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