Supporting knowledge creation and sharing by building a standardised interconnected repository of biodiversity data | Zenodo

“This EOSC in practice story was developed within the Cos4cloud project and targets a very wide user base as it is addressed to any researchers, teachers, students, companies, institutions and, more generally, anyone interested in knowing, studying or analysing biodiversity information.

The story presents Cos4Bio, a co-designed, interoperable and open-source service that integrates biodiversity observations from multiple citizen observatories in one place, allowing experts to save time in the species identification process and get access to an enormous number of biodiversity observations. This resource is available on the EOSC Portal Catalogue and Marketplace …”

Supporting knowledge creation and sharing by building a standardised interconnected repository of biodiversity data | EOSC Portal

“This EOSC in practice story targets a very wide user base as it is addressed to any researchers, teachers, students, companies, institutions and, more generally, anyone interested in knowing, studying or analysing biodiversity information. It was developed within the Cos4cloud project….

Cos4Bio is a co-designed, interoperable and open-source service that integrates biodiversity observations from multiple citizen observatories in one place, allowing experts to save time in the species identification process and get access to an enormous number of biodiversity observations….”

The Vast Library of Life: 15 Years of the BHL Portal – Biodiversity Heritage Library

“It seems like we are on an anniversary splurge. In April, I marked my 10th year as BHL Program Director. Today is a more important date in BHL history. May 9, 2007 marked the official launch of BHL content on the web. We celebrated that day with one of our first BHL blog posts (Biodiversity Heritage Library and Encyclopedia of Life Launch!). On that launch date, BHL had 306 titles, 3,236 volumes, and 1,271,664 pages of taxonomic literature. Today, BHL has grown to become a global consortium of natural history, botanical, research, and national libraries and hosts over 60 million pages and more than 281,000 volumes….”

How research is being transformed by open data and AI | Popular Science

“How iNaturalist can correctly recognize (most of the time, at least) different living organisms is thanks to a machine-learning model that works off of data collected by its original app, which first debuted in 2008 and is simply called iNaturalist. Its goal is to help people connect to the richly animated natural world around them. 

The iNaturalist platform, which boasts around 2 million users, is a mashup of social networking and citizen science where people can observe, document, share, discuss, learn more about nature, and create data for science and conservation. Outside of taking photos, the iNaturalist app has extended capabilities compared to the gamified Seek. It has a news tab, local wildlife guides, and organizations can also use the platform to host data collection “projects” that focus on certain areas or certain species of interest. 

When new users join iNaturalist, they’re prompted to check a box that allows them to share their data with scientists (although you can still join if you don’t check the box). Images and information about their location that users agree to share are tagged with a creative commons license, otherwise, it’s held under an all-rights reserved license. About 70 percent of the app’s data on the platform is classified as creative commons. “You can think of iNaturalist as this big open data pipe that just goes out there into the scientific community and is used by scientists in many ways that we’re totally surprised by,” says Scott Loarie, co-director of iNaturalist. …

But with an ever-growing amount of data, our ability to wrangle these numbers and stats manually becomes virtually impossible. “You would only be able to handle these quantities of data using very advanced computing techniques. This is part of the scientific world we live in today,” Durant adds….

Another problem that researchers have to consider is maintaining the quality of big datasets, which can impinge on the effectiveness of analytics tools. This is where the peer-review process plays an important role….”

 

Biodiversity Community Integrated Knowledge Library (BiCIKL)

“BiCIKL will catalyse a culture change in the way biodiversity data is identified, linked, integrated and re-used across the research cycle. We will cultivate a more transparent, trustworthy and efficient research ecosystem.

BiCIKL will launch a new European starting community of key research infrastructures, researchers, citizen scientists and other stakeholders in the biodiversity and life sciences based on open science practices through access to data, tools and services.

BiCIKL is building the Biodiversity Knowledge Hub (BKH) – a single knowledge portal to interlinked and machine-readable FAIR data (Findable, Accessible, Interoperable and Reusable) using unique stable identifiers on specimens, genomics, observations, taxonomy and publications….”

 

Library as Laboratory: Analyzing Biodiversity Literature at Scale

“Imagine the great library of life, the library that Charles Darwin said was necessary for the “cultivation of natural science” (1847). And imagine that this library is not just hundreds of thousands of books printed from 1500 to the present, but also the data contained in those books that represents all that we know about life on our planet. That library is the Biodiversity Heritage Library (BHL) The Internet Archive has provided an invaluable platform for the BHL to liberate taxonomic names, species descriptions, habitat description and much more. Connecting and harnessing the disparate data from over five-centuries is now BHL’s grand challenge. The unstructured textual data generated at the point of digitization holds immense untapped potential. Tim Berners-Lee provided the world with a semantic roadmap to address this global deluge of dark data and Wikidata is now executing on his vision. As we speak, BHL’s data is undergoing rapid transformation from legacy formats into linked open data, fulfilling the promise to evaporate data silos and foster bioliteracy for all humankind….”

First-of-its-kind global catalog of bird shapes yields ecological ‘gold mine’ | Science | AAAS

“Now, a team of 115 researchers from 30 countries, led by Sheard’s Ph.D. adviser, Imperial College London ecologist Joseph Tobias, has published anatomical measurements of all 11,009 living bird species—not just passerines such as robins, but everything from ducks and penguins to vultures and ostriches. “It’s a gold mine,” says geneticist Nancy Chen of the University of Rochester, who was not involved in the project.

The open-source data set, called AVONET, debuts this month in a special issue of Ecology Letters along with papers describing its value for studying bird evolution and ecology, as well as the impact of changes in climate and habitat on vulnerable species. “For the first time, we are gaining a global, quantitative perspective on bird biodiversity, which is really amazing,” says ecologist Brian Enquist of the University of Arizona….”

AVONET: morphological, ecological and geographical data for all birds – Tobias – 2022 – Ecology Letters – Wiley Online Library

Abstract:  Functional traits offer a rich quantitative framework for developing and testing theories in evolutionary biology, ecology and ecosystem science. However, the potential of functional traits to drive theoretical advances and refine models of global change can only be fully realised when species-level information is complete. Here we present the AVONET dataset containing comprehensive functional trait data for all birds, including six ecological variables, 11 continuous morphological traits, and information on range size and location. Raw morphological measurements are presented from 90,020 individuals of 11,009 extant bird species sampled from 181 countries. These data are also summarised as species averages in three taxonomic formats, allowing integration with a global phylogeny, geographical range maps, IUCN Red List data and the eBird citizen science database. The AVONET dataset provides the most detailed picture of continuous trait variation for any major radiation of organisms, offering a global template for testing hypotheses and exploring the evolutionary origins, structure and functioning of biodiversity.

 

Biodiversity Community Integrated Knowledge Library (BiCIKL)

Abstract:  BiCIKL is an European Union Horizon 2020 project that will initiate and build a new European starting community of key research infrastructures, establishing open science practices in the domain of biodiversity through provision of access to data, associated tools and services at each separate stage of and along the entire research cycle. BiCIKL will provide new methods and workflows for an integrated access to harvesting, liberating, linking, accessing and re-using of subarticle-level data (specimens, material citations, samples, sequences, taxonomic names, taxonomic treatments, figures, tables) extracted from literature. BiCIKL will provide for the first time access and tools for seamless linking and usage tracking of data along the line: specimens > sequences > species > analytics > publications > biodiversity knowledge graph > re-use.

 

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

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

 

“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

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

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

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

“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.”