Tobias Kuhn's research while affiliated with Vrije Universiteit Amsterdam and other places
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Publications (26)
With the rapidly increasing amount of scientific literature, it is getting continuously more difficult for researchers in different disciplines to keep up-to-date with the recent findings in their field of study. Processing scientific articles in an automated fashion has been proposed as a solution to this problem, but the accuracy of such processi...
Data integration is an essential task in the open world of the Semantic Web. Many approaches have been proposed that achieve such integration by linking related entities across data providers, but they lack the support for in-depth documentation of the involved processes such as the creation, manipulation and evaluation of links. As a consequence,...
Understanding the complexity of restricted research data is vitally important in the current new era of Open Science. While the FAIR Guiding Principles have been introduced to help researchers to make data Findable, Accessible, Interoperable and Reusable, it is still unclear how the notions of FAIR and Openness can be applied in the context of rest...
UNSTRUCTURED
This is the authors' responses to peer review reports related to MS#34979.
With the rapidly increasing amount of scientific literature,it is getting continuously more difficult for researchers in different disciplines to be updated with the recent findings in their field of study.Processing scientific articles in an automated fashion has been proposed as a solution to this problem,but the accuracy of such processing remai...
BACKGROUND
In the poorly studied field of physician suicide, various factors can contribute to misinformation or information distortion, which in turn can influence evidence-based policies and prevention of suicide in this unique population.
OBJECTIVE
The aim of this paper is to use nanopublications as a scientific publishing approach to establish...
The use of semantic technologies is gaining significant traction in science communication with a wide array of applications in disciplines including the Life Sciences, Computer Science, and the Social Sciences. Languages like RDF, OWL, and other formalisms based on formal logic are applied to make scientific knowledge accessible not only to human r...
Scientific publishing is the means by which we communicate and share scientific knowledge, but this process currently often lacks transparency and machine-interpretable representations. Scientific articles are published in long coarse-grained text with complicated structures, and they are optimized for human readers and not for automated means of o...
It is essential for the advancement of science that researchers share, reuse and reproduce each other’s workflows and protocols. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of research data, and emphasize the importance of making digital objects findable and reusable by others. The question of how to ap...
Scientific publishing is the means by which we communicate and share scientific knowledge, but this process currently often lacks transparency and machine-interpretable representations. Scientific articles are published in long coarse-grained text with complicated structures, and they are optimized for human readers and not for automated means of o...
In the poorly studied field of physician suicide, various fac-tors can contribute to misinformation or information distor-tion, which in turn can influence evidence-based policies and prevention of suicide in this unique population. Here, we report on the use of nanopublications as a scientific publishing approach to establish a citation network of...
Nanopublication is a data publishing model which has a great potential for the representation of scientific results allowing interoperability, data integration and exchange of scientific findings. But this model suffer of the lack of an appropriate standard methodology to produce complete and interoperable citations providing both data identificati...
It is essential for the advancement of science that scientists and researchers share, reuse and reproduce workflows and protocols used by others. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of research data, and emphasize a number of important points regarding the means by which digital objects are foun...
Scientific publishing seems to be at a turning point. Its paradigm has stayed basically the same for 300 years but is now challenged by the increasing volume of articles that makes it very hard for scientists to stay up to date in their respective fields. In fact, many have pointed out serious flaws of current scientific publishing practices, inclu...
Scientific publishing seems to be at a turning point. Its paradigm has stayed basically the same for 300 years but is now challenged by the increasing volume of articles that makes it very hard for scientists to stay up to date in their respective fields. In fact, many have pointed out serious flaws of current scientific publishing practices, inclu...
In this paper we discuss the role of the Nanopublication (nanopub) model for scholarly publications with particular focus on the citation of nanopubs. To this end, we contribute to the state-of-the-art in data citation by proposing: the nanocitation framework that defines the main steps to create a text snippet and a machine-readable citation given...
In this paper we discuss the role of the Nanopublication (nanopub) model for scholarly publications with particular focus on the citation of nanopubs.
The number of scientific articles has grown rapidly over the years and there are no signs that this growth will slow down in the near future. Because of this, it becomes increasingly difficult to keep up with the latest developments in a scientific field. To address this problem, we present here an approach to help researchers learn about the lates...
Climate change, vaccination, abortion, Trump: Many topics are surrounded by fierce controversies. The nature of such heated debates and their elements have been studied extensively in the social science literature. More recently, various computational approaches to controversy analysis have appeared, using new data sources such as Wikipedia, which...
The number of scientific articles has grown rapidly over the years and there are no signs that this growth will slow down in the near future. Because of this, it becomes increasingly difficult to keep up with the latest developments in a scientific field. To address this problem, we present here an approach to help researchers learn about the lates...
Climate change, vaccination, abortion, Trump: Many topics are surrounded by fierce controversies. The nature of such heated debates and their elements have been studied extensively in the social science literature. More recently, various computational approaches to controversy analysis have appeared, using new data sources such as Wikipedia, which...
Citations
... The Open Research Knowledge Graph project (ORKG) [1,18] ambitions to represent all that can be found in a research paper: this is wider than experiments, but experiments have reproducibility requirements which lead their descriptions to go beyond what is available in papers. Some work have proposed the expression of experiments [24], of hypotheses [9] or claims [3]. On the experimental side: the researchobject project has provided a way to describe protocols [14] as well as SMART protocols [11]. ...
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... This can be used to identify provenance information in hierarchical graphs [5]. A proposal for the structured use of several named graphs are nano publications [2] that also explicitly support provenance. ...
... A recent work on ontological consideration to scientific workflows is presented by Celebi et al., 78 with the objective of enhancing reproducibility of results in scientific research in general. Although the research on scientific-workflow-related ontology is currently premature, our case-based survey suggests that adopting standard domain-specific ontology such as BattINFO in the BIG-MAP project or developing specific case-based ontology that accommodates peculiarities of one's research can encourage better collaboration and help mitigate cognitive burden related to reproducing/validating the results of one's peers in both large-and small-scale collaborations. ...
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... Response: We greatly appreciate the comment from the reviewer and note that we have clarified the data source used in this proof-of-concept study in a Data Source subsection of the Methods. The authors had already used the final reference list from the published article, not the MedRxiv preprint [15], for this study. The reference has been updated in the reference list of this manuscript. ...
... Nanopublication has been applied for scientific research. Currently, converting existing relational databases (such as DisGeNet, a gene-disease association knowledge database) to nanopublications (Fabris, Kuhn, & Silvello, 2020) or storing and computing triples at online platforms such as The Open Pharmaceutical Triple Store (Open PHACTS, a pharmaceutical semantic triple discovery platform) (Williams et al., 2012) are two representatives of nanopublication applications. However, the nanopublication model has not been widely utilized in clinical research and practice. ...
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... In previous research we have applied nanopublications to implement a semantic and fine-grained model for reviewing (Bucur et al., 2019), and have extended this to semantically represent the full structure of (classical) scientific articles with their reviews and review responses as a single network of nanopublications (Bucur et al., 2020). In order to get closer to our vision of genuine semantic publishing, however, we need to represent not just the structure but also the main content of these articles, most importantly their main scientific claims. ...
... To promote the reuse of nanopublications and increase acceptance, scholars have recently proposed a nanocitation format that can cite individual nanopublications and allocate credits to the contributor. Therefore, it is possible to design bibliometric indicators, conduct fine-grained analysis of knowledge units, and combine them with current scientific research (Fabris, Kuhn, & Silvello, 2019). ...
... Hence, interactive notebooks can transform how experimental results are exchanged in biomedical research. In this direction, several academic journals now support the Jupyter Notebook as a legitimate component of a publication, for example, the journal F1000 Research 9 , or as an acceptable format type to submit articles, for example, the journal Data Science 10 . However, generating interactive notebooks requires high level of computer programming expertise which is uncommon among experimental biologists. ...
... While it is important to try to process the vast amount of existing scientific literature that has the form of long English texts (and sometimes long texts in other languages), we should also think about how we can improve the way how 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 (Kuhn and Dumontier, 2017), where the machine-interpretable formal semantics cover the main scientific claims the work is making. Nanopublications (Groth et al., 2010), which are small RDF-based semantic packages, have emerged as a powerful concept and technology for enabling such genuine semantic publishing. ...
... Methodological research at the intersection of NLP, information retrieval and machine learning is aimed at detecting, classifying or verifying (scientific) claims and discourse [11,18,19,24,25], and is a key facilitator for large-scale interdisciplinary analysis of science discourse. Prior works often focus on actual scholarly publications [14,21], where the formality of language differs substantially from science claims in online news and social media, e.g., Twitter. ...
