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Initial beta build for OMOP Waveform Extension ETL#65

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briangow wants to merge 4 commits into
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bg_waveform_extension_1
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Initial beta build for OMOP Waveform Extension ETL#65
briangow wants to merge 4 commits into
devfrom
bg_waveform_extension_1

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@briangow

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Overview
This PR introduces an initial (beta) build path for OMOP Waveform Extension ETL tables using pre-extracted waveform metadata inputs.

Context
The Python waveform metadata extraction process is currently maintained in a separate repository. Once that process is finalized, it may be incorporated into this repository.

Source metadata inputs
The ETL expects two source tables populated by the extraction script:

waveform_files_all
subject_id, person_id, hadm_id, visit_occurrence_id, visit_detail_id, location, waveform_folders, record_id, group_id, mimic_start, mimic_end, session_start, session_end, file_start, file_end, src_file, trg_file

waveform_channels_all
person_id, visit_occurrence_id, visit_detail_id, group_id, session_start, session_end, file_start, file_end, src_file, trg_file, channel_name, sample_units, sample_rate, sample_rate_units, gain, gain_units, segment_length

What this PR includes:

  • Adds initial SQL ETL build logic for OMOP Waveform Extension targets.
  • Uses waveform_files_all and waveform_channels_all as source metadata interfaces.
  • Applies waveform-specific concept mappings as part of the build. Some waveform-specific vocabulary content is currently supplied via the Tufts CVB repository, and additional terms/mappings will be added over time.

Scope and maturity
This PR establishes the initial/beta end-to-end waveform ETL framework and will be expanded and refined in subsequent updates.

Out of scope
This PR does not build the WAVEFORM_FEATURE table.

@odikia

odikia commented Jun 12, 2026

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@briangow , thanks for the work! will plan to review soon. Any firm deadlines I should be aware of? Should be well before next WG meeting, but just grounding in known milestones

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2 participants