vocab-pop

OHDSI Vocabulary / Population Browser

• overall goals:
  • make individual OHDSI vocabularies more approachable
  • facilitate understanding of OHDSI's vocabularies and concepts, relationships between them, and their prevelance in a specific CDM
  • facilitate translation from individual source concepts for cohort or phenotype definition and for ETL work
  • facilitate development or translation of concept sets
  • provide tools and interface for classification/granularity selection in other contexts (e.g., patient profiles)
  • towards these ends:
    • develop detailed requirements, designs, and prototypes
    • implement in ATLAS if and when resources are available
• use cases:
  • define a cohort or phenotype (needed by ATLAS users):
    • translate existing phenotype definition (e.g., set of ICD-9 codes for some condition) from a source vocabulary into a target vocabulary
  • explore the whole set of OHDSI vocabularies:
    • needed in Athena
    • to improve and debug the vocabularies
    • in general
    • only for concepts in user's CDM
    • for a specific domain:
      • e.g., provider specialty, show record counts for all values including zero counts for specialties not used; maybe also show corresponding source values and source values that weren't able to be mapped to a target. (provider.specialty_concept_id, provider.specialty_source_value, provider.specialty_source_concept_id, care_site.specialty_concept_id, care_site.specialty_source_value)
    • to better understand relationships between source and target domains
    • to better understand classifications available
  • source(s) to target(s):
    • find mapped or matching codes, classification or standard
    • in target code(s) selected, see which source codes are added or left out and counts of corresponding patient records
  • find a concept:
    • have immediate feedback on CDM records with concept
    • see relationships to other concepts and be encouraged to assure one has chosen correctly
  • explore my popupaltion:
    • overall
    • in terms of some domain
    • defining a subpopulation (same as 1)
    • intersecion of subpopulations
  • Patrick's SNOMED navigation strategy:
    • using related concepts filter on Class, choose Has ancestor of from Relationship facet, filter on Distance facet
  • compare vocabulary version as per (http://forums.ohdsi.org/t/new-vocabulary-population-visualization-working-group/2187/17?u=sigfried_gold)[Peter's post]
• notes and to-dos:
  • other systems to get ideas from:
    • http://outins.com/
    • http://jigsaw.io/
    • http://www.ephir.com/
    • http://www.aviz.fr/Research/Nodetrix
  • javascript libraries to consider using:
    • https://www.golden-layout.com/examples/
  • to-dos:
    • integrate ERD maybe:
      • http://www.ohdsi.org/web/wiki/lib/exe/fetch.php?media=documentation:omop_cdm_v5_erd.pdf
    • source record count:
      • show these as existing in cdm but not available through query
      • also show ancestor concepts with their descendant record counts
      • only show classification concepts that have a descendant record count
    • default to showing 4 main domains (condition, drug, procedure, measurement)