HackingLimno2025

Notebooks and code for the Hacking Limno 2025 Workshop on biodiversity data.

Accompanying presentation

The Global Ocean Observing System (GOOS), with NOAA's U.S. Integrated Ocean Observing System (IOOS) as part of it, uses Biological and Ecological Essential Ocean Variables (BioEco EOVs) to standardize ocean observing data from communities like the Marine Biodiversity Observation Network (MBON). The GOOS Biology and BioEco Variables focus on the abundance and distribution of key aquatic organisms. Using predefined lists of species, one can query biological occurrence data from the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF). After querying, users can analyze OBIS and GBIF occurrence data to study the abundance and distribution of these BioEco Variables. This occurrence data can then be combined with gridded and tabular environmental data served by ERDDAP to further analyze into products (e.g. species distribution models). In this workshop we will demonstrate the tools and techniques for assessing ecosystem health using this open science framework.

steps

1. find relevant OBIS & ERDDAP data
2. build OBIS samples table
3. add environmental data to samples table from ERDDAP
4. use samples table to characterize taxa
   • what environments does the taxa live in
   • SDM model

references

Notebooks in progress:

• tylar pyobis-corals based
• TODO: erdappy query
• erdap + obis sampling to create occurence+environmental table
• samples into SDM

data sources

• list of EOV aphiaIDs
• seascapes (lots of environmental information in one product)

SDM examples & frameworks Ideas:

example	env. data sources	framework	ref
daniel furman	worldClim	scikitlearn	ref
Google	worldClim, SRTM elevation, global forest cover	Google Earth Engine	ref
elapid	NA	elapid	ref

pyobis examples

• query & display corals
• query for specific dataset

other obis examples

• robis EOV H3 grids
• robis EOV queries

Session title: Mapping biodiversity indicator species using open data

Lead(s):

Tylar Murray (tylar.murray@usf.edu, murray.tylar@gmail.com), Mathew Biddle (mathew.biddle@noaa.gov)

Date:

July 21-23

Duration:

1.5hrs

Abstract:

The Global Ocean Observing System (GOOS), with NOAA's U.S. Integrated Ocean Observing System (IOOS) as part of it, uses Biological and Ecological Essential Ocean Variables (BioEco EOVs) to standardize ocean observing data from communities like the Marine Biodiversity Observation Network (MBON). The GOOS Biology and BioEco Variables focus on the abundance and distribution of key aquatic organisms. Using predefined lists of species, one can query biological occurrence data from the Ocean Biodiversity Information System (OBIS) and the Global Biodiversity Information Facility (GBIF). After querying, users can analyze OBIS and GBIF occurrence data to study the abundance and distribution of these BioEco Variables. This occurrence data can then be combined with gridded and tabular environmental data served by ERDDAP to further analyze into products (e.g. species distribution models). In this workshop we will demonstrate the tools and techniques for assessing ecosystem health using this open science framework.

Resources:

• Robis query to OBIS for EOVs: https://ioos.github.io/ioos_code_lab/content/code_gallery/data_analysis_and_visualization_notebooks/2024-09-13-OBIS_EOVs.html
• Using pyobis - https://ioos.github.io/ioos_code_lab/content/code_gallery/data_access_notebooks/2022-11-23_pyobis_example.html
• Searching for data across multiple ERDDAPs: https://ioos.github.io/ioos_code_lab/content/code_gallery/data_access_notebooks/2021-10-19-multiple-erddap-search.html