Category: Comparative Cytogenetics

Interoperable biodiversity data extracted from literature through open-ended queries

OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System. 

The OpenBiodiv contribution to BiCIKL

Apart from coordinating the Horizon 2020-funded project BiCIKL, scholarly publisher and technology provider Pensoft has been the engine behind what is likely to be the first production-stage semantic system to run on top of a reasonably-sized biodiversity knowledge graph.

OpenBiodiv is a biodiversity database containing knowledge extracted from scientific literature, built as an Open Biodiversity Knowledge Management System. 

As of February 2023, OpenBiodiv contains 36,308 processed articles; 69,596 taxon treatments; 1,131 institutions; 460,475 taxon names; 87,876 sequences; 247,023 bibliographic references; 341,594 author names; and 2,770,357 article sections and subsections.

In fact, OpenBiodiv is a whole ecosystem comprising tools and services that enable biodiversity data to be extracted from the text of biodiversity articles published in data-minable XML format, as in the journals published by Pensoft (e.g. ZooKeys, PhytoKeys, MycoKeys, Biodiversity Data Journal), and other taxonomic treatments – available from Plazi and Plazi’s specialised extraction workflow – into Linked Open Data.

“I believe that OpenBiodiv is a good real-life example of how the outputs and efforts of a research project may and should outlive the duration of the project itself. Something that is – of course – central to our mission at BiCIKL.”

explains Prof Lyubomir Penev, BiCIKL’s Project Coordinator and founder and CEO of Pensoft.

“The basics of what was to become the OpenBiodiv database began to come together back in 2015 within the EU-funded BIG4 PhD project of Victor Senderov, later succeeded by another PhD project by Mariya Dimitrova within IGNITE. It was during those two projects that the backend Ontology-O, the first versions of RDF converters and the basic website functionalities were created,”

he adds.

At the time OpenBiodiv became one of the nine research infrastructures within BiCIKL tasked with the provision of virtual access to open FAIR data, tools and services, it had already evolved into a RDF-based biodiversity knowledge graph, equipped with a fully automated extraction and indexing workflow and user apps.

Currently, Pensoft is working at full speed on new user apps in OpenBiodiv, as the team is continuously bringing into play invaluable feedback and recommendation from end-users and partners at BiCIKL. 

As a result, OpenBiodiv is already capable of answering open-ended queries based on the available data. To do this, OpenBiodiv discovers ‘hidden’ links between data classes, i.e. taxon names, taxon treatments, specimens, sequences, persons/authors and collections/institutions. 

Thus, the system generates new knowledge about taxa, scientific articles and their subsections, the examined materials and their metadata, localities and sequences, amongst others. Additionally, it is able to return information with a relevant visual representation about any one or a combination of those major data classes within a certain scope and semantic context.

Users can explore the database by either typing in any term (even if misspelt!) in the search engine available from the OpenBiodiv homepage; or integrating an Application Programming Interface (API); as well as by using SPARQL queries.

On the OpenBiodiv website, there is also a list of predefined SPARQL queries, which is continuously being expanded.

Sample of predefined SPARQL queries at OpenBiodiv.

“OpenBiodiv is an ambitious project of ours, and it’s surely one close to Pensoft’s heart, given our decades-long dedication to biodiversity science and knowledge sharing. Our previous fruitful partnerships with Plazi, BIG4 and IGNITE, as well as the current exciting and inspirational network of BiCIKL are wonderful examples of how far we can go with the right collaborators,”

concludes Prof Lyubomir Penev.

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

You can also follow Pensoft on Twitter, Facebook and Linkedin and use #OpenBiodiv on Twitter.

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.

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 OA Switchboard on Twitter and Linkedin.

Mosquito populations give a new insight into the role of Caucasus in evolution

We know that the Caucasus is a relatively large mountainous region, situated between Black and the Caspian seas. In its turn, it is divided into three subregions: Ciscaucasia, Greater Caucasus and Transcaucasia, also known as South Caucasus.

A closer look into the chromosome structure of mosquito larvae of a curious group of species (Chironomus “annularius” sensu Strenzke (1959)), collected from the three localities, has allowed Dr Mukhamed Karmokov of the Tembotov Institute of Ecology of Mountain territories at the Russian Academy of Science to figure out how the specificity of the Caucasian region has simultaneously unified its fauna geographically, yet has divided it evolutionarily. His paper is published in the open access journal Comparative Cytogenetics.

Having collected a sufficient amount of mosquito larvae, the researcher managed to study the chromosome structure, rearrangements and possible peculiarities of the separate Caucasian populations, in order to compare them.

Additionally, he analysed their relations to earlier known populations from Europe, Siberia, Kazakhstan and North America.

Amongst the curious peculiarities Karmokov identified in the chromosome structure of the studied larvae were some rearrangements which appear unique to Caucasus. Furthermore, he found that despite the close geographic proximity, the genetic distance between the Caucasian populations is quite significant, even While not enough to determine them as separate species, it could prove them as separate subspecies.

In conclusion, the scientist notes that the obtained data confirm that the Caucasian populations of the studied species have complex genetic structure and provide evidence for microevolution processes in the region.

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Original source:

Karmokov MKh (2018) Karyotype characteristics and chromosomal polymorphism of Chironomus “annularius” sensu Strenzke (1959) (Diptera, Chironomidae) from the Caucasus region. Comparative Cytogenetics 12(3): 267-284. https://doi.org/10.3897/CompCytogen.v12i3.25832

New butterfly species discovered in Russia with an unusual set of 46 chromosomes

What looked like a population of a common butterfly species turned out to be a whole new organism, and, moreover – one with a very peculiar genome organisation.

Discovered by Vladimir Lukhtanov, entomologist and evolutionary biologist at the Zoological Institute in St. Petersburg, Russia, and Alexander Dantchenko, entomologist and chemist at the Moscow State University, the startling discovery was named South-Russian blue (Polyommatus australorossicus). It was found flying over the northern slopes of the Caucasus mountains in southern Russia. The study is published in the open access journal Comparative Cytogenetics.

“This publication is the long-awaited completion of a twenty-year history,” says Vladimir Lukhtanov.

In the mid-nineties, Vladimir Lukhtanov, together with his students and collaborators, started an exhaustive study of Russian butterflies using an array of modern and traditional research techniques. In 1997, Alexander Dantchenko who was mostly focused on butterfly ecology, sampled a few blue butterfly specimens from northern slopes of the Caucasus mountains. These blues looked typical at first glance and were identified as Azerbaijani blue (Polyommatus aserbeidschanus).

However, when the scientists looked at them under a microscope, it became clear that they had 46 chromosomes – a very unusual number for this group of the blue butterflies and exactly the same count as in humans.

Having spent twenty years studying the chromosomes of more than a hundred blue butterfly species and sequencing DNA from all closely related species, the researchers were ready to ascertain the uniqueness of the discovered butterfly and its chromosome set.

Throughout the years of investigation, it has become clear that caterpillars of genetically related species in the studied butterfly group feed on different, but similar plants. This discovery enables entomologists to not only discover new butterfly species with the help of botanic information, but also protect them.

“We are proud of our research,” says Vladimir Lukhtanov. “It contributes greatly to both the study of biodiversity and understanding the mechanisms of biological evolution.”

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Original source:

Lukhtanov VA, Dantchenko AV (2017) A new butterfly species from south Russia revealed through chromosomal and molecular analysis of the Polyommatus (Agrodiaetus) damonides complex (Lepidoptera, Lycaenidae). Comparative Cytogenetics 11(4): 769-795. https://doi.org/10.3897/CompCytogen.v11i4.20072

New butterfly species discovered in Israel for the first time in 109 years

Vladimir Lukhtanov, entomologist and evolutionary biologist at the Zoological Institute in St. Petersburg, Russia, made a startling discovery: what people had thought was a population of a common species, turned out to be a whole new organism and, moreover – one with an interesting evolutionary history. This new species is named Acentria’s fritillary (Melitaea acentria) and was found flying right over the slopes of the popular Mount Hermon ski resort in northern Israel. It is described in the open access journal Comparative Cytogenetics.

“To me, it was a surprise that no one had already discovered it,” says Vladimir Lukhtanov.

“Thousands of people had observed and many had even photographed this beautifully coloured butterfly, yet no one recognised it as a separate species. The lepidopterists (experts in butterflies and moths) had been sure that the Hermon samples belonged to the common species called Persian fritillary (Melitaea persea), because of their similar appearance, but nobody made the effort to study their internal anatomy and DNA”.

In 2012, Vladimir Lukhtanov, together with his students, initiated an exhaustive study of Israeli butterflies using an array of modern and traditional research techniques. In 2013, Asya Novikova (until 2012, a master’s student at St. Petersburg University and, from 2013, a PhD student at the Hebrew University, Jerusalem) sampled a few fritillaries from Mt. Hermon.

It was at that time when the researchers noticed that the specimens “didn’t look right” – their genitalia appeared different from those of the typical Persian fritillary. Over the next few years, Lukhtanov and his students studied this population in-depth. They carried out sequencing DNA from the specimens and found that they had a unique molecular signature – very different from the DNA of any other fritillary.

The Acentria’s fritillary seems to be endemic in northern Israel and the neighbouring territories of Syria and Lebanon. Its evolutionary history is likely to prove interesting.

“The species is probably one of a handful of butterflies known to have arisen through hybridisation between two other species in the past,” says Lukhtanov. “This process is known to be common in plants, but scientists have only recently realised it might also be present in butterflies.”

This is the first new butterfly species discovered and described from the territory of Israel in 109 years.

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Original source:

Lukhtanov VA (2017) A new species of Melitaea from Israel, with notes on taxonomy, cytogenetics, phylogeography and interspecific hybridization in the Melitaea persea complex (Lepidoptera, Nymphalidae). Comparative Cytogenetics 11(2): 325-357. https://doi.org/10.3897/CompCytogen.v11i2.12370