Anita de Waard

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A workflow-centric research object bundles a workflow, the provenance of the results obtained by its enactment, other digital objects that are relevant for the experiment (papers, datasets, etc.), and annotations that semantically describe all these objects. In this paper, we propose a model to specify workflow-centric research objects, and show how the(More)
Biological knowledge is increasingly represented as a collection of (entity-relationship-entity) triplets. These are queried, mined, appended to papers, and published. However, this representation ignores the argumentation contained within a paper and the relationships between hypotheses, claims and evidence put forth in the article. In this paper, we(More)
This thesaurus-based search system uses automatic indexing, RDF-based querying, and concept-based visualization of results to support exploration of large online document repositories. Innovative research institutes rely on the availability of complete and accurate information about new research and development. Information providers such as Elsevier make(More)
The exploration of large information spaces is a difficult task, especially if the user is not familiar with the terminology used to describe information. Conceptual models of a domain in terms of thesauri or ontologies can leverage this problem to some extend. In order to be useful, there is a need for interactive tools for exploring large information sets(More)
Despite the advent of computer-centered ways of creating and accessing scientific knowledge, the format of the scientific research article has remained basically unchanged. We have developed a model of a more appropriate form for research publications to structure scientific articles, based on a rhetorical structure which is ubiquitous in (natural) science(More)
With the advancement of technology and the wide adoption of ontologies as knowledge representation formats, in the last decade, a handful of models were proposed for the externalization of the rhetoric and argumentation captured within scientific publications. Conceptually, most of these models share a similar representation form of the scientific(More)
Our goal is to develop a new format for scientific research articles, which will facilitate their use in a computer-assisted environment. By explicitly marking up rhetorical and knowledge elements in the text, an attempt is made to optimally represent the argumentation contained within the article. To this end, a structure of discourse segments and their(More)
To enable better representations of biomedical argumentation over collections of research papers, we propose a model and a lightweight ontology to represent interpersonal, discourse-based, data-driven reasoning. This model is applied to a collection of scientific documents, to show how it can be applied in practice. We present three biomedical applications(More)
To manage the flood of information that threatens to engulf (life-)scientists, an abundance of computer-aided tools are being developed. These tools aim to provide access to the knowledge conveyed within a collection of research papers, without actually having to read the papers. Many of these tools focus on text mining, by looking for specific(More)