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PRCRMP biodiversity notebook #24

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#65
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PRCRMP biodiversity notebook#24
#65
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MathewBiddle
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Notebook ideaFor new notebook proposals

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@MathewBiddle
MathewBiddle
opened on Sep 3, 2021

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: ioos/notebooks_demos#378

Activity

  1. MathewBiddle
    added
    Notebook ideaFor new notebook proposals
    on Sep 3, 2021

  2. MathewBiddle commented on Feb 8, 2022

    @MathewBiddle
    MathewBiddle
    on Feb 8, 2022
    ContributorAuthor

    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

  3. MathewBiddle
    added a commit that references this issue on Feb 11, 2022

    Draft PRCRMP notebook

    4c61c67

  4. MathewBiddle commented on Aug 16, 2022

    @MathewBiddle
    MathewBiddle
    on Aug 16, 2022
    ContributorAuthor

    Let's use pyobis to do this...

  5. MathewBiddle
    self-assigned this
    on Oct 4, 2023
  6. MathewBiddle
    added this to IOOS CodeLabon Jul 17, 2025
  7. github-project-automation
    moved this to To Do in IOOS CodeLabon Jul 17, 2025
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