How we plan to publish 1 000 bio-logging datasets to GBIF and OBIS

Talk at Living Data 2025 in Bogota, Colombia - October 23, 2025.

Abstract: https://livingdata2025.com/program.html?abstract=7005380

Transcript

1. Peter Desmet INBO, Belgium How we plan to publish 1 000 bio-logging datasets to GBIF and OBIS Image by OpenStreetMap contr., CARTO, Peter Desmet
2. Peter Desmet Authors Sanne Govaert Pieter Huybrechts Jonathan Pye Claudia Meneses Sarah Davidson Photo by Misjel Decleer, VLIZ
3. - Expensive/disruptive to collect - Useful beyond movement ecology research - We want to - Increase discoverability & use through GBIF and OBIS - Retain provenance - Be consistent across realm and technique Bio-logging data Photo by INBO GBIF: Global Biodiversity Information Facility OBIS: Ocean Biodiversity Information System
4. Software - Automate transformation to Darwin Core - One for each source system - Movebank: movepub R package inbo.github.io/movepub - European Tracking Network: etn R package inbo.github.io/etn - Ocean Tracking Network: export function bit.ly/otn-ipython-utils library(movepub) (dataset <- read_package("https://zenodo.org/records/10053903/fi les/datapackage.json")) #> A Data Package with 3 resources: #> • reference-data #> • gps #> • acceleration #> For more information, see <https://doi.org/10.5281/zenodo.10053903>. write_dwc(dataset, ".") #> ── Reading data ── #> #> ℹ Taxa found in reference data and their WoRMS AphiaID: #> Haematopus ostralegus: 147436 #> #> ── Transforming data to Darwin Core ── #> #> ── Writing files ── #> #> • ./occurrence.csv #> • ./meta.xml #> • ./emof.csv
5. Measurement Measurement Measurement Measurement Measurement Measurement Deployment Position Position Darwin Core Deployment Measurement Capture Tagging Release Position Recapture Measurement Measurement Measurement Measurement Measurement - Deployment = parent event - Child events share parentEventID and organismID - Capture, etc. = human obs. - Positions = machine obs. - Downsampled to 1st record per hour, indicated in dataGeneralizations - Biometrics, settings = measurements Figure by Peter Desmet
6. Retain provenance - Refer to source in metadata - Source DOI in datasetID - Record identifiers in eventID & occurrenceID - Source system in collectionCode - Need for eventType controlled vocabulary (“tag attachment”, “gps”, etc.) Image by GBIF
7. - Combine bio-logging data with other occurrence data - MBON’s A-BioTrack project marinebon.org/biotrack/ - Boom & Kissling (2024) doi.org/10.1111/ecog.07246 - Visualize bio-logging data across systems - bit.ly/moveVisGBIF Use Figure by Peter Desmet
8. - Standardization - Use standard bio-logging formats as input? (e.g. ATO ato.trackyverse.org) - Use Darwin Core Data Package? - Discoverability - Mobilize more datasets - GBIF hosted portal - 357 datasets & 13M occurrences so far Wanna join? Get in touch! Next steps Image by OpenStreetMap contr., OpenMapTiles, GBIF
9. Thank you! peter.desmet@inbo.be bit.ly/1000-biologging This work was funded by NLBIF (MOVE2GBIF), EU (DTO-BioFlow, B3), Research Foundation - Flanders (LifeWatch) & Canada Foundation for Innovation (Major Science Initiatives - OTN). Photo by Jim Abernethy, OTN