Category Archives: oa.biodiversity

Dynamic visualisation of million?tip trees: The OneZoom project – Wong – – Methods in Ecology and Evolution – Wiley Online Library

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Abstract:  

 

The complete tree of life is now available, but methods to visualise it are still needed to meet needs in research, teaching and science communication. Dynamic visualisation of million-tip trees requires many challenges in data synthesis, data handling and computer graphics to be overcome.
Our approach is to automate data processing, synthesise data from a wide range of available sources, then to feed these data to a client-side visualisation engine in parts. We develop a way to store the whole tree topology locally in a highly compressed form, then dynamically populate metadata such as text and images as the user explores.
The result is a seamless and smooth way to explore the complete tree of life, including images and metadata, even on relatively old mobile devices.
The underlying methods developed have applications that transcend tree of life visualisation. For the whole complete tree, we describe automated ID mappings between well known resources without resorting to taxonomic name resolution, automated methods to collate sets of public domain representative images for higher taxa, and an index to measure public interest of individual species.
The visualisation layout and the client user interface are both abstracted components of the codebase enabling other zoomable tree layouts to be swapped in, and supporting multiple applications including exhibition kiosks and digital art.
After 10 years of work, our tree of life explorer is now broadly complete, it has attracted nearly 1.5 million online users, and is backed by a novel long-term sustainability plan. We conclude our description of the OneZoom project by suggesting the next challenges that need to be solved in this field: extinct species and guided tours around the tree.”

“The Google Earth of Biology” – Visually Stunning Tree of All Known Life Unveiled Online

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“The OneZoom explorer – available at onezoom.org – maps the connections between 2.2 million living species, the closest thing yet to a single view of all species known to science. The interactive tree of life allows users to zoom in to any species and explore its relationships with others, in a seamless visualisation on a single web page. The explorer also includes images of over 85,000 species, plus, where known, their vulnerability to extinction.

OneZoom was developed by Imperial College London biodiversity researcher Dr. James Rosindell and University of Oxford evolutionary biologist Dr. Yan Wong. In a paper published today in Methods in Ecology and Evolution, Drs Wong and Rosindell present the result of over ten years of work, gradually creating what they regard as “the Google Earth of biology.” …”

Dr. Wong added: “It’s extraordinary how much research there is still to be done. Building the OneZoom tree of life was only possible through sophisticated methods to gather and combine existing data – it would have been impossible to curate all this by hand.”

Open Data Practices among Users of Primary Biodiversity Data | BioScience | Oxford Academic

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Abstract:  Presence-only biodiversity data are increasingly relied on in biodiversity, ecology, and conservation research, driven by growing digital infrastructures that support open data sharing and reuse. Recent reviews of open biodiversity data have clearly documented the value of data sharing, but the extent to which the biodiversity research community has adopted open data practices remains unclear. We address this question by reviewing applications of presence-only primary biodiversity data, drawn from a variety of sources beyond open databases, in the indexed literature. We characterize how frequently researchers access open data relative to data from other sources, how often they share newly generated or collated data, and trends in metadata documentation and data citation. Our results indicate that biodiversity research commonly relies on presence-only data that are not openly available and neglects to make such data available. Improved data sharing and documentation will increase the value, reusability, and reproducibility of biodiversity research.

Creating a Campaign to Increase Open Access to Research on Climate Science and Biodiversity: A joint initiative of Creative Commons, EIFL and SPARC

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Open Science No Text Logo

Open Science No Text. By: Greg Emmerich. CC BY-SA 3.0

As the United Nations Climate Change Conference, officially known as the 26th Conference of Parties, or COP26, continues in Glasgow, Scotland, I’m pleased to share some good news. The Open Society Foundations approved funding for Creative Commons, SPARC and EIFL to lead a global campaign promoting open access to climate and biodiversity research. This is a promising new strategy to encourage governments, foundations, institutes, universities and environmental organizations to use “open” to accelerate progress towards solving the climate crisis and to preserve global biodiversity. Catherine Stihler, CC’s CEO and a native of Scotland, publicly announced the campaign during her keynote at the University of St Andrews’ Power to the people event and will have the opportunity to announce the campaign at a COP26 fringe event – Open UK: Open Technology for Sustainability – on 11 November. CC is particularly happy to have the opportunity to work closely with our longtime allies in the open access movement to ensure that this effort is truly a global campaign, and hope that this initiative will help to provide a blueprint for future funding of similar collaborative campaigns.

Additional Detail

Climate change, and the resulting harm to our global biodiversity, is one of the world’s most pressing challenges. The complexity of the climate crisis requires collaborative global interventions that center on equity and evidence-based mitigation practices informed by multidisciplinary research. Many researchers, governments, and global environmental organizations recognize the importance of the open sharing of research to accelerate progress, but lack cohesive strategies and mechanisms to facilitate effective knowledge sharing and collaboration across disciplinary and geographic borders. 

During the COVID-19 crisis, the power of open access to democratize knowledge sharing, accelerate discovery, promote research collaboration, and bring together the efforts of global stakeholders to tackle the pandemic took center stage. Scientists embraced the immediate, open sharing of preprints, research articles, data and code. This embrace of openness contributed to the rapid sequencing and sharing of the virus’ genome, the quick development of therapeutics, and the fastest development of effective vaccines in human history. The lessons learned during the pandemic can – and should – be applied to accelerate progress on other urgent problems facing society. 

The goal of this project is to create a truly global campaign to promote open access, open science and open data as effective enabling strategies to accelerate progress towards solving the climate crisis and preserving global biodiversity. It will develop effective messaging, strategies, and tactics to empower stakeholders currently leading critical climate and biodiversity work to embed open practices and policies in their operations, and make open sharing of research the default.  

We expect to identify the most important climate and biodiversity research publications not already OA and coordinate a campaign to open those publications, remove legal and policy barriers to applying open licenses to research articles, influence key funders (governments, foundations, and institutes) of climate science and biodiversity research to adopt and implement strong OA policies, and identify opportunities to open climate and biodiversity educational resources so students, teachers and citizens can learn about these global challenges and help contribute to solutions.

We will encourage global environment organizations to adopt open licensing policies to ensure all their content is free to be reused, built upon and shared for the global public good, delivering on their SDG commitments. We will engage with researchers, universities and policy makers in the Global South to ensure inclusive outcomes throughout.

We will share additional news on this campaign as it progresses.

The post Creating a Campaign to Increase Open Access to Research on Climate Science and Biodiversity: A joint initiative of Creative Commons, EIFL and SPARC appeared first on Creative Commons.

Closing the knowledge-action gap in conservation with open science

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Abstract:  The knowledge-action gap in conservation science and practice occurs when research outputs do not result in actions to protect or restore biodiversity. Among the diverse and complex reasons for this gap, three barriers are fundamental: knowledge is often unavailable to practitioners, challenging to interpret, and/or difficult to use. Problems of availability, interpretability, and useability are solvable with open science practices. We consider the benefits and challenges of three open science practices for use by conservation scientists and practitioners. First, open access publishing makes the scientific literature available to all. Second, open materials (methods, data, code, and software) increase the transparency and (re)use potential of research findings. Third, open education resources allow conservation professionals (scientists and practitioners) to acquire the skills needed to make use of research outputs. The long-term adoption of open science practices would help researchers and practitioners achieve conservation goals more quickly and efficiently, in addition to reducing inequities in information sharing. However, short-term costs for individual researchers (insufficient institutional incentives to engage in open science and knowledge mobilization) remain a challenge to overcome. Finally, we caution against a passive approach to sharing that simply involves making information available. We advocate for a proactive stance towards transparency, communication, collaboration, and capacity building that involves seeking out and engaging with potential users to maximize the environmental and societal impact of conservation science.

 

Let me count the ways: Obstacles and opportunities for access to conservation literature | IUCN World Conservation Congress 2020

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“The panel discussion aims to offer an opportunity for conversation among the all-too-often siloed players responsible for producing and providing access to conservation literature—researchers, librarians, and publishers—to spark ideas and ultimately, solutions, for how to ensure access to literature and strengthen the scientific underpinnings of nature conservation efforts.”

IUCN To Boost Open Access To Conservation Knowledge | Scoop News

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“Thanks to a 3-year grant from the Arcadia Fund – a charitable fund of Lisbet Rausing and Peter Baldwin – the International Union for Conservation of Nature (IUCN) will be able to promote and improve researchers’ open access to high-quality conservation knowledge.

The grant will support IUCN in advancing and promoting principles of open access through scholarly communications amongst IUCN’s membership and expert network. It will also allow IUCN to digitize its back catalogue of publications and to develop an open access policy….”

Keep digital sequence information a common good

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“The political debate surrounding digital sequence information (DSI) on genetic resources under the Convention on Biological Diversity (CBD) has garnered immense interest and raised concern across the international scientific community. At the last CBD Conference of the Parties (COP 14), parties formally “agreed to resolve their differences” and, thus, with COP 15 set for October 2021, a decision on DSI and access and benefit-sharing (ABS) approaches.

Disrupting the flow of open DSI has the potential to not only severely hinder basic research and biodiversity conservation, but also innovation more broadly. This includes science and technology that addresses challenges in food security, health, biodiversity loss, and climate change worldwide, which could ultimately undermine progress on the Sustainable Development Goals (SDGs). What’s at stake is best highlighted by the global SARS-CoV-2 pandemic: diagnostic kits within weeks of virus discovery, vaccines ten months later, and ongoing surveillance for variants, all possible thanks to rapid DNA sequencing and open DSI….” 

Biodiversity Digitization 2021 | iDigBio

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“The first two decades of the 21st century have seen huge gains in the digitization and mobilization of the world’s biodiversity data. Natural history museums and biodiversity collections on virtually every continent have collaborated across the globe to develop and harness a suite of emerging technologies and efficiencies. These tools have liberated data from millions of species occurrence and biodiversity specimen records and fueled an ever-expanding network of high-quality research. This conference is dedicated to celebrating these successes and to inspiring development of an even greater palette of accomplishments in the decades to come. To provide a world update on these achievements, the U.S. National Museum of Natural History – Smithsonian (NMNH), Integrated Digitized Biocollections (iDigBio), and Global Biodiversity Information Facility (GBIF) cordially invite you to attend Biodiversity Digitization: Celebrating a Decade of Progress, a jointly sponsored virtual event to be held September 22-23, 2021.”

Biodiversity Literature Repository

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“The Biodiversity Literature Repository (BLR) has been growing from a community on Zenodo to be a service dedicated to liberate and make open access, FAIR (findable, accessible, interoperable and reusable) data hidden in the hundreds of millions of pages of scholarly publications.

It is built on top of Zenodo, a digital repository hosted at CERN, which provides a sustainable and robust infrastructure for long tail research data, which can consist of small datasets that otherwise would be lost.

Originally a collaboration between Zenodo, Plazi and Pensoft, BLR began as a repository for taxonomic publications which lacked Digital Object Identifiers (DOI) and thus were effectively orphaned from the network of online citations. As it grew its scope expanded to morphed into a highly interlinked repository that focuses on include illustrations and taxonomic treatments contained in publications with all these content types interlinked among themselves and enhanced with and rich metadata.

The source data for BLR are scholarly publications that are most often in PDF or html format but sometimes in XML formats whose structured data facilitates the automated data extraction.

The largest data users are the Global Biodiversity Information Facility (GBIF) and the United States’ National Center for Biotechnology Information (NCBI).

Support of BLR comes from the Arcadia Fund and the three partner institutions Zenodo, Plazi and Pensoft.”

Biodiversity Heritage Library and Plazi: Biodiversity Literature Repository

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“This document describes the cooperation and collaboration of BHL and Plazi, on common goals. It outlines common goals and areas of common interests, and clarifies key areas of responsibility. The digital arena allows building a large corpus of literature and from that a “graph” of knowledge or knowledge graph through identification, extraction and linking of data. It provides an emerging access platform to the knowledge beyond the conventional traditional human-reader focused access. It allows new modes of access, including text and data mining, search, visualization and the discovery of new findings based on the accessibility of data. This knowledge graph does not replace existing media, but rather complements them. In the case of biodiversity sciences, it is based on both the estimated 500 Million pages of biodiversity literature and on increasingly born-digital publications. In biodiversity, the very rich data centric publications with the highly sophisticated implicit citation networks are a perfect base to build such a knowledge graph. In order to build the knowledge graph, the data in the publications must be liberated and made open, findable, accessible, interoperable, reusable (FAIR) for machine use. This is the necessary additional step after the digitization of existing literature….”

Language extinction triggers the loss of unique medicinal knowledge | PNAS

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Abstract:  The United Nations proclamation of 2022–2032 as the International Decade of Indigenous Languages aims to raise global awareness about their endangerment and importance for sustainable development. Indigenous languages contain the knowledge that communities have about their surrounding plants and the services they provide. The use of plants in medicine is a particularly relevant example of such ecosystem services. Here, we find that most medicinal knowledge is linguistically unique—i.e., known by a single language—and more strongly associated with threatened languages than with threatened plants. Each indigenous language is therefore a unique reservoir of medicinal knowledge—a Rosetta stone for unraveling and conserving nature’s contributions to people.

 

The Global Extinction of Languages Is Threatening a Vital Type of Human Knowledge

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“As human languages are driven to extinction around the world, a verbal encyclopedia of medical knowledge is on the brink of being forgotten.

Among 12,495 medicinal uses for plants in indigenous communities, new research has found over 75 percent of those plants are each tied to just one local language. If these unique words trickle out of use, so too may the knowledge they contain….

Language extinction is a tragic phenomenon that’s been occurring worldwide, as languages spoken by precious few people are replaced by larger ones. Roughly one language ceases to be spoken every four months, and 3,054 languages are currently endangered around the world….

The vast majority of plant species in the study were found to have medical properties described in just one indigenous language, many of which are themselves endangered….

In North America, for instance, the authors found waning indigenous languages held 86 percent of all unique knowledge on plant medicine. In the northwest Amazon, on the other hand, 100 percent of medicinal plant knowledge is restricted to languages on the edge of extinction. …”

What Is BHL’s New Persistent Identifier Working Group DOI’ng? – Biodiversity Heritage Library

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“In October 2020, BHL launched a new working group with a momentous goal: to make the content on BHL persistently discoverable, citable and trackable using DOIs (Digital Object Identifiers)….

BHL has been retrospectively minting DOIs for historic publications since 2011, but the focus has primarily been on monographs. BHL’s new Persistent Identifier Working Group (PIWG) is (at least initially) focusing on journal articles. Minting DOIs for articles on BHL is a far more complex and time-consuming task than minting DOIs for monographs. This is because article DOIs need article data: every journal volume uploaded onto BHL must be accompanied by journal and volume data, but there is no requirement that contributors provide article data….

COVID-19 provided an unexpected opportunity to make a considerable dent in this work. With no access to scanners or library materials, a number of BHL contributors, including Harvard University Libraries, Muséum National d’Histoire Naturelle and BHL Australia, pivoted from making new content accessible to making their existing content on BHL more discoverable. For example, BHL Australia’s digitisation volunteers gathered, gap filled and checked article-level metadata for over 30,000 articles in 2020….”

Science Academies of G-7 Nations Call for Action to Reach Net-Zero Emissions, Reverse Declines in Biodiversity, and Improve Data-Sharing to Prepare for Future Health Emergencies | National Academies

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“Science academies from the G-7 nations today issued three statements recommending that their governments take urgent action to build a net-zero emissions, climate-resilient future, reverse global declines in biodiversity, and improve data-sharing for future health emergencies.   

The statements are intended to inform discussions during the G-7 summit in June to be held in the United Kingdom, as well as ongoing policymaking….”