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

Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences

Recently, a number of organisations have called for open access to scientific information and especially to the data obtained from publicly funded research, among which the Royal Society report and the European Commission press release are particularly notable. It has long been accepted that building research on the foundations laid by other scientists is both effective and efficient. Regrettably, some disciplines, chemistry being one, have been slow to recognise the value of sharing and have thus been reluctant to curate their data and information in preparation for exchanging it. The very significant increases in both the volume and the complexity of the datasets produced has encouraged the expansion of e-Research, and stimulated the development of methodologies for managing, organising, and analysing "big data". We review the evolution of cheminformatics, the amalgam of chemistry, computer science, and information technology, and assess the wider e-Science and e-Research perspective. Chemical information does matter, as do matters of communicating data and collaborating with data. For chemistry, unique identifiers, structure representations, and property descriptors are essential to the activities of sharing and exchange. Open science entails the sharing of more than mere facts: for example, the publication of negative outcomes can facilitate better understanding of which synthetic routes to choose, an aspiration of the Dial-a-Molecule Grand Challenge. The protagonists of open notebook science go even further and exchange their thoughts and plans. We consider the concepts of preservation, curation, provenance, discovery, and access in the context of the research lifecycle, and then focus on the role of metadata, particularly the ontologies on which the emerging chemical Semantic Web will depend. Among our conclusions, we present our choice of the "grand challenges" for the preservation and sharing of chemical information

Status Report of the DPHEP Study Group: Towards a Global Effort for Sustainable Data Preservation in High Energy Physics

Data from high-energy physics (HEP) experiments are collected with significant financial and human effort and are mostly unique. An inter-experimental study group on HEP data preservation and long-term analysis was convened as a panel of the International Committee for Future Accelerators (ICFA). The group was formed by large collider-based experiments and investigated the technical and organisational aspects of HEP data preservation. An intermediate report was released in November 2009 addressing the general issues of data preservation in HEP. This paper includes and extends the intermediate report. It provides an analysis of the research case for data preservation and a detailed description of the various projects at experiment, laboratory and international levels. In addition, the paper provides a concrete proposal for an international organisation in charge of the data management and policies in high-energy physics

Analysis and Synthesis of Metadata Goals for Scientific Data

The proliferation of discipline-specific metadata schemes contributes to artificial barriers that can impede interdisciplinary and transdisciplinary research. The authors considered this problem by examining the domains, objectives, and architectures of nine metadata schemes used to document scientific data in the physical, life, and social sciences. They used a mixed-methods content analysis and Greenberg’s (2005) metadata objectives, principles, domains, and architectural layout (MODAL) framework, and derived 22 metadata-related goals from textual content describing each metadata scheme. Relationships are identified between the domains (e.g., scientific discipline and type of data) and the categories of scheme objectives. For each strong correlation (\u3e0.6), a Fisher’s exact test for nonparametric data was used to determine significance (p \u3c .05). Significant relationships were found between the domains and objectives of the schemes. Schemes describing observational data are more likely to have “scheme harmonization” (compatibility and interoperability with related schemes) as an objective; schemes with the objective “abstraction” (a conceptual model exists separate from the technical implementation) also have the objective “sufficiency” (the scheme defines a minimal amount of information to meet the needs of the community); and schemes with the objective “data publication” do not have the objective “element refinement.” The analysis indicates that many metadata-driven goals expressed by communities are independent of scientific discipline or the type of data, although they are constrained by historical community practices and workflows as well as the technological environment at the time of scheme creation. The analysis reveals 11 fundamental metadata goals for metadata documenting scientific data in support of sharing research data across disciplines and domains. The authors report these results and highlight the need for more metadata-related research, particularly in the context of recent funding agency policy changes

1st INCF Workshop on Sustainability of Neuroscience Databases

The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability

Development of a pilot data management infrastructure for biomedical researchers at University of Manchester – approach, findings, challenges and outlook of the MaDAM Project

Management and curation of digital data has been becoming ever more important in a higher education and research environment characterised by large and complex data, demand for more interdisciplinary and collaborative work, extended funder requirements and use of e-infrastructures to facilitate new research methods and paradigms. This paper presents the approach, technical infrastructure, findings, challenges and outlook (including future development within the successor project, MiSS) of the ‘MaDAM: Pilot data management infrastructure for biomedical researchers at University of Manchester’ project funded under the infrastructure strand of the JISC Managing Research Data (JISCMRD) programme. MaDAM developed a pilot research data management solution at the University of Manchester based on biomedical researchers’ requirements, which includes technical and governance components with the flexibility to meet future needs across multiple research groups and disciplines