Skip to content
/ sophy Public

Southern Ocean phytoplakton observations stored in a relational SQL database

License

Notifications You must be signed in to change notification settings

ayushnag/sophy

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

SOPHY: Southern Ocean Phytoplankton Database

License

  • UW Oceanography
  • Made by Ayush Nag and Hannah Joy-Warren

In situ observations combined with phytoplankton taxonomies, ocean fronts, and ocean sectors

  • Built with SQLite and Python
  • Helper functions to make accessing data easy
  • Visualizations to see data over time, regions, and biological parameters
  • Data: sophy.xlsx

Environment and package setup

Create new environment

To explore the data in table form through a web browser using Datasette

  1. conda create -n sophyvenv datasette pandas jupyter tqdm
  2. conda activate sophyvenv
  3. Run the cell for Option 1 in sophy.ipynb to build sophy.db
  4. datasette sophy.db -o

To visualize the data using a Jupyter Notebook

  1. conda create -n sophyvenv geopandas cartopy jupyter seaborn tqdm
  2. conda activate sophyvenv
  3. Follow the steps in sophy.ipynb for sample queries and plotting

Data Sources

  • Palmer Station Antartica LTER (lter)
  • Phytobase (phytobase)
    • Righetti, D., Vogt, M., Zimmermann, N. E., Guiry, M. D., and Gruber, N.: PhytoBase: A global synthesis of open-ocean phytoplankton occurrences, Earth Syst. Sci. Data, 12, 907–933, https://doi.org/10.5194/essd-12-907-2020, 2020.
  • AMT Cruises (AMT)

Note: This database modifies the original datasets and is NOT a replacement for the original datasets.