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A new pilot project by Pensoft and Knowledge Pixels breaks scientific knowledge into FAIR and interlinked snippets of precise information
As you might have already heard, Knowledge Pixels: an innovative startup tech company aiming to revolutionise scientific publishing and knowledge sharing by means of nanopublications – recently launched a pilot project with the similarly pioneering open-science journal Research Ideas and Outcomes (RIO), in a first of several upcoming collaborations between the software developer and the open-access scholarly publisher Pensoft.
“The way how science is performed has dramatically changed with digitalisation, the Internet, and the vast increase in data, but the results are still shared in basically the same form and language as 300 years ago: in narrative text, like a story. These narratives are not precise and not directly interpretable by machines, thereby not FAIR. Even the latest impressive AI tools like ChatGPT can only guess (and sometimes ‘hallucinate’) what the authors meant exactly and how the results compare,”
said Philipp von Essen and Tobias Kuhn, the two founders of Knowledge Pixels in a press announcement.
So, in order to bridge the gap between authors and their readers and fellow researchers – whether humans or computers – the partners launched several workflows to bi-directionally link scientific publications from RIO Journal to nanopublications. We will explain and demonstrate these workflows in a bit.
Now, first, let’s see what nanopublications are and how they contribute to scientific knowledge, researchers and scholarship as a whole.
What are nanopublications?
General structure of a nanopublication:
“the smallest unit of publishable information”,
as explained by Knowledge Pixel on nanopub.net.
Basically, a nanopublication – unlike a research article – is just a tiny snippet of a scientific finding (e.g. medication X treats disease Y), which exists as a complete and straightforward piece of information stored on a decentralised server network in a specially structured format, so that it is readable for humans, but also “understandable” and actionable for computers and their algorithms.
A nanopublication may also be an assertion related to an existing research article meant to support, comment, update or complement the reported findings.
In fact, nanopublications as a concept have been with us for quite a while now. Ever since the rise of the Semantic Web, to be exact. At the end of the day, it all boils down to providing easily accessible information that is only a click away from additional useful and relevant content. The thing is, technological advancement has only recently begun to catch up with the concept of nanopublications. Today, we are one step closer to another revolution in scientific publishing, thanks to the emergence and increasing adoption of what we call knowledge graphs.
“As pioneers in the semantic open access scientific publishing field for over a decade now, at Pensoft we 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: the open-access scholarly publisher behind the very first semantically enhanced research article in the biodiversity domain, published back in 2010 in the ZooKeys journal.
Why nanopublications?
Apart from enabling computer algorithms with wholesome access to published research findings, nanopublications allow for the knowledge snippets that they are intended to communicate to be fully understandable and actionable. With nanopublications, each byte of knowledge is interconnected and traceable back to its author(s) and scientific evidence.
By granting computers the capability of exchanging information between users and platforms, 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.
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.
By linking assertions to a publication by means of nanopublications allows the original authors and their fellow researchers to keep knowledge up to date as new findings emerge either in support or contradiction to previous information.
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.
A scientific issue that would definitely benefit from an additional layer of provenance and, specifically, a workflow allowing for new updates to be linked to previous publications is the biodiversity domain, where species treatments, taxon names, biotic interactions and phylogenies are continuously being updated, reworked and even discarded for good. This is why an upcoming collaboration between Pensoft and Knowledge Pixels will also involve the Biodiversity Data Journal (stay tuned!)
What can you do in RIO?
Now, let’s have a look at the *nano* opportunities already available at RIO Journal.
The integration between RIO and Nanodash: the environment developed by Knowledge Pixels where users edit and publish their nanopublications is available at any article published in the journal.
Add reaction to article
This function allows any reader to evaluate and record an opinion about any article using a simple template. The opinion is posted as a nanopublication displayed on the article page, bearing the timestamp and the name of the creator.
All one needs to do is go to a paper, locate the Nanopubs tab in the menu on the left and click on the Add reaction command to navigate to the Nanodash workspace accessible to anyone registered on ORCiD.
Within the simple Nanodash workspace, the user can provide the text of the nanopublication; define its relation to the linked paper using the Citation Typing Ontology (CiTO); update its provenance and add information (e.g. licence, extra creators) by inserting extra elements.
To do this, the Knowledge Pixels team has created a ready-to-use nanopublication template, where the necessary details for the RIO paper and the author that secure the linkage have already been pre-filled.
Post an inline comment as a nanopublication
Another opportunity for readers and authors to add further meaningful information or feedback to an already published paper is by attaching an inline comment and then exporting it to Nanodash, so that it becomes a nanopublication. To do this, users will simply need to select some text with a left click, type in the comment, and click OK. Now, their input will be available in the Comment tab designed to host simple comments addressing the authors of the publication.
While RIO has long been supporting features allowing for readers to publicly share comments and even CrossRef-registered post-publication peer reviews along the articles, the nanopublications integration adds to the versatile open science-driven arsenal of feedback tools. More precisely, the novel workflow is especially useful for comments that provide a particularly valuable contribution to a research topic.
To make a comment into a nanopublication the user needs to locate the comment in the tab, and click on the Post as Nanopub command to access the Nanodash environment.
Add a nanopublication while writing your manuscript
A functionality available from ARPHA Writing Tool – the online collaborative authoring environment that underpins the manuscript submission process at several journals published by Pensoft, including RIO Journal – allows for researchers to create a list of nanopublications within their manuscripts.
By doing so, not only do authors get to highlight their key statements in a tabular view within a separate pre-designated Nanopublications section, but they also make it easier for reviewers and scientific editors to focus on and evaluate the very foundations of the paper.
By incorporating a machine algorithm-friendly structure for the main findings of their research paper, authors ensure that AI assistants, for example, will be more likely to correctly ‘read’, ‘interpret’ and deliver the knowledge reported in the publication for the next users and their prompts. Furthermore, fellow researchers who might want to cite the paper will also have an easier time citing the specific statement from within the cited source, so that their own readers – be it human, or AI – will make the right links and conclusions.
Within a pre-designated article template at RIO – regardless of the paper type selected – authors have the option to either paste a link to an already available nanopublication or manage their nanopublication via the Nanodash environment by following a link. Customised for the purposes of RIO, the Nanodash workspace will provide them with all the information needed to guide them through the creation and publication of their nanopublications.
Why Research Ideas and Outcomes, a.k.a. RIO Journal?
Why did Knowledge Pixels and Pensoft opt to run their joint pilot at no other journal within the Pensoft portfolio of open-access scientific journals but the Research Ideas and Outcomes (RIO)?
Well, one may argue that there simply was no better choice than an academic outlet that was initially designed to serve as “the open-science journal”: something it has been honourably recognised for by SPARC in 2016, only one year since its launch.
Innovative since day #1, back in 2015, RIO surfaced as an academic outlet to publish a whole lot of article types, reporting on scientific work from across the research process, starting from research ideas, grant proposals and workshop reports.
After all, back in 2015, when it was only a handful of funders who required Data and Software Management Plans to be made openly and publicly, RIO was already providing a platform to publish those as easily citable research outputs, complete with DOI and registration on Crossref. In the spirit of transparency, RIO has always operated an open and public by default peer review policy.
More recently, RIO introduced a novel collections workflow which allows, for example, project coordinators, to provide a one-stop access point for publications and all kinds of valuable outputs resulting from their projects regardless of their publication source.
Bottom line is, RIO has always stood for innovation, transparency, openness and FAIRness in scholarly publishing and communication, so it was indeed the best fit for the nanopublication pilot with Knowledge Pixels.
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We encourage you to try the nanopublications workflow yourself by going to https://riojournal.com/articles, and posting your own assertion to an article of your choice!
Don’t forget to also sign up for the RIO Journal’s newsletter via the Email alert form on the journal’s website and follow it on Twitter, Facebook, Linkedin and Mastodon.