Category: BISS Journal

Nanopublications tailored to biodiversity data

Novel nanopublication workflows and templates for associations between organisms, taxa and their environment are the latest outcome of the collaboration between Knowledge Pixels and Pensoft.

First off, why nanopublications?

Nanopublications complement human-created narratives of scientific knowledge with elementary, machine-actionable, simple and straightforward scientific statements that prompt sharing, finding, accessibility, citability and interoperability. 

By making it easier to trace individual findings back to their origin and/or follow-up updates, nanopublications also help to better understand the provenance of scientific data. 

With the nanopublication format and workflow, authors make sure that key scientific statements – the ones underpinning their research work – are efficiently communicated in both human-readable and machine-actionable manner in line with FAIR principles. Thus, their contributions to science are better prepared for a reality driven by AI technology.

The machine-actionability of nanopublications is a standard due to each assertion comprising a subject, an object and a predicate (type of relation between the subject and the object), complemented by provenance, authorship and publication information. A unique feature here is that each of the elements is linked to an online resource, such as a controlled vocabulary, ontology or standards. 

Now, what’s new?

As a result of the partnership between high-tech startup Knowledge Pixels and open-access scholarly publisher and technology provider Pensoft, authors in Biodiversity Data Journal (BDJ) can make use of three types of nanopublications:

  1. Nanopublications associated with a manuscript submitted to BDJ. This workflow lets authors add a Nanopublications section within their manuscript while preparing their submission in the ARPHA Writing Tool (AWT). Basically, authors ‘highlight’ and ‘export’ key points from their papers as nanopublications to further ensure the FAIRness of the most important findings from their publications.
  1. Standalone nanopublication related to any scientific publication, regardless of its author or source. This can be done via the Nanopublications page accessible from the BDJ website. The main advantage of standalone nanopublication is that straightforward scientific statements become available and FAIR early on, and remain ready to be added to a future scholarly paper.
  1. Nanopublications as annotations to existing scientific publications. This feature is available from several journals published on the ARPHA Platform, including BDJ. By attaching an annotation to the entire paper (via the Nanopublication tab) or a text selection (by first adding an inline comment, then exporting it as a nanopublication), a reader can evaluate and record an opinion about any article using a simple template based on the Citation Typing Ontology (CiTO).

Nanopublications for biodiversity data?

At Biodiversity Data Journal (BDJ), authors can now incorporate nanopublications within their manuscripts to future-proof the most important assertions on biological taxa and organisms or statements about associations of taxa or organisms and their environments. 

On top of being shared and archived by means of a traditional research publication in an open-access peer-reviewed journal, scientific statements using the nanopublication format will also remain ‘at the fingertips’ of automated tools that may be the next to come looking for this information, while mining the Web.

Using the nanopublication workflows and templates available at BDJ, biodiversity researchers can share assertions, such as:

So far, the available biodiversity nanopublication templates cover a range of associations, including those between taxa and individual organisms, as well as between those and their environments and nucleotide sequences. 

Nanopublication template customised for biodiversity research publications available from Nanodash.

As a result, those easy-to-digest ‘pixels of knowledge’ can capture and disseminate information about single observations, as well as higher taxonomic ranks. 

The novel domain-specific publication format was launched as part of the collaboration between Knowledge Pixels – an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing and the open-access scholarly publisher Pensoft.

… so, what exactly is a nanopublication?

General structure of a nanopublication:

“the smallest unit of publishable information”,

as explained on nanopub.net.

Basically, a nanopublication – unlike a research article – is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists as a reusable and cite-able pieces of a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms.

These semantic statements expressed in community-agreed terms, openly available through links to controlled vocabularies, ontologies and standards, are not only freely accessible to everyone in both human-readable and machine-actionable formats, but also easy-to-digest for computer algorithms and AI-powered assistants.

In short, nanopublications allow us to browse and aggregate such findings as part of a complex scientific knowledge graph. Therefore, nanopublications bring us one step closer to the next revolution in scientific publishing, which started with the emergence and increasing adoption of knowledge graphs. 

“As pioneers in the semantic open access scientific publishing field for over a decade now, we at Pensoft are deeply engaged with making research work actually available at anyone’s fingertips. What once started as breaking down paywalls to research articles and adding the right hyperlinks in the right places, is time to be built upon,”

said Prof. Lyubomir Penev, founder and CEO at Pensoft, which had published the very first semantically enhanced research article in the biodiversity domain back in 2010 in the ZooKeys journal.

Why are nanopublications necessary?

By letting computer algorithms access published research findings in a structured format, nanopublications allow for the knowledge snippets that they are intended to communicate to be fully understandable and actionable. With nanopublications, each of those fragments of scientific information is interconnected and traceable back to its author(s) and scientific evidence. 

A nanopublication is a tiny snippet of a precise and structured scientific finding (e.g. medication X treats disease Y), which exists within a growing knowledge graph stored on a decentralised server network in a format that it is readable for humans, but also “understandable” and actionable for computers and their algorithms. Illustration by Knowledge Pixels. 

By building on shared knowledge representation models, these data become Interoperable (as in the I in FAIR), so that they can be delivered to the right user, at the right time, in the right place , ready to be reused (as per the R in FAIR) in new contexts. 

Another issue nanopublications are designed to address is research scrutiny. Today, scientific publications are produced at an unprecedented rate that is unlikely to cease in the years to come, as scholarship embraces the dissemination of early research outputs, including preprints, accepted manuscripts and non-conventional papers.

A network of interlinked nanopublications could also provide a valuable forum for scientists to test, compare, complement and build on each other’s results and approaches to a common scientific problem, while retaining the record of their cooperation each step along the way. 

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We encourage you to try the nanopublications workflow yourself when submitting your next biodiversity paper to Biodiversity Data Journal. 

Community feedback on this pilot project and suggestions for additional biodiversity-related nanopublication templates are very welcome!

This Nanopublications for biodiversity workflow was created with a partial support of the European Union’s Horizon 2020 BiCIKL project under grant agreement No 101007492 and in collaboration with Knowledge Pixels AG.The tool uses data and API services of ChecklistBank, Catalogue of Life, GBIF, GenBank/ENA, BOLD, Darwin Core, Environmental Ontology (ENVO), Relation Ontology (RO), NOMEN, ZooBank, Index Fungorum, MycoBank, IPNI, TreatmentBank, and other resources. 

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On the journal website: https://bdj.pensoft.net/, you can find more about the unique features and workflows provided by the Biodiversity Data Journal (BDJ), including innovative research paper formats (e.g. Data Paper, OMICS Data Paper, Software Description, R Package, Species Conservation Profiles, Alien Species Profile), expert-provided data audit for each data paper submission, automated data export and more.

Don’t forget to also sign up for the BDJ newsletter via the Email alert form on the journal’s homepage and follow it on Twitter and Facebook.

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How it works: Nanopublications linked to articles in RIO Journal

Earlier this year, Knowledge Pixels and Pensoft presented several routes for readers and researchers to contribute to research outputs – either produced by themselves or by others – through nanopublications generated through and visualised in Pensoft’s cross-disciplinary Research Ideas and Outcomes (RIO) journal, which uses the same nanopublication workflows.

This October, TDWG 2023 is coming up to Tasmania & online

As in previous years, the abstracts – already getting published in the BISS journal – are giving a sneak peek of the event!

The annual TDWG conference will be taking place 9-13 October in Tasmania, Australia. Once again, the event will be running in a hybrid format. 

This year, the TDWG conference is hosted by Atlas of Living Australia – the Australian node of GBIF – the Global Biodiversity Information Facility and the National Research Collections Australia.

For an eighth year in a row, all conference abstracts will be submitted to TDWG via the Association’s own journal: Biodiversity Information Science and Standards (BISS Journal), published by Pensoft and powered by the end-to-end publishing platform ARPHA. Using the ‘mini-paper’ format, participants are not only openly and efficiently sharing their work with the world, but they also get to enjoy many features typically exclusive to ‘standard’ research papers, including DOI registration on Crossref, semantic enrichment and structural elements (e.g., tables, figures), all of which are stored as easily exported data.

Apart from an abstract submission portal, BISS Journal also serves as a permanent, openly accessible scholarly source for all contributions concerning the creation, maintenance, and promotion of open community-driven data standards to enable sharing and use of biodiversity data for all.

Learn more about the unique features of BISS and explore past TDWG abstract collections compiled for TDWG’s previous conferences. 

As in previous years, the abstracts will be published ahead of the event itself to provide the community with a sneak preview of the conference. The 2023 collection of abstracts, will allow readers to explore the abstracts by session (e.g., symposia, posters, contributed presentations, keynotes). Sometime after the conference, check out the media tab on most abstracts for slides presented and a link to session video when it is posted on TDWG’s YouTube channel.

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Visit the TDWG 2023 conference website for more information about the scientific program, registration, abstract submission and more. Ahead, during and after the conference, join the conversation on Twitter and Mastodon via #tdwg2023.

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Don’t forget to also follow TDWG (Twitter, Facebook and Mastodon), BISS Journal (Twitter and Facebook) and Pensoft (Twitter and Facebook) on social media.

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Can’t wait until TDWG 2023? Use the time to relive last year’s TDWG 2022 in this blog post and view the TDWG 2022: The Aftermovie.
#TDWG2022 recap: TDWG and Pensoft welcomed 400 biodiversity information experts from 41 countries in Sofia

Pensoft among the first 27 publishers to share prices & services via the Journal Comparison Service by Plan S

All journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.

In support of transparency and openness in scholarly publishing and academia, the scientific publisher and technology provider Pensoft joined the Journal Comparison Service (JCS) initiative by cOAlition S, an alliance of national funders and charitable bodies working to increase the volume of free-to-read research. 

As a result, all journals published by Pensoft – each using the publisher’s self-developed ARPHA Platform – provide extensive and transparent information about their costs and services in line with the Plan S principles.

The JCS was launched to aid libraries and library consortia – the ones negotiating and participating in Open Access agreements with publishers – by providing them with everything they need to know in order to determine whether the prices charged by a certain journal are fair and corresponding to the quality of the service. 

According to cOAlition S, an increasing number of libraries and library consortia from Europe, Africa, North America, and Australia have registered with the JCS over the past year since the launch of the portal in September 2021.

While access to the JCS is only open to librarians, individual researchers may also make use of the data provided by the participating publishers and their journals. 

This is possible through an integration with the Journal Checker Tool, where researchers can simply enter the name of the journal of interest, their funder and affiliation (if applicable) to check whether the scholarly outlet complies with the Open Access policy of the author’s funder. A full list of all academic titles that provide data to the JCS is also publicly available. By being on the list means a journal and its publisher do not only support cOAlition S, but they also demonstrate that they stand for openness and transparency in scholarly publishing.

“We are delighted that Pensoft, along with a number of other publishers, have shared their price and service data through the Journal Comparison Service. Not only are such publishers demonstrating their commitment to open business models and cultures but are also helping to build understanding and trust within the research community.”

said Robert Kiley, Head of Strategy at cOAlition S. 

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About cOAlition S:

On 4 September 2018, a group of national research funding organisations, with the support of the European Commission and the European Research Council (ERC), announced the launch of cOAlition S, an initiative to make full and immediate Open Access to research publications a reality. It is built around Plan S, which consists of one target and 10 principles. Read more on the cOAlition S website.

About Plan S:

Plan S is an initiative for Open Access publishing that was launched in September 2018. The plan is supported by cOAlition S, an international consortium of research funding and performing organisations. Plan S requires that, from 2021, scientific publications that result from research funded by public grants must be published in compliant Open Access journals or platforms. Read more on the cOAlition S website.

One Biodiversity Knowledge Hub to link them all: BiCIKL 2nd General Assembly

The FAIR Data Place – the key and final product of the partnership – is meant to provide scientists with all types of biodiversity data “at their fingertips”

The Horizon 2020 – funded project BiCIKL has reached its halfway stage and the partners gathered in Plovdiv (Bulgaria) from the 22nd to the 25th of October for the Second General Assembly, organised by Pensoft. 

The BiCIKL project will launch a new European 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’s goal is to create a centralised place to connect all key biodiversity data by interlinking 15 research infrastructures and their databases. The 3-year European Commission-supported initiative kicked off in 2021 and involves 14 key natural history institutions from 10 European countries.

BiCIKL is keeping pace as expected with 16 out of the 48 final deliverables already submitted, another 9 currently in progress/under review and due in a few days. Meanwhile, 21 out of the 48 milestones have been successfully achieved.

Prof. Lyubomir Penev (BiCIKL’s project coordinator Prof. Lyubomir Penev and CEO and founder of Pensoft) opens the 2nd General Assembly of BiCIKL in Plovdiv, Bulgaria.

The hybrid format of the meeting enabled a wider range of participants, which resulted in robust discussions on the next steps of the project, such as the implementation of additional technical features of the FAIR Data Place (FAIR being an abbreviation for Findable, Accessible, Interoperable and Reusable).

This FAIR Data Place online platform – the key and final product of the partnership and the BiCIKL initiative – is meant to provide scientists with all types of biodiversity data “at their fingertips”.

This data includes biodiversity information, such as detailed images, DNA, physiology and past studies concerning a specific species and its ‘relatives’, to name a few. Currently, the issue is that all those types of biodiversity data have so far been scattered across various databases, which in turn have been missing meaningful and efficient interconnectedness.

Additionally, the FAIR Data Place, developed within the BiCIKL project, is to give researchers access to plenty of training modules to guide them through the different services.

Halfway through the duration of BiCIKL, the project is at a turning point, where crucial discussions between the partners are playing a central role in the refinement of the FAIR Data Place design. Most importantly, they are tasked with ensuring that their technologies work efficiently with each other, in order to seamlessly exchange, update and share the biodiversity data every one of them is collecting and taking care of.

By Year 3 of the BiCIKL project, the partners agree, when those infrastructures and databases become efficiently interconnected to each other, scientists studying the Earth’s biodiversity across the world will be in a much better position to build on existing research and improve the way and the pace at which nature is being explored and understood. At the end of the day, knowledge is the stepping stone for the preservation of biodiversity and humankind itself.

“Needless to say, it’s an honour and a pleasure to be the coordinator of such an amazing team spanning as many as 14 partnering natural history and biodiversity research institutions from across Europe, but also involving many global long-year collaborators and their infrastructures, such as Wikidata, GBIF, TDWG, Catalogue of Life to name a few,”

said BiCIKL’s project coordinator Prof. Lyubomir Penev, CEO and founder of Pensoft.

“I see our meeting in Plovdiv as a practical demonstration of our eagerness and commitment to tackle the long-standing and technically complex challenge of breaking down the silos in the biodiversity data domain. It is time to start building freeways between all biodiversity data, across (digital) space, time and data types. After the last three days that we spent together in inspirational and productive discussions, I am as confident as ever that we are close to providing scientists with much more straightforward routes to not only generate more biodiversity data, but also build on the already existing knowledge to form new hypotheses and information ready to use by decision- and policy-makers. One cannot stress enough how important the role of biodiversity data is in preserving life on Earth. These data are indeed the groundwork for all that we know about the natural world”  

Prof. Lyubomir Penev added.
Christos Arvanitidis (CEO of LifeWatch ERIC) at the 2nd General Assembly of the BiCIKL project.

Christos Arvanitidis, CEO of LifeWatch ERIC, added:

“The point is: do we want an integrated structure or do we prefer federated structures? What are the pros and cons of the two options? It’s essential to keep the community united and allied because we can’t afford any information loss and the stakeholders should feel at home with the Project and the Biodiversity Knowledge Hub.”

Joe Miller, Executive Secretary and Director at GBIF, commented:

“We are a brand new community, and we are in the middle of the growth process. We would like to already have answers, but it’s good to have this kind of robust discussion to build on a good basis. We must find the best solution to have linkages between infrastructures and be able to maintain them in the future because the Biodiversity Knowledge Hub is the location to gather the community around best practices, data and guidelines on how to use the BiCIKL services… In order to engage even more partners to fill the eventual gaps in our knowledge.”

Joana Pauperio (biodiversity curator at EMBL-EBI) at the 2nd General Assembly of the BiCIKL project.

“BiCIKL is leading data infrastructure communities through some exciting and important developments”  

said Dr Guy Cochrane, Team Leader for Data Coordination and Archiving and Head of the European Nucleotide Archive at EMBL’s European Bioinformatics Institute (EMBL-EBI).

“In an era of biodiversity change and loss, leveraging scientific data fully will allow the world to catalogue what we have now, to track and understand how things are changing and to build the tools that we will use to conserve or remediate. The challenge is that the data come from many streams – molecular biology, taxonomy, natural history collections, biodiversity observation – that need to be connected and intersected to allow scientists and others to ask real questions about the data. In its first year, BiCIKL has made some key advances to rise to this challenge,”

he added.

Deborah Paul, Chair of the Biodiversity Information Standards – TDWG said:

“As a partner, we, at the Biodiversity Information Standards – TDWG, are very enthusiastic that our standards are implemented in BiCIKL and serve to link biodiversity data. We know that joining forces and working together is crucial to building efficient infrastructures and sharing knowledge.”

The project will go on with the first Round Table of experts in December and the publications of the projects who participated in the Open Call and will be founded at the beginning of the next year.

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Learn more about BiCIKL on the project’s website at: bicikl-project.eu

Follow BiCIKL Project on Twitter and Facebook. Join the conversation on Twitter at #BiCIKL_H2020.

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All BiCIKL project partners:

#TDWG2022 recap: TDWG and Pensoft welcomed 400 biodiversity information experts from 41 countries in Sofia

For the 37th time, experts from across the world to share and discuss the latest developments surrounding biodiversity data and how they are being gathered, used, shared and integrated across time, space and disciplines.

Between 17th and 21st October, about 400 scientists and experts took part in a hybrid meeting dedicated to the development, use and maintenance of biodiversity data, technologies, and standards across the world.

This year, the conference was hosted by Pensoft in collaboration with the National Museum of Natural History (Bulgaria) and the Institute of Biodiversity and Ecosystem Research at the Bulgarian Academy of Science. It ran under the theme “Stronger Together: Standards for linking biodiversity data”.

For the 37th time, the global scientific and educational association Biodiversity Information Standards (TDWG) brought together experts from all over the globe to share and discuss the latest developments surrounding biodiversity data and how they are being gathered, used, shared and integrated across time, space and disciplines.

This was the first time the event happened in a hybrid format. It was attended by 160 people on-site, while another 235 people joined online. 

The TDWG 2022 conference saw plenty of networking and engaging discussions with as many as 160 on-site attendees and another 235 people, who joined the event remotely.

The conference abstracts, submitted by the event’s speakers ahead of the meeting, provide a sneak peek into their presentations and are all publicly available in the TDWG journal Biodiversity Information Science and Standards (BISS).

“It’s wonderful to be in the Balkans and Bulgaria for our Biodiversity Information and Standards (TDWG) 2022 conference! Everyone’s been so welcoming and thoughtfully engaged in conversations about biodiversity information and how we can all collaborate, contribute and benefit,”

said Deborah Paul, Chair of TDWG, a biodiversity informatics specialist and community liaison at the University of Illinois, Prairie Research Institute‘s Illinois Natural History Survey and also an active participant in the Society for the Preservation of Natural History Collections (SPNHC), the Entomological Collections Network (ECN), ICEDIG, the Research Data Alliance (RDA), and The Carpentries.

“Our TDWG mission is to create, maintain and promote the use of open, community-driven standards to enable sharing and use of biodiversity data for all,”

she added.
Prof Lyubomir Penev (Pensoft) and Deborah Paul (TDWG) at TDWG 2022.

“We are proud to have been selected to be the hosts of this year’s TDWG annual conference and are definitely happy to have joined and observed so many active experts network and share their know-how and future plans with each other, so that they can collaborate and make further progress in the way scientists and informaticians work with biodiversity information,”  

said Pensoft’s founder and CEO Prof. Lyubomir Penev.

“As a publisher of multiple globally renowned scientific journals and books in the field of biodiversity and ecology, at Pensoft we assume it to be our responsibility to be amongst the first to implement those standards and good practices, and serve as an example in the scholarly publishing world. Let me remind you that it is the scientific publications that present the most reliable knowledge the world and science has, due to the scrutiny and rigour in the review process they undergo before seeing the light of day,”

he added.

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In a nutshell, the main task and dedication of the TDWG association is to develop and maintain standards and data-sharing protocols that support the infrastructures (e.g., The Global Biodiversity Information Facility – GBIF), which aggregate and facilitate use of these data, in order to inform and expand humanity’s knowledge about life on Earth.

It is the goal of everyone at TDWG to let scientists interested in the world’s biodiversity to do their work efficiently and in a manner that can be understood, shared and reused.

It is the goal of everyone volunteering their time and expertise to TDWG to enable the scientists interested in the world’s biodiversity to do their work efficiently and in a manner that can be understood, shared and reused by others. After all, biodiversity data underlie everything we know about the natural world.

If there are optimised and universal standards in the way researchers store and disseminate biodiversity data, all those biodiversity scientists will be able to find, access and use the knowledge in their own work much more easily. As a result, they will be much better positioned to contribute new knowledge that will later be used in nature and ecosystem conservation by key decision-makers.

On Monday, the event opened with welcoming speeches by Deborah Paul and Prof. Lyubomir Penev in their roles of the Chair of TDWG and the main host of this year’s conference, respectively.

The opening ceremony continued with a keynote speech by Prof. Pavel Stoev, Director of the Natural History Museum of Sofia and co-host of TDWG 2022. 

Prof. Pavel Stoev (Natural History Museum of Sofia) with a presentation about the known and unknown biodiversity of Bulgaria during the opening plenary session of TDWG 2022.

He walked the participants through the fascinating biodiversity of Bulgaria, but also the worrying trends in the country associated with declining taxonomic expertise. 

He finished his talk with a beam of hope by sharing about the recently established national unit of DiSSCo, whose aim – even if a tad too optimistic – is to digitise one million natural history items in four years, of which 250,000 with photographs. So far, one year into the project, the Bulgarian team has managed to digitise more than 32,000 specimens and provide images to 10,000 specimens.

The plenary session concluded with a keynote presentation by renowned ichthyologist and biodiversity data manager Dr. Richard L. Pyle, who is also a manager of ZooBank – the key international database for newly described species.

Keynote presentation by Dr Richard L. Pyle (Bishop Museum, USA) at the opening plenary session of TDWG 2022.

In his talk, he highlighted the gaps in the ways taxonomy is being used, thereby impeding biodiversity research and cutting off a lot of opportunities for timely scientific progress.

“There are simple things we can do to change how we use taxonomy as a tool that would dramatically improve our ability to conduct science and understand biodiversity. There is enormous value and utility within existing databases around the world to understand biodiversity, how threatened it is, what impacts human activity has (especially climate change), and how to optimise the protection and preservation of biodiversity,”

he said in an interview for a joint interview by the Bulgarian News Agency and Pensoft.

“But we do not have easy access to much of this information because the different databases are not well integrated. Taxonomy offers us the best opportunity to connect this information together, to answer important questions about biodiversity that we have never been able to answer before. The reason meetings like this are so important is that they bring people together to discuss ways of using modern informatics to greatly increase the power of the data we already have, and prioritise how we fill the gaps in data that exist. Taxonomy, and especially taxonomic data integration, is a very important part of the solution.”

Pyle also commented on the work in progress at ZooBank ten years into the platform’s existence and its role in the next (fifth) edition of the International Code of Zoological Nomenclature, which is currently being developed by the International Commission of Zoological Nomenclature (ICZN). 

“We already know that ZooBank will play a more important role in the next edition of the Code than it has for these past ten years, so this is exactly the right time to be planning new services for ZooBank. Improvements at ZooBank will include things like better user-interfaces on the web to make it easier and faster to use ZooBank, better data services to make it easier for publishers to add content to ZooBank as part of their publication workflow, additional information about nomenclature and taxonomy that will both support the next edition of the Code, and also help taxonomists get their jobs done more efficiently and effectively. Conferences like the TDWG one are critical for helping to define what the next version of ZooBank will look like, and what it will do.”

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During the week, the conference participants had the opportunity to enjoy a total of 140 presentations; as well as multiple social activities, including a field trip to Rila Monastery and a traditional Bulgarian dinner.

TDWG 2022 conference participants document their species observations on their way to Rila Monastery.

While going about the conference venue and field trip localities, the attendees were also actively uploading their species observations made during their stay in Bulgaria on iNaturalist in a TDWG2022-dedicated BioBlitz. The challenge concluded with a total of 635 observations and 228 successfully identified species.

Amongst the social activities going on during TDWG 2022 was a BioBlitz, where the conference participants could uploade their observations made in Bulgaria on iNaturalist and help each other successfully identify the specimens.

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In his interview for the Bulgarian News Agency and Pensoft, Dr Vincent Smith, Head of the Informatics Division at the Natural History Museum, London (United Kingdom), co-founder of DiSSCo, the Distributed System of Scientific Collections, and the Editor-in-Chief of Biodiversity Data Journal, commented: 

“Biodiversity provides the support systems for all life on Earth. Yet the natural world is in peril, and we face biodiversity and climate emergencies. The consequences of these include accelerating extinction, increased risk from zoonotic disease, degradation of natural capital, loss of sustainable livelihoods in many of the poorest yet most biodiverse countries of the world, challenges with food security, water scarcity and natural disasters, and the associated challenges of mass migration and social conflicts.

Solutions to these problems can be found in the data associated with natural science collections. DiSSCo is a partnership of the institutions that digitise their collections to harness their potential. By bringing them together in a distributed, interoperable research infrastructure, we are making them physically and digitally open, accessible, and usable for all forms of research and innovation. 

At present rates, digitising all of the UK collection – which holds more than 130 million specimens collected from across the globe and is being taken care of by over 90 institutions – is likely to take many decades, but new technologies like machine learning and computer vision are dramatically reducing the time it will take, and we are presently exploring how robotics can be applied to accelerate our work.”

Dr Vincent Smith, Head of the Informatics Division at the Natural History Museum, London, co-founder of DiSSCo, and Editor-in-Chief of Biodiversity Data Journal at the TDWG 2022 conference.

In his turn, Dr Donat Agosti, CEO and Managing director at Plazi – a not-for-profit organisation supporting and promoting the development of persistent and openly accessible digital taxonomic literature – said:

“All the data about biodiversity is in our libraries, that include over 500 million pages, and everyday new publications are being added. No person can read all this, but machines allow us to mine this huge, very rich source of data. We do not know how many species we know, because we cannot analyse with all the scientists in this library, nor can we follow new publications. Thus, we do not have the best possible information to explore and protect our biological environment.”

Dr Donat Agosti demonstrating the importance of publishing biodiversity data in a structured and semantically enhanced format in one of his presentations at TDWG 2022.

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At the closing plenary session, Gail Kampmeier – TDWG Executive member and one of the first zoologists to join TDWG in 1996 – joined via Zoom to walk the conference attendees through the 37-year history of the association, originally named the Taxonomic Databases Working Group, but later transformed to Biodiversity Information Standards, as it expanded its activities to the whole range of biodiversity data. 

“While this presentation is about TDWG’s history as an organisation, its focus will be on the heart of TDWG: its people. We would like to show how the organisation has evolved in terms of gender balance, inclusivity actions, and our engagement to promote and enhance diversity at all levels. But more importantly, where do we—as a community—want to go in the future?”,

reads the conference abstract of her colleague at TDWG Dr Visotheary Ung (CNRS-MNHN) and herself.

Then, in the final talk of the session, Deborah Paul took to the stage to present the progress and key achievements by the association from 2022.

She gave a special shout-out to the TDWG journal: Biodiversity Information Science and Standards (BISS), where for the 6th consecutive year, the participants of the annual conference submitted and published their conference abstracts ahead of the event. 

Deborah Paul reminds that – apart from the conference abstracts – the TDWG journal: Biodiversity Information Science and Standards (BISS) also welcomes full-lenght articles that demonstrate the development or application of new methods and approaches in biodiversity informatics.

Launched in 2017 on the Pensoft’s publishing platform ARPHA, the journal provides the quite unique and innovative opportunity to have both abstracts and full-length research papers published in a modern, technologically-advanced scholarly journal. In her speech, Deborah Paul reminded that BISS journal welcomes research articles that demonstrate the development or application of new methods and approaches in biodiversity informatics in the form of case studies.

Amongst the achievements of TDWG and its community, a special place was reserved for the Horizon 2020-funded BiCIKL project (abbreviation for Biodiversity Community Integrated Knowledge Library), involving many of the association’s members. 

Having started in 2021, the 3-year project, coordinated by Pensoft, brings together 14 partnering institutions from 10 countries, and 15 biodiversity under the common goal to create a centralised place to connect all key biodiversity data by interlinking a total of 15 research infrastructures and their databases.

Deborah Paul also reported on the progress of the Horizon 2020-funded project BiCIKL, which involves many of the TDWG members. BiCIKL’s goal is to create a centralised place to connect all key biodiversity data by interlinking 15 key research infrastructures and their databases.

In fact, following the week-long TDWG 2022 conference in Sofia, a good many of the participants set off straight for another Bulgarian city and another event hosted by Pensoft. The Second General Assembly of BiCIKL took place between 22nd and 24th October in Plovdiv.

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You can also explore highlights and live tweets from TDWG 2022 on Twitter via #TDWG2022.
The Pensoft team at TDWG 2022 were happy to become the hosts of the 37th TDWG conference.

Pensoft’s ARPHA Publishing Platform integrates with OA Switchboard to streamline reporting to funders of open research

By the time authors open their inboxes to the message their work is online, a similar notification will have also reached their research funder.

Image credit: OA Switchboard.

By the time authors – who have acknowledged third-party financial support in their research papers submitted to a journal using the Pensoft-developed publishing platform: ARPHA – open their inboxes to the congratulatory message that their work has just been published and made available to the wide world, a similar notification will have also reached their research funder.

This automated workflow is already in effect at all journals (co-)published by Pensoft and those published under their own imprint on the ARPHA Platform, as a result of the new partnership with the OA Switchboard: a community-driven initiative with the mission to serve as a central information exchange hub between stakeholders about open access publications, while making things simpler for everyone involved.

All the submitting author needs to do to ensure that their research funder receives a notification about the publication is to select the supporting agency or the scientific project (e.g. a project supported by Horizon Europe) in the manuscript submission form, using a handy drop-down menu. In either case, the message will be sent to the funding body as soon as the paper is published in the respective journal.

“At Pensoft, we are delighted to announce our integration with the OA Switchboard, as this workflow is yet another excellent practice in scholarly publishing that supports transparency in research. Needless to say, funding and financing are cornerstones in scientific work and scholarship, so it is equally important to ensure funding bodies are provided with full, prompt and convenient reports about their own input.”

comments Prof Lyubomir Penev, CEO and founder of Pensoft and ARPHA.

 

“Research funders are one of the three key stakeholder groups in OA Switchboard and are represented in our founding partners. They seek support in demonstrating the extent and impact of their research funding and delivering on their commitment to OA. It is great to see Pensoft has started their integration with OA Switchboard with a focus on this specific group, fulfilling an important need,”

adds Yvonne Campfens, Executive Director of the OA Switchboard.

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About the OA Switchboard:

A global not-for-profit and independent intermediary established in 2020, the OA Switchboard provides a central hub for research funders, institutions and publishers to exchange OA-related publication-level information. Connecting parties and systems, and streamlining communication and the neutral exchange of metadata, the OA Switchboard provides direct, indirect and community benefits: simplicity and transparency, collaboration and interoperability, and efficiency and cost-effectiveness.

About Pensoft:

Pensoft is an independent academic publishing company, well known worldwide for its novel cutting-edge publishing tools, workflows and methods for text and data publishing of journals, books and conference materials.

All journals (co-)published by Pensoft are hosted on Pensoft’s full-featured ARPHA Publishing Platform and published in a way that ensures their content is as FAIR as possible, meaning that it is effortlessly readable, discoverable, harvestable, citable and reusable by both humans and machines.

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Follow Pensoft on Twitter, Facebook and Linkedin.
Follow OA Switchboard on Twitter and Linkedin.

This October, the hybrid TDWG 2022 conference will address standards for linking biodiversity data

From 17th to 21st October 2022, the Biodiversity Information Standards (TDWG) conference – to be held in Sofia – will run under the theme “Stronger Together: Standards for linking biodiversity data”.

Between 17th and 21st October 2022, the Biodiversity Information Standards (TDWG) conference – to be held in Sofia, Bulgaria – will run under the theme “Stronger Together: Standards for linking biodiversity data”.

The event will be hosted by scholarly publisher and technology provider Pensoft, in collaboration with the National Museum of Natural History, and the Institute of Biodiversity and Ecosystem Research at the Bulgarian Academy of Sciences. This year, the event will be welcoming participants in-person, as well as virtually.

In addition to opening and closing plenaries, the conference will feature 14 symposia and a mix of other formats that include lightning talks, a workshop, and panel discussion, and contributed oral presentations and virtual posters. 

For a seventh year in a row, all abstracts submitted to the annual conference are made publicly available in the dedicated TDWG journal: Biodiversity Information Science and Standards (BISS Journal).

Thus, the abstracts – published ahead of the event itself – are not only permanently and freely available in a ‘mini-paper’ format, but will also provide conference participants with a sneak peek into what’s coming at the much anticipated conference.

Learn more about the unique features of BISS.

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Register and find more about the TDWG 2022 conference on Pensoft Event Manager.

See the Call for Abstracts and learn how to submit your abstract today.

Visit the TDWG conference website.

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Ahead, during and after the conference, join the conversation on Twitter via #tdwg2022.

Don’t forget to also follow TDWG (Twitter and Facebook), BISS Journal (Twitter and Facebook) and Pensoft (Twitter and Facebook) on social media.

Not Your Typical Conference Abstract #TDWG2021

TDWG 2021, the virtual conference of Biodiversity Information Standards (TDWG) being held 18–22 October, issued a call for abstracts representing presentations in fifteen symposia, as well as posters (including infographics), and contributed oral presentations appropriate to the conference theme Connecting the world of biodiversity data: uniting people, processes, and tools. Registration is now open, with the deadline for abstract submission set to 2 August 2021.

Joint blog post by #TDWG2021 Program Committee and Pensoft Editorial Team

TDWG 2021, the virtual conference of Biodiversity Information Standards (TDWG) being held 18–22 October, issued a call for abstracts representing presentations in fifteen symposia, as well as posters (including infographics), and contributed oral presentations appropriate to the conference theme Connecting the world of biodiversity data: uniting people, processes, and tools. Registration is now open, with the deadline for abstract submission set to 2 August 2021. 

Detailed instructions have also been made available to guide authors through the process. Abstract publication costs are included in the conference registration. All presenters must be fully registered before their abstracts can be published. 

Why are these not your typical conference abstracts? 

In short, each published abstract is a mini-paper designed to entice conference participants to attend your presentation, but, even more importantly, to let you provide something more enduring, a snapshot of your research progress the size of a written elevator pitch.

Using Pensoft’s ARPHA writing tool, you can enhance your abstract, so that it includes figures, keywords, references, and supplementary materials. Slides, posters, and video links can also be added to the abstract’s media tab after the conference, to build a well-rounded understanding of your work. TDWG’s open access Pensoft journal, Biodiversity Information Science and Standards (BISS), will even provide metrics about views, downloads, citations, or even online mentions of your abstract. 

Benefits of publishing your TDWG conference abstract: 

  • Free and open access to your abstract ahead of the conference via the society’s open access Pensoft journal, Biodiversity Information Science and Standards (BISS) 
  • A Digital Object Identifier (DOI), a unique, persistent, and citable reference assigned to each abstract 
  • Distribution of abstracts under the terms of Creative Commons attribution licenses, either CC BY 4.0 (default) or CC0 (by request).
  • Review provided by at least two editors for each abstract.
  • Readers can comment or ask questions within the Comment tab in the publication. Authors may also use the Comment tab for updates or errata.
  • Automatic linking of your abstract to your author record via ORCID and/or Web of Science (Publons) ResearcherID.
  • To prompt discoverability, all articles, including abstracts, are automatically harvested upon publication by a range of indexers, from AGRIS to ZDB.
  • Technical editors are cited as part of the article metadata. 
  • Abstracts are associated with the conference session in which they were presented.
  • Easy to create buzz around your presentation by sharing your abstract on Twitter, Facebook, Mendeley, Reddit, or via email with a single click thanks to share buttons.

While BISS is currently known as (just) a place to publish conference proceedings, this is a misconception. Authors are encouraged to publish full articles of methods, standards, guidelines, case studies, software descriptions, forum papers, editorials, correspondence, data or software reviews. BISS provides a discount on the article processing charges (APCs) for TDWG members.

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Join the conversation around this year’s Biodiversity Information Standards (TDWG) conference on Twitter via #TDWG2021.

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Visit BISS Journal website at: https://biss.pensoft.net/ and follow on Twitter and Facebook.

Integration of Freshwater Biodiversity Information for Decision-Making in Rwanda

Teams from Ghana, Malawi, Namibia and Rwanda during the inception meeting of the African Biodiversity Challenge Project in Kigali, Rwanda. Photo by Yvette Umurungi.

The establishment and implementation of a long-term strategy for freshwater biodiversity data mobilisation, sharing, processing and reporting in Rwanda is to support environment monitoring and the implementation of Rwanda’s National Biodiversity Strategy (NBSAP). In addition, it is to also help us understand how economic transformation and environmental change is affecting freshwater biodiversity and its resulting ecosystem services.

As part of this strategy, the Center of Excellence in Biodiversity and Natural Resource Management (CoEB) at the University of Rwanda, jointly with the Rwanda Environment Management Authority (REMA) and the Albertine Rift Conservation Society (ARCOS), are implementing the African Biodiversity Challenge (ABC) project “Integration of Freshwater Biodiversity Information for Decision-Making in Rwanda.”

The conference abstract for this project has been published in the open access journal Biodiversity Information Science and Standards (BISS). 

The CoEB has a national mandate to lead on biodiversity data mobilisation and implementation of the NBSAP in collaboration with REMA. This includes digitising data from reports, conducting analyses and reporting for policy and research, as indicated in Rwanda’s NBSAP.

The collation of the data will follow the international standards and will be available online, so that they can be accessed and reused from around the world. In fact, CoEB aspires to become a Global Biodiversity Informatics Facility (GBIF) node, thereby strengthening its capacity for biodiversity data mobilisation.

Data use training for the African Biodiversity Challenges at the South African National Biodiversity Institute (SANBI), South Africa. Photo by Yvette Umurungi.

The mobilised data will be organised using GBIF standards, and the project will leverage the tools developed by GBIF to facilitate data publication. Additionally, it will also provide an opportunity for ARCOS to strengthen its collaboration with CoEB as part of its endeavor to establish a regional network for biodiversity data management in the Albertine Rift Region.

The project is expected to conclude with at least six datasets, which will be published through the ARCOS Biodiversity Information System. These are to include three datasets for the Kagera River Basin; one on freshwater macro-invertebrates from the Congo and Nile Basins; one for the Rwanda Development Board archive of research reports from protected areas; and one from thesis reports from master’s and bachelor’s students at the University of Rwanda.

The project will also produce and release the first “Rwandan State of Freshwater Biodiversity”, a document which will describe the status of biodiversity in freshwater ecosystems in Rwanda and present socio-economic conditions affecting human interactions with this biodiversity.

The page of Center of Excellence in Biodiversity and Natural Resource Management (CoEB) at University of Rwanda on the Global Biodiversity Information Facility portal. Image by Yvette Umurungi.

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The ABC project is a competition coordinated by the South African National Biodiversity Institute (SANBI) and funded by the JRS Biodiversity Foundation. The competition is part of the JRS-funded project, “Mobilising Policy and Decision-making Relevant Biodiversity Data,” and supports the Biodiversity Information Management activities of the GBIF Africa network.

 

Original source:

Umurungi Y, Kanyamibwa S, Gashakamba F, Kaplin B (2018) African Biodiversity Challenge: Integrating Freshwater Biodiversity Information to Guide Informed Decision-Making in Rwanda. Biodiversity Information Science and Standards 2: e26367. https://doi.org/10.3897/biss.2.26367