Table of Contents

Minutes_Meeting_01062016

Attendees

Hua Xu, Jon Duke, George Hripcsak, Karthik Natarajan, Anupama Gururaj, Mark Khayter, Min Jiang, Don Torok, Alexandre Yahi, Andrew Williams

Agenda

  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
  5. Discussion

Minutes

  1. General IRB document for use of clinical text and approval from all contributors, post online - Almost completed
  2. Collect minimum set of modifiers for all clinical entities that support use of rule to derive clinical concepts: Alex
    • cTAKES is being run on clinical notes programmatically. Alex will present the minimal model in the next meeting.
  3. Aggregate and share note-type metadata from various sources: Karthik
    • LOINC note type mapping would be a very useful resource. We should generate hierarchical representation of note-types as an ontology. Karthik will present his work to date at the next meeting.
    • Existing ontology for note types to be shared : Vanderbilt (Hua) and Regenstrief (Jon)
  4. Simple search set up for MT samples: MinPresentation
    • Presentation clinical_text_search_engine_01_06.pdf
    • The interface being developed should present a summary with visualization for patients/notes.
    • We will add Boolean query options to improve the search
    • We will implement a Ranking algorithm
    • Assign fake patient ID's to the notes to generate the visualization portion.
    • Generate a program like Circe to define the patient cohort
    • Next steps: How to move the data from textual searches stored in a table outside of OMOP to the OMOP?
      • Structured searches from CDW and textual searches can be combined using existing strategies. Jon will share the slides of his presentation on combining data from different searches
      • Run NLP on the ElasticSearch to extract information
  5. Wrappers for cTAKES and Metamap
  6. Report on the WG - Hua will generate and share with the members for comments
  7. The best ways to represent textual data need to be determined

Action Items

  1. Minimal Model Presentation - Alex
  2. Note-type mapping Presentation - Karthink
  3. Share existing ontologies from Vanderbilt (Hua) and Regenstrief (Jon)
  4. Share strategies for combining data from different searches - Jon
  5. Report on WG for commenting - Hua
  6. Wrappers for cTAKES and Metamap - Min
  7. Improvements to search engine set up using MT samples - Min
  8. Textual Data Representation - Discussion