Did You Ask for Citations? An Insight into Preprint Citations en route to Open Science

Abstract:  This study investigates citation patterns between 2017 and 2020 for preprints published in three preprint servers, one specializing in biology (bioRxiv), one in chemistry (ChemRxiv), and another hosting preprints in all disciplines (Research Square). Showing evidence that preprints are now regularly cited in peer reviewed journal articles, books, and conference papers, the outcomes of this investigation further substantiate the value of open science also in relation to citation-based metrics on which the evaluation of scholarship continues to rely on. This analysis will be useful to inform new research-based education in today’s scholarly communication. View Full-Text

 

Frontiers | The FAANG Data Portal: Global, Open-Access, “FAIR”, and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes | Genetics

Abstract:  The Functional Annotation of ANimal Genomes (FAANG) project is a worldwide coordinated action creating high-quality functional annotation of farmed and companion animal genomes. The generation of a rich genome-to-phenome resource and supporting informatic infrastructure advances the scope of comparative genomics and furthers the understanding of functional elements. The project also provides terrestrial and aquatic animal agriculture community powerful resources for supporting improvements to farmed animal production, disease resistance, and genetic diversity. The FAANG Data Portal (https://data.faang.org) ensures Findable, Accessible, Interoperable and Reusable (FAIR) open access to the wealth of sample, sequencing, and analysis data produced by an ever-growing number of FAANG consortia. It is developed and maintained by the FAANG Data Coordination Centre (DCC) at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI). FAANG projects produce a standardised set of multi-omic assays with resulting data placed into a range of specialised open data archives. To ensure this data is easily findable and accessible by the community, the portal automatically identifies and collates all submitted FAANG data into a single easily searchable resource. The Data Portal supports direct download from the multiple underlying archives to enable seamless access to all FAANG data from within the portal itself. The portal provides a range of predefined filters, powerful predictive search, and a catalogue of sampling and analysis protocols and automatically identifies publications associated with any dataset. To ensure all FAANG data submissions are high-quality, the portal includes powerful contextual metadata validation and data submissions brokering to the underlying EMBL-EBI archives. The portal will incorporate extensive new technical infrastructure to effectively deliver and standardise FAANG’s shift to single-cellomics, cell atlases, pangenomes, and novel phenotypic prediction models. The Data Portal plays a key role for FAANG by supporting high-quality functional annotation of animal genomes, through open FAIR sharing of data, complete with standardised rich metadata. Future Data Portal features developed by the DCC will support new technological developments for continued improvement for FAANG projects.

 

Converting Access Microbiology to an open research platform: focus group and AI review tool research results | Microbiology Society

Abstract:  The Microbiology Society will be launching an open research platform in October 2021. Developed using funding from the Wellcome Trust and the Howard Hughes Medical Institute (HHMI), the platform will combine our current sound-science journal, Access Microbiology, with artificial intelligence (AI) review tools and many of the elements of a preprint server. In an effort to improve the rigour, reproducibility and transparency of the academic record, the Access Microbiology platform will host both preprints of articles and their Version of Record (VOR) publications, as well as the reviewer reports, Editor’s decision, authors’ response to reviewers and the AI review reports. To ensure the platform meets the needs of our community, in February 2020 we conducted focus group meetings with various stakeholders. Using articles previously submitted to Access Microbiology, we undertook testing of a range of potential AI review tools and investigated the technical feasibility and utility of including these tools as part of the platform. In keeping with the open and transparent ethos of the platform, we present here a summary of the focus group feedback and AI review tool testing.

 

Meet the new Faculty Opinions Score – Faculty Opinions Blog

“Traditional citation metrics, such as the journal impact factor, can frequently act as biased measurements of research quality and contribute to the broken system of research evaluation. Academic institutions and funding bodies are increasingly moving away from relying on citation metrics towards greater use of transparent expert opinion. 

Faculty Opinions has championed this cause for two decades, with over 230k recommendations made by our 8000+ Faculty Members, and we are excited to introduce the next step in our evolution – a formidable mark of research quality – the new Faculty Opinions Score….

The Faculty Opinions Score assigns a numerical value of research publications in Biology and Medicine, to quantify their impact and quality compared to other publications in their field. 

The Faculty Opinions Score is derived by combining our unique star-rated Recommendations on individual publications, made by world-class experts, with bibliometrics to produce a radically new metric in the research evaluation landscape. 

 

 

 

Key properties of the Faculty Opinions Score: 

A score of zero is assigned to articles with no citations and no recommendations. 
The average score of a set of recommended articles has an expected value of 10. However, articles with many recommendations or highly cited articles may have a much higher score. There is no upper bound. 
Non-recommended articles generally score lower than recommended articles. 
Recommendations contribute more to the score than bibliometric performance. In other words, expert recommendations increase an article’s score (much) more than citations do….”

New metric ‘leverages opinions of 8,000 experts’ | Research Information

“Faculty Opinions has introduced a new metric in the research evaluation landscape, leveraging the opinions of more than 8,000 experts. 

The Faculty Opinions Score is designed to be an early indicator of an article’s future impact and a mark of research quality. The company describes the implications for researchers, academic institutions and funding bodies as ‘promising’….”

iDigBio receives $20 million from NSF to sustain U.S. museum digitization efforts – Florida Museum Science

“The National Science Foundation has awarded iDigBio nearly $20 million to continue its mission of digitizing natural history collections nationwide, making them available online to researchers, educators and community scientists around the world.

For the past decade, iDigBio, a collaborative program based at the Florida Museum of Natural History at the University of Florida, has led the push to digitize the estimated 1 billion biological specimens held in U.S. museums. These online records of animals, plants and other organisms serve as a searchable archive of life and help researchers identify species in danger of extinction, track the spread of invaders, study how climate change is reshaping ecosystems and possibly predict the next pandemic.

Thanks to iDigBio’s coordination, training and community-building efforts, about 40% of specimens in U.S. collections are now represented in the program’s portal, comprising one of the largest virtual collections of Earth’s biodiversity and contributing to more than 2,000 studies so far….”

ManyBirds: A multi-site collaborative Open Science approach to avian cognition and behaviour research

Abstract:  Comparative cognitive and behaviour research aims to investigate cognitive evolution by comparing performance in different species to understand how these abilities have evolved. Ideally, this requires large and diverse samples, however, these can be difficult to obtain by single labs or institutions, leading to potential reproducibility and generalisation issues with small, less representative samples. To help mitigate these issues, we are establishing a multi-site collaborative Open Science approach called ManyBirds, with the aim of providing new insight into the evolution of avian cognition and behaviour through large-scale comparative studies, following the lead of exemplary ManyPrimates, ManyBabies and ManyDogs projects. Here, we outline a) why we should study birds, including the origin of modern birds, avian brains, convergent evolution of cognition, and the replicability crisis; b) the current state of the avian cognition field, including a ‘snapshot’ review; c) the ManyBirds project, with plans, infrastructure, limitations, implications and future directions. In sharing this process, we hope that this may be useful for other researchers in devising similar projects in other taxa, like non-avian reptiles or mammals, and to encourage further collaborations with ManyBirds and related ManyX projects. Ultimately, we hope to promote collaboration between ManyX projects to allow for wider investigation of the evolution of cognition across all animals, including potentially humans.

 

Vegetation of planet Earth: Researchers publish unique database as open access

It’s a treasure trove of data: The global geodatabase of vegetation plots “sPlotOpen” is now freely accessible. It contains data on vegetation from 114 countries and from all climate zones on Earth. The database was compiled by an international team of researchers led by Martin Luther University Halle-Wittenberg (MLU), the German Centre for Integrative Biodiversity Research (iDiv) and the French National Centre for Scientific Research (CNRS). Researchers around the world finally have a balanced, representative dataset of the Earth’s vegetation at their disposal, as the team reports in the journal Global Ecology & Biogeography.

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.