Workflows Allowing Creation of Journal Article Supporting Information and Findable, Accessible, Interoperable, and Reusable (FAIR)-Enabled Publication of Spectroscopic Data

Authors : Agustin Barba, Santiago Dominguez, Carlos Cobas, David P. Martinsen, Charles Romain, Henry S. Rzepa; Felipe Seoane

There is an increasing focus on the part of academic institutions, funding agencies, and publishers, if not researchers themselves, on preservation and sharing of research data. Motivations for sharing include research integrity, replicability, and reuse.

One of the barriers to publishing data is the extra work involved in preparing data for publication once a journal article and its supporting information have been completed.

In this work, a method is described to generate both human and machine-readable supporting information directly from the primary instrumental data files and to generate the metadata to ensure it is published in accordance with findable, accessible, interoperable, and reusable (FAIR) guidelines.

Using this approach, both the human readable supporting information and the primary (raw) data can be submitted simultaneously with little extra effort.

Although traditionally the data package would be sent to a journal publisher for publication alongside the article, the data package could also be published independently in an institutional FAIR data repository.

Workflows are described that store the data packages and generate metadata appropriate for such a repository. The methods both to generate and to publish the data packages have been implemented for NMR data, but the concept is extensible to other types of spectroscopic data as well.

URL : Workflows Allowing Creation of Journal Article Supporting Information and Findable, Accessible, Interoperable, and Reusable (FAIR)-Enabled Publication of Spectroscopic Data

DOI : https://doi.org/10.1021/acsomega.8b03005

Survey on Scientific Shared Resource Rigor and Reproducibility

Authors : Kevin L. Knudtson, Robert H. Carnahan, Rebecca L. Hegstad-Davies, Nancy C. Fisher, Belynda Hicks, Peter A. Lopez, Susan M. Meyn, Sheenah M. Mische, Frances Weis-Garcia, Lisa D. White, Katia Sol-Church

Shared scientific resources, also known as core facilities, support a significant portion of the research conducted at biomolecular research institutions.

The Association of Biomolecular Resource Facilities (ABRF) established the Committee on Core Rigor and Reproducibility (CCoRRe) to further its mission of integrating advanced technologies, education, and communication in the operations of shared scientific resources in support of reproducible research.

In order to first assess the needs of the scientific shared resource community, the CCoRRe solicited feedback from ABRF members via a survey. The purpose of the survey was to gain information on how U.S. National Institutes of Health (NIH) initiatives on advancing scientific rigor and reproducibility influenced current services and new technology development.

In addition, the survey aimed to identify the challenges and opportunities related to implementation of new reporting requirements and to identify new practices and resources needed to ensure rigorous research.

The results revealed a surprising unfamiliarity with the NIH guidelines. Many of the perceived challenges to the effective implementation of best practices (i.e., those designed to ensure rigor and reproducibility) were similarly noted as a challenge to effective provision of support services in a core setting. Further, most cores routinely use best practices and offer services that support rigor and reproducibility.

These services include access to well-maintained instrumentation and training on experimental design and data analysis as well as data management. Feedback from this survey will enable the ABRF to build better educational resources and share critical best-practice guidelines.

These resources will become important tools to the core community and the researchers they serve to impact rigor and transparency across the range of science and technology.

DOI : https://dx.doi.org/10.7171%2Fjbt.19-3003-001

Lost or found? Discovering data needed for research

Authors : Kathleen Gregory, Paul Groth, Andrea Scharnhorst, Sally Wyatt

Finding or discovering data is a necessary precursor to being able to reuse data, although relatively little large-scale empirical evidence exists about how researchers discover, make sense of and (re)use data for research.

This study presents evidence from the largest known survey investigating how researchers discover and use data that they do not create themselves.

We examine the data needs and discovery strategies of respondents, propose a typology for data (re)use and probe the role of social interactions and other research practices in data discovery, with the aim of informing the design of community-centric solutions and policies.

URL : https://arxiv.org/abs/1909.00464

How libraries can support society publishers to accelerate their transition to full and immediate OA and Plan S

Authors : Alicia Wise, Lorraine Estelle

The relationship between libraries and society publishers has not previously been a close one. While transactions have in the past been mediated by third parties, larger commercial publishers or agents, there is now an opportunity for strategic new collaborations as societies seek to transition to open access (OA) and deploy business models compliant with Plan S.

Wellcome, UK Research and Innovation (UKRI) and the Association of Learned and Professional Society Publishers (ALPSP) commissioned Information Power Ltd to undertake to support society publishers in accelerating their transition to OA in alignment with Plan S.

Outcomes demonstrate support in principle from library consortia and their members to repurpose existing expenditure to help society publishers to successfully make a full transition to OA.

Principles to inform the short- and medium-term development of OA transformative agreements have been co-developed by consortium representatives and publishers to inform development of an OA transformative agreement toolkit.

URL : How libraries can support society publishers to accelerate their transition to full and immediate OA and Plan S

DOI : http://doi.org/10.1629/uksg.477

Is Scholarly Publishing Like Rock and Roll?

Author : David W. Lewis

This article uses Alan B. Krueger’s analysis of the music industry in his book Rockonomics: A Backstage Tour of What the Music Industry Can Teach Us About Economics and Life as a lens to consider the structure of scholarly publishing and what could happen to scholarly publishing going forward.

Both the music industry and scholarly publishing are facing disruption as their products become digital. Digital content provides opportunities to a create a better product at lower prices and in the music industry this has happened. Scholarly publishing has not yet done so.

Similarities and differences between the music industry and scholarly publishing will be considered. Like music, scholarly publishing appears to be a superstar industry. Both music and scholarly publishing are subject to piracy, which threatens revenue, though Napster was a greater disrupter than Sci-Hub seems to be.

It also appears that for a variety of reasons market forces are not effective in driving changes in business models and practices in scholarly publishing, at least not at the rate we would expect given the changes in technology. After reviewing similarities and differences, the prospects for the future of scholarly publishing will be considered.

URL : Is Scholarly Publishing Like Rock and Roll?

URL : http://hdl.handle.net/1805/20430

Public Views on Models for Accessing Genomic and Health Data for Research: Mixed Methods Study

Authors : Kerina H Jones, Helen Daniels, Emma Squires, David V Ford

Background

The literature abounds with increasing numbers of research studies using genomic data in combination with health data (eg, health records and phenotypic and lifestyle data), with great potential for large-scale research and precision medicine.

However, concerns have been raised about social acceptability and risks posed for individuals and their kin. Although there has been public engagement on various aspects of this topic, there is a lack of information about public views on data access models.

Objective

This study aimed to address the lack of information on the social acceptability of access models for reusing genomic data collected for research in conjunction with health data.

Models considered were open web-based access, released externally to researchers, and access within a data safe haven.

Methods

Views were ascertained using a series of 8 public workshops (N=116). The workshops included an explanation of benefits and risks in using genomic data with health data, a facilitated discussion, and an exit questionnaire.

The resulting quantitative data were analyzed using descriptive and inferential statistics, and the qualitative data were analyzed for emerging themes.

Results

Respondents placed a high value on the reuse of genomic data but raised concerns including data misuse, information governance, and discrimination. They showed a preference for giving consent and use of data within a safe haven over external release or open access.

Perceived risks with open access included data being used by unscrupulous parties, with external release included data security, and with safe havens included the need for robust safeguards.

Conclusions: This is the first known study exploring public views of access models for reusing anonymized genomic and health data in research.

It indicated that people are generally amenable but prefer data safe havens because of perceived sensitivities. We recommend that public views be incorporated into guidance on models for the reuse of genomic and health data.

URL : Public Views on Models for Accessing Genomic and Health Data for Research: Mixed Methods Study

DOI : https://doi.org/10.2196/14384

COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations

Authors : Ivan Heibi, Silvio Peroni, David Shotton

In this paper, we present COCI, the OpenCitations Index of Crossref open DOI-to-DOI citations (this http URL). COCI is the first open citation index created by OpenCitations, in which we have applied the concept of citations as first-class data entities, and it contains more than 445 million DOI-to-DOI citation links derived from the data available in Crossref.

These citations are described in RDF by means of the newly extended version of the OpenCitations Data Model (OCDM).

We introduce the workflow we have developed for creating these data, and also show the additional services that facilitate the access to and querying of these data via different access points: a SPARQL endpoint, a REST API, bulk downloads, Web interfaces, and direct access to the citations via HTTP content negotiation.

Finally, we present statistics regarding the use of COCI citation data, and we introduce several projects that have already started to use COCI data for different purposes.

URL : https://arxiv.org/abs/1904.06052