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 readers but also to automated systems. These approaches have mostly focused on the structure of scientific publications themselves, on the used scientific methods and equipment, or on the structure of the used datasets. The core claims or hypotheses of scientific work have only been covered in a shallow manner, such as by linking mentioned entities to established identifiers. In this research, we therefore want to find out whether we can use existing semantic formalisms to fully express the content of high-level scientific claims using formal semantics in a systematic way. Analyzing the main claims from a sample of scientific articles from all disciplines, we find that their semantics are more complex than what a straight-forward application of formalisms like RDF or OWL account for, but we managed to elicit a clear semantic pattern which we call the "super-pattern". We show here how the instantiation of the five slots of this super-pattern leads to a strictly defined statement in higher-order logic. We successfully applied this super-pattern to an enlarged sample of scientific claims. We show that knowledge representation experts, when instructed to independently instantiate the super-pattern with given scientific claims, show a high degree of consistency and convergence given the complexity of the task and the subject. These results therefore open the door on the longer run for allowing researchers to express their high-level scientific findings in a manner they can be automatically interpreted. This in turn will allow for automated consistency checking, question answering, aggregation, and much more.

BackgroundBiological networks have a growing importance for the interpretation of high-throughput “omics” data. Integrative network analysis makes use of statistical and combinatorial methods to extract smaller subnetwork modules, and performs enrichment analysis to annotate the modules with ontology terms or other available knowledge. This process results in an annotated module, which retains the original network structure and includes enrichment information as a set system. A major bottleneck is a lack of tools that allow exploring both network structure of extracted modules and its annotations.ResultsThis paper presents a visual analysis approach that targets small modules with many set-based annotations, and which displays the annotations as contours on top of a node-link diagram. We introduce an extension of self-organizing maps to lay out nodes, links, and contours in a unified way. An implementation of this approach is freely available as the Cytoscape app Conclusions accurately conveys small and annotated modules consisting of several dozens of proteins and annotations. We demonstrate that facilitates the interpretation of integrative network analysis results in a guided case study. This study has resulted in a novel biological insight regarding the virally-encoded G-protein coupled receptor US28.

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 organization and access. Peer reviewing is the main method of quality assessment, but these peer reviews are nowadays rarely published and their own complicated structure and linking to the respective articles are not accessible. In order to address these problems and to better align scientific publishing with the principles of the Web and Linked Data, we propose here an approach to use nanopublications as a unifying model to represent in a semantic way the elements of publications, their assessments, as well as the involved processes, actors, and provenance in general. To evaluate our approach, we present a dataset of 627 nanopublications representing an interlinked network of the elements of articles (such as individual paragraphs) and their reviews (such as individual review comments). Focusing on the specific scenario of editors performing a meta-review, we introduce seven competency questions and show how they can be executed as SPARQL queries. We then present a prototype of a user interface for that scenario that shows different views on the set of review comments provided for a given manuscript, and we show in a user study that editors find the interface useful to answer their competency questions. In summary, we demonstrate that a unified and semantic publication model based on nanopublications can make scientific communication more effective and user-friendly. IntroductionScientific publishing is about how we disseminate, share and assess research. Despite the fact that technology has changed how we perform and disseminate research, there is much more potential for scientific publishing to become a more transparent and more efficient process, and to improve on the age-old paradigms of journals, articles, and peer reviews [3,28]. With scientific publishing often

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, including the lack of accuracy and efficiency of the reviewing process. To address some of these problems, we apply here the general principles of the Web and the Semantic Web to scientific publishing, focusing on the reviewing process. We want to determine if a fine-grained model of the scientific publishing workflow can help us make the reviewing processes better organized and more accurate, by ensuring that review comments are created with formal links and semantics from the start. Our contributions include a novel model called Linkflows that allows for such detailed and semantically rich representations of reviews and the reviewing processes. We evaluate our approach on a manually curated dataset from several recent Computer Science journals and conferences that come with open peer reviews. We gathered ground-truth data by contacting the original reviewers and asking them to categorize their own review comments according to our model. Comparing this ground truth to answers provided by model experts, peers, and automated techniques confirms that our approach of formally capturing the reviewers' intentions from the start prevents substantial discrepancies compared to when this information is later extracted from the plain-text comments. In general, our analysis shows that our model is well understood and easy to apply, and it revealed the semantic properties of such review comments.

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