User Tools

Site Tools


projects:workgroups:nlp-wg

This is an old revision of the document!


OHDSI Natural Language Processing Working Group

Objective

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.

Project Lead

Hua Xu

Project Co-leads

Jon Duke, Nigam Shah, Noemie Elhadad

Plan

  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

Participants

  • Hua Xu
  • 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
  • Anupama Gururaj
  • 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

Upcoming Meeting Dates

  • April 11th, 2018
  • May 9th, 2018
  • June 13th, 2018
  • July 11th, 2018
  • August 8th, 2018
  • September 12th, 2018
  • October 10th, 2018
  • November 14th, 2018
  • December 12th, 2018

Repository

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

Proposal for concepts detected by NLP

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

Start Date

August 2015

WG Agenda/Minutes/Recordings

Meetings

  Schedule: Second Wednesday of every month at 2pm Eastern Time 
  
  JULY MEETING IS CANCELLED

The next meeting will be on August 8th, 2018

  
  Call-in: 
  1) Dial +1 (571) 317-3122 (United States) 
     Please see below for international call-in numbers
  2) Enter conference ID: 707-196-421 
  Screen Sharing: [[https://global.gotomeeting.com/join/707196421]]
  More phone numbers
  * Australia : +61 2 8355 1039
  * Austria : +43 7 2088 2172
  * Belgium : +32 (0) 42 68 0180
  * Canada : +1 (647) 497-9379
  * Denmark : +45 89 88 05 39
  * Finland : +358 (0) 931 58 4588
  * France : +33 (0) 170 950 589
  * Germany : +49 (0) 692 5736 7301
  * Ireland : +353 (0) 15 360 757
  * Italy : +39 0 294 75 15 37
  * Netherlands : +31 (0) 108 080 116
  * New Zealand : +64 9 801 0294
  * Norway : +47 21 51 81 86
  * Spain : +34 911 23 4248
  * Sweden : +46 (0) 852 500 516
  * Switzerland : +41 (0) 435 0824 41
  * United Kingdom : +44 (0) 330 221 0099
projects/workgroups/nlp-wg.1531250882.txt.gz · Last modified: 2018/07/10 19:28 by anu_gururaj2