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NOTE_NLP

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README.md
README.md
 
 
check_etl.sql
check_etl.sql
 
 
etl.sql
etl.sql
 
 
extract_section.sql
extract_section.sql
 
 
load.sql
load.sql
 
 
nlp.md
nlp.md
 
 
section_list.csv
section_list.csv
 
 

README.md

Link to CommonDataModel

  • NOTE_NLP

  • is a contribution table

  • note_id is a foreign key to note table

Source Tables (mimic)

noteevents

  • sections have not been yet mapped to a standard terminology. CDO (standard from loinc) recently gave up (see #13)
  • extracted section covers automatically extracted section that present at least 1% in the notes
  • the resulting section have been manualy mapped together by Ivan Lerner (section_concept_id)
  • the detailed level is left into section_source_concept_id
  • notes in error in mimic were note extracted

Examples

explanation of section_source_concept_id

SELECT concept_name, section_source_concept_id, count(1)
FROM note_nlp
JOIN concept ON section_source_concept_id = concept_id
GROUP by 1, 2 ORDER BY 3 desc LIMIT 20;
concept_name section_source_concept_id count
Heart rhythm: 2001067175 9958
Respiratory / Chest: 2001067198 5440
Cardiovascular: 2001067189 4498
No particular Section 2001066541 4446
IVF: 2001067188 3924
HISTORY: 2001067383 3920
Abdominal: 2001067200 3816
IMPRESSION: 2001067379 3710
Neurologic: 2001067185 3555
Allergies: 2001067155 3519
Drains: 2001067165 3112
Peripheral Vascular: 2001067207 2788
Lines: 2001067183 2752
HPI: 2001067197 2520
Disposition: 2001067187 2448
RUL Lung Sounds: 2001067547 2380
LLL Lung Sounds: 2001067548 2380
LUL Lung Sounds: 2001067546 2380
RLL Lung Sounds: 2001067549 2380
BP: 2001067168 2334

how to access to one section

-- the 5 first section
SELECT lexical_variant
FROM note_nlp
WHERE section_source_concept_id = 2001067155                      -- concept.concept_name = 'Allergies'
limit 5 ;
lexical_variant
Allergies:
Penicillins
Unknown;
Allergies:
Penicillins
Unknown;
Allergies:
Penicillins
Unknown;
Allergies:
Penicillins
Unknown;
Allergies:
Penicillins
Unknown;