This is a space to ask questions and discuss the content of Data Use Club Practical Session on accessing and downloading species information: Data Use Club practical sessions: accessing and downloading species information (which will take place on the 16th of May 2024).
You are welcome to ask questions in advance on the topic here.
We will share the presentation links here afterwards.
The recorded webinar is available here: Data Use Club practical sessions: accessing and downloading species information on Vimeo
Here are the resources and referenced mentioned during the webinar:
- Taxon Core Terms: Darwin Core Quick Reference Guide - Darwin Core
- GBIF Extensions: GBIF Registered Extensions
- Data Use Club recorded webinar - Name matching and the GBIF Taxonomic Backbone: Data Use Club - practical session 4 - recording and resources
- Data Use Club recorded webinar - Introduction to the API, rgbif and pygbif: Data use club - practical session 3 - recording and resources
- Blogpost about the species API: (Almost) everything you want to know about the GBIF Species API - GBIF Data Blog
- Species API documentation: Species API :: Technical Documentation
- Access “treatment” information for a given taxon: treatments endpoint · Issue #1385 · gbif/portal16 · GitHub
- Wikidata: https://www.wikidata.org/
- Wikidata-related forum thread: https://discourse.gbif.org/t/given-a-gbif-human-readable-webpage-for-a-species-how-to-find-the-api-call-for-each-item-on-the-page/
- Accessing invasive species information: On species pages list if considered invasive by countries · Issue #883 · gbif/portal16 · GitHub
- API call to get all extinct taxa across any checklist on GBIF: https://api.gbif.org/v1/species/search?rank=SPECIES&isExtinct=true
- Limited to the GBIF backbone: https://api.gbif.org/v1/species/search?rank=SPECIES&isExtinct=true&datasetKey=d7dddbf4-2cf0-4f39-9b2a-bb099caae36c
- Export all extinct names from COL: http://api.checklistbank.org/dataset/3LR/export.txt?extinct=true
- Only from a certain group “Trilobites taxonID=TRL”: http://api.checklistbank.org/dataset/3LR/export.txt?taxonID=TRL&extinct=true
- Checklistbank: https://www.checklistbank.org
- Checklistbank API documentation: https://api.checklistbank.org
- Checklistbank API tutorial: backend/API.md at master · CatalogueOfLife/backend · GitHub
- Checklistbank tutorial for cross dataset search: ChecklistBank tutorial
- Checklistbank tutorial for checklist comparison: ChecklistBank tutorial
- Next Data Use Club webinar: Data Use Club practical sessions: cloud computing services
Some Q&A and comments that are not in the recording but were shared and answered in the chat:
I have experienced that the “isExtinct” flag is often not set correctly, especially for taxa that actually are extinct
Yes, it is not receiving much attention currently and there are lots of gaps and wrongly flagged species. The COL is starting this year to clean up bits, e.g. by adding integrity checks like comparing the extinct status of a genus, family and its species. We also start to integrate PaleoBio DataBase again this year. It is likely worse in the GBIF backbone where we aggregate the extinct flag from many sources automatically.
I have an experience when downloading data from gbif there are field names in csv that are not complete e.g. georeferen, preparatio, dispositio…
That should not be. Please leave a feedback issue so we can take a look
Issues · gbif/portal-feedback · GitHub.
Feel free to add your own questions here as well.