ayushnag / sophy

Southern Ocean phytoplakton observations stored in a relational SQL database

SOPHY: Southern Ocean Phytoplankton Database

• 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

• Miniconda is recommended

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)
  • Palmer Station Antarctica LTER and N. Waite. 2022. Merged discrete water-column data from annual PAL LTER field seasons at Palmer Station, Antarctica, from 1991 to 2021. ver 1. Environmental Data Initiative. https://doi.org/10.6073/pasta/7358be99bd7ec1c73293893defb289d3 (Accessed 2023-02-13).
• 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)
  • Rees, A., Robinson, C., Smyth, T., Aiken, J., Nightingale, P., & Zubkov, M. (2015). 20 years of the Atlantic Meridional Transect-AMT. Limnology and Oceanography Bulletin, 24(4), 101-107.
  • https://doi.org/10.1002/lob.10069
  • https://www.amt-uk.org/

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

sophy's Issues

Let's add a license

Up to you and @hljw which one, but let's get a license in here. UW tends to recommend MIT and BSD as do I.