Notes

RO crates

https://www.researchobject.org/ro-crate/

What is an RO-Crate? An RO-Crate is a Research Object (or RO) formed of a collection of data (a crate) and a special ro-crate-metadata.json file which describes the collection.

The collection may contain any kind of research data - papers, data files, software, references to other research, and so on. It may be a folder full of files, an abstract grouping of connected references, or a combination of both.

The ro-crate-metadata.json file (also known as the RO-Crate Metadata Document) is a plain text file, readable by humans and machines, that includes metadata for each item within the collection - the authors, license, identifier, provenance, and so on. Any folder can be turned into an RO-Crate by adding an ro-crate-metadata.json file.

Researchers can distribute their work as an RO-Crate to ensure their data travels with its metadata, so that key components are correctly tracked, archived, and attributed.

RO-Crate uses the JSON-LD format, which is based on JSON. The ro-crate-metadata.json file can be written by hand or by using one of the existing tools. Some workflow managers (such as Galaxy) support exporting RO-Crates from their web interface.

Below is an example of an ro-crate-metadata.json file, which describes rainfall data published by an Australian institute under a Creative Commons license:

https://www.researchobject.org/ro-crate/about_ro_crate

https://www.researchobject.org/ro-crate/background#research-object-background

https://biodt.eu/

https://github.com/BioDT/biodt-familiar

An illustration of a circle formed by smaller circles Intelligence for sustainable trade Trase provides data and insight that empowers business, government and civil society to eliminate deforestation and transition towards more sustainable and equitable agricultural supply chains.

https://trase.earth/

Nature first

WHAT IS NATURE FIRST? The goal of Nature FIRST is to develop predictive, proactive and preventative capabilities for nature conservation stakeholders by combining theoretic premises from the sciences of ecology and environmental forensics with empirical environmental observations (satellite-based & on-site) into a Proof of Principle that is tested and demonstrated in 4 European areas, covering 6 biogeographical regions.

https://www.naturefirst.info/

Crane Radar

With the Crane Radar, you can track Cranes in real time and anticipate where they can be spotted in the next few hours. We hope you enjoy your sightings!

Before every Winter, cranes migrate from cold Scandinavia to warmer areas in France and Spain, and back again before the Spring. Hence, highest changes to see them flying are in October-November and February-March.

Every minute the position(s) of spotted cranes are recalculated. Click on the binocular to get details about the original observation. Zoom in to get more accurate estimates.

https://sensingclues.org/craneradar

BEEHAVE

Honey bees face numerous challenges, including intensive agriculture, diseases, and fluctuations in nectar and pollen availability. The Digital Twin prototype will assess landscape quality to provide practical insights into honey bee performance and honey production.

Honey bees, or Apis mellifera, are vital pollinators and honey producers. Their well-being is closely tied to the landscapes they inhabit, where a continuous supply of nectar and pollen is essential, especially during periods when mass-flowering crops like oilseed rape are unavailable.

https://biodt.eu/news/first-operational-prototype-digital-twin-biodt

Omic BON

raissa.meyer@awi.de

https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giad068/7252077

The founding charter of the Omic Biodiversity Observation Network (Omic BON)

Omic BON The Omic Biodiversity Observation Network (Omic BON) aims to promote coordinated biomolecular observations for global insight and action.

Omic BON is a thematic BON focused on the study of genes, transcripts, proteins, metabolites, and other biomolecules in organisms or environmental materials. Omics enables biodiversity observation at the molecular scale across environments and geographies. Omic BON will complement thematic BONs focused on environments (Marine BON, Freshwater BON, Soil BON), as well as national and regional BONs. Omic BON will additionally closely work with the GEO BON Genetic Composition Working Group.

Omic BON will coordinate its growing partnership to establish a distributed, global biomolecular observatory. Its first round of priorities will be promoting intercalibration of biomolecular observing technologies, the development of globally harmonized practices, standards, and protocols. It provides a forum for international stakeholders to align approaches using existing and new biomolecular technologies. Omic BON also promotes alignment of omic cyberinfrastructures and raises awareness of the societal implications of omics observation (e.g., in the ethical, legal, and policy domains).

Omic BON will be coordinating effort along five major axes: (1) localized omic observatories, (2) networks of observing platforms, (3) data infrastructures, (4) curated and long-term stores of biosamples, and (5) (meta)data standardization bodies.

Tuesday 18 June 2024

Workshop/Panel debate/Training Forum Tuesday, June 18, 11:30 – 13:00 PD-2 Unleashing biodiversity's secrets through integrated and scaled genomic science solutions Addressing the global biodiversity crisis requires an understanding of the diversity of life on Earth, how that diversity functions and interacts, and how biodiversity responds to different environmental pressures. Two key strands of genomic science provide opportunities to develop solutions to address the complex challenges of delivering knowledge to improve our capabilities for effective biomonitoring, biodiversity conservation, and species discovery. DNA barcoding is transforming the speed of completion of the inventory of life on Earth and providing the foundations of global biomonitoring systems. Genome sequencing is transforming understanding at the genetic level and delivering knowledge of how species adapt to environmental change. This panel discussion aims to bring together experts from these two domains of genomic science in an open forum to (1) introduce the current state-of-the-art to the wider community of stakeholders in biodiversity research and policy; and (2) debate the priorities for addressing challenges and seizing opportunities needed to accelerate and integrate genomic science solutions into practices that enhance the efficacy of management interventions and biomonitoring programmes with state-of-the-art genomic tools. The organisers of this panel discussion are coordinating the first large-scale pan-European effort to develop and strengthen functioning communities of practice in biodiversity genomics, the Biodiversity Genomics Europe (BGE) Project (https://biodiversitygenomics.eu/). The BGE Project is building European capacity, production, and applications in biodiversity genomics, from field sampling to DNA sequencing followed by data processing and analysis to drive applications in biomonitoring, conservation, and bioeconomy. The panel will comprise two representatives of the BGE Project as well as one representative each from the global umbrella networks the International Barcode of Life (iBOL) and the Earth BioGenome Project (EBP).

Organizers and Panellists Robert Waterhouse – Swiss Institute of Bioinformatics (Switzerland): organiser, moderator Dimitris Koureas – Naturalis Biodiversity Center (Netherlands): organiser, panellist

Failed to foresee the issues related to Nagoya protocol

Camila Mazzoni – Leibniz Institute for Zoo and Wildlife Research (Germany): organiser, panellist Rutger Vos – Naturalis Biodiversity Center (Netherlands): panellist

https://www.naturalis.nl/en/science/researchers/rutger-vos

Bioinformatics

Harris Lewin – Earth Biogenome Project: panellist

EBP - Earth BioGenome Project started 2018 58 differents projects. A network of networks https://www.earthbiogenome.org/

https://goat.genomehubs.org/projects/EBP

We have to sequence where the biodiversity is located (to bypass/adress Nagoya issues) Evaluation the Return On Investment of the EBP is a major challenge

4.7 Billions $$ is the "magic number"

EBP sections at protocols.io https://www.protocols.io/

Think about establishing an EMI section there also ?

Arts in Lab

https://artistsinlabs.ch/

https://swissnex.org/brazil/news/fungi-cosmology/

Jose Melo Ferreira – Research Center in Biodiversity and Genetic Resources (Portugal): panellist

https://www.cibio.up.pt/en/people/details/jose-melo-ferreira/

Parallel Session (oral) Flüela Tuesday, June 18, 14:30 – 16:00 SCICOM_15.1 Opening up and preparing scientific publications for the chatGPT-age Our scientific understanding of biodiversity is traditionally communicated through scientific publications and reports in a format geared towards the human reader. The sheer number of publications produced annually, and a backlog of hundreds of millions of pages make it impossible to keep up with this knowledge, even for a restricted topic. Also the discovery of new relevant publications is challenging, albeit in a digital world this could be instantaneous. This has an impact from reviewing the state and changes in biodiversity and its causes to measuring and understanding the impact of recommendations. It contributes to a North-South divide of access to this information, and it is not suited to make use of fledgling artificial intelligence applications to mine and discover the wealth embedded in this data. Recent developments in converting scientific publications or publishing them from the beginning in machine-actionable, semantic blocks of text are leading a way forwards for example to access data about species or discover biotic interactions. Furthermore, since these blocks of text or data are made findable, accessible, interoperable and reusable (FAIR data) through the Biodiversity Literature Repository (BLR) and the biodiversityPMC, this opens scientific publications to everybody, as well as to advanced data analytic and artificial tools. It also enables customizing the annotations in publications for domain specific purposes, for example to support reporting in IPBES. In this session an overview will be provided of how to access biodiversity data through the biodiversityPMC and BLR, how publications can be processed after publishing or published in machine actionable ways to import into biodiversityPMC and BLR, and how the data is being used. Part of the session will include representative invited lectures the other part will be used for a discussion with potential stakeholders. Confirmed speakers Laurence Bénichou, Muséum national d’Histoire naturelle, Paris, France Rainer Krug, Department of Evolutionary Biology and Environmental Studies. University of Zürich, Zurich, Switzerland Patrick Ruch, Swiss Institute of Bioinformatics, Carouge, Switzerland Fabio Rinaldi, Dalle Molle Institute for Artificial Intelligence (IDSIA), Viganello, Switzerland Rob Waterhouse, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland Conveners Donat Agosti, Plazi, Zinggstrasse 16, 3007 Bern, Switzerland, agosti@plazi.org Laurence Bénichou, Muséum national d’Histoire naturelle, Paris, France, laurence.benichou@mnhn.fr Patrick Ruch, University of Applied Sciences Geneva (HES-SO) / SIB Swiss Institute of Bioinformatics, Carouge, Switzerland, patrick.ruch@hesge.ch 559 LITERATURE WORKFLOWS IN IPBES - HOW THEY WOULD PROFIT FROM ENRICHED PUBLICATIONS Oral Presenter: Rainer M. Krug (Zürich, Switzerland) 14:30 – 14:45 15 min 667 WHERE ARE WE TODAY IN REGARD TO FINDING, ACCESSING AND MINING LITERATURE? Oral Presenter: Patrick Ruch (Carouge, Switzerland) 14:45 – 14:55 10 min 632 HOW DO WE GET THERE? A 7* SCHEME OF GETTING “OPEN FAIR PUBLICATIONS” Oral Presenter: Donat Agosti (Bern, Switzerland) 14:55 – 15:05 10 min 622 DEVELOPMENT IN PUBLISHING BIODIVERSITY Oral Presenter: Laurence Benichou (Paris, France) 15:05 – 15:15 10 min 631 MACHINE LEARNING FOR COLLECTION OF ARTHROPOD ORGANISMAL AND ECOLOGICAL TRAITS Speaker: Joseph Cornelius (Lugano, Switzerland) 15:15 – 15:25 10 min Discussion Session SCICOM_15.1

ChatGPT alternatives

Gemini (google) Ecosia chat

Wednesday 19 June 2024

Daniel Schrag Professor of Geology, Professor of Environmental Science and Engineering, and Co-Director of the Science, Technology, and Public Policy Program at the Harvard University, schrag@eps.harvard.edu

Parallel Session (oral) Sertig Wednesday, June 19, 09:30 – 11:00 PHIETH_9.1a Philosophies of biodiversity conservation In this session we welcome contributions that discuss different questions concerning biodiversity conservation from the perspective of philosophy, ethics and political theory. Particularly welcome are papers that address the general theme of the conference, from science to action. Potential other topics include: • The philosophy of valuing and protecting biodiversity • Justice and politics in biodiversity conservation, including such issues as ownership of genetic resources, democracy and biodiversity, transparency of biodiversity data, bio/ecosecurity • Ethical analysis of different conservation techniques and strategies such as de-extinction, natural vs. artificial biodiversity conservation, assisted migration, ecological restoration and rewilding • Analysis and critique of the biodiversity concept in environmental philosophy and promising alternative concepts We are open to presentations from different philosophical positions and traditions. We organise two sessions during the conference, and presentations will be grouped by their content with one session dedicated to more abstract deliberations in terms of conceptual analysis, value-theory, biodiversity as a philosophical problem etc. and a second session being primarily dedicated to application/policy-orientated normative questions. Especially welcome are abstracts that focus on a philosophical analysis of science, ethics, and policy. The WBF conference attracts an interdisciplinary academic audience that is interested in different aspects of biodiversity conservation. Therefore, we emphasize that presentations should address an interdisciplinary audience. Interested presenters will also have the opportunity to share their presentations in form of draft papers with the other thematic session participants before the conference to allow for further in-depth exchange (optional pre-read papers). Conveners Markku Oksanen, Department of Social Sciences, University of Eastern Finland, P.O.Box 1627, 70211 Kuopio, Finland, markku.oksanen@uef.fi Anna Deplazes Zemp, Department of Molecular Life Sciences, University of Zurich, anna.deplazeszemp@uzh.ch

252 CONSERVING BIODIVERSITY THROUGH EATING: IS THERE A CASE FOR VEGANISM?

Oral Presenter: Markku Oksanen (Kuopio, Finland) 09:30 – 09:45 15 min

https://fr.wikipedia.org/wiki/Lepomis_gibbosus

### 371 SHOULD NON-HUMAN ORGANISMS HAVE A RIGHT TO A LIVABLE LOCALITY? Oral Presenter: Simona Capisani (Durham, United Kingdom) 09:45 – 10:00 15 min

373 THREE DIMENSIONS OF URGENCY

Oral Presenter: Yasha Rohwer (Wilsonville, United States) Oral Presenter: Evelyn Brister (Rochester, United States) 10:00 – 10:15 15 min

3 dimensions of the concept of Urgency. Rarely well defined

408 SUSTAINABILITY AND HABITAT RIGHTS

Oral Presenter: Anna Wienhues (Oslo, Norway) 10:15 – 10:30 15 min

777 WHY BIODIVERSITY ETHICS?

Oral Presenter: Gesine Schepers (Bielefeld, Germany)

Plenary Lecture Plenary hall Thursday, June 20, 08:00 – 09:30 Ple_Thu_1 Plenary Thursday morning The diversity of life is constantly evolving and changing - forming the Tree of Life. The Tree of Life can be regarded as a unifying framework that can inform biodiversity conservation. Successful conservation of biodiversity also requires to recognise nature as a stakeholder. Our task is to recognise the needs of fellow species and to listening to nature to redress and correct past mistakes, and to move to a future where nature is restored to its rightful place.

Speakers: Jesús Pinto-Ledezma Evolutionary and quantitative ecologist, Department of Ecology, Evolution & Behavior at the University of Minnesota, United States, jpintole@umn.edu

Wynter Jamieson Worsthorne Intuitive Interspecies Communicator, founder Animaltalk Africa, wynter@animaltalkafrica.co.za 830 THE TREE OF LIFE AS A FOUNDATION FOR BASIC AND APPLIED RESEARCH Oral Presenter: Jesús Pinto-Ledezma (St. Paul, United States) 08:00 – 08:45 45 min 835 CONSULTING AND CO-CREATING WITH MOTHER NATURE FOR POSITIVE TRANSFORMATION Oral Presenter: Wynter J. Worsthorne (Sunvalley, South Africa)

Parallel Session (oral) Wisshorn Thursday, June 20, 09:30 – 11:00 HWBSDG_6.11 The Earth Metabolome Initiative Life is a complex, dynamic and yet precise interplay of chemical structures and their reactions, orchestrated across dimensions and scales – from the forming and breaking of chemical bonds to the cycling of carbon and nutrients through ecosystems, and from the diversification of molecules to the diversification of all species on Earth. These processes and their participants – metabolites – govern relationships of living beings to each other and the Earth system. Humans depend on the metabolites of other organisms for nutrition and medicines. Yet we have identified only a minute fraction (~0.02%) of the millions of metabolites estimated to be produced across the Tree of Life. This fundamental aspect of biodiversity is a treasure chest yet to be unlocked, and with every species lost it is sinking out of reach. By describing the ensemble of metabolites – the metabolome – of every organism, the Earth Metabolome Initiative (EMI) aims to reveal the mechanisms that orchestrate and maintain living systems. This information will be digitized and organized in an open knowledge base and accompanied by a metabolome biobank. An ongoing pilot project, the Digital Botanical Gardens Initiative (DBGI), is now developing open science workflows for digitization of chemodiversity from botanical collections. We expect the EMI to identify new ways to conserve, use and manage chemodiversity sustainably, thus directly contributing to the UN’s Sustainable Development Goals. This open session aims to bring together and align EMI members with researchers, practitioners and societal actors. Presentations will focus on the challenge posed by the EMI: to catalog, contextualize, interpret, and make open Earth’s chemodiversity. In doing so, we will evaluate how the EMI can advance life sciences, benefit society, and protect biodiversity – as well as invite participants to discuss and contribute to the future of the Earth Metabolome Initiative as it evolves. Conveners Pierre-Marie Allard, COMMONS Lab, Department of Biology, University of Fribourg, Chemin du Musée, 10 – CH1700 Fribourg, Switzerland, pierre-marie.allard@unifr.ch Emmanuel Defossez, Functional Ecology Laboratory, Institute of Biology, University of Neuchâtel, emmanuel.defossez@unine.ch Meredith C. Schuman, Spatial Genetics, Departments of Geography and Chemistry, University of Zurich, meredithchristine.schuman@uzh.ch The Earth Metabolome Initiative, an introduction. Oral Presenter: Pierre-Marie Allard (Fribourg, Switzerland) 09:30 – 09:45 15 min

814 THE EARTH BIOGENOME PROJECT: PROGRESS ON BIOLOGY’S MOONSHOT Oral Presenter: Harris Lewin (Tempe, United States) 09:45 – 10:15

inititate with Genome10K

2015-2017 strat of the EBP Sequencing the genome of all eukaryotik life 1.8 M species over 10 years. Launched at the Wellcome trust in London and WEF

GOAT created at the Wlcomme Sanger for the EBP

EBP coordinating council as for ambitions to set standards for the EBP and the related hubs

Standards recommendation for the Earth BioGenome Project

Develop standards EARLY in the project

EBP Committe Chairs

Governance structurebut NOT a legal entity

Collection, identifying and storing of the organisms is the bottelneck.

30 min 368 OCEAN METABOLOMICS FOR MARINE CHEMICAL ECOLOGY AND DRUG DISCOVERY RESEARCH Oral Presenter: Deniz Tasdemir (Kiel, Germany) 10:15 – 10:30 15 min

Most equipped centre for marine sample collection. They operate worldwide Ecometabolomics

514 GENOMIC DATA PRODUCTION SYSTEMS TO CATALOGUE AND EXPLORE EUKARYOTIC BIODIVERSITY Oral Presenter: Robert Waterhouse (Lausanne, Switzerland) 10:30 – 10:45 15 min

Note EMI: we need to show % of IUCN

587 MOLECULAR FEATURES OF PUSH-PULL INTERCROPPING SYSTEMS IN EAST AFRICA Oral Presenter: Jakob Lang (Zurich, Switzerland)

European Cell Atlas

Select a couple of pilots