EBVOSC : From raw biodiversity data to operational indicators through the Essential Biodiversity Variables

This project has been accepted as a case study by the Global Open Science Cloud - GOSC -

Keywords

Essential Biodiversity Variables, FAIR, workflow, ecoinformatics, metadata, Galaxy-E, GEO-BON, biodiversity observatories, Ecological Metadata Language

Introduction

Data integration in biodiversity science is complex, essentially because  framework harmonizing data and methods is lacking. Getting interoperable data from raw, heterogeneous and scattered datasets to measure and understand the spatio-temporal dynamics of biodiversity from local to global scales is both necessary and challenging. Essential Biodiversity Variables (EBVs) represent a relevant framework for identifying appropriate data to be collated and for creating and implementing analytical workflows, from raw data to EBV data products.

Our aim is to operationalize EBV indicators by targeting the highest levels of FAIRness (Findable, Accessible, Interoperability, Reusable) for both data and source code implementation, so that data and tools can be widely shared and reused. 

A number of open standards, tools, platforms used by international infrastructures. In particular, we are already engaged with the Galaxy platform initiative for source code management and use; the DataOne network of data catalogs; the Ecological Metadata Language standard for data management; the 2021-2023 BiodiFAIRse GO FAIR IN roadmap; and GEO BON’s roadmap (“Improve the acquisition, coordination and delivery of biodiversity observations and related services to users including decision makers and the scientific community”). In relation with the GOSC vision, EBVOSC will seek to utilize, contribute to and ensure interoperability with these initiatives.

Details are in the caption following the image

from Kissling et al, 2017

Significance of the case study

The EBVOSC case study aims to demonstrate that a better mobilization of such data can readily generate EBVs and associated biodiversity indicators through automated and regular updating.

For the biodiversity scientific community, EBV operationalization is a hot topic that raises several IT challenges (data structuration and sharing, source code review standardization and dissemination), thereby delaying our ability to respond quickly to face current biodiversity and climate emergencies. EBVOSC will provide an open and transparent comprehensive EBV operationalization pilot addressing these issues.

For the broader research community, EBVOSC will build on existing international standards, approaches and initiatives regarding data and workflows, thus benefiting communities in life, climate, and earth sciences as well as the humanities community, by linking biodiversity indicators to socio-economic measurements. 

For society and stakeholders, operationalizing the EBV concept in a FAIR and transparent way is extremely important for people’s awareness on the biodiversity and climate crises through trusted indicators.

Research challenges and societal benefits

In line with international goals, measuring biodiversity state and dynamics in a transparent, reproducible and harmonized way, in line with driving forces and human pressures would have genuine societal benefits. By detecting change at species, population or community up to socio-ecosystems, they may allow appraising and reporting key and robust information at national and international levels (CBD, IPBES).

From Gonzalez A. et al., 2023. A global biodiversity observing system to unite monitoring and guide action. Nature in Ecology and Evolution. https://doi.org/10.1038/s41559-023-02171-0

Data requirement for the case study

Data from several biomes, both within and between BONs, will be gathered to demonstrate the portability and the reusability of EBV workflows. Extensive and well structured datasets (in particular nationwide surveys from each national BON) are candidate data for immediate EBV operationalization. Nevertheless, harmonization efforts would be required to make such data fully interoperable & reusable based on the highest degree of FAIRness.

Statement of the problem(s) that need to be addressed by GOSC

Dealing with multiple, scattered and heterogeneous data collection systems at all scales from gene to ecosystems, measuring biodiversity over large scales remains particularly complex. Based on existing approaches used by other domains such as climate or earth sciences, EBVOSC will propose methods to collate, harmonize and process contrasted in-situ data (e.g. field work and captor networks), and potentially together with remote-sensing data, by means of high performance computing tools and services. Existing efforts are not sufficient today to rapidly cope with the need of raw biodiversity data sharing and indicators production.

EBVOSC proposes an innovative way to address important challenges related to biodiversity indicators for facilitating existing biodiversity indicators production, and broad understanding.

Engagement with the GOSC Initiative 

EBVOSC proposes to contribute substantially to GOSC working groups (Strategy, governance and sustainability / Policy and legal / Technical infrastructure / Data interoperability) from the biodiversity domain point of view. Nevertheless, EVBOSC is focusing on approaches and  technologies that will also benefit other scientific domains.

Deliverables

Case Study Co-chairs

 

Who is creating this case study?

Outreach

Workshop SFE² GFO EEF

This projet has been presented at the joint meeting, Internatinal Conference on ecological sciences the 23th of November 2022, at Metz (France)

[The workshop presentation is available here]

 

EBVs data portal

This PNDB portal is a view of PNDB datasets corresponding to the "GEO BON EBV operationalization pilot" France is experimenting