This Python package builds gridded datasets of WoRMS aligned marine species distributions as GeoParquet based on the OBIS and GBIF occurrence snapshots. The package currently supports Geohash and H3 grid output.
When using this data product, please copy the citations provided below:
OBIS (2024). speciesgrids (version 0.1.0). https://github.com/iobis/speciesgrids
GBIF.org (1 May 2024) GBIF Occurrence Data https://doi.org/10.15468/dl.ubwn8z
OBIS (25 October 2023) OBIS Occurrence Snapshot. Ocean Biodiversity Information System. Intergovernmental Oceanographic Commission of UNESCO. https://obis.org.
World Register of Marine Species. Available from https://www.marinespecies.org at VLIZ. Accessed 2024-05-01. doi:10.14284/170.
IUCN. 2023. The IUCN Red List of Threatened Species. Version 2023-1. https://www.iucnredlist.org. Accessed on 13 May 2024.
Gearty W, Chamberlain S (2022). rredlist: IUCN Red List Client. R package version 0.7.1, https://CRAN.R-project.org/package=rredlist.
A number of grids are available for download from S3:
aws s3 cp --recursive s3://obis-products/speciesgrids .import geopandas
filters = [("AphiaID", "==", 141433)]
gdf = geopandas.read_parquet("../h3_7/", filters=filters)
gdf.explore(column="records", cmap="viridis", legend=True, tiles="CartoDB positron")
gdf.set_index("h3_07", inplace=True)
gdf = gdf.h3.h3_to_geo_boundary()
gdf.explore(column="records", cmap="viridis", legend=True, tiles="CartoDB positron")
Other data usage examples are available as notebooks.
The following source datasets need to be prepared:
- OBIS occurrence snapshot
- GBIF occurrence snapshot
- WoRMS export (taxon and species profile tables)
- IUCN Red List export
- GBIF taxonomic backbone to WoRMS taxonomy from ChecklistBank
Adapt the file paths and grid configuration in speciesgrids/__main__.py and run:
python -m speciesgridsaws s3 sync geohash_4 s3://obis-products/speciesgrids/geohash_4
aws s3 sync h3_7 s3://obis-products/speciesgrids/h3_7