Generating reproducible workflows for the publication of open and FAIR data

Talk at Research Data Management & Data Stewardship: much more than a FAIRytale in Brussels, Belgium - December 12, 2019.

1. 12 December 2019, Brussels Peter Desmet & Lien Reyserhove Generating repeatable workflows for the publication of open and FAIR data
2. Hi!
3. Research data management
4. Open data publication
5. Research software development
7. We want to study (invasive) alien species to inform/guide environmental policy
8. Reporting on invasive alien species
9. •  What species? •  Where are they? •  How are they getting here? •  What is their impact? •  Future distributions? •  Future impact? Alien species in Belgium
10. What species are alien in Belgium?
11. Let’s check the Alien species checklist for Belgium
12. We don’t have one! And certainly not one that is verified, open and FAIR
13. We do have A number of authoritative checklist with a more specialized scope
14. Data for alien plants
15. Data for alien plants
16. Open & FAIR? Checklist Open Findable Accessible Inter- operable Reusable
17. Data for alien molluscs
18. Open & FAIR? Checklist Open Findable Accessible Inter- operable Reusable
19. Checklist Open Findable Accessible Inter- operable Reusable How to go from …
20. Checklist Open Findable Accessible Inter- operable Reusable … to open & FAIR data?
21. Checklist Open Findable Accessible Inter- operable Reusable … to open & FAIR data? Unified
22. TrIAS data publication workflow
23. Workflow 1.  Data management Tidy data
24. Authors can manage their own data
25. Tidy data (Wickham 2014)
26. Tidy data (Wickham 2014) Each row is an observation
27. Each column is a variable Tidy data (Wickham 2014)
28. Tidy data (Wickham 2014) Each table is an observational unit
29. Setup a repository
30. Template structure
31. Upload raw data
32. Workflow 1.  Data management 2.  Standardization Tidy data Interoperable
33. Darwin Core
34. Darwin Core
35. Darwin Core
36. Reproducible data transformation
37. Literate programming (R Markdown)
38. Generate standardized data
39. Repeatable
40. Repeatable
41. Collaborative
42. Versioned
43. Workflow 1.  Data management 2.  Standardization 3.  Documentation Tidy data Interoperable Understandable
44. Documenting with metadata
45. Bringing it all together
46. Bringing it all together
47. Workflow 1.  Data management 2.  Standardization 3.  Documentation 4.  Publication Tidy data Interoperable Understandable Open
48. Publishing data
49. Published data
50. Published data
51. Workflow 1.  Data management 2.  Standardization 3.  Documentation 4.  Publication 5.  Registration Tidy data Interoperable Understandable Open FAIR
52. Global Biodiversity Information Facility
53. Registering a dataset with GBIF
54. Dataset on GBIF
55. FAIR metadata
56. FAIR data
57. Alien molluscs
58. Checklist Open Findable Accessible Inter- operable Reusable FAIR datasets
59. Going even further
60. 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
61. Checklist Open Findable Accessible Inter- operable Reusable Creating a unified checklist Unified
62. Multiple checklists on GBIF
63. Using GBIF as an infrastructure
64. Repeatable process
65. Documented process
66. FAIR unified checklist
67. We now have an Alien species checklist for Belgium
68. Going even further
69. Checklist-based indicators
70. Open occurrence data
71. Occurrence-based indicators
72. Reproducible, open & fair
73. trias-project.be
74. 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