Biodiversity Literature Repository

“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

“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

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

“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

“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

“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….”

Access to biodiversity for food production: Reconciling open access digital sequence information with access and benefit sharing: Molecular Plant

“Over the last 40 years or so, a complex web of international legal agreements was developed that regulate the access, transfer, and use of plant genetic resources. These include the Convention on Biological Diversity (CBD), the Nagoya Protocol, and the International Treaty on Plant Genetic Resources (Figure 1). In developing these legal regimes, policy makers struggled to balance a number of conflicting demands. These included ensuring that access providers share in the benefits that arise from the use of their genetic resources; that users who value-add to genetic resources can protect their innovations via intellectual property; and, at the same time, that scientists and breeders have ongoing access to genetic resources. While there are problems with the existing regimes, they have reached an uneasy compromise of sorts….”

 

 

Access to biodiversity for food production: Reconciling open assess digital sequence information with access and benefit sharing – ScienceDirect

“Over the last forty years or so, a complex web of international legal agreements were developed that regulate the access, transfer, and use of plant genetic resources. These include the Convention on Biological Diversity (CBD), the Nagoya Protocol, and the International Treaty on Plant Genetic Resources (Figure 1). In developing these legal regimes, policy makers struggled to balance a number of conflicting demands. These included ensuring that access providers share in the benefits that arise from the use of their genetic resources; that users who value-add to genetic resources can protect their innovations via intellectual property; and, at the same time, that scientists and breeders have ongoing access to genetic resources. While there are problems with the existing regimes, they have reached an uneasy compromise of sorts. In recent years, dramatic changes in the life sciences have threatened to undermine this complex and fragile balance (Unamba et al., 2015). These changes have been facilitated by new genomic technologies such as gene editing and synthetic biology (McDaniel and Weiss, 2005), by improved and cheaper sequencing technologies (Schaffer, 2007) which rapidly increased the availability of DNA sequence data, and advances in whole genome sequencing (Figure 1). Genomics is now a major source of data, rivalling big data disciplines like astronomy in the pace of data acquisition, storage, and analysis (Stephens et al., 2015). Open access international data repositories, such as GenBank, the DNA Databank of Japan, and European Molecular Biological Laboratory, that house a huge amount of DNA sequencerelated data (estimated at over 1.5 billion sequences) (WiLDSI , 2020) facilitate the sharing and use of digital sequence information (DSI) (Ad Hoc Technical Group on Digital Sequence Information 2015). The scientific value of public databases largely comes from the aggregation of data that allows scientists to identify patterns across the stored sequences (WiLDSI, 2020)….”

APEC Open Science Webinar & The 2020 APEC Science Prize For Innovation, Research & Education (ASPIRE)

The Academy of Science Malaysia (ASM), together with the Ministry of Science Technology and Innovation Malaysia (MOSTI) and the International Science Council-Regional Office for Asia and the Pacific (ISC ROAP) is pleased to invite you to the APEC Policy Sharing Webinar on Open Science & The 2020 ASPIRE Award Ceremony. The COVID-19 pandemic has triggered the need for sharing of data and information at an unprecedented scale which can be fulfilled by the paradigm of Open Science. Open Science represents a new approach to the scientific process based on cooperative work and new ways of disseminating knowledge by using digital technologies and new collaborative tools to address global challenges. The Webinar is aimed to build a community of purpose that works together to identify platform governance measures and technical know-how; and serves as a medium to share best practices in APEC economies and international policies for platform governance. An APEC PPSTI Statement on Open Science will be developed during the Webinar to promote engagement and knowledge sharing among APEC Economies through Open Science. In conjunction with APEC 2020, The Webinar will also feature the award ceremony of 2020 APEC Science Prize for Innovation, Research and Education (ASPIRE). It is an annual award which recognizes young scientists who have demonstrated a commitment to excellence in scientific research. The theme for this year is Biodiversity for a Prosperous Economy.

Access to scientific literature by the conservation community [PeerJ]

Abstract:  Access to the scientific literature is perceived to be a challenge to the biodiversity conservation community, but actual level of literature access relative to needs has never been assessed globally. We examined this question by surveying the constituency of the International Union for Conservation of Nature (IUCN) as a proxy for the conservation community, generating 2,285 responses. Of these respondents, ?97% need to use the scientific literature in order to support their IUCN-related conservation work, with ?50% needing to do so at least once per week. The crux of the survey revolved around the question, “How easy is it for you currently to obtain the scientific literature you need to carry out your IUCN-related work?” and revealed that roughly half (49%) of the respondents find it not easy or not at all easy to access scientific literature. We fitted a binary logistic regression model to explore factors predicting ease of literature access. Whether the respondent had institutional literature access (55% do) is the strongest predictor, with region (Western Europe, the United States, Canada, Australia and New Zealand) and sex (male) also significant predictors. Approximately 60% of respondents from Western Europe, the United States, Canada, Australia and New Zealand have institutional access compared to ?50% in Asia and Latin America, and ?40% in Eastern Europe and in Africa. Nevertheless, accessing free online material is a popular means of accessing literature for both those with and without institutional access. The four journals most frequently mentioned when asked which journal access would deliver the greatest improvements to the respondent’s IUCN-related work were Conservation Biology, Biological Conservation, Nature, and Science. The majority prefer to read journal articles on screen but books in hard copy. Overall, it is apparent that access to the literature is a challenge facing roughly half of the conservation community worldwide.

 

Biologer: an open platform for collecting biodiversity data

Abstract:  Background

We have developed a new platform named “Biologer” intended for recording species observations in the field (but also from literature resources and collections). The platform is created as user-friendly, open source, multilingual software that is compatible with Darwin Core standard and accompanied by a simple Android application. It is made from the user’s perspective, allowing everyone to choose how they share the data. Project team members are delegated by involved organisations. The team is responsible for development of the platform, while local Biologer communities are engaged in data collection and verification.

New information

Biologer has been online and available for use in Serbia since 2018 and was soon adopted in Croatia and Bosnia and Herzegovina. In total, we have assembled 536 users, who have collected 163,843 species observation records data from the field and digitalised 33,458 literature records. The number of active users and their records is growing daily. Out of the total number of gathered data, 89% has been made open access by the users, 10% is accessible on the scale of 10×10 km and only 1% is closed. In the future, we plan to provide a taxonomic data portal that could be used by local and national initiatives in Eastern Europe, aggregate all data into a single web location, create detailed data overview and enable fluent communication between users.

Biologer: an open platform for collecting biodiversity data

Abstract:  Background

We have developed a new platform named “Biologer” intended for recording species observations in the field (but also from literature resources and collections). The platform is created as user-friendly, open source, multilingual software that is compatible with Darwin Core standard and accompanied by a simple Android application. It is made from the user’s perspective, allowing everyone to choose how they share the data. Project team members are delegated by involved organisations. The team is responsible for development of the platform, while local Biologer communities are engaged in data collection and verification.

New information

Biologer has been online and available for use in Serbia since 2018 and was soon adopted in Croatia and Bosnia and Herzegovina. In total, we have assembled 536 users, who have collected 163,843 species observation records data from the field and digitalised 33,458 literature records. The number of active users and their records is growing daily. Out of the total number of gathered data, 89% has been made open access by the users, 10% is accessible on the scale of 10×10 km and only 1% is closed. In the future, we plan to provide a taxonomic data portal that could be used by local and national initiatives in Eastern Europe, aggregate all data into a single web location, create detailed data overview and enable fluent communication between users.

iNaturalist – SciStarter

“iNaturalist is a place where you can record what you see in nature, meet other nature lovers, and learn about the natural world. It is also a crowdsourced species identification system and an organism occurrence recording tool. You can use it to record your own observations, get help with identifications, collaborate with others to collect this kind of information for a common purpose, or access the observational data collected by iNaturalist users.

From hikers to hunters, birders to beach-combers, the world is filled with naturalists, and many of us record what we find. What if all those observations could be shared online? You might discover someone who finds beautiful wildflowers at your favorite birding spot, or learn about the birds you see on the way to work. If enough people recorded their observations, it would be like a living record of life on Earth that scientists and land managers could use to monitor changes in biodiversity, and that anyone could use to learn more about nature.

That’s the vision behind iNaturalist.org. So if you like recording your findings from the outdoors, or if you just like learning about life, join us!”

Plazi and Pensoft join forces to let biodiversity knowledge of coronaviruses hosts out | EurekAlert! Science News

“Pensoft’s flagship journal ZooKeys invites free-to-publish research on key biological traits of SARS-like viruses potential hosts and vectors; Plazi harvests and brings together all relevant data from legacy literature to a reliable FAIR-data repository.”

Access to Scientific Literature by the Conservation Community | bioRxiv

AbsAccess to the scientific literature is perceived to be a challenge to the biodiversity conservation community, but actual level of literature access relative to needs has never been assessed globally. We examined this question by surveying the constituency of the International Union for Conservation of Nature (IUCN) as a proxy for the conservation community, generating 2,285 responses. Of these respondents, ~97% need to use the scientific literature in order to support their IUCN-related conservation work, with ~50% needing to do so at least once per week. The crux of the survey revolved around the question, “How easy is it for you currently to obtain the scientific literature you need to carry out your IUCN-related work?” and revealed that roughly half (49%) of the respondents find it not easy or not at all easy to access scientific literature. We fitted a binary logistic regression model to explore factors predicting ease of literature access. Whether the respondent had institutional literature access (55% do) is the strongest predictor, with region (Western Europe, the United States, Canada, Australia and New Zealand) and gender (male) also significant predictors. Approximately 60% of respondents from Western Europe, the United States, Canada, Australia and New Zealand have institutional access compared to ~50% in Asia and Latin America, and ~40% in Eastern Europe and in Africa. Nevertheless, accessing free online material is a popular means of accessing literature for both those with and without institutional access. The four journals most frequently mentioned when asked which journal access would deliver the greatest improvements to the respondent’s IUCN-related work were Conservation Biology, Biological Conservation, Nature, and Science. The majority prefer to read journal articles on screen but prefer to read books in hard copy. Overall, it is apparent that access to the literature is a challenge facing roughly half of the conservation community worldwide.