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Add GBIF to the metadata sources #125

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BethYates opened this issue Jun 24, 2024 · 1 comment
Closed

Add GBIF to the metadata sources #125

BethYates opened this issue Jun 24, 2024 · 1 comment
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feature Requests for new features good first issue Good for newcomers

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@BethYates
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BethYates commented Jun 24, 2024

Description of feature

Add GBIF to the set of sources queried by the genome metadata subworkflow

@BethYates BethYates added enhancement Improvement of the existing features feature Requests for new features good first issue Good for newcomers and removed enhancement Improvement of the existing features labels Jun 24, 2024
@BethYates BethYates changed the title Add GBIF as a datasource for the genome notes metadata subworkflow Add GBIF to the metadata sources Jun 24, 2024
@BethYates
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To close this issue you will need to download and parse a json file from GBIF and feed the parsed file into the combine metadata process in the genome_metadata subworkflow. This will most likely need it's own custom process as you actually need to fetch and parse two files to get the information we need in a 2 step process. First query https://api.gbif.org/ using genus and species https://api.gbif.org/v1/species/match?verbose=true&genus=Felis&species=catus and then use the usageKey id returned by this to do a species lookup https://api.gbif.org/v1/species/2435022 from here you can get the authorship field which is what we want to retrieve

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feature Requests for new features good first issue Good for newcomers
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