48,988 research outputs found
The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web
Research in life sciences is increasingly being conducted in a digital and
online environment. In particular, life scientists have been pioneers in
embracing new computational tools to conduct their investigations. To support
the sharing of digital objects produced during such research investigations, we
have witnessed in the last few years the emergence of specialized repositories,
e.g., DataVerse and FigShare. Such repositories provide users with the means to
share and publish datasets that were used or generated in research
investigations. While these repositories have proven their usefulness,
interpreting and reusing evidence for most research results is a challenging
task. Additional contextual descriptions are needed to understand how those
results were generated and/or the circumstances under which they were
concluded. Because of this, scientists are calling for models that go beyond
the publication of datasets to systematically capture the life cycle of
scientific investigations and provide a single entry point to access the
information about the hypothesis investigated, the datasets used, the
experiments carried out, the results of the experiments, the people involved in
the research, etc. In this paper we present the Research Object (RO) suite of
ontologies, which provide a structured container to encapsulate research data
and methods along with essential metadata descriptions. Research Objects are
portable units that enable the sharing, preservation, interpretation and reuse
of research investigation results. The ontologies we present have been designed
in the light of requirements that we gathered from life scientists. They have
been built upon existing popular vocabularies to facilitate interoperability.
Furthermore, we have developed tools to support the creation and sharing of
Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page
A Linked Data Approach to Sharing Workflows and Workflow Results
A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the âMaterials and Methodsâ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find associated resources and integrate them as data and services. We present initial steps towards preserving bioinformatics âmaterials and methodsâ by exploiting the workflow paradigm for capturing the design of a data analysis pipeline, and RDF to link the workflow, its component services, run-time provenance, and a personalized biological interpretation of the results. An example shows the reproduction of the unique graph of an analysis procedure, its results, provenance, and personal interpretation of a text mining experiment. It links data from Taverna, myExperiment.org, BioCatalogue.org, and ConceptWiki.org. The approach is relatively âlight-weightâ and unobtrusive to bioinformatics users
Semantic Integration of Cervical Cancer Data Repositories to Facilitate Multicenter Association Studies: The ASSIST Approach
The current work addresses the unifi cation of Electronic Health Records related to cervical cancer into a single medical knowledge source, in the context of the EU-funded ASSIST research project. The project aims to facilitate the research for cervical precancer and cancer through a system that virtually unifi es multiple patient record repositories, physically located in different medical centers/hospitals, thus, increasing fl exibility by allowing the formation of study groups âon demandâ and by recycling patient records in new studies. To this end, ASSIST uses semantic technologies to translate all medical entities (such as patient examination results, history, habits, genetic profi le) and represent them in a common form, encoded in the ASSIST Cervical Cancer Ontology. The current paper presents the knowledge elicitation approach followed, towards the defi nition and representation of the diseaseâs medical concepts and rules that constitute the basis for the ASSIST Cervical Cancer Ontology. The proposed approach constitutes a paradigm for semantic integration of heterogeneous clinical data that may be applicable to other biomedical application domains
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A short survey of discourse representation models
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 publication, i.e. as a series of interconnected elementary knowledge items. The main differences are given by the terminology used, the types of rhetorical and/or argumentation relations connecting the knowledge items and the foundational theories supporting these relations. This paper analyzes the state of the art and provides a concise comparative overview of the ïŹve most prominent discourse representation models, with the goal of sketching an uniïŹed model for discourse representation
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