Retrieve biodiversity data from the web
This process retrieves biodiveryity data, i.e. occurrences for various species, from the sources GBIF, iNaturalist and VertNet. For more details, please ask BOKU.
pan-european use case AquaINFRA R
| Id | Title | Data Type | Description |
|---|---|---|---|
| species_names_list | Species names to download (list of species) | string | List of species. If you have a url to the dataset, use the option below. |
| species_names_url | Data with species names to download | string | URL to a table containing the occurrences from any source. This can be the outcome of the match-data process. |
| colname_species | Species column name | string | If the data provided in the data path is a dataframe, indicate here the column name with species names. |
| databases | Database names | array | List of databases to consider. Only "gbif, inat, vertnet" supported. |
| gbif_limit | Max number (GBIF) | integer | The maximum number of data points that are being retrieved from GBIF. |
| inaturalist_limit | Max number (iNaturalist) | integer | The maximum number of data points that are being retrieved from iNaturalist. |
| vertnet_limit | Max number (VertNet) | integer | The maximum number of data points that are being retrieved from VertNet. |
| study_area_bbox | Area of Interest as a bounding box | object | A bounding box: {'bbox': [south, west, north, east]} (see https://docs.ogc.org/is/18-062r2/18-062r2.html#bounding-box-value) |
| study_area_shapefile | Area of Interest as shapefile | string | URL to the zipped input shapefile containing the study areas inside which you would like to retrieve occurrences. |
| study_area_geojson_url | Area of Interest as GeoJSON | string | URL to the input GeoJSON file containing the study areas inside which you would like to retrieve occurrences. |
| study_area_geojson | Area of Interest as a GeoJSON object | object | Directly post the GeoJSON containing the study areas inside which you would like to retrieve occurrences. |
| percentage_correctness | Species name correctness in percent | number | A number indicating the percentage of species name correctness that should be allowed to be replaced. High values ensure a perfect match from the standard database. |
| synonym_check | Consider synonyms from standard databases like FishBase | boolean | YES, if synoymns species names should be returned from FishBase during data checks before data download. |
| Id | Title | Description |
|---|---|---|
| biodiversity_data | Combined occurrences | A table containing the combined occurrences inside the study area. |
Educational resources and documentation
Jobs
Browse jobsLinks
- GitHub repo (text/html)
- Process description as JSON (application/json)
- Process description as HTML (text/html)
- Jobs list as HTML (text/html)
- Jobs list as JSON (application/json)
- Execution for this process as JSON (application/json)
Execution modes
- Synchronous
- Asynchronous