <semicolon-separated list of observationss>


  Text:
  Title: Exploring Celiac Disease: A Case Analysis of Multi-Systemic Symptoms and Effective Dietary Intervention in a Young Female.
  Keywords: celiac disease (cd); dermatitis herpetiformis; intraepithelial lymphocytes; iron deficiency anemia (ida); ttg-iga antibodies
  PMID: 37736457
  Abstract: This study presents the case of a 23-year-old woman diagnosed with celiac disease (CD), a condition triggered by an immune response to gluten, leading to inflammation in the small intestine. The patient manifested typical gastrointestinal symptoms, including diarrhea, abdominal pain, and vomiting, complemented by extra-intestinal signs such as fatigue and skin rashes. Diagnosis was corroborated through the presence of tTG-IgA antibodies and distinct histological changes in the duodenum. A notable finding was the patient's iron deficiency anemia, directly linked to the duodenal damage caused by CD. Effective management, encompassing a strict gluten-free diet and iron supplementation, resulted in marked improvement in her condition. This case accentuates the significance of early CD detection, especially in patients exhibiting a combination of gastrointestinal and extra-intestinal symptoms. Emphasis is placed on the pivotal role of timely diagnosis, adherence to a gluten-free regimen, and sustained monitoring to ensure patient well-being and prevent complications.Copyright © 2023, Ahmed et al.

  ===

extracted_object:
  observations:
    - celiac disease
    - dermatitis herpetiformis
    - intraepithelial lymphocytes
    - iron deficiency anemia
    - ttg-iga antibodies

So the container object isn't being parsed as expected.

[caufieldjh]

Will need slot descriptions before this works properly anyway

[caufieldjh]

This breaks when patient height and weight aren't provided because the resulting None-like values won't validate.

[caufieldjh]

Synthetic notes for testing this schema are here: https://github.com/monarch-initiative/ontogpt-experiments/tree/main/experiments/dietician/synthetic_notes

[caufieldjh]

This will still need some more tuning but it works for now.