B-Cubed: Leveraging analysis-ready biodiversity datasets and cloud computing for timely and actionable biodiversity monitoring

Transcript

1. Biodiversity Building Blocks for Policy
   B-Cubed
   Leveraging analysis-ready biodiversity
   datasets and cloud computing for timely
   and actionable biodiversity monitoring
   TDWG 2023, Hobart, Australia
   Peter Desmet
   

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2. Biodiversity Building Blocks for Policy
   New Horizon Europe project
   

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3. Biodiversity Building Blocks for Policy
   Opportunity
   Global biodiversity crisis
   requires rapid, reliable
   and repeatable
   biodiversity monitoring
   data which decision
   makers can use to
   evaluate policy.
   Challenge
   B-Cubed is
   standardizing access to
   biodiversity data,
   empowering
   policymakers to address
   the impacts of biodiversity
   change.
   Aim
   Such information – from
   local to global level and
   within relevant timescales
   – calls for an improved
   integration of data on
   biodiversity from
   different sources.
   

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4. Biodiversity Building Blocks for Policy
   Essential Biodiversity
   Variables (EBV)
   ● Data cube with 3 dimensions
   ○ Taxonomic
   ○ Temporal
   ○ Spatial
   ● Each with extent, resolution
   and uncertainty
   ● Measurements (count)
   Kissling et al. (2018) doi.org/10.1111/brv.12359
   

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5. Biodiversity Building Blocks for Policy
   Species occurrence cube
   SELECT
   taxon,
   year,
   round(lat) || '_' || round(lon)
   AS grid_cell,
   count(*)
   FROM
   occurrences
   GROUP BY
   taxon, year, grid_cell
   taxon year grid_cell count
   Vespa
   crabro
   2020 50_3 15
   Vespa
   crabro
   2020 50_4 14
   Vespa
   crabro
   2020 50_5 4
   Vespa
   crabro
   2020 51_3 20
   Vespa
   crabro
   2021 50_3 11
   Vespa
   crabro
   2021 50_4 9
   Vespa
   velutina
   2020 50_3 4
   Vespa
   velutina
   2020 50_4 2
   Vespa
   velutina
   2021 50_3 16
   Vespa
   velutina
   2021 50_4 5
   Desmet et al. (2023) bit.ly/D2_1_v1
   

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6. Biodiversity Building Blocks for Policy
   Spatial grid assignment
   ● Spatial reference grid
   ○ EEA (1x1 km, 10x10 km)
   ○ QDGC (15x15 min, 30x30 min)
   ○ MGRS (1x1 m, 10x10 m)
   ● Assign occurrence to grid
   ○ Take into account uncertainty
   ○ Random assignment within
   uncertainty
   Oldoni et al. (2020)
   doi.org/10.1101/2020.03.23.983601
   

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7. Biodiversity Building Blocks for Policy
   Spatial grid assignment
   SELECT
   taxon,
   year,
   eea_grid_code(
   lat, lon, coord_uncertainty,
   size = "10km",
   assignment = "random"
   ) AS grid_cell,
   count(*)
   FROM
   occurrences
   GROUP BY
   taxon, year, grid_cell
   taxon year grid_cell count
   Vespa
   crabro
   2020 10kmE380N3
   11
   2
   Vespa
   crabro
   2020 10kmE380N3
   12
   2
   Vespa
   crabro
   2020 10kmE380N3
   12
   0 (no row)
   Vespa
   crabro
   2020 10kmE381N3
   11
   5
   Vespa
   crabro
   2021 10kmE380N3
   11
   3
   Vespa
   crabro
   2021 10kmE380N3
   12
   2
   Vespa
   velutina
   2020 10kmE380N3
   11
   1
   Vespa
   velutina
   2020 10kmE380N3
   12
   1
   Vespa
   velutina
   2021 10kmE380N3
   11
   7
   Vespa
   velutina
   2021 10kmE380N3
   12
   2
   

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8. Biodiversity Building Blocks for Policy
   SELECT
   taxon,
   year,
   count(*),
   count_higher(*, "genus")
   AS count_genus,
   FROM
   occurrences
   GROUP BY
   taxon, year
   Sampling bias taxon year count count_genu
   s
   Vespa
   crabro
   2020 15152 20361
   Vespa
   crabro
   2021 15055 20533
   Vespa
   crabro
   2022 20655 38641
   Vespa
   crabro
   2023 1805 7192
   Vespa
   velutina
   2020 3683 20361
   Vespa
   velutina
   2021 3825 20533
   Vespa
   velutina
   2022 16259 38641
   Vespa
   velutina
   2023 5108 7192
   

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9. Biodiversity Building Blocks for Policy
   Using cubes in B-Cubed
   ● Modeled cubes
   ○ Suitability cube
   ○ Dissimilarity cube
   ○ Network invasibility cube
   ● Indicators
   ○ Phylogenetic indicators
   ○ Impact of alien taxa indicators
   ○ Robustness indicators
   

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10. Biodiversity Building Blocks for Policy
    Automated
    workflows
    Cloud
    computing
    Policy aligned
    Tutorials Case studies FAIR and open
    

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11. Biodiversity Building Blocks for Policy
    New GBIF download
    service
    ● Search & filter occurrences
    ○ Improved temporal processing
    ○ Filters to exclude occurrences
    ● Define cube
    ○ Dimensions
    ○ Output format (CSV, Parquet,
    NetCDF)
    ○ Destination (GBIF, cloud
    provider)
    ● DOI + Metadata
    

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12. Biodiversity Building Blocks for Policy
    Hackathon
    ● Innovate with data cubes!
    ○ Interoperability with other data
    ○ Visualizations, integrations
    ○ Engage with the community
    ● Location: Brussels, Belgium
    ● Save the date: 2-5 April 2024
    

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13. Biodiversity Building Blocks for Policy
    Thank you
    ● Presentation:
    bit.ly/tdwg-2023-b-cubed
    ● DOI: 10.3897/biss.7.110734
    ● Website: b-cubed.eu
    ● Twitter/X: @BCubedProject
    ● LinkedIn: B-Cubed Project
    Quentin Groom
    Laura Abraham
    Tim Adriaens
    Lissa Breugelmans
    David A. Clarke
    Miguel A. Fernández
    Louise Hendrickx
    Cang Hui
    Sabrina Kumschick
    Matilde Martini
    Melodie McGeoch
    Teodor Metodiev
    Joe Miller
    Co-authors
    Damiano Oldoni
    Henrique M. Pereira
    Cristina Preda
    Tim Robertson
    Duccio Rocchini
    Hanno Seebens
    Heliana Teixeira
    Maarten Trekels
    John R.Wilson
    Nikol Yovcheva
    Tsungai Zengeya
    Peter Desmet
    

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