Étiquette : open science

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Text data mining and data quality management for research information systems in the context of open data and open science

Authors : Otmane Azeroual, Gunter Saake, Mohammad Abuosba, Joachim Schöpfel

In the implementation and use of research information systems (RIS) in scientific institutions, text data mining and semantic technologies are a key technology for the meaningful use of large amounts of data.

It is not the collection of data that is difficult, but the further processing and integration of the data in RIS. Data is usually not uniformly formatted and structured, such as texts and tables that cannot be linked.

These include various source systems with their different data formats such as project and publication databases, CERIF and RCD data model, etc. Internal and external data sources continue to develop.

On the one hand, they must be constantly synchronized and the results of the data links checked. On the other hand, the texts must be processed in natural language and certain information extracted.

Using text data mining, the quality of the metadata is analyzed and this identifies the entities and general keywords. So that the user is supported in the search for interesting research information.

The information age makes it easier to store huge amounts of data and increase the number of documents on the internet, in institutions’ intranets, in newswires and blogs is overwhelming.

Search engines should help to specifically open up these sources of information and make them usable for administrative and research purposes. Against this backdrop, the aim of this paper is to provide an overview of text data mining techniques and the management of successful data quality for RIS in the context of open data and open science in scientific institutions and libraries, as well as to provide ideas for their application. In particular, solutions for the RIS will be presented.

URL : https://arxiv.org/abs/1812.04298

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The principles of tomorrow’s university

Authors : Daniel S. Katz, Gabrielle Allen, Lorena A. Barba, Devin R. Berg, Holly Bik, Carl Boettiger, Christine L. Borgman, C. Titus Brown, Stuart Buck, Randy Burd, Anita de Waard, Martin Paul Eve, Brian E. Granger, Josh Greenberg, Adina Howe, Bill Howe, May Khanna, Timothy L. Killeen, Matthew Mayernik, Erin McKiernan, Chris Mentzel, Nirav Merchant, Kyle E. Niemeyer, Laura Noren, Sarah M. Nusser, Daniel A. Reed, Edward Seidel, MacKenzie Smith, Jeffrey R. Spies, Matt Turk, John D. Van Horn, Jay Walsh

In the 21st Century, research is increasingly data- and computation-driven. Researchers, funders, and the larger community today emphasize the traits of openness and reproducibility.

In March 2017, 13 mostly early-career research leaders who are building their careers around these traits came together with ten university leaders (presidents, vice presidents, and vice provosts), representatives from four funding agencies, and eleven organizers and other stakeholders in an NIH- and NSF-funded one-day, invitation-only workshop titled « Imagining Tomorrow’s University. »

Workshop attendees were charged with launching a new dialog around open research – the current status, opportunities for advancement, and challenges that limit sharing.

The workshop examined how the internet-enabled research world has changed, and how universities need to change to adapt commensurately, aiming to understand how universities can and should make themselves competitive and attract the best students, staff, and faculty in this new world.

During the workshop, the participants re-imagined scholarship, education, and institutions for an open, networked era, to uncover new opportunities for universities to create value and serve society.

They expressed the results of these deliberations as a set of 22 principles of tomorrow’s university across six areas: credit and attribution, communities, outreach and engagement, education, preservation and reproducibility, and technologies.

Activities that follow on from workshop results take one of three forms. First, since the workshop, a number of workshop authors have further developed and published their white papers to make their reflections and recommendations more concrete.

These authors are also conducting efforts to implement these ideas, and to make changes in the university system.

Second, we plan to organise a follow-up workshop that focuses on how these principles could be implemented.

Third, we believe that the outcomes of this workshop support and are connected with recent theoretical work on the position and future of open knowledge institutions.

URL : The principles of tomorrow’s university

DOI : https://doi.org/10.12688/f1000research.17425.1

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Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

Authors : Joshua D. Wallach, Kevin W. Boyack, John P. A. Ioannidis

Currently, there is a growing interest in ensuring the transparency and reproducibility of the published scientific literature. According to a previous evaluation of 441 biomedical journals articles published in 2000–2014, the biomedical literature largely lacked transparency in important dimensions.

Here, we surveyed a random sample of 149 biomedical articles published between 2015 and 2017 and determined the proportion reporting sources of public and/or private funding and conflicts of interests, sharing protocols and raw data, and undergoing rigorous independent replication and reproducibility checks.

We also investigated what can be learned about reproducibility and transparency indicators from open access data provided on PubMed. The majority of the 149 studies disclosed some information regarding funding (103, 69.1% [95% confidence interval, 61.0% to 76.3%]) or conflicts of interest (97, 65.1% [56.8% to 72.6%]).

Among the 104 articles with empirical data in which protocols or data sharing would be pertinent, 19 (18.3% [11.6% to 27.3%]) discussed publicly available data; only one (1.0% [0.1% to 6.0%]) included a link to a full study protocol. Among the 97 articles in which replication in studies with different data would be pertinent, there were five replication efforts (5.2% [1.9% to 12.2%]).

Although clinical trial identification numbers and funding details were often provided on PubMed, only two of the articles without a full text article in PubMed Central that discussed publicly available data at the full text level also contained information related to data sharing on PubMed; none had a conflicts of interest statement on PubMed.

Our evaluation suggests that although there have been improvements over the last few years in certain key indicators of reproducibility and transparency, opportunities exist to improve reproducible research practices across the biomedical literature and to make features related to reproducibility more readily visible in PubMed.

URL : Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017

DOI : https://doi.org/10.1371/journal.pbio.2006930

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Dimensions of open research: critical reflections on openness in the ROER4D project

Authors : Thomas William King, Cheryl-Ann Hodgkinson-Williams, Michelle Willmers, Sukaina Walji

Open Research has the potential to advance the scientific process by improving the transparency, rigour, scope and reach of research, but choosing to experiment with Open Research carries with it a set of ideological, legal, technical and operational considerations.

Researchers, especially those in resource-constrained situations, may not be aware of the complex interrelations between these different domains of open practice, the additional resources required, or how Open Research can support traditional research practices.

Using the Research on Open Educational Resources for Development (ROER4D) project as an example, this paper attempts to demonstrate the interrelation between ideological, legal, technical and operational openness; the resources that conducting Open Research requires; and the benefits of an iterative, strategic approach to one’s own Open Research practice.

In this paper we discuss the value of a critical approach towards Open Research to ensure better coherence between ‘open’ ideology (embodied in strategic intention) and ‘open’ practice (the everyday operationalisation of open principles).

URL : Dimensions of open research: critical reflections on openness in the ROER4D project

Alternative location : https://www.openpraxis.org/index.php/OpenPraxis/article/view/285

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Open Science by Design

Contributors : National Academies of Sciences, Engineering, and Medicine; Policy and Global Affairs; Board on Research Data and Information; Committee on Toward an Open Science Enterprise

Openness and sharing of information are fundamental to the progress of science and to the effective functioning of the research enterprise. The advent of scientific journals in the 17th century helped power the Scientific Revolution by allowing researchers to communicate across time and space, using the technologies of that era to generate reliable knowledge more quickly and efficiently.

Harnessing today’s stunning, ongoing advances in information technologies, the global research enterprise and its stakeholders are moving toward a new open science ecosystem.

Open science aims to ensure the free availability and usability of scholarly publications, the data that result from scholarly research, and the methodologies, including code or algorithms, that were used to generate those data.

Open Science by Design is aimed at overcoming barriers and moving toward open science as the default approach across the research enterprise.

This report explores specific examples of open science and discusses a range of challenges, focusing on stakeholder perspectives. It is meant to provide guidance to the research enterprise and its stakeholders as they build strategies for achieving open science and take the next steps.

URL : https://www.nap.edu/catalog/25116/open-science-by-design-realizing-a-vision-for-21st-century

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Leveraging Concepts in Open Access Publications

Authors : Andrea Bertino, Luca Foppiano, Laurent Romary, Pierre Mounier

Aim

This paper addresses the integration of a Named Entity Recognition and Disambiguation (NERD) service within a group of open access (OA) publishing digital platforms and considers its potential impact on both research and scholarly publishing.

This application, called entity-fishing, was initially developed by Inria in the context of the EU FP7 project CENDARI (Lopez et al., 2014) and provides automatic entity recognition and disambiguation against Wikipedia and Wikidata. Distributed with an open-source licence, it was deployed as a web service in the DARIAH infrastructure hosted at the French HumaNum.

Methods

In this paper, we focus on the specific issues related to its integration on five OA platforms specialized in the publication of scholarly monographs in social sciences and humanities as part of the work carried out within the EU H2020 project HIRMEOS (High Integration of Research Monographs in the European Open Science infrastructure).

Results and Discussion

In the following sections, we give a brief overview of the current status and evolution of OA publications and how HIRMEOS aims to contribute to this.

We then give a comprehensive description of the entity-fishing service, focusing on its concrete applications in real use cases together with some further possible ideas on how to exploit the generated annotations.

Conclusions

We show that entity-fishing annotations can improve both research and publishing process. Entity-fishing annotations can be used to achieve a better and quicker understanding of the specific and disciplinary language of certain monographs and so encourage non-specialists to use them.

In addition, a systematic implementation of the entity-fishing service can be used by publishers to generate thematic indexes within book collections to allow better cross-linking and query functions.

URL : https://hal.inria.fr/hal-01900303/

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Identifying the challenges in implementing open science

Authors : Sarah E. Ali-Khan, Antoine Jean, E. Richard Gold

Areas of open science (OS) policy and practice are already relatively well-advanced in several countries and sectors through the initiatives of some governments, funders, philanthropy, researchers and the community. Nevertheless, the current research and innovation system, including in the focus of this report, the life sciences, remains weighted against OS.

In October 2017, thought-leaders from across the world gathered at an Open Science Leadership Forum in the Washington DC office of the Bill and Melinda Gates Foundation to share their views on what successful OS looks like.

We focused on OS partnerships as this is an emerging model that aims to accelerate science and innovation. These outcomes are captured in a first meeting report: Defining Success in Open Science.

On several occasions, these conversations turned to the challenges that must be addressed and new policies required to effectively and sustainably advance OS practice.

Thereupon, in this report, we describe the concerns raised and what is needed to address them supplemented by our review of the literature, and suggest the stakeholder groups that may be best placed to begin to take action.

It emerges that to be successful, OS will require the active engagement of all stakeholders: while the research community must develop research questions, identify partners and networks, policy communities need to create an environment that is supportive of experimentation by removing barriers.

This report aims to contribute to ongoing discussions about OS and its implementation. It is also part of a step-wise process to develop and mobilize a toolkit of quantitative and qualitative indicators to assist global stakeholders in implementing high value OS collaborations.

Currently in co-development through an open and international process, this set of measures will allow the generation of needed evidence on the influence of OS partnerships on research, innovation, and critical social and economic goals.

URL : Identifying the challenges in implementing open science

DOI : http://dx.doi.org/10.12688/mniopenres.12805.1