BY-COVID WP5 T5.2 Baseline Use Case

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BY-COVID WP5 T5.2 Baseline Use Case

@id ./
name [?] BY-COVID WP5 T5.2 Baseline Use Case
@type Dataset
description [?] This publication corresponds to the Research Objects (RO) of the Baseline Use Case proposed in T.5.2 (WP5) in the BY-COVID project on “COVID-19 Vaccine(s) effectiveness in preventing SARS-CoV-2 infection”.
funder [?] European Commission
datePublished [?] 2023-04-19
author [?]
conformsTo [?]
codeRepository [?] https://github.com/by-covid/BY-COVID_WP5_T5.2_baseline-use-case
hasPart [?]
distribution [?] https://github.com/by-covid/BY-COVID_WP5_T5.2_baseline-use-case/archive/refs/heads/main.zip
identifier [?] https://doi.org/10.5281/zenodo.6913045
cite-as [?] https://w3id.org/ro/doi/10.5281/zenodo.6913045
isBasedOn [?]
keywords [?] COVID-19, vaccines, comparative effectiveness, causal inference, international comparison, SARS-CoV-2, common data model, directed acyclic graph, synthetic data
license [?] Creative Commons Attribution 4.0 International
dateModified [?] 2023-10-05
publisher [?] BY-COVID
funding [?] HORIZON-INFRA-2021-EMERGENCY-01 101046203
mentions [?]
url [?] https://by-covid.github.io/BY-COVID_WP5_T5.2_baseline-use-case/
version [?] 1.2.0
assesses [?] Research Question: How effective have the SARS-CoV-2 vaccination programmes been in preventing SARS-CoV-2 infections?
material [?] Cohort definition: All individuals (from 5 to 115 years old, included) vaccinated with at least one dose of the SARS-CoV-2 vaccine (any of the available brands) and all individuals eligible to be vaccinated with a documented positive diagnosis (irrespective of the type of test) for a SARS-CoV-2 infection during the data extraction period.
materialExtent [?] Inclusion criteria: All people vaccinated with at least one dose of the COVID-19 vaccine (any of the available brands) in an area of residence. Any person eligible to be vaccinated (from 5 to 115 years old, included) with a positive diagnosis (irrespective of the type of test) for SARS-CoV-2 infection (COVID-19) during the period of data extraction. Exclusion criteria: People not eligible for the vaccine (from 0 to 4 years old, included)
publishingPrinciples [?] Study Design: An observational retrospective longitudinal study to assess the effectiveness of the SARS-CoV-2 vaccines in preventing SARS-CoV-2 infections using routinely collected social, health and care data from several countries. A causal model was established using Directed Acyclic Graphs (DAGs) to map domain knowledge, theories and assumptions about the causal relationship between exposure and outcome.
temporalCoverage [?] Study Period: From the date of the first documented SARS-CoV-2 infection in each country to the most recent date in which data is available at the time of analysis. Roughly from 01-03-2020 to 30-06-2022, depending on the country.
usageInfo [?] The scripts (software) included in the publication are offered "as-is", without warranty, and disclaiming liability for damages resulting from using it. The software is released under the CC-BY-4.0 licence, which gives you permission to use the content for almost any purpose (but does not grant you any trademark permissions), so long as you note the license and give credit.
releaseNotes [?] - Updated Causal model to eliminate the consideration of 'vaccination_schedule_cd' as a mediator - Adjusted the study period to be consistent with the Study Protocol - Updated 'sex_cd' as a required variable - Added 'chronic_liver_disease_bl' as a comorbidity at the individual level - Updated 'socecon_lvl_cd' at the area level as a recommended variable -Added crosswalks for the definition of 'chronic_liver_disease_bl' in a separate sheet -Updated the 'vaccination_schedule_cd' reference to the 'Vaccine' node in the updated DAG -Updated the description of the 'confirmed_case_dt' and 'previous_infection_dt' variables to clarify the definition and the need for a single registry per person
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about [?]


Go to: European Commission

@id https://ror.org/00k4n6c32
name [?] European Commission
@type Organization
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funder [?]


Go to: Francisco Estupiñán-Romero



Go to: Nina Van Goethem



Go to: Marjan Meurisse



Go to: Javier González-Galindo



Go to: Enrique Bernal-Delgado



Go to: Process Run Crate

@id https://w3id.org/ro/wfrun/process/0.1
name [?] Process Run Crate
@type CreativeWork
version [?] 0.1
Items that reference this one
conformsTo [?] BY-COVID WP5 T5.2 Baseline Use Case


Go to: Workflow Run Crate

@id https://w3id.org/ro/wfrun/workflow/0.1
name [?] Workflow Run Crate
@type CreativeWork
version [?] 0.1
Items that reference this one
conformsTo [?] BY-COVID WP5 T5.2 Baseline Use Case


Go to: Workflow RO-Crate

@id https://w3id.org/workflowhub/workflow-ro-crate/1.0
name [?] Workflow RO-Crate
@type CreativeWork
version [?] 1.0
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conformsTo [?]


BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment - Analytical pipeline

@id vaccine_effectiveness_analytical_pipeline/
name [?] BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment - Analytical pipeline
@type Dataset
description [?] Reproducable analytical pipeline to apply causal inference techniques using distributed observational data
datePublished [?] 2023-04-26
author [?]
version [?] 1.0.0
url [?] https://github.com/by-covid/BY-COVID_WP5_T5.2_baseline-use-case/tree/main/vaccine_effectiveness_analytical_pipeline
hasPart [?]
Items that reference this one
hasPart [?] BY-COVID WP5 T5.2 Baseline Use Case


⬇️ Download: BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment - Causal Model



COVID-19 vaccine(s) effectiveness assessment (synthetic dataset)

@id vaccine_effectiveness_common_data_model_specification/
name [?] COVID-19 vaccine(s) effectiveness assessment (synthetic dataset)
@type Dataset
description [?] Synthetic data set to test the causal model proposed by the baseline use case in BY-COVID WP5 assessing the effectiveness of the COVID-19 vaccine(s)
datePublished [?] 2023-01-26
version [?] 1.1.0
identifier [?] https://doi.org/10.5281/zenodo.6913045
url [?] https://zenodo.org/record/7572373
creator [?]
contributor [?]
distribution [?] vaccine_effectiveness_synthetic_pop_10k_v.1.1.0
hasPart [?]
keywords [?]
  • synthetic data
  • dataset
  • covid-19
  • vaccines
  • effectiveness
  • causal model
license [?] Creative Commons Attribution 4.0 International
mainEntity [?] Quarto script sourcing consecutive scripts of the analytical pipeline (QMD)
spatialCoverage [?] Europe
subjectOf [?] Metadata for Common data model specification
temporalCoverage [?] 01-01-2020/31-12-2024
variableMeasured [?]
  • person_id: undefined
  • age_nm: undefined
  • sex_cd: undefined
  • socecon_lvl_cd: undefined
  • residence_area_cd: undefined
  • country_cd: undefined
  • foreign_bl: undefined
  • exitus_dt: undefined
  • exitus_bl: undefined
  • essential_worker_bl: undefined
  • institutionalized_bl: undefined
  • dose_1_brand_cd: undefined
  • dose_1_dt: undefined
  • dose_2_brand_cd: undefined
  • dose_2_dt: undefined
  • dose_3_brand_cd: undefined
  • dose_3_dt: undefined
  • number_doses: undefined
  • fully_vaccinated_dt: undefined
  • fully_vaccinated_bl: undefined
  • vaccination_schedule_cd: undefined
  • confirmed_case_dt: undefined
  • confirmed_case_bl: undefined
  • previous_infection_dt: undefined
  • previous_infection_bl: undefined
  • test_type_cd: undefined
  • variant_cd: undefined
  • diabetes_bl: undefined
  • obesity_bl: undefined
  • heart_failure_bl: undefined
  • copd_bl: undefined
  • solid_tumor_without_metastasis_bl: undefined
  • chronic_kidney_disease_bl: undefined
  • sickle_cell_disease_bl: undefined
  • hypertension_bl: undefined
  • blood_cancer_bl: undefined
  • transplanted_bl: undefined
  • hiv_infection_bl: undefined
  • primary_immunodeficiency_bl: undefined
  • immunosuppression_bl: undefined
  • pregnancy_bl: undefined
Items that reference this one
hasPart [?]
about [?]
mainEntity [?] COVID-19 vaccine effectiveness data model specification dataspice (JSON)


BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment - Data Management Plan



BY-COVID - WP5 - Baseline Use Case: SARS-CoV-2 vaccine effectiveness assessment - Study protocol



Common data model specification



⬇️ Download: Diagram of analytical pipeline

@id analytical-pipeline.png
name [?] Diagram of analytical pipeline
@type
  • File
  • ImageObject
about [?] Quarto script sourcing consecutive scripts of the analytical pipeline (QMD)
Items that reference this one
hasPart [?] BY-COVID WP5 T5.2 Baseline Use Case
image [?] Quarto script sourcing consecutive scripts of the analytical pipeline (QMD)


⬇️ Download: Conceptual phases

@id conceptual-phase.png
name [?] Conceptual phases
@type
  • File
  • ImageObject
description [?] From Causal model, via a data model spec to generation of synthetic data
about [?]
Items that reference this one
hasPart [?] BY-COVID WP5 T5.2 Baseline Use Case


⬇️ Download: README.md

@id README.md
@type File
author [?]
encodingFormat [?] text/markdown
about [?] BY-COVID WP5 T5.2 Baseline Use Case
Items that reference this one
hasPart [?] BY-COVID WP5 T5.2 Baseline Use Case
object [?] RO-Crate metadata created based on README and dataspice JSON-LD


Go to: https://github.com/by-covid/BY-COVID_WP5_T5.2_baseline-use-case/archive/refs/heads/main.zip













Go to: Creative Commons Attribution 4.0 International

@id https://spdx.org/licenses/CC-BY-4.0
name [?] Creative Commons Attribution 4.0 International
@type Thing
identifier [?] CC-BY-4.0
url [?] https://creativecommons.org/licenses/by/4.0/
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license [?]


Go to: BY-COVID

@id https://by-covid.eu/
name [?] BY-COVID
@type Project
description [?] BeYond-COVID, make data from COVID-19 and other infectious diseases open and accessible to everyone
url [?] https://by-covid.eu/
funding [?] HORIZON-INFRA-2021-EMERGENCY-01 101046203
Items that reference this one
publisher [?] BY-COVID WP5 T5.2 Baseline Use Case


Go to: HORIZON-INFRA-2021-EMERGENCY-01 101046203

@id https://doi.org/10.3030/101046203
name [?] HORIZON-INFRA-2021-EMERGENCY-01 101046203
@type Grant
funder [?] European Commission
identifier [?] https://doi.org/10.3030/101046203
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funding [?]


Generating HTML from QMD

@id #qmd-generation
name [?] Generating HTML from QMD
@type CreateAction
endTime [?] 2022-07-27T12:00:00+01:00
instrument [?] Quarto
object [?] COVID-19 vaccine effectiveness causal model v.1.1.0 (QMD)
result [?] COVID-19 vaccine effectiveness causal model v.1.1.0 (HTML)
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mentions [?] BY-COVID WP5 T5.2 Baseline Use Case


Execution of pandas-profiling for exploratory data analysis

@id #panda-analysis
name [?] Execution of pandas-profiling for exploratory data analysis
@type CreateAction
endTime [?] 2022-05-27T09:52:32.926250
instrument [?] pandas-profiling v3.1.0
object [?]
result [?]
startTime [?] 2022-05-27T09:52:29.847284
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mentions [?] BY-COVID WP5 T5.2 Baseline Use Case


dataspice JSON-LD created from CSV templates



Second (?) execution of Jupyter Notebook to generate 650k synthetic dataset

@id #notebook-execution-650k
name [?] Second (?) execution of Jupyter Notebook to generate 650k synthetic dataset
@type CreateAction
description [?] Note that this CSV has only 650k entries, but the Notebook code is meant to crate 1M entries. A modified notebook must have been executed.
endTime [?] 2022-05-24
instrument [?] COVID-19 vaccine effectiveness synthetic dataset generation script (IPYNB)
result [?] Synthetic dataset with 650k entries
Items that reference this one
mentions [?] BY-COVID WP5 T5.2 Baseline Use Case


Execution of Jupyter Notebook to generate 10k synthetic dataset

@id #notebook-execution-1M
name [?] Execution of Jupyter Notebook to generate 10k synthetic dataset
@type CreateAction
endTime [?] 2022-05-24
instrument [?] COVID-19 vaccine effectiveness synthetic dataset generation script (IPYNB)
result [?] vaccine_effectiveness_synthetic_dataset/vaccines_effectiveness_synthetic_pop_10k_v.1.1.0.csv
Items that reference this one
mentions [?] BY-COVID WP5 T5.2 Baseline Use Case


RO-Crate metadata created based on README and dataspice JSON-LD

@id #metadata-creation
name [?] RO-Crate metadata created based on README and dataspice JSON-LD
@type CreateAction
actionStatus [?] http://schema.org/CompletedActionStatus
agent [?] Stian Soiland-Reyes
endTime [?] 2023-01-06
object [?]
result [?] ro-crate-metadata.json
Items that reference this one
mentions [?] BY-COVID WP5 T5.2 Baseline Use Case