Category Archives: oa.biodiversity

BiCIKL continues to update project outcomes in own collection in RIO Journal |

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“The dynamic open-science project collection of BiCIKL, titled “Towards interlinked FAIR biodiversity knowledge: The BiCIKL perspective” (doi: 10.3897/rio.coll.105), continues to grow, as the project progresses into its third year and its results accumulate ever so exponentially. 

Following the publication of three important BiCIKL deliverables: the project’s Data Management Plan, its Visual identity package and a report, describing the newly built work?ow and tools for data extraction, conversion and indexing and the user applications from OpenBiodiv, there are currently 30 research outcomes in the BiCIKL collection that have been shared publicly to the world, rather than merely submitted to the European Commission.

Shortly after the BiCIKL project started in 2021, a project-branded collection was launched in the open-science scholarly journal Research Ideas and Outcomes (RIO). There, the partners have been publishing – and thus preserving – conclusive research papers, as well as early and interim scientific outputs….”

Open data to achieve the EU green transition | data.europa.eu

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“To achieve the EU Green Deal and a to achieve a fair green and digital transition across Europe, access to data (open as well as private) is crucial. These data can provide users with information, e.g. through interactive maps or dashboards. It can also be used to create services that open the way to and speed up the process towards, for example, climate neutrality, reduction of greenhouse gas (GHG) emissions, improvement of energy efficiency and restoring biodiversity….

Across Europe, public institutions and private companies are using (open) data to develop services. Some examples are:…”

 

A new open-access platform to bring greater oversight of deforestation risks – SPOTT.org | SPOTT.org

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“ZSL [Zoological Society of London], as a sub-grantee alongside Global Canopy, will be launching a revolutionary platform in 2022 bringing together the best data available on corporate exposure to, and reporting on, deforestation and other related environmental, social and governance (ESG) issues.

The project aims to provide market-leading data to help financial institutions identify risks and find opportunities for sustainable investments to meet the growing demand for responsible financial products in light of the biodiversity and climate crises.

The database will be underpinned by the data collected through ZSL’s SPOTT assessments, Global Canopy’s Forest 500 assessments and the Stockholm Environment Institute, Global Canopy and Neural Alpha’s Trase Supply Chains and Trase Finance data, and will be aligned with the Accountability Framework Initiative and its guidance.

Supported by a five-year grant from the Norwegian government, the resulting data and metrics will provide a more comprehensive view of company performance on deforestation, conversion and associated human rights risks. The dataset will also provide broader coverage of the most exposed forest risk supply chains (in particular: palm oil, soy, timber, pulp, rubber and cattle products) and geographies where corporate performance data on these topics is currently missing. By mapping and integrating data from aligned initiatives and external datasets, more complete and in-depth coverage of corporate performance data will be available….”

Wikidata and the bibliography of life [PeerJ]

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Abstract:  Biological taxonomy rests on a long tail of publications spanning nearly three centuries. Not only is this literature vital to resolving disputes about taxonomy and nomenclature, for many species it represents a key source—indeed sometimes the only source—of information about that species. Unlike other disciplines such as biomedicine, the taxonomic community lacks a centralised, curated literature database (the “bibliography of life”). This article argues that Wikidata can be that database as it has flexible and sophisticated models of bibliographic information, and an active community of people and programs (“bots”) adding, editing, and curating that information.

 

Celebrating 30 years of scholarly publishing at Pensoft! | Blog

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“Openly accessible and digital-first since the very start, the ZooKeys journal was born on a sunny morning in California during the Entomological Society of America meeting in 2007, when Prof Lyubomir Penev and his renowned colleague Dr Terry Erwin from the Smithsonian Institution agreed over breakfast that zoologists from around the world could indeed use a new-age taxonomic journal. What the community at the time was missing was a scholarly outlet that would not only present a smooth fast track for their research papers, while abiding by the highest and most novel standards in the field, but do so freely and openly to any reader at any time and in any place. Fast forward to 2021, ZooKeys remains the most prolific open-access journal in zoology….”

 

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

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“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

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“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

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“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

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“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)

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“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

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“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

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“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

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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)

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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

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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.”