Format

• GBIF Infrastructure: Data processing has a detailed description of the flow
  • occurrences.txt is an improved/cleaned/formalized verbatim.txt
  • metadata
    • meta.xml has list of all colum data types etc.
      • for all files in the zip!
      • columns links lead to DCMI: DCMI Metadata Terms
    • metadata.xml is things like download doi, license, number of rows, etc.
• .zips are in Darwin format: FAQ
  • Because there are cases when both single and double quotes etc., and neither '/" as quotechar work.

  df = vx.read_csv(DS_LOCATION,convert="verbatim.hdf5",progress=True, sep="\t",quotechar=None,quoting=3,chunk_size=500_000)
  

Tools

• GBIF .zip parser lib:
  • BelgianBiodiversityPlatform/python-dwca-reader: 🐍 A Python package to read Darwin Core Archive (DwC-A) files.
  • Tried it, took a long time both for the zip and directory, so I gave up
• gbif/pygbif: GBIF Python client
  • API client, can also do graphs etc., neat!

Analysis

Things to try:

• limit number of columns through pd.read_csv.usecols()¹ to the ‘interesting’ ones
  • optionally take a smaller subset of the dataset and drop all NaNs
  • take column indexes from meta.xml
  • See if someone already did this:BelgianBiodiversityPlatform/python-dwca-reader: 🐍 A Python package to read Darwin Core Archive (DwC-A) files.