Author : Sofia Zapounidou
This thesis studies the library data and the way that linked data technologies may affect libraries. The thesis aims to contribute to the research regarding the devel-opment and implementation of a framework for the integration of bibliographic data in the semantic web.
It seeks to make sound propositions for the interopera-bility of conceptual bibliographic models, as well as for future library systems and search environments integrating bibliographic information.
Authors : Maria A.M. Heijne, Wilma J.S.M. van Wezenbeek
In this paper, the authors – both of whom are library directors and involved in the contract negotiations with the bigger scientific publishers – present the conditions that formed the Dutch approach in these negotiations.
A combination of clear political support, a powerful delegation, a unique bargaining model and fidelity to their principles geared the Dutch to their success in achieving open access. The authors put these joint license and open access negotiations in the perspective of open science and show that they are part of the transition towards open access.
URL : https://edoc.hu-berlin.de/handle/18452/19356
Author : Silvio Peroni
Semantic Publishing involves the use of Web and Semantic Web technologies and standards for the semantic enhancement of a scholarly work so as to improve its discoverability, interactivity, openness and (re-)usability for both humans and machines.
Recently, people have suggested that the semantic enhancements of a scholarly work should be undertaken by the authors of that scholarly work, and should be considered as integral parts of the contribution subjected to peer review. However, this requires that the authors should spend additional time and effort adding such semantic annotations, time that they usually do not have available.
Thus, the most pragmatic way to facilitate this additional task is to use automated services that create the semantic annotation of authors’ scholarly articles by parsing the content that they have already written, thus reducing the additional time required of the authors to that for checking and validating these semantic annotations.
In this article, I propose a generic approach called compositional and iterative semantic enhancement (CISE) that enables the automatic enhancement of scholarly papers with additional semantic annotations in a way that is independent of the markup used for storing scholarly articles and the natural language used for writing their content.
URL : Automating semantic publishing
Alternative location : https://content.iospress.com/articles/data-science/ds012
Author : Ana Sofia Figueiredo
Initiatives for sharing research data are opportunities to increase the pace of knowledge discovery and scientific progress. The reuse of research data has the potential to avoid the duplication of data sets and to bring new views from multiple analysis of the same data set.
For example, the study of genomic variations associated with cancer profits from the universal collection of such data and helps in selecting the most appropriate therapy for a specific patient. However, data sharing poses challenges to the scientific community.
These challenges are of ethical, cultural, legal, financial, or technical nature. This article reviews the impact that data sharing has in science and society and presents guidelines to improve the efficient sharing of research data.
Authors : Catherine Heeney, Shona M. Kerr
Issues of balancing data accessibility with ethical considerations and governance of a genomics research biobank, Generation Scotland, are explored within the evolving policy landscape of the past ten years. During this time data sharing and open data access have become increasingly important topics in biomedical research.
Decisions around data access are influenced by local arrangements for governance and practices such as linkage to health records, and the global through policies for biobanking and the sharing of data with large-scale biomedical research data resources and consortia.
We use a literature review of policy relevant documents which apply to the conduct of biobanks in two areas: support for open access and the protection of data subjects and researchers managing a bioresource.
We present examples of decision making within a biobank based upon observations of the Generation Scotland Access Committee. We reflect upon how the drive towards open access raises ethical dilemmas for established biorepositories containing data and samples from human subjects.
Despite much discussion in science policy literature about standardisation, the contextual aspects of biobanking are often overlooked. Using our engagement with GS we demonstrate the importance of local arrangements in the creation of a responsive ethical approach to biorepository governance.
We argue that governance decisions regarding access to the biobank are intertwined with considerations about maintenance and viability at the local level. We show that in addition to the focus upon ever more universal and standardised practices, the local expertise gained in the management of such repositories must be supported.
A commitment to open access in genomics research has found almost universal backing in science and health policy circles, but repositories of data and samples from human subjects may have to operate under managed access, to protect privacy, align with participant consent and ensure that the resource can be managed in a sustainable way.
Data access committees need to be reflexive and flexible, to cope with changing technology and opportunities and threats from the wider data sharing environment. To understand these interactions also involves nurturing what is particular about the biobank in its local context.
URL : Balancing the local and the universal in maintaining ethical access to a genomics biobank
Authors : Alexander Garcia, Federico Lopez, Leyla Garcia, Olga Giraldo, Victor Bucheli, Michel Dumontier
A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies.
In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology.
We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language.
We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io.
Authors : Ming-yueh Tsay, Tai-luan Wu, Ling-li Tseng
This study examines the completeness and overlap of coverage in physics of six open access scholarly communication systems, including two search engines (Google Scholar and Microsoft Academic), two aggregate institutional repositories (OAIster and OpenDOAR), and two physics-related open sources (arXiv.org and Astrophysics Data System).
The 2001–2013 Nobel Laureates in Physics served as the sample. Bibliographic records of their publications were retrieved and downloaded from each system, and a computer program was developed to perform the analytical tasks of sorting, comparison, elimination, aggregation and statistical calculations.
Quantitative analyses and cross-referencing were performed to determine the completeness and overlap of the system coverage of the six open access systems.
The results may enable scholars to select an appropriate open access system as an efficient scholarly communication channel, and academic institutions may build institutional repositories or independently create citation index systems in the future. Suggestions on indicators and tools for academic assessment are presented based on the comprehensiveness assessment of each system.