Authors : Xiaoling Chen, Anupama E Gururaj, Burak Ozyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-eui Kim, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Claudiu Farcas, Todd Johnson, Ron Margolis, George Alter, Susanna-Assunta Sansone, Ian M Fore, Lucila Ohno-Machado, Jeffrey S Grethe, Hua Xu
Finding relevant datasets is important for promoting data reuse in the biomedical domain, but it is challenging given the volume and complexity of biomedical data. Here we describe the development of an open source biomedical data discovery system called DataMed, with the goal of promoting the building of additional data indexes in the biomedical domain.
Materials and Methods
DataMed, which can efficiently index and search diverse types of biomedical datasets across repositories, is developed through the National Institutes of Health–funded biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) consortium.
It consists of 2 main components: (1) a data ingestion pipeline that collects and transforms original metadata information to a unified metadata model, called DatA Tag Suite (DATS), and (2) a search engine that finds relevant datasets based on user-entered queries.
In addition to describing its architecture and techniques, we evaluated individual components within DataMed, including the accuracy of the ingestion pipeline, the prevalence of the DATS model across repositories, and the overall performance of the dataset retrieval engine.
Results and Conclusion
Our manual review shows that the ingestion pipeline could achieve an accuracy of 90% and core elements of DATS had varied frequency across repositories. On a manually curated benchmark dataset, the DataMed search engine achieved an inferred average precision of 0.2033 and a precision at 10 (P@10, the number of relevant results in the top 10 search results) of 0.6022, by implementing advanced natural language processing and terminology services.
Currently, we have made the DataMed system publically available as an open source package for the biomedical community.
DOI : https://doi.org/10.1093/jamia/ocx121
Authors : Renata Gonçalves Curty, Kevin Crowston, Alison Specht, Bruce W. Grant, Elizabeth D. Dalton
The value of sharing scientific research data is widely appreciated, but factors that hinder or prompt the reuse of data remain poorly understood. Using the Theory of Reasoned Action, we test the relationship between the beliefs and attitudes of scientists towards data reuse, and their self-reported data reuse behaviour.
To do so, we used existing responses to selected questions from a worldwide survey of scientists developed and administered by the DataONE Usability and Assessment Working Group (thus practicing data reuse ourselves).
Results show that the perceived efficacy and efficiency of data reuse are strong predictors of reuse behaviour, and that the perceived importance of data reuse corresponds to greater reuse. Expressed lack of trust in existing data and perceived norms against data reuse were not found to be major impediments for reuse contrary to our expectations.
We found that reported use of models and remotely-sensed data was associated with greater reuse. The results suggest that data reuse would be encouraged and normalized by demonstration of its value.
We offer some theoretical and practical suggestions that could help to legitimize investment and policies in favor of data sharing.
URL : Attitudes and norms affecting scientists’ data reuse
DOI : https://doi.org/10.1371/journal.pone.0189288
Authors : Daniel S. Falster, Richard G. FitzJohn, Matthew W. Pennell, William K. Cornwell
The sharing and re-use of data has become a cornerstone of modern science. Multiple platforms now allow quick and easy data sharing. So far, however, data publishing models have not accommodated on-going scientific improvements in data: for many problems, datasets continue to grow with time — more records are added, errors fixed, and new data structures are created. In other words, datasets, like scientific knowledge, advance with time.
We therefore suggest that many datasets would be usefully published as a series of versions, with a simple naming system to allow users to perceive the type of change between versions. In this article, we argue for adopting the paradigm and processes for versioned data, analogous to software versioning.
We also introduce a system called Versioned Data Delivery and present tools for creating, archiving, and distributing versioned data easily, quickly, and cheaply. These new tools allow for individual research groups to shift from a static model of data curation to a dynamic and versioned model that more naturally matches the scientific process.
URL : Versioned data: why it is needed and how it can be achieved (easily and cheaply)
DOI : https://doi.org/10.7287/peerj.preprints.3401v1
Author : Frank Andreas Sposito
Data curation is often defined as the practice of maintaining, preserving, and enhancing research data for long-term value and reusability. The role of data reuse in the data curation lifecycle is critical: increased reuse is the core justification for the often sizable expenditures necessary to build data management infrastructures and user services.
Yet recent studies have shown that data are being shared and reused through open data repositories at much lower levels than expected. These studies underscore a fundamental and often overlooked challenge in research data management that invites deeper examination of the roles and responsibilities of data curators.
This presentation will identify key barriers to data reuse, data quality and user trust, and propose a framework for implementing reuser-centric strategies to increase data reuse.
Using the concept of a “data reuse plan” it will highlight repository-based approaches to improve data quality and user trust, and address critical areas for innovation for data curators working in the absence of repository support.
URL : What do data curators care about? Data quality, user trust, and the data reuse plan
Alternative location : http://library.ifla.org/id/eprint/1797
Authors : Devan Ray Donaldson, Shawn Martin, Thomas Proffen
Even though the importance of sharing data is frequently discussed, data sharing appears to be limited to a few fields, and practices within those fields are not well understood. This study examines perspectives on sharing neutron data collected at Oak Ridge National Laboratory’s neutron sources.
Operation at user facilities has traditionally focused on making data accessible to those who create them. The recent emphasis on open data is shifting the focus to ensure that the data produced are reusable by others.
This mixed methods research study included a series of surveys and focus group interviews in which 13 data consumers, data managers, and data producers answered questions about their perspectives on sharing neutron data.
Data consumers reported interest in reusing neutron data for comparison/verification of results against their own measurements and testing new theories using existing data. They also stressed the importance of establishing context for data, including how data are produced, how samples are prepared, units of measurement, and how temperatures are determined.
Data managers expressed reservations about reusing others’ data because they were not always sure if they could trust whether the people responsible for interpreting data did so correctly.
Data producers described concerns about their data being misused, competing with other users, and over-reliance on data producers to understand data. We present the Consumers Managers Producers (CMP) Model for understanding the interplay of each group regarding data sharing.
We conclude with policy and system recommendations and discuss directions for future research.
URL : Understanding Perspectives on Sharing Neutron Data at Oak Ridge National Laboratory
DOI : http://doi.org/10.5334/dsj-2017-035
Authors : Irene V. Pasquetto, Bernadette M. Randles, Christine L. Borgman
While science policy promotes data sharing and open data, these are not ends in themselves. Arguments for data sharing are to reproduce research, to make public assets available to the public, to leverage investments in research, and to advance research and innovation.
To achieve these expected benefits of data sharing, data must actually be reused by others. Data sharing practices, especially motivations and incentives, have received far more study than has data reuse, perhaps because of the array of contested concepts on which reuse rests and the disparate contexts in which it occurs.
Here we explicate concepts of data, sharing, and open data as a means to examine data reuse. We explore distinctions between use and reuse of data.
Lastly we propose six research questions on data reuse worthy of pursuit by the community: How can uses of data be distinguished from reuses? When is reproducibility an essential goal? When is data integration an essential goal? What are the tradeoffs between collecting new data and reusing existing data? How do motivations for data collection influence the ability to reuse data? How do standards and formats for data release influence reuse opportunities?
We conclude by summarizing the implications of these questions for science policy and for investments in data reuse.
URL : On the Reuse of Scientific Data
DOI : http://doi.org/10.5334/dsj-2017-008
Participation in Open Data initiatives require two semi-independent actions: the sharing of data produced by a researcher or group, and a consumer of shared data. Consumers of shared data range from people interested in validating the results of a given study to transformers of the data.
These transformers can add value to the dataset by extracting new relationships and information. The relationship between producers and consumers can be modeled in a game-theoretic context, namely by using a Prisoners’ Dilemma (PD) model to better understand potential barriers and benefits of sharing.
In this paper, we will introduce the problem of data sharing, consider assumptions about economic versus social payoffs, and provide simplistic payoff matrices of data sharing.
Several variations on the payoff matrix are given for different institutional scenarios, ranging from the ubiquitous acceptance of Open Science principles to a context where the standard is entirely non-cooperative. Implications for building a CC-BY economy are then discussed in context.
URL : Data Reuse as a Prisoner’s Dilemma: the social capital of open science
DOI : https://doi.org/10.1101/093518