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AtlasOfLivingAustralia / data-management

Data management issue tracking
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Harvest invasive species from GBIF #952

Open peggynewman opened 11 months ago

peggynewman commented 11 months ago

It may be useful for biosecurity authorities to be able to see global occurrences of species considered to be invasive in Australia.

Using this List of Invasive Species Derived from DAFF and DCCEEW biosecurity Lists

Use the GBIF species API https://www.gbif.org/developer/species (probably /parser/name POST) to match to the GBIF taxonomy, then download occurrence records from GBIF for these. Make the process rerunnable.

Create a data resource in the ALA. Load records into test to review.

Sherrin-ALA commented 11 months ago

Occurrence records for Australia I presume.

peggynewman commented 11 months ago

No, global. Refer first sentence.

Sherrin-ALA commented 11 months ago

Oops. I think the relevant API calls here are: To get the taxonID - match?name in the first instance. https://api.gbif.org/v1/species/match?name=Acarapis%20woodi

If matched to a species - will return speciesKey in the response. In this example : "speciesKey":4542910 Will return a confidence level for the match - we may wish to set a minimum confidence level.

To get a straight count of occurrences: https://api.gbif.org/v1/occurrence/count?taxonKey=4542910 To get a complete list of occurrence records: https://api.gbif.org/v1/occurrence/search?taxonKey=4542910 To limit it to a country - use the ISO two letter country code: https://api.gbif.org/v1/occurrence/search?taxonKey=4542910&country=US

For reference - https://www.gbif.org/occurrence/search?taxon_key=4542910