Tag: Plazi

BiCIKL partners sign the Leiden Declaration on FAIR Digital Objects

Key figures from Naturalis Biodiversity Center, Plazi and Pensoft were amongst the first to sign the Declaration at the closing session of the First International Conference on FAIR Digital Objects (FDO2022)

Several of the BiCIKL partners signed the Leiden Declaration on FAIR Digital Objects, thereby committing to “a new environment that works as a truly meaningful data space,” as framed by the organisers of the conference, whose first instalment turned out to be the perfect occasion for the formal publication of the pact. 

Key figures from Naturalis Biodiversity Center, Plazi and Pensoft were amongst the first to sign the Declaration at the closing session of the First International Conference on FAIR Digital Objects (FDO2022), which took place in October 2022 in Leiden, the Netherlands, where it was hosted by the Naturalis Biodiversity Center.

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The conference brought together key international technical, scientific, industry and science-policy stakeholders with the aim to boost the development and implementation of FAIR Digital Objects (FDOs) worldwide. It was organised by the FDO Forum, an initiative supported by major global initiatives and by a variety of regional and national initiatives with the shared goal to achieve a better coherence amongst the increasing number of initiatives working on FDO-based designs and implementations.  

By joining the Declaration’s signees, the BiCIKL partners formally committed to:

  • Support the FAIR guiding principles to be applied (ultimately) to each digital object in a web of FAIR data and services;  
  • Support open standards and protocols;
  • Support data and services to be as open as possible, and only as restricted as necessary;
  • Support distributed solutions where useful to achieve robustness and scalability, but recognise the need for centralised approaches where necessary;
    • Support the restriction of standards and protocols to the absolute minimum;
    • Support freedom to operate wherever possible;
    • Help to avoid monopolies and provider lock-in wherever possible.

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During the event, Plazi and Pensoft held a presentation demonstrating how their Biodiversity Literature Repository turns taxonomic treatments ‘locked’ in legacy scientific literature into FAIR Digital Objects. As a result of the collaboration between Plazi and Pensoft – a partnership long-preceding their involvement in BiCIKL – this workflow has also been adapted to modern-day publishing, in order to FAIRify data as soon as it is published.

A slide from the Plazi presentation at the FDO2022, Leiden, the Netherlands. Credit: Plazi.

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Ahead of FDO2022, all submitted conference abstracts – including the one associated with Plazi’s presentation – were made publicly available in a collection of their own in Pensoft’s open-science journal Research Ideas and Outcomes (RIO). Thus, not only did the organisers make the conference outputs available to the participants early on, so that they can familiarise themselves with the upcoming talks and topics in advance, but they also ensure that the contributions are permanently preserved and FAIR in their own turn. 

The conference collection, guest edited by Tina Loo (Naturalis Biodiversity Center), contains a total of 51 conference abstracts, where each is published in HTML, XML and PDF formats, and assigned with its own persistent identifier (DOI) just like the collection in its entirety (10.3897/rio.coll.190).

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Read more about the declaration and sign it yourself from this link. You can also follow the FDO Forum on Twitter (@FAIRDOForum).

Special ZooKeys memorial volume open to submissions to commemorate our admirable founding Editor-in-Chief Terry Erwin

In recognition of the love and devotion that Terry expressed for the study of the World’s biodiversity, ZooKeys invites contributions to this memorial issue, covering all subjects falling within the area of systematic zoology. Titled “Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020)”.

In tribute to our beloved friend and founding Editor-in-Chief, Dr Terry Erwin, who passed away on 11th May 2020, we are planning a special memorial volume to be published on 11 May 2021, the date Terry left us. Terry will be remembered by all who knew him for his radiant spirit, charming enthusiasm for carabid beetles and never-ceasing exploration of the world of biodiversity! 

In recognition of the love and devotion that Terry expressed for study of the World’s biodiversity, ZooKeys invites contributions to this memorial issue, titled “Systematic Zoology and Biodiversity Science: A tribute to Terry Erwin (1940-2020)”, to all subjects falling within the area of systematic zoology. Of special interest are papers recognising Terry’s dedication to collection based research, massive biodiversity  surveys and origin of biodiversity hot spot areas. The Special will be edited by John Spence, Achille Casale, Thorsten Assmann, James Liebherr and Lyubomir Penev.

Article processing charges (APCs) will be waived for: (1) Contributions to systematic biology and diversity of carabid beetles, (2) Contributions from Terry’s students and (3) Contributions from his colleagues from the Smithsonian Institution. The APC for articles which do not fall in the above categories will be discounted at 30%.

The submission deadline is 31st December 2020.

Contributors are also invited to send memories and photos which shall be published in a special addendum to the volume.

The memorial volume will also include a joint project of Plazi, Pensoft and the Biodiversity Literature Repository aimed at extracting of taxonomic data from Terry Erwin’s publications and making it easily accessible to the scientific community.

Research on bats and pangolins – potential vectors of zoonotic pandemics like COVID-19 – invited to a free-to-publish special issue in ZooKeys

Captively bred pangolins. 
Photo by Hua L. et al., taken from their study on the current status, problems and future prospects of captive breeding of pangolins, openly accessible in ZooKeys at: https://doi.org/10.3897/zookeys.507.6970

Accepted papers will be published free of charge in recognition of the emergency of the current global situation

Was it the horseshoe bat or could it rather be one of the most traded mammal in the world: the pangolin, at the root of the current devastating pandemic that followed the transmission of the zoonotic SARS-CoV-2 virus to a human host, arguably after infected animal products reached poorly regulated wet markets in Wuhan, China, last year? 

To make matters worse, the current situation is no precedent. Looking at the not so distant past, we notice that humanity has been repeatedly falling victim to viral deadly outbreaks, including Zika, Ebola, the Swine flu, the Spanish flu and the Plague, where all are linked to an animal host that at one point, under specific circumstances transferred the virus to people. 

Either way, here’s a lesson humanity gets to learn once again: getting too close to wildlife is capable of opening the gates to global disasters with horrific and irreversible damage on human lives, economics and ecosystems. What is left for us to understand is how exactly these transmission pathways look like and what are the factors making certain organisms like the bat and the pangolin particularly efficient vectors of diseases such as COVID-19 (Coronavirus). This crucial knowledge could’ve been easier for us to grasp had we only obtained the needed details about those species on time.

Aligning with the efforts of the biodiversity community, such as the recently announced DiSSCo and CETAF COVID-19 Task Force, who intend to create an efficient network of taxonomists, collection curators and other experts from around the globe and equip them with the tools and large datasets needed to combat the unceasing pandemic, the open-access peer-reviewed scholarly journal ZooKeys invites researchers from across the globe to submit their work on the biology of bats and pangolins to a free-to-publish special issue. 

The effort will be coordinated with the literature digitisation provider Plazi, who will extract and liberate data on potential hosts from various journals and publishers. In this way, these otherwise hardly accessible data will be re-used to support researchers in generation of new hypotheses and knowledge on this urgent topic.

By providing further knowledge on these sources and vectors of zoonotic diseases, this collection of publications could contribute with priceless insights to make the world better prepared for epidemics like the Coronavirus and even prevent such from happening in the future. 

Furthermore, by means of its technologically advanced infrastructure and services, including expedite peer review and publication processes, in addition to a long list of indexers and databases where publications are registered, ZooKeys will ensure the rapid publication of those crucial findings, and will also take care that once they get online, they will immediately become easy to discover, cite and built on by any researcher, anywhere in the world. 

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The upcoming “Biology of bats and pangolins” special issue is to add up to some excellent examples of previous research on the systematics, biology and distribution of pangolins and bats published in ZooKeys. 

In their review paper from 2015, Chinese scientists looked into the issues and prospects around captive breeding of pangolins. A year later, their colleagues at South China Normal University provided further insights into captive breeding, in addition to new data on the reproductive parameters of Chinese pangolins.

Back in 2013, a Micronesian-US research studied the taxonomy, distribution and natural history of flying fox bats inhabiting the Caroline Islands (Micronesia). A 2018 joint study on bat diversity in Sri Lanka focused on chiropteran conservation and management; while a more recent article on the cryptic diversity and range extension of the big-eyed bats in the genus Chiroderma. 

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For more information, visit ZooKeys website. 

Follow ZooKeys on Twitter and Facebook.

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References:

Buden D, Helgen K, Wiles G (2013) Taxonomy, distribution, and natural history of flying foxes (Chiroptera, Pteropodidae) in the Mortlock Islands and Chuuk State, Caroline Islands. ZooKeys 345: 97-135. https://doi.org/10.3897/zookeys.345.5840

Edirisinghe G, Surasinghe T, Gabadage D, Botejue M, Perera K, Madawala M, Weerakoon D, Karunarathna S (2018) Chiropteran diversity in the peripheral areas of the Maduru-Oya National Park in Sri Lanka: insights for conservation and management. ZooKeys 784: 139-162. https://doi.org/10.3897/zookeys.784.25562

Hua L, Gong S, Wang F, Li W, Ge Y, Li X, Hou F (2015) Captive breeding of pangolins: current status, problems and future prospects. ZooKeys 507: 99-114. https://doi.org/10.3897/zookeys.507.6970

Lim BK, Loureiro LO, Garbino GST (2020) Cryptic diversity and range extension in the big-eyed bat genus Chiroderma (Chiroptera, Phyllostomidae). ZooKeys 918: 41-63. https://doi.org/10.3897/zookeys.918.48786

Zhang F, Wu S, Zou C, Wang Q, Li S, Sun R (2016) A note on captive breeding and reproductive parameters of the Chinese pangolin, Manis pentadactyla Linnaeus, 1758. ZooKeys 618: 129-144. https://doi.org/10.3897/zookeys.618.8886

Data mining applied to scholarly publications to finally reveal Earth’s biodiversity

At a time when a million species are at risk of extinction, according to a recent UN report, ironically, we don’t know how many species there are on Earth, nor have we noted down all those that we have come to know on a single list. In fact, we don’t even know how many species we would have put on such a list.

The combined research including over 2,000 natural history institutions worldwide, produced an estimated ~500 million pages of scholarly publications and tens of millions of illustrations and species descriptions, comprising all we currently know about the diversity of life. However, most of it isn’t digitally accessible. Even if it were digital, our current publishing systems wouldn’t be able to keep up, given that there are about 50 species described as new to science every day, with all of these published in plain text and PDF format, where the data cannot be mined by machines, thereby requiring a human to extract them. Furthermore, those publications would often appear in subscription (closed access) journals.

The Biodiversity Literature Repository (BLR), a joint project ofPlazi, Pensoft and Zenodo at CERN, takes on the challenge to open up the access to the data trapped in scientific publications, and find out how many species we know so far, what are their most important characteristics (also referred to as descriptions or taxonomic treatments), and how they look on various images. To do so, BLR uses highly standardised formats and terminology, typical for scientific publications, to discover and extract data from text written primarily for human consumption.

By relying on state-of-the-art data mining algorithms, BLR allows for the detection, extraction and enrichment of data, including DNA sequences, specimen collecting data or related descriptions, as well as providing implicit links to their sources: collections, repositories etc. As a result, BLR is the world’s largest public domain database of taxonomic treatments, images and associated original publications.

Once the data are available, they are immediately distributed to global biodiversity platforms, such as GBIF–the Global Biodiversity Information Facility. As of now, there are about 42,000 species, whose original scientific descriptions are only accessible because of BLR.

The very basic principle in science to cite previous information allows us to trace back the history of a particular species, to understand how the knowledge about it grew over time, and even whether and how its name has changed through the years. As a result, this service is one avenue to uncover the catalogue of life by means of simple lookups.

So far, the lessons learned have led to the development of TaxPub, an extension of the United States National Library of Medicine Journal Tag Suite and its application in a new class of 26 scientific journals. As a result, the data associated with articles in these journals are machine-accessible from the beginning of the publishing process. Thus, as soon as the paper comes out, the data are automatically added to GBIF.

While BLR is expected to open up millions of scientific illustrations and descriptions, the system is unique in that it makes all the extracted data findable, accessible, interoperable and reusable (FAIR), as well as open to anybody, anywhere, at any time. Most of all, its purpose is to create a novel way to access scientific literature.

To date, BLR has extracted ~350,000 taxonomic treatments and ~200,000 figures from over 38,000 publications. This includes the descriptions of 55,800 new species, 3,744 new genera, and 28 new families. BLR has contributed to the discovery of over 30% of the ~17,000 species described annually.

Prof. Lyubomir Penev, founder and CEO of Pensoft says,

“It is such a great satisfaction to see how the development process of the TaxPub standard, started by Plazi some 15 years ago and implemented as a routine publishing workflow at Pensoft’s journals in 2010, has now resulted in an entire infrastructure that allows automated extraction and distribution of biodiversity data from various journals across the globe. With the recent announcement from the Consortium of European Taxonomic Facilities (CETAF) that their European Journal of Taxonomy is joining the TaxPub club, we are even more confident that we are paving the right way to fully grasping the dimensions of the world’s biodiversity.”

Dr Donat Agosti, co-founder and president of Plazi, adds:

“Finally, information technology allows us to create a comprehensive, extended catalogue of life and bring to light this huge corpus of cultural and scientific heritage – the description of life on Earth – for everybody. The nature of taxonomic treatments as a network of citations and syntheses of what scientists have discovered about a species allows us to link distinct fields such as genomics and taxonomy to specimens in natural history museums.”

Dr Tim Smith, Head of Collaboration, Devices and Applications Group at CERN, comments:

“Moving the focus away from the papers, where concepts are communicated, to the concepts themselves is a hugely significant step. It enables BLR to offer a unique new interconnected view of the species of our world, where the taxonomic treatments, their provenance, histories and their illustrations are all linked, accessible and findable. This is inspirational for the digital liberation of other fields of study!”

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Additional information:

BLR is a joint project led by Plazi in partnership with Pensoft and Zenodo at CERN.

Currently, BLR is supported by a grant from Arcadia, a charitable fund of Lisbet Rausing and Peter Baldwin.

Plazi and the Biodiversity Literature Repository (BLR) awarded EUR 1.1 million from Arcadia Fund to grant free access to biodiversity data

Plazi has received a grant of EUR 1.1 million from Arcadia – the charitable fund of Lisbet Rausing and Peter Baldwin – to liberate data, such as taxonomic treatments and images, trapped in scholarly biodiversity publications.

The project will expand the existing corpus of the Biodiversity Literature Repository (BLR), a joint venture of Plazi and Pensoft, hosted on Zenodo at CERN. The project aims to add hundreds of thousands of figures and taxonomic treatments extracted from publications, and further develop and hone the tools to search through the corpus.

The BLR is an open science community platform to make the data contained in scholarly publications findable, accessible, interoperable and reusable (FAIR). BLR is hosted on Zenodo, the open science repository at CERN, and maintained by the Switzerland-based Plazi association and the open access publisher Pensoft.

In its short existence, BLR has already grown to a considerate size: 35,000+ articles have been added, and extracted from 600+ journals. From these articles, more than 180,000 images have also been extracted and uploaded to BLR, and 225,000+ sub-article components, including biological names, taxonomic treatments or equivalent defined blocks of text have been deposited at Plazi’s TreatmentBank. Additionally, over a million bibliographic references have been extracted and added to Refbank.

The articles, images and all other sub-article elements are fully FAIR compliant and citable. In case an article is behind a paywall, a user can still access its underlying metadata, the link to the original article, and use the DOI assigned to it by BLR for persistent citation.

“Generally speaking, scientific illustrations and taxonomic treatments, such as species descriptions, are one of the best kept ‘secrets’ in science as they are neither indexed, nor are they citable or accessible. At best, they are implicitly referenced,” said Donat Agosti, president of Plazi. “Meanwhile, their value is undisputed, as shown by the huge effort to create them in standard, comparative ways. From day one, our project has been an eye-opener and a catalyst for the open science scene,” he concluded.

Though the target scientific domain is biodiversity, the Plazi workflow and tools are open source and can be applied to other domains – being a catalyst is one of the project’s goals.

While access to biodiversity images has already proven useful to scientists, but also inspirational to artists, for example, the people behind Plazi are certain that such a well-documented, machine-readable interface is sure to lead to many more innovative uses.

To promote BLR’s approach to make these important data accessible, Plazi seeks collaborations with the community and publishers, to remove hurdles in liberating the data contained in scholarly publications and make them FAIR.

The robust legal aspects of the project are a core basis of BLR’s operation. By extracting the non-copyrightable elements from the publications and making them findable, accessible and re-usable for free, the initiative drives the move beyond the PDF and HTML formats to structured data.

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To participate in the project or for further questions, please contact Donat Agosti, President at Plazi at info@plazi.org

 

Additional information:

About Plazi:

Plazi is an association supporting and promoting the development of persistent and openly accessible digital taxonomic literature. To this end, Plazi maintains TreatmentBank, a digital taxonomic literature repository to enable archiving of taxonomic treatments; develops and maintains TaxPub, an extension of the National Library of Medicine / National Center for Biotechnology Informatics Journal Article Tag Suite for taxonomic treatments; is co-founder of the Biodiversity Literature Repository at Zenodo, participates in the development of new models for publishing taxonomic treatments in order to maximize interoperability with other relevant cyberinfrastructure components such as name servers and biodiversity resources; and advocates and educates about the vital importance of maintaining free and open access to scientific discourse and data. Plazi is a major contributor to the Global Biodiversity Information Facility.

About Arcadia Fund:

Arcadia is a charitable fund of Lisbet Rausing and Peter Baldwin. It supports charities and scholarly institutions that preserve cultural heritage and the environment. Arcadia also supports projects that promote open access and all of its awards are granted on the condition that any materials produced are made available for free online. Since 2002, Arcadia has awarded more than $500 million to projects around the world.

Novel cybercatalog of flower-loving flies suggests the digital future of taxonomy

Charting Earth’s biodiversity is the goal of taxonomy and to do so the scientists need to create an extensive citation network based on several hundred million pages of scientific literature. By providing a novel taxonomic ‘cybercatalog’ of southern African flower-loving (apiocerid) flies, Drs. Torsten Dikow and Donat Agosti demonstrate how the network of taxonomic knowledge can be made available through links provided to online data providers. Their work is available in the open-access Biodiversity Data Journal.

The present research showcases that the information cannot only be made available to the reader who follows the links, but also to machines that use the growing number of digital, online resources that are linked through persistent identifiers.

Primary data providers for taxonomic information such as species names (ZooBank), specimen images (Morphbank), species descriptions (Plazi), and digitized literature (BHL, Biodiversity Heritage Library; BioStor; and BLR, Biodiversity Literature Repository) play an important role in making data on species available in electronic form. Aggregators such as the Global Biodiversity Information Facility (GBIF) and the Encyclopedia of Life (EoL) gather this information automatically to distribute it even further to audiences beyond the reach of the life sciences.

In contrast to previous species catalogs, in cybercatalogs access to information is provided through links to open-access, online data repositories such as the ones listed above. Taxonomists and other users can now access this literature, species descriptions, and specimen records immediately without a search in a natural history library or collection. The cybercatalog takes advantage of a new publishing platform within the Biodiversity Data Journal that makes it easy to upload species information and links to data about these species through a CheckList template. Furthermore, the Biodiversity Data Journal now allows future updates and re-publications of the cybercatalog with the new unique persistent identifier (DOI, Digital Object Identifier) whenever a new species is described or other taxonomic changes take place.

The authors argue that cybercatalogs are indeed the future of taxonomic catalogs since the online data in them are easily accessible to anyone.

“It is a taxonomist’s dream to have online access to all previously published information on a species and through this step the discipline of taxonomy can (re-)position itself as a central resource within the life sciences and beyond to the public and society at large,” add the authors. “Online access will also help to narrow the gap between the South and the North as a fantastic example of unhindered access to our knowledge of the global biological diversity, which is increasingly under pressure from human populations.”

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For the realization of this project Plazi and Pensoft were partially supported by the EC-FP7 EU BON project (ENV 30845) (Building the European Biodiversity Observation Network).

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Original source:

Dikow T, Agosti D (2015) Utilizing online resources for taxonomy: a cybercatalog of Afrotropical apiocerid flies (Insecta: Diptera: Apioceridae). Biodiversity Data Journal 3: e5707. doi: 10.3897/BDJ.3.e5707