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Building an end-to-end open source data platform for clinical data Alberto Labarga PyData London 2023

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https://github.com/bsc-health-data/pydatalondon23-modern-data-stack

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Telecommunications Engineer Working as Head of Health Data @BSC More than 20 years teaching open data - open source – open science

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Data is big

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My God, it’s full of data!

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Data is the new oil

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Modern data stack

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The modern data stack is one framework used to conceptualize how different data tools work together to allow a complete data journey.

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Modern Data Stack ● Infraestructure as code

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Modern Data Stack ● Infraestructure as code ● From Datawarehouse to Lakehouse

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Modern Data Stack ● Infraestructure as code ● From Datawarehouse to Lakehouse ● From ETL to ELT

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Modern Data Stack ● Infraestructure as code ● From Datawarehouse to Lakehouse ● From ETL to ELT ● Data governance and observability

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Modern Data Stack ● Infraestructure as code ● From Datawarehouse to Lakehouse ● From ETL to ELT ● Data governance and observability ● Self-service analytics

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Ingestion Storage Sources Trasformation Data analytics Orchestration Gobernance Data quality

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(Clinical) Data is complicated

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https://ohdsi.github.io/CommonDataModel/

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https://athena.ohdsi.org

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https://github.com/bsc-health-data/pydatalondon23-modern-data-stack

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What about Python?

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https://gitlab.com/meltano/sdk/-/tree/main/cookiecutter

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https://docs.getdbt.com/docs/building-a-dbt-project/building-models/python-models

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https://github.com/open-metadata/openmetadata-demo/blob/main/mlmodel-cicd/mlmodel_cicd.py

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https://github.com/open-metadata/openmetadata-demo/tree/main/custom-connector/

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FRIDAY SATURDAY

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Thanks!