Observational Health Data Sciences and Informatics

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Please find the slides from the meeting below:

{{ :projects:workgroups:nlp_wg_meeting_20190109_v2.pdf |}}

Please find the recording of the meeting below:

{{ :projects:workgroups:2019-01-09_13.07_ohdsi-nlp-wg.mp4 |}}

====== Action items updates: ======

===== 2018 Summary =====
  * Delivered NLP Tools (https://github.com/OHDSI/NLPTools)
  * Wrappers for converting existing NLP systems (MetaMap, cTAKES, CLAMP) outputs to CDM NLP tables
  * Mapping of CUIs to standard terminology in CDM
  * Other ongoing projects
  * Mapping of Note Types to LOINC/standard vocabulary 
  * Landscape Analysis of section identifier systems and proposal of a standard terminology for use 
  * Extension and standardization of concept-modifiers from NLP systems

===== 2019 Aims =====
  * Evaluate and revise textual CDM tables by sharing practical issues and lessons learnt during ETL for processing textual data into CDM
  * Develop tools (within Atlas) to facilitate uses of NLP data for cohort building/phenotyping 
      - Collaborate with eMERGE consortium: 
          - Presentation by Yuan Luo on March 13th, 2019
  * Conduct cross-site studies that use textual data
  * Continue developing other NLP resources

===== Ongoing Projects =====
  * Mapping of Note Types to LOINC/standard vocabulary – Karthik Natarajan, Ruth Reeves, and Jon Duke 
    - Karthik hopes to start working on this again, last progress was an evaluation against rule based system with Med (naive Bayes approach)
    - Notes shared with Jon, loaded report names and generated n-grams, need to be tagged per ideas for mapping, Karthik to find somebody to tag/annotate, not accounting yet for linking them back to OMOP vocabulary, note-type needs to be standardized, the LOINC document ontology and Radlax are flattened here, both Note_type and Note_class are present, needs to be reviewed, leverage Jon's tool here
  * Landscape Analysis of section identifier systems and proposal of a standard terminology for use – Hua Xu and Karthik Natarajan 
    - use SecTagger?, no other updates, Mitre has a tool called Zoner, need to review current Section Header tools, Stephane will share the terminology he has
  * Mapping of CUIs to standard terminology – Juan Banda, need to add link to Juan's repo in the OHDSI NLP repo
  * Standardization of term_modifiers and values – Hua Xu

===== Presentation =====
==== Enterprise NLP needs ====
  * Fast deployment of NLP solutions through
  - Task scheduling 
  - Resource management (distributed, scalable)
  * Visual Analytics
  - Search NLP outputs
  - Extract information for research – phenotyping  
  * Enhanced security
   - Multi-user
   - Configurable
  * Demo by Ergin Soysal
Observational Health Data Sciences and Informatics

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