The primary goal of the NLP working group is to promote the use of textual information from Electronic Health Records (EHRs) for observational studies under the OHDSI umbrella. To facilitate this objective, the group will develop methods and software that can be implemented to utilize clinical text for studies by the OHDSI community.

Hua Xu

Jon Duke, Nigam Shah, Noemie Elhadad

1. IRB for use of clinical text
2. Clinical text data storage and representation schema
3. NLP tools/pipelines for ETL
4. Use cases, e.g, phenotyping for cohort selection using NLP outputs

1. Rules for defining term_exists – led by Stephane Meystre - COMPLETED
2. Mapping of CUIs to standard terminology – Juan Banda - COMPLETED - https://github.com/thepanacealab/OHDSIananke
3. Mapping of Note Types to LOINC/standard vocabulary –Karthik Natarajan, Ruth Reeves, Jon Duke and Hua Xu– Report type list discussion
4. Landscape Analysis of section identifier systems and proposal of a standard terminology for use – Hua Xu, Karthik Natarajan
5. Examples and rules for term_temporal – led by George Hripsack (Sunny)
6. Standardization of term_modifiers and values – Hua Xu

1. Mapping of Note Types to LOINC/standard vocabulary –Karthik Natarajan, Ruth Reeves, Jon Duke and Hua Xu– Report type list discussion
2. Landscape Analysis of section identifier systems and proposal of a standard terminology for use – Hua Xu, Karthik Natarajan
3. Examples and rules for term_temporal – led by George Hripsack (Sunny)
4. Standardization of term_modifiers and values – Hua Xu
5. Evaluate and revise textual CDM tables by sharing practical issues and lessons learnt during ETL for processing textual data into CDM, Usecases – Ruth Reeves,
6. Develop tools (within Atlas) to facilitate uses of NLP data for cohort building/phenotyping : Collaborate with eMERGE consortium:
7. Conduct cross-site studies that use textual data
8. Continue developing other NLP resources

• Hua Xu
• Anupama Gururaj
• Nigam Shah
• Noemie Elhadad
• Jon Duke
• Alexandre Yahi
• Thomas Ginter
• Olga Patterson
• George Hripsack
• Vojtech Huser
• Mark Khayter
• Karthik Natarajan
• Min Jiang
• Scott DuVall
• Abraham Hartzema
• David Sontag
• Arnab Bose
• Lian Hu
• Jan A Kors
• J van Der Lei
• Peter R Rijnbeek
• Vivienne Zhu
• Bob Patterson
• Michael Gurley
• Xiaoling Chen
• Hongfang Liu
• Hong Yu
• Stephane Meystre
• Timothy Miller
• Wendy Chapman
• Feifan Liu
• Paris Nicolas
• Mark Dredze
• Masoud Rouhizadeh
• Malcolm McRoberts
• Nishanth Parameshwar Pavinkurve
• Carol Friedman

• March 13th, 2019
• April 10th, 2019
• May 8th, 2019
• June 12th, 2019
• July 10th, 2019

• NLP Tools in OHDSI GitHub https://github.com/OHDSI/NLPTools
• OHDSIananke https://github.com/thepanacealab/OHDSIananke

create a new table called NOTE_NLP with the following columns

• note_id (integer) links to NOTE.note_id (foreign key)
• note_concept_id (integer) concept_id of a term found in the note
• certainty (real number 0-100) how certain is the NLP pipeline that this concept is present in the note
• offset position of where in the note was the concept detected
• span (integer) number of characters from offset where the concept was detected
• negation_flag (string of length 1 (or boolean)) indicates if the concept is negated

16ohdsi_nlp_schema_updated.pdf

https://docs.google.com/document/d/1ykYVJTQ5MuI7eh_Nk7xzt44EzNjVs71nq2LIsC_RlOg/edit

August 2015

1. WG_meeting_10072015
2. WG_meeting_11042015
3. WG_meeting_01062016
4. WG_meeting_02032016
5. WG_meeting_03092016
6. WG_meeting_04132016
7. WG_meeting_04202016
8. WG_meeting_06142017
9. WG_meeting_07122017
10. WG_meeting_09132017
11. WG_meeting_10112017
12. WG_meeting_12122017
13. WG_meeting_01102018
14. WG_meeting_02142018
15. WG_meeting_03142018
16. WG_meeting_04142018
17. WG_meeting_05092018
18. WG_meeting_06132018
19. WG_meeting_09122018
20. WG_meeting_11142018
21. WG_meeting_01092019
22. WG_meeting_02132019

  Schedule: Second Wednesday of every month at 2pm Eastern Time

THE DECEMBER MEETING IS CANCELLED

  
  The next meeting will be on March 13th, 2019
  
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    * May 8th
    * June 12th
    * July 10th
  
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