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The Future of Science Publishing – Focus on Nanopublications and Formalization Papers

reflective, hexagonal architectural forms looking towards a distant tree-lined horizon

28 March 2022 | Carmel McNamara, IOS Press, NL
Celebrating its 35th anniversary this year, IOS Press will share perspectives and insights into science publishing developments during a symposium on March 31, 2022. Prior to the event, this blog post highlights the latest research of one of the speakers in the technical session, Tobias Kuhn from Vrije Universiteit Amsterdam. Dr. Kuhn is the co-Editor-in-Chief of Data Science and guest editor of a new special issue, together with his colleague Cristina-Iulia Bucur, which aims to demonstrate for the first time that scientific articles can be formalized and therefore machine-interpretable – including the main scientific claims.

Making the publishing process transparent and machine-interpretable

by Carmel McNamara, IOS Press, NL

Celebrating its 35th anniversary this year, IOS Press will share perspectives and insights into science publishing developments during a symposium on March 31, 2022. Prior to the event, this blog post highlights the latest research of one of the speakers in the technical session, Tobias Kuhn from Vrije Universiteit Amsterdam. Dr. Kuhn is the co-Editor-in-Chief of Data Science and guest editor of a new special issue, together with his colleague Cristina-Iulia Bucur, which aims to demonstrate for the first time that scientific articles can be formalized and therefore machine-interpretable – including the main scientific claims.

IOS Press was founded in 1987.  Since then, developments within scholarly publishing  have continued at a rapid pace, some anticipated by forward-thinking leaders in the field, while others have been unforeseen. Reflecting on the 30th anniversary celebration in 2017, the company’s founder and director Einar Fredriksson, PhD stated: “IOS Press is based on an academic publishing tradition commenced by learned societies and continued into the 20th century by specialized book-sellers and private sector publishers. With the arrival of computer networks and the Web in conjunction with a rapid growth of research and number of publications, and an increased interest among public sector institutions and funding agencies, our working environment is constantly changing.” 

The company has a strong focus on innovation and is committed to investment in innovation. Current investigations include transparency and reproducibility, the incorporation of semantic entities for published metadata, and the development and application of proprietary software. Primary goals are to prioritize accessibility and strive for advancements in semantic publishing concentrating on the dissemination of scientific knowledge. As part of this initiative, the linked machine-readable metadata from all IOS Press journals and books are publicly available via LD Connect and users are invited to explore the data freely (read more in this blog post). 

IOS Press is committed to addressing forward-looking topics, and these will be in evidence during the upcoming symposium to celebrate its 35th anniversary. Presenting during the technical session, Tobias Kuhn will share insights into nanopublications. He explains: "We need to find better ways to publish scientific findings to make them interpretable by software. I will show how we can let researchers formally represent and publish their own findings, and will report on our recent experiences in what could be the first steps in a new era of scientific publishing."

white interconnected hexagons

 

Semantic web technologies and nanopublications

The importance of published articles being interpretable and readable by machines is without doubt. However, there are still some areas of scholarly publishing that are clinging to the past, such as adhering to formats that are optimized for print use, such as PDF files, for all journal articles – even if it is an online-only journal. This topic was covered in a Labs blog post (see here), in which Cristina-Iulia Bucur first shared ideas for transforming scholarly articles into small, interlinked snippets of data. She states: “In our approach, we argue for a new system of scientific publishing that contains smaller, fine-grained, formal – machine-interpretable – representations of scientific knowledge that are linked together in a big knowledge network in a web-like fashion in a way that these publications do not need to be necessarily linked to a journal or a traditional publication and can be publication entities by themselves. Moreover, semantic technologies make possible the decomposition of traditional science articles into constituent machine-readable parts that are linked not only with one another, but also to other related fine-grained parts of knowledge on the Web following the linked data principles.”

Now, the Data Science special issue goes one step further. It introduces the brand new concept of “formalization papers” – which are nanopublication-based semantic publications whose novelty lies in the formalization of a previously published scientific claim. The editors Tobias Kuhn and Cristina-Iulia Bucur state that the aim of the special issue is to demonstrate for the first time that scientific articles can be formalized and therefore machine-interpretable – including the main scientific claims: “A formalization paper contributes a semantic formalization of one of the main claims of an already published scientific article. Its novelty therefore lies solely in the formalization of a claim, not the claim itself. The authors of such formalization papers consequently take credit for the way in which the formalization is done, but not for the original claim (unless that claim happens to come from the same authors).” Discover more about this topic via the extract of the special issue’s editorial listed in Box 1.
 

Box 1: Semantic Publishing with Formalization Papers

The vast majority of existing approaches of making scientific texts machine-readable have one thing in common: they take the current paradigm of scientific articles for granted and therefore take them as their starting point to extract information. While it is important to try to process the enormous amount of existing scientific literature that takes the form of long English texts (and sometimes long texts in other languages), we should also think about how we can improve the way in which we publish scientific insights in the first place. An important aspect of this is the vision of semantic publishing, which we mean here in the sense of genuine semantic publishing, where the machine-interpretable formal semantics cover the main scientific claims the work is making. Nanopublications, which are small RDF-based semantic packages, have emerged as a powerful concept and technology for enabling such genuine semantic publishing.

In the past, nanopublications were used to implement a semantic and fine-grained model for reviewing, and this was extended to semantically represent the full structure of (classical) scientific articles with their reviews and review responses as a single network of nanopublications. In order to get closer to the vision of genuine semantic publishing, however, not just the structure, but also the main content of these articles needs to be represented, most importantly their main scientific claims. To that aim, a semantic template called the “super-pattern” was proposed to represent the meaning of scientific claims in formal logic.

The publication of the special issue with formalization papers in the Data Science journal shows not only that nanopublications and the super-pattern can be used to implement the basic steps and entities of a journal workflow, but also that authors of such formalization papers can be taught to use these in order to publish in a novel journal publication workflow as the publication of the special issue demonstrates. We found that the super-pattern can be well understood conceptually, and that its application in a practical setting is feasible.

 

This text is extracted from the editorial by Tobias Kuhn and Cristina-Iulia Bucur in Data Science, Volume 5, Issue 1 (March 2022).

 

reflective hexagonal architectural element with a view to a distant horizon

 

Looking to the future for science publishing

Tobias Kuhn will be discussing this brand new semantic publishing development during the upcoming IOS Press symposium (more details of how to watch his presentation are included below). He will join a host of other expert scholars who will be sharing personal perspectives on what’s next for the industry and where the future of the field lies.

 

We invite you to join the celebration online and keep an eye on this blog for highlights from the event!

IOS Press 35th Anniversary Celebration: Symposium

March 31, 2022 | Watch the livestream from 13:45–17:00 & view contributions online

The 35th anniversary of IOS Press will be celebrated on March 31, 2022 with a symposium entitled “The Future of Science Publishing – Personal Views.” Presentations by a host of international speakers will shed light on current developments within their field and what they see ahead of us in the future of publishing. There will be two parts to the event – a Tech Session and a Key Editors Session. To view the full line-up, click here

We are very pleased that we can invite the IOS Press global audience to join the livestream of the symposium online. There will also be a number of contributions and presentations in addition to the live event that will be accessible via the event website page in due course and will be available to view throughout this anniversary year!

IOS Press 35 years logo (dark blue)

 

Technical developments for the scientific publishing industry have also been highlighted on this blog – from the article about blockchain technology to one of the initial posts on the site covering FAIR data. View other related blog posts via the links below.