Download data from EurOBIS using the LifeWatch/EMODnet-Biology Web Feature Services
The eurobis R package allows you to download data from EurOBIS.
You can query on:
- Dataset: provide the Integrated Marine Information System (IMIS) unique identifier for datasets DasID.
- Taxon: use a scientific name (e.g. the sea turtle Caretta caretta) or a WoRMS AphiaID (e.g. 137205)
- Traits: get all occurrences that are benthos. Or zooplankton. Or both. Powered by WoRMS.
- Time: just give start and end dates.
- Geographically: it allows to query on more than 300 records from the Marine Regions Gazetteer by giving the MRGID. Or just pass the area of your interest as a polygon written in as Well Known Text
- Other important classifications as IUCN Red List, MSDF Indicators or Habitats Directive and CITES Annexes.
Or create your own selection using the EMODnet Biology toolbox. Just copy the webservice URL and paste in R.
Installation
You can install the development version from GitHub with devtools:
devtools::install_github("lifewatch/eurobis")Get occurrences
Use the eurobis_occurrences() family of functions to query data.
A basic example is:
library(eurobis)
# Get one single dataset
dataset <- eurobis_occurrences_basic(dasid = 8045)
#> Loading ISO 19139 XML schemas...
#> Loading ISO 19115 codelists...
#> Loading IANA mime types...
#> No encoding supplied: defaulting to UTF-8.
#> ✓ Downloading layer: EMODnet EurOBIS Basic Occurrence Data
#> ℹ The Basic Occurrence Data download provides you data for the following 8 essential terms: datasetid, datecollected, decimallongitude, decimallatitude, coordinateuncertaintyinmeters, scientificname, aphiaid, scientificnameaccepted. For more information, please consult: https://www.emodnet-biology.eu/emodnet-data-format.
dplyr::glimpse(dataset)
#> Rows: 52
#> Columns: 11
#> $ gml_id <fct> eurobis-obisenv_basic.fid--7af1e85b_1818…
#> $ id <int> 28821850, 28822197, 28822700, 28822829, …
#> $ datasetid <chr> "http://www.emodnet-biology.eu/data-cata…
#> $ datecollected <dttm> 2020-05-04, 2020-03-02, 2020-03-02, 202…
#> $ decimallongitude <dbl> -8.73902, -8.73902, -8.73902, -8.73902, …
#> $ decimallatitude <dbl> 40.61773, 40.61773, 40.61773, 40.61773, …
#> $ coordinateuncertaintyinmeters <dbl> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5…
#> $ scientificname <chr> "Zostera marina", "Zostera marina", "Zos…
#> $ aphiaid <chr> "http://marinespecies.org/aphia.php?p=ta…
#> $ scientificnameaccepted <chr> "Zostera subg. Zostera marina", "Zostera…
#> $ geometry <POINT [°]> POINT (-8.73902 40.61773), POINT (…To see the list of datasets, use:
eurobis_list_datasets()
#> # A tibble: 1,221 × 2
#> id name
#> <chr> <chr>
#> 1 5685 1507-1997 Paul F. Clark North East Atlantic Crab Atlas
#> 2 5688 1778-1998 Ivor Rees North Wales Marine Fauna Ad-hoc sightings shore an…
#> 3 5666 1915-2016 Marine Strategy Framework Directive (MSFD) Collation of inva…
#> 4 1884 2005-Ongoing UK MarLIN Shore Thing timed search results
#> 5 6430 2009 University of Plymouth Wave Hub, Cornwall towed underwater video …
#> 6 6421 2010 University of Plymouth Guernsey towed underwater video benthic su…
#> 7 6693 2011 University of Plymouth Falmouth towed underwater video maerl and …
#> 8 6691 2012-2013 University of Plymouth Falmouth maerl bed infauna and sedime…
#> 9 5670 2012-ongoing UK Offshore Marine Conservation Zone (MCZ) Survey Data
#> 10 6692 2012 University of Plymouth Falmouth towed underwater video maerl and …
#> # … with 1,211 more rowsFor detailed information run:
help(eurobis_occurrences)Query by traits
Use the functional_group argument:
# Get one single dataset
dataset <- eurobis_occurrences_basic(dasid = 8045, functional_groups = "angiosperms")
#> ✓ Downloading layer: EMODnet EurOBIS Basic Occurrence Data
#> ℹ The Basic Occurrence Data download provides you data for the following 8 essential terms: datasetid, datecollected, decimallongitude, decimallatitude, coordinateuncertaintyinmeters, scientificname, aphiaid, scientificnameaccepted. For more information, please consult: https://www.emodnet-biology.eu/emodnet-data-format.
dplyr::glimpse(dataset)
#> Rows: 52
#> Columns: 11
#> $ gml_id <fct> eurobis-obisenv_basic.fid--7af1e85b_1818…
#> $ id <int> 28821850, 28822197, 28822700, 28822829, …
#> $ datasetid <chr> "http://www.emodnet-biology.eu/data-cata…
#> $ datecollected <dttm> 2020-05-04, 2020-03-02, 2020-03-02, 202…
#> $ decimallongitude <dbl> -8.73902, -8.73902, -8.73902, -8.73902, …
#> $ decimallatitude <dbl> 40.61773, 40.61773, 40.61773, 40.61773, …
#> $ coordinateuncertaintyinmeters <dbl> 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5…
#> $ scientificname <chr> "Zostera marina", "Zostera marina", "Zos…
#> $ aphiaid <chr> "http://marinespecies.org/aphia.php?p=ta…
#> $ scientificnameaccepted <chr> "Zostera subg. Zostera marina", "Zostera…
#> $ geometry <POINT [°]> POINT (-8.73902 40.61773), POINT (…See the full list of queriable traits in the exported dataset
species_traits:
tibble::as_tibble(species_traits)
#> # A tibble: 32 × 4
#> category group selection selectid
#> <chr> <chr> <chr> <chr>
#> 1 Species group Functional group algae Algae
#> 2 Species group Functional group angiosperms Angiosperms
#> 3 Species group Functional group benthos Benthos
#> 4 Species group Functional group birds Birds
#> 5 Species group Functional group mammals Mammals
#> 6 Species group Functional group phytoplankton phytoplankton
#> 7 Species group Functional group pisces pisces
#> 8 Species group Functional group reptiles Reptiles
#> 9 Species group Functional group zooplankton zooplankton
#> 10 Species importance to society CITES Annex I 28_280_0
#> # … with 22 more rowsQuery by location
You can also filter by location, either using the Marine Regions Gazetteer Identifier (MRGID) or passing any polygon as Well Known Text.
eurobis_occurrences_basic(mrgid = 5688, geometry = "POLYGON ((-9.099426 40.33016, -9.099426 40.9788, -8.366089 40.9788, -8.366089 40.33016, -9.099426 40.33016))")To help drawing the area of your interest, you can use
eurobis_map_draw(). You can draw here a polygon interactively:
selected_area <- eurobis_map_draw()
#> POLYGON ((-9.099426 40.33016, -9.099426 40.9788, -8.366089 40.9788, -8.366089 40.33016, -9.099426 40.33016))
eurobis_occurrences_full(geometry = selected_area)To help choosing the MRGID from Marine Regions, see the list of queriable regions with:
eurobis_list_regions()
#> # A tibble: 303 × 3
#> id nameEN placetype
#> <chr> <chr> <chr>
#> 1 21899 Adriatic Sea Marine Ecoregion of the World (MEOW)
#> 2 3314 Adriatic Sea IHO Sea Area
#> 3 3315 Aegean Sea IHO Sea Area
#> 4 21900 Aegean Sea Marine Ecoregion of the World (MEOW)
#> 5 5670 Albanian Exclusive Economic Zone EEZ
#> 6 25614 Albanian part of the Adriatic Sea Marine Region
#> 7 25622 Albanian part of the Ionian Sea Marine Region
#> 8 21897 Alboran Sea Marine Ecoregion of the World (MEOW)
#> 9 3324 Alboran Sea IHO Sea Area
#> 10 8378 Algerian Exclusive Economic Zone EEZ
#> # … with 293 more rowsOr select the MRGIDs of you interest with the family of functions
eurobis_map_regions_*: these will open a leaflet map including the
layers, read via Web Map Services (WMS).
# MEOW Ecoregions
eurobis_map_regions_ecoregions()
# Exclusive Economic Zones (EEZ)
eurobis_map_regions_eez()
# International Hydrographic Office areas (IHO)
eurobis_map_regions_iho()
# Marine Regions intersection of EEZ and IHO. Named as Marine Region in eurobis_list_regions()
eurobis_map_regions_eez_iho()
# EMODnet-Biology Reporting Areas
eurobis_map_regions_reportingareas()See the manual with:
help(eurobis_map_regions)Note that passing both an MRGID and a geometry does not restrict to the selected area within the MRGID record, but adds both data fetched from the selected data and the MRGID record.
Why an EurOBIS R package? Didn’t exist an OBIS package already?
Yes, you could also use the OBIS R
package robis. The main advantage of
the eurobis R package is the functionality to query on species traits.
Disclaimer
If data are extracted from the EMODnet Biology for secondary analysis resulting in a publication, the appropriate source should be cited.
The downloaded data should be cited as: EMODnet Biology (yyyy) Fulll Occurrence Data and parameters downloaded from the EMODnet Biology Project (www.emodnet-biology.eu). Available online at www.emodnet-biology.eu/toolbox, consulted on yyyy-mm-dd.
Regarding the citation of the individual datasets, the following guidelines should be taken into account:
- If any individual data source of EurOBIS constitutes a significant proportion of the downloaded and used records (e.g. more than 10% of the data is derived from a single source), the individual data source should also be cited.
- If any individual data source of EurOBIS constitutes a substantial proportion of the downloaded and used records (e.g. more than 25% of the data is derived from a single source or the data is essential to arrive at the conclusion of the analysis), the manager or custodian of this data set should be contacted.
- In any case, it may be useful to contact the data custodian directly. The data custodian might have additional data available that may strengthen the analysis or he/she might be able to provide additional helpful information that may not be apparent from the provided metadata.
- The data may not be redistributed without the permission of the appropriate data owners. If data are extracted from the EMODnet Data Portal for redistribution, please contact us at bio@emodnet.eu.
