How to manage and publish biodiversity data

Talk at the BiodivScen Data Management Workshop in Helsinki, Finland - May 14, 2019.

Transcript

1. How to manage and
   publish biodiversity data
   BiodivScen Data Management Workshop
   14 May 2019 - Helsinki
   Peter Desmet
   

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2. Open science lab for biodiversity
   At the Research Institute for Nature and Forest
   (INBO) in Belgium.
   We offer technical support to researchers in the
   projects we collaborate in.
   Our support is mainly focused on open data
   publication and research software development.
   @oscibio
   

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3. Managing biodiversity data
   

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4. You’re not alone
   Managing data is hard, but a lot already exists.
   Please don’t reinvent the wheel if you don’t
   have to.
   

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5. Platforms
   Look for existing platforms
   before creating your own
   

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6. Many systems exist to manage biological collection
   information - iDigBio.org
   Biological collection databases
   

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7. Citizen science infrastructure for recording (photo)
   observations: smartphone app, species image
   recognition, community validation - inaturalist.org
   iNaturalist
   

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8. Customizable and open: create projects, add custom
   fields to observations, API, species image recognition
   iNaturalist
   

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9. Manage and analyse tracking data, has own
   repository - www.movebank.org
   Movebank
   

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10. It is expensive to develop and maintain one:
    collaborate with others if you do so!
    No platform yet?
    

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11. Data standards
    

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12. TDWG - www.tdwg.org
    Biodiversity Information Standards
    

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13. TDWG maintained standard to express biodiversity
    information: glossary of terms - dwc.tdwg.org
    Darwin Core
    

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14. Most popular way to package biodiversity data: data
    as CSV files (core + extensions), metadata as XML
    Darwin Core Archive
    

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15. Used to standardize information in a field: requires
    community input
    Vocabularies
    

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16. Not biodiversity oriented, but makes data widely
    compatible - www.opengeospatial.org/standards
    Open Geospatial Consortium
    

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17. Licenses
    Don’t create your own licence!
    

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18. Standardized licenses to grant or clarify copyright
    permissions for creative works -
    creativecommons.org
    Creative Commons
    

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19. Creative Commons Zero is the most appropriate
    license for scientific (biodiversity) data
    CC0 for scientific data
    

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20. Getting credit for your data is a community and
    technical issue
    Don’t use a license to get credit
    

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21. Publishing biodiversity data
    

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22. Find a repository
    To archive your data,
    following the FAIR principles
    

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24. Generic research repository: free, easy to use, close
    to unlimited size, has API, managed by CERN
    Zenodo
    

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25. To find mostly domain-specific repositories
    (“databases”) and standards - fairsharing.org
    FAIRsharing
    

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26. Easiest and most interoperable way to publish
    species occurrences and checklists
    Integrated Publishing Toolkit (IPT)
    

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27. Publishing data
    to the largest
    biodiversity information infrastructure
    

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28. Global Biodiversity Information Facility
    GBIF - www.gbif.org
    

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29. Species recorded at a specific place and time
    1.3 billion occurrence records
    

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30. Human observations: citizen science, monitoring
    Machine observations: GPS tracking, camera traps
    Specimens: preserved, fossil or living collections
    Sampling events: sample with associated
    measurements
    Occurrence data
    

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31. Taxonomic checklist: synonymy, classification
    Regional checklist: species distribution
    Thematic checklist: species properties (e.g.
    invasive)
    … and species data
    

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32. Request endorsement to become a data publisher
    Standardize your data into Darwin Core
    Document your data with standardized metadata
    Choose a license: CC0, CC-BY, CC-BY-NC
    Register your dataset to make it discoverable
    How to publish data to GBIF
    

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33. Make use of the Integrated Publishing Toolkit (IPT).
    Ask national node for existing data hosting centres
    How to publish data to GBIF
    

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34. Make use of one the platforms that already publishes
    data to GBIF
    How to publish data to GBIF
    

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35. GBIF services
    What you get in return
    

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36. Registered datasets get a DOI, are findable through
    GBIF website and API, and citations are tracked
    Discoverability
    

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37. Registered datasets get a DOI, are findable through
    GBIF website and API, and citations are tracked
    Discoverability
    

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38. Data search
    Darwin Core standardization allows cross-dataset
    search through website and API
    

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39. Backbone taxonomy
    All data gets matched to a backbone taxonomy →
    unique ID, higher classification, synonymy resolution
    

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40. Reproducible downloads
    Any query can be downloaded, gets a DOI and there
    are clear citation guidelines
    

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41. Distributed, active community supporting data
    publishers and users
    Community
    

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42. E.g. Tracking Invasive Alien Species (TrIAS) uses
    GBIF as a starting point doi.org/10.15468/xoidmd
    Infrastructure that can be build upon
    

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43. You’re not alone
    A lot already exists. Please don’t reinvent the
    wheel if you don’t have to.
    

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44. Thank you!
    @peterdesmet
    Desmet P (2019) How to manage and publish
    biodiversity data http://bit.ly/biodivscen-talk
    

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