International Journal of Digital Curation
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Building a Bridge Between Journal Articles and Research Data: The PKP-Dataverse Integration Project
Get PDFA growing number of funding agencies and international scholarly organizations are requesting that research data be made more openly available to help validate and advance scientific research. Thus, this is an opportune moment for research data repositories to partner with journal editors and publishers in order to simplify and improve data curation and publishing practices. One practical example of this type of cooperation is currently being facilitated by a two year (2012-2014) one million dollar Sloan Foundation grant, integrating two well-established open source systems: the Public Knowledge Project’s (PKP) Open Journal Systems (OJS), developed by Stanford University and Simon Fraser University; and Harvard University’s Dataverse Network web application, developed by the Institute for Quantitative Social Science (IQSS). To help make this interoperability possible, an OJS Dataverse plugin and Data Deposit API are being developed, which together will allow authors to submit their articles and datasets through an existing journal management interface, while the underlying data are seamlessly deposited into a research data repository, such as the Harvard Dataverse. This practice paper will provide an overview of the project, and a brief exploration of some of the specific challenges to and advantages of this integration
Persistent Identifiers for Scholarly Assets and the Web: The Need for an Unambiguous Mapping
Get PDFPersistent IDentifiers (PIDs), such as DOIs, Handles and ARK identifiers, play a significant role in the identification of a wide variety of assets that are created and used in scholarly endeavours, including research papers, datasets, images, etc. Motivated by concerns about long-term persistence, among others, PIDs are minted outside the information access protocol of the day, HTTP. Yet, value-added services targeted at both humans and machines routinely assume or even require resources identified by means of HTTP URIs in order to make use of off-the-shelf components like web browsers and servers. Hence, an unambiguous bridge is required between the PID-oriented paradigm that is widespread in research communication and the HTTP-oriented web, semantic web and linked data environment. This paper describes the problem, and a possible solution towards defining and deploying such an interoperable bridge
The PBase Scientific Workflow Provenance Repository
Get PDFScientific workflows and their supporting systems are becoming increasingly popular for compute-intensive and data-intensive scientific experiments. The advantages scientific workflows offer include rapid and easy workflow design, software and data reuse, scalable execution, sharing and collaboration, and other advantages that altogether facilitate “reproducible science”. In this context, provenance – information about the origin, context, derivation, ownership, or history of some artifact – plays a key role, since scientists are interested in examining and auditing the results of scientific experiments. However, in order to perform such analyses on scientific results as part of extended research collaborations, an adequate environment and tools are required. Concretely, the need arises for a repository that will facilitate the sharing of scientific workflows and their associated execution traces in an interoperable manner, also enabling querying and visualization. Furthermore, such functionality should be supported while taking performance and scalability into account. With this purpose in mind, we introduce PBase: a scientific workflow provenance repository implementing the ProvONE proposed standard, which extends the emerging W3C PROV standard for provenance data with workflow specific concepts. PBase is built on the Neo4j graph database, thus offering capabilities such as declarative and efficient querying. Our experiences demonstrate the power gained by supporting various types of queries for provenance data. In addition, PBase is equipped with a user friendly interface tailored for the visualization of scientific workflow provenance data, making the specification of queries and the interpretation of their results easier and more effective
Leveraging High Performance Computing for Managing Large and Evolving Data Collections
Get PDFThe process of developing a digital collection in the context of a research project often involves a pipeline pattern during which data growth, data types, and data authenticity need to be assessed iteratively in relation to the different research steps and in the interest of archiving. Throughout a project’s lifecycle curators organize newly generated data while cleaning and integrating legacy data when it exists, and deciding what data will be preserved for the long term. Although these actions should be part of a well-oiled data management workflow, there are practical challenges in doing so if the collection is very large and heterogeneous, or is accessed by several researchers contemporaneously. There is a need for data management solutions that can help curators with efficient and on-demand analyses of their collection so that they remain well-informed about its evolving characteristics. In this paper, we describe our efforts towards developing a workflow to leverage open science High Performance Computing (HPC) resources for routinely and efficiently conducting data management tasks on large collections. We demonstrate that HPC resources and techniques can significantly reduce the time for accomplishing critical data management tasks, and enable a dynamic archiving throughout the research process. We use a large archaeological data collection with a long and complex formation history as our test case. We share our experiences in adopting open science HPC resources for large-scale data management, which entails understanding usage of the open source HPC environment and training users. These experiences can be generalized to meet the needs of other data curators working with large collections
DataShare: Empowering Researcher Data Curation
Get PDFResearchers are increasingly being asked to ensure that all products of research activity – not just traditional publications – are preserved and made widely available for study and reuse as a precondition for publication or grant funding, or to conform to disciplinary best practices. In order to conform to these requirements, scholars need effective, easy-to-use tools and services for the long-term curation of their research data. The DataShare service, developed at the University of California, is being used by researchers to: (1) prepare for curation by reviewing best practice recommendations for the acquisition or creation of digital research data; (2) select datasets using intuitive file browsing and drag-and-drop interfaces; (3) describe their data for enhanced discoverability in terms of the DataCite metadata schema; (4) preserve their data by uploading to a public access collection in the UC3 Merritt curation repository; (5) cite their data in terms of persistent and globally-resolvable DOI identifiers; (6) expose their data through registration with well-known abstracting and indexing services and major internet search engines; (7) control the dissemination of their data through enforceable data use agreements; and (8) discover and retrieve datasets of interest through a faceted search and browse environment. Since the widespread adoption of effective data management practices is highly dependent on ease of use and integration into existing individual, institutional, and disciplinary workflows, the emphasis throughout the design and implementation of DataShare is to provide the highest level of curation service with the lowest possible technical barriers to entry by individual researchers. By enabling intuitive, self-service access to data curation functions, DataShare helps to contribute to more widespread adoption of good data curation practices that are critical to open scientific inquiry, discourse, and advancement
From Project to Strategic Vision: Taking the Lead in Research Data Management Support at the University of Sydney Library
Get PDFThis paper explores three stories, each occurring a year apart, illustrating an evolution toward a strategic vision for Library leadership in supporting research data management at the University of Sydney. The three stories describe activities undertaken throughout the Seeding the Commons project and beyond, as the establishment of ongoing roles and responsibilities transition the Library from project partner to strategic leader in the delivery of research data management support. Each story exposes key ingredients that characterise research data management support: researcher engagement; partnerships; and the complementary roles of policy and practice
Editorial
Get PDFAlexander Ball, Production Editor, introduces Volume 9, Issue 2 (2014) of the International Journal of Digital Curation
Controlled Vocabulary Standards for Anthropological Datasets
Get PDFThis article seeks to outline the use of controlled vocabulary standards for qualitative datasets in cultural anthropology, which are increasingly held in researcher-accessible government repositories and online digital libraries. As a humanistic science that can address almost any aspect of life with meaning to humans, cultural anthropology has proven difficult for librarians and archivists to effectively organize. Yet as anthropology moves onto the web, the challenge of organizing and curating information within the field only grows. In considering the subject classification of digital information in anthropology, I ask how we might best use controlled vocabularies for indexing digital anthropological data. After a brief discussion of likely concerns, I outline thesauri which may potentially be used for vocabulary control in metadata fields for language, location, culture, researcher, and subject. The article concludes with recommendations for those existing thesauri most suitable to provide a controlled vocabulary for describing digital objects in the anthropological world
Publishing and Pushing: Mixing Models for Communicating Research Data in Archaeology
Get PDFWe present a case study of data integration and reuse involving 12 researchers who published datasets in Open Context, an online data publishing platform, as part of collaborative archaeological research on early domesticated animals in Anatolia. Our discussion reports on how different editorial and collaborative review processes improved data documentation and quality, and created ontology annotations needed for comparative analyses by domain specialists. To prepare data for shared analysis, this project adapted editor-supervised review and revision processes familiar to conventional publishing, as well as more novel models of revision adapted from open source software development of public version control. Preparing the datasets for publication and analysis required significant investment of effort and expertise, including archaeological domain knowledge and familiarity with key ontologies. To organize this work effectively, we emphasized these different models of collaboration at various stages of this data publication and analysis project. Collaboration first centered on data editors working with data contributors, then widened to include other researchers who provided additional peer-review feedback, and finally the widest research community, whose collaboration is facilitated by GitHub’s version control system. We demonstrate that the “publish” and “push” models of data dissemination need not be mutually exclusive; on the contrary, they can play complementary roles in sharing high quality data in support of research. This work highlights the value of combining multiple models in different stages of data dissemination
eBird: Curating Citizen Science Data for Use by Diverse Communities
Get PDFIn this paper we describe eBird, a highly successful citizen science project. With over 150,000 participants worldwide and an accumulation of over 140,000,000 bird observations globally in the last decade, eBird has evolved into a major tool for scientific investigations in diverse fields such as ornithology, computer science, statistics, ecology and climate change. eBird’s impact in scientific research is grounded in careful data curation practices that pay attention to all stages of the data lifecycle, and attend to the needs of stakeholders engaged in that data lifecycle. We describe the important aspects of eBird, paying particular attention to the mechanisms to improve data quality; describe the data products that are available to the global community; investigate some aspects of the downloading community; and demonstrate significant results that derive from the use of openly-available eBird data