PRCRMP biodiversity notebook

[MathewBiddle]

If you are opening an issue regarding an existing notebook/code or the webpage just ignore the instructions below. If you want to suggest a notebook for the code gallery please answer these questions:

• [ ] What is language(s) for used in the example?
• [ ] Is it focused on a particular module/software or an IOOS data service?
• [ ] Can you provide a minimum example of the expected code and results in a notebook?

Please provide a detailed description of the suggested example below: Bathymetry contours on a map. Puerto Rico PRCRMP has a Demo of MBON portal. I would like to do something where we bring the coral data in and include bathymetry contours, somewhat repeating the PRCRMP demo - benthic portion of the demo. The product can be found at https://mbon.ioos.us/#data/1 in MBON portal. I don’t want to repeat the effort, but I’d like to do something with these data. Example making contour map from netCDF data at NCEI:

import xarray as xr
url = 'https://www.ngdc.noaa.gov/thredds/dodsC/regional/northern_california_36_msl_2005.nc'
ds = xr.open_dataset(url)  
ds.Band1.plot.contour(levels=50)

Initial steps:

1. Ingest PRCRMP data from OBIS (using robis in R)
2. Get bathymetry data (using Python)
3. Translate R response into Pythonese.
4. Make interactive graphics

xref: https://github.com/ioos/notebooks_demos/issues/378

[MathewBiddle]

I think we should replace this notebook idea with the notebook I generated here [1]. That notebook shows how to query the OBIS API in python and parse the responses into a few figures. IT might be easy enough to bring in bathymetry data if it's something we need?

Things to fix:

• [ ] Identify a specific order/family/genus/species to make a distribution plot of
• [ ] (Optional) Resolve deprecation warnings
• [ ] Histogram distribution along latitudes/longitudes as subplots to map
• [ ] Ensure y/x-axis distribution is somehow 'linked' to latitudes/longitudes on the map
• [ ] Clean up comments/code and add a narrative.

[1] https://github.com/MathewBiddle/bio_ice/blob/main/create_map_from_OBIS_API.ipynb

[MathewBiddle]

Let's use pyobis to do this...