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. …”

Abuse of ORCID’s weaknesses by authors who use paper mills | SpringerLink

Abstract:  In many countries around the world that use authorship and academic papers for career advancement and recognition, the accurate identity of participating authors is vital. ORCID (Open Researcher and Contributor ID), an author disambiguation tool that was created in 2012, is being vociferously implemented across a wide swathe of journals, including by many leading publishers. In some countries, authors who publish in indexed journals, particularly in journals that carry a Clarivate Analytics’ Journal Impact Factor, are rewarded, sometimes even monetarily. A strong incentive to cheat and abuse the publication ethos thus exists. There has been a recent spike in the detection of papers apparently derived from paper mills that have multiple issues with figures. The use of such figures across many papers compromises the integrity of the content in all those papers, with widespread ramifications for the integrity of the biomedical literature and of journals that may be gamed by academics. The use of ORCID does not guarantee the authenticity of authors associated with a paper mill-derived paper, nor does it fortify the paper’s integrity. These weaknesses of ORCID may dampen trust in this tool, especially if the ORCID platform is being populated by “ghost” (empty) ORCID accounts of academics whose identities cannot be clearly verified, or disposable accounts (perhaps created by paper mill operators) that are used only once, exclusively to pass the paper submission step. Open-source forensic tools to assist academics, editors and publishers to detect problematic figures, and more stringent measures by ORCID to ensure robust author identity verification, are urgently required to protect themselves, and the wider biomedical literature.

 

Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols | Nucleic Acids Research | Oxford Academic

Abstract:  Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interoperability and Reusability (FAIR) of computational resources, thereby promoting the reproducibility of complex bioinformatics analyses. Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a centralized catalogue of scientific software. The ready-to-use packaging of hundreds of tools and workflows, combined with the implementation of interoperability standards, enables users to launch analyses across multiple environments. Dockstore is widely used, more than twenty-five high-profile organizations share analysis collections through the platform in a variety of workflow languages, including the Broad Institute’s GATK best practice and COVID-19 workflows (WDL), nf-core workflows (Nextflow), the Intergalactic Workflow Commission tools (Galaxy), and workflows from Seven Bridges (CWL) to highlight just a few. Here we describe the improvements made over the last four years, including the expansion of system integrations supporting authors, the addition of collaboration features and analysis platform integrations supporting users, and other enhancements that improve the overall scientific reproducibility of Dockstore content.

 

 

SORTEE (SOCIETY FOR OPEN, RELIABLE, AND TRANSPARENT ECOLOGY AND EVOLUTIONARY BIOLOGY)

“SORTEE is a service organization which brings together researchers working to improve reliability and transparency through cultural and institutional changes in ecology, evolutionary biology, and related fields broadly defined. Anyone interested in improving research in these disciplines is welcome to join, regardless of experience. The society is international in scope, membership, and objectives.is a service organization which brings together researchers working to improve reliability and transparency through cultural and institutional changes in ecology, evolutionary biology, and related fields broadly defined. Anyone interested in improving research in these disciplines is welcome to join, regardless of experience. The society is international in scope, membership, and objectives….”

 

Fee-free Open Access publishing in leading biological science journals now available to researchers in developing and transition economy countries

“From Albania to Zimbabwe, researchers in 30 developing and transition economy countries can benefit from immediate and fee-free Open Access publishing in The Company of Biologists’ subscription journals following a Read & Publish agreement with Electronic Information for Libraries (EIFL).

This landmark agreement runs until 31 December 2023 and institutional members of EIFL-partner library consortia in eligible countries can participate free of charge.

Researchers in eligible countries will be able to publish an uncapped number of Open Access research articles in Development, Journal of Cell Science and Journal of Experimental Biology without paying an article processing charge (APC). They will also benefit from free and unlimited access to the journals and their archives dating back to 1853….”