Generating reproducible workflows for the publication of open and FAIR data

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12 December 2019, Brussels Peter Desmet & Lien Reyserhove Generating repeatable workflows for the publication of open and FAIR data

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Hi!

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Research data management

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Open data publication

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Research software development

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No content

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We want to study (invasive) alien species to inform/guide environmental policy

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Reporting on invasive alien species

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•  What species? •  Where are they? •  How are they getting here? •  What is their impact? •  Future distributions? •  Future impact? Alien species in Belgium

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What species are alien in Belgium?

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Let’s check the Alien species checklist for Belgium

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We don’t have one! And certainly not one that is verified, open and FAIR

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We do have A number of authoritative checklist with a more specialized scope

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Data for alien plants

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Data for alien plants

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Open & FAIR? Checklist Open Findable Accessible Inter- operable Reusable

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Data for alien molluscs

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Open & FAIR? Checklist Open Findable Accessible Inter- operable Reusable

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Checklist Open Findable Accessible Inter- operable Reusable How to go from …

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Checklist Open Findable Accessible Inter- operable Reusable … to open & FAIR data?

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Checklist Open Findable Accessible Inter- operable Reusable … to open & FAIR data? Unified

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TrIAS data publication workflow

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Workflow 1.  Data management Tidy data

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Authors can manage their own data

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Tidy data (Wickham 2014)

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Tidy data (Wickham 2014) Each row is an observation

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Each column is a variable Tidy data (Wickham 2014)

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Tidy data (Wickham 2014) Each table is an observational unit

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Setup a repository

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Template structure

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Upload raw data

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Workflow 1.  Data management 2.  Standardization Tidy data Interoperable

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Darwin Core

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Darwin Core

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Darwin Core

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Reproducible data transformation

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Literate programming (R Markdown)

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Generate standardized data

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Repeatable

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Repeatable

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Collaborative

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Versioned

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Workflow 1.  Data management 2.  Standardization 3.  Documentation Tidy data Interoperable Understandable

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Documenting with metadata

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Bringing it all together

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Bringing it all together

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Workflow 1.  Data management 2.  Standardization 3.  Documentation 4.  Publication Tidy data Interoperable Understandable Open

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Publishing data

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Published data

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Published data

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Workflow 1.  Data management 2.  Standardization 3.  Documentation 4.  Publication 5.  Registration Tidy data Interoperable Understandable Open FAIR

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Global Biodiversity Information Facility

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Registering a dataset with GBIF

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Dataset on GBIF

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FAIR metadata

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FAIR data

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Alien molluscs

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Checklist Open Findable Accessible Inter- operable Reusable FAIR datasets

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Going even further

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Imagine a future where dynamically, from year to year, we can track the progression of alien species (AS), identify emerging species, assess their current and future risk and timely inform policy in a seamless data-driven workflow. One that is built on open science and open data infrastructures. By using international biodiversity standards and facilities, we would ensure interoperability, repeatability and sustainability. This would make the process adaptable to future requirements in an evolving IAS policy landscape both locally and internationally. Mission

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Checklist Open Findable Accessible Inter- operable Reusable Creating a unified checklist Unified

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Multiple checklists on GBIF

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Using GBIF as an infrastructure

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Repeatable process

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Documented process

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FAIR unified checklist

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We now have an Alien species checklist for Belgium

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Going even further

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Checklist-based indicators

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Open occurrence data

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Occurrence-based indicators

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Reproducible, open & fair

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trias-project.be

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Thank you! Peter Desmet & Lien Reyserhove (2019) Generating reproducible workflows for the publication of open and FAIR data. Presentation. http://bit.ly/trias-open-fair @trias_project Tracking Invasive Alien Species (TrIAS) trias-project.be @oscibio Open science lab for biodiversity oscibio.inbo.be @peterdesmet