Meeting Notes - Analyticsphere/ehr-pipeline-documentation GitHub Wiki

11/21/24 Kick-off meeting with Eddy

  • Attendies: EF, JP
  • JP gave EF access to Analyticsphere GitHub organization
  • JP initiated IAM process for EF to access BigQuery
  • Discussed current EHR resources and scripts for using OHDSI packages with Connect data
  • Discussed 5 steps for EHR ingestion from GCS to BQ- documented here
  • Set up Wiki
  • Discussed GH Issues and Project (kanban) for project management- GH project linked here
  • Action Items
    • Follow up on GCP access
    • EF to set up RStudio, rJava, jdbc drivers, etc

. . .

07/01/24 Kick-off

  • Attendees: NG, JP, RS, SM
  • NG discussed EHR WG presentation
  • Action items from NG:
    • Determine number of records per participant for each table
    • Identify concepts in data relavent to cervical cancer

07/03/24

  • Antendees: JP, RS, SM
  • Discussed initial README.md and documentation strategy
  • Discussed OHDSI software tools that map to each of our objectives
  • Action items:
    • everyone: Familiarize ourselves with the CDM/OHDSI documentation and tools.
    • RS: #1 Add Connect_ID's to all CDM tables from HP [DONE]
    • MS:
      • #2 Generate counts of records per person for each table. [DONE]
      • Make histogram. [DONE]
    • JP: #3 Get generate_ares_data.R up and running with our BigQuery data.

07/09/24

  • Antendees: JP, RS, SM
  • Recapped progress from 4/3
    • RS:
      • added Connect_ID to each CDM table, saved well-documented query. Suggested formalizing progress with scheduled query when loading data.
      • RS noted that the death table has individuals that lack a Connect_ID in the death table
      • Need to confirm that identify which individuals lack Connect_ID's and confirm that those with Connect_ID's are consented, etc. #4
    • SM:
      • Connected to BQ from R (after much permissioning/authentication troubleshooting).
      • Generated histograms of record counts per participant for each table.
    • JP:
      • Demonstrated ATLAS
      • Discussed successes/troubles with DatabaseConnector
      • Discussed codes for cervical screenings and results detailed in tables above
  • Action Items:
    • RS: Check if the Cervical screening concepts are in HP EHR data set. [DONE]
    • SM:
      • Meet with Rebecca [DONE]
      • Generate PDF with histograms for each table. #2 [DONE]
    • JP:
      • Determine why DatabaseConnector doesn't point to a specific project [DONE]
      • Continue working on getting ACHILLES, DQD, ARES and ATLAS running [ONGOING]

07/24/24

  • Attendees: JP, RS, SM
  • Soyoun shared her poster. JP & RS to provide feedback this week.
  • JP gave update on new table delivery from HealthPartners
    • CONNECT_ID now populated. Same as PERSON_ID.
    • SOURCE_CONCEPT_VALUE is a useful field condition_occurance table
  • Discussed Book of OHDSI documentation on CDM.
  • Action:
    • JP, RS to review soyoun's poster
    • SM to complete poster & read Book of OHDSI documentation on the CDM.
      • Try to understand how concept hierarchy is organized.
    • RS to look up OMOP concepts for Cervical Screenings etc. given new OMOP codes.
    • RS to explore the Cohort construction and evaluation section HADES R packages
      • JP specifically interested in:
        • PhenotypeLibrary for exploring existing cohort definitions
        • Capr for defining new cohorts or concept sets.
    • JP run Achilles and DQD with a test (Eunomia) as Proof-of-Concept