Archives des mots-clés : biomedical research

How Do Scientists Define Openness? Exploring the Relationship Between Open Science Policies and Research Practice

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Authors : Nadine Levin, Sabina Leonelli, Dagmara Weckowska, David Castle, John Dupré

This article documents how biomedical researchers in the United Kingdom understand and enact the idea of “openness.”

This is of particular interest to researchers and science policy worldwide in view of the recent adoption of pioneering policies on Open Science and Open Access by the U.K. government—policies whose impact on and implications for research practice are in need of urgent evaluation, so as to decide on their eventual implementation elsewhere.

This study is based on 22 in-depth interviews with U.K. researchers in systems biology, synthetic biology, and bioinformatics, which were conducted between September 2013 and February 2014.

Through an analysis of the interview transcripts, we identify seven core themes that characterize researchers’ understanding of openness in science and nine factors that shape the practice of openness in research.

Our findings highlight the implications that Open Science policies can have for research processes and outcomes and provide recommendations for enhancing their content, effectiveness, and implementation.

URL : How Do Scientists Define Openness? Exploring the Relationship Between Open Science Policies and Research Practice

Alternative location : http://bst.sagepub.com/content/early/2016/09/30/0270467616668760.abstract

Chinese Postgraduate Medical Students Researching for Publication

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Author : Yongyan Li

The value of including a research component in medical students’ training programs has been widely recognized. Nevertheless, examples of how this may be done are rarely found in the literature.

The case study reported in this short paper aimed to address this gap in the literature by investigating how a group of postgraduate students attached to the Orthopedics Department of a major hospital in China engaged in research for publication.

Fourteen students were interviewed, and their “mission lists” were analyzed to reveal the students’ research profiles, the sources of their research ideas, and their data collection activities.

The study showed that the students pursued more clinical than basic research topics, their research topics often fell under their immediate supervisors’ larger projects, and the students were actively engaged in the gathering of research data on the wards and at the outpatient clinic.

The reported study does not claim generalizability of its findings. More of such reports from various settings in different parts of the world are needed to enhance constructive exchanges and mutual learning.

URL : Chinese Postgraduate Medical Students Researching for Publication

DOI : http://dx.doi.org/10.3390/publications4030025

Open access publishing trend analysis: statistics beyond the perception

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Authors : Elisabetta Poltronieri, Elena Bravo, Moreno Curti, Maurizio Ferri, Cristina Mancini

Introduction

The purpose of this analysis was twofold: to track the number of open access journals acquiring impact factor, and to investigate the distribution of subject categories pertaining to these journals. As a case study, journals in which the researchers of the National Institute of Health (Istituto Superiore di Sanità) in Italy have published were surveyed.

Method

Data were collected by searching open access journals listed in the Directory of Open Access Journals ) then compared with those having an impact factor as tracked by the Journal Citation Reports for the years 2010-2012. Journal Citation Reports subject categories were matched with Medical Subject Headings to provide a larger content classification.

Analysis

A survey was performed to determine the Directory journals matching the Journal Citation Reports list, and their inclusion in a given subject area.

Results

In the years 2010-2012, an increase in the number of journals was observed for Journal Citation Reports (+ 4.93%) and for the Directory (+18.51%). The discipline showing the highest increment was medicine (315 occurrences, 26%).

Conclusions

From 2010 to 2012, the number of open access journals with impact factor has gradually risen, with a prevalence for journals relating to medicine and biological science disciplines, suggesting that authors prefer to publish more than before in open access journals.

URL : http://www.informationr.net/ir/21-2/paper712.html

 

Agreements between Industry and Academia on Publication Rights : A Retrospective Study of Protocols and Publications of Randomized Clinical Trials

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Authors : Benjamin Kasenda, Erik von Elm, John J. You, Anette Blümle, Yuki Tomonaga, Ramon Saccilotto et al.

Background

Little is known about publication agreements between industry and academic investigators in trial protocols and the consistency of these agreements with corresponding statements in publications.

We aimed to investigate (i) the existence and types of publication agreements in trial protocols, (ii) the completeness and consistency of the reporting of these agreements in subsequent publications, and (iii) the frequency of co-authorship by industry employees.

Methods and Findings

We used a retrospective cohort of randomized clinical trials (RCTs) based on archived protocols approved by six research ethics committees between 13 January 2000 and 25 November 2003.

Only RCTs with industry involvement were eligible. We investigated the documentation of publication agreements in RCT protocols and statements in corresponding journal publications. Of 647 eligible RCT protocols, 456 (70.5%) mentioned an agreement regarding publication of results. Of these 456, 393 (86.2%) documented an industry partner’s right to disapprove or at least review proposed manuscripts; 39 (8.6%) agreements were without constraints of publication.

The remaining 24 (5.3%) protocols referred to separate agreement documents not accessible to us. Of those 432 protocols with an accessible publication agreement, 268 (62.0%) trials were published. Most agreements documented in the protocol were not reported in the subsequent publication (197/268 [73.5%]).

Of 71 agreements reported in publications, 52 (73.2%) were concordant with those documented in the protocol. In 14 of 37 (37.8%) publications in which statements suggested unrestricted publication rights, at least one co-author was an industry employee.

In 25 protocol-publication pairs, author statements in publications suggested no constraints, but 18 corresponding protocols documented restricting agreements.

Conclusions

Publication agreements constraining academic authors’ independence are common. Journal articles seldom report on publication agreements, and, if they do, statements can be discrepant with the trial protocol.

URL : Agreements between Industry and Academia on Publication Rights : A Retrospective Study of Protocols and Publications of Randomized Clinical Trials

DOI : http://dx.doi.org/10.1371/journal.pmed.1002046

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

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Authors : Andra Waagmeester,  Martina Kutmon, Anders Riutta, Ryan Miller,  Egon L. Willighagen, Chris T.  Evelo , Alexander R. Pico

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data.

The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org.

Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries.

In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web.

WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development.

We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

URL : Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

DOI : http://dx.doi.org/10.1371/journal.pcbi.1004989

Assessment of and Response to Data Needs of Clinical and Translational Science Researchers and Beyond

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Objective and Setting

As universities and libraries grapple with data management and “big data,” the need for data management solutions across disciplines is particularly relevant in clinical and translational science (CTS) research, which is designed to traverse disciplinary and institutional boundaries.

At the University of Florida Health Science Center Library, a team of librarians undertook an assessment of the research data management needs of CTS researchers, including an online assessment and follow-up one-on-one interviews.

Design and Methods

The 20-question online assessment was distributed to all investigators affiliated with UF’s Clinical and Translational Science Institute (CTSI) and 59 investigators responded. Follow-up in-depth interviews were conducted with nine faculty and staff members.

Results

Results indicate that UF’s CTS researchers have diverse data management needs that are often specific to their discipline or current research project and span the data lifecycle. A common theme in responses was the need for consistent data management training, particularly for graduate students; this led to localized training within the Health Science Center and CTSI, as well as campus-wide training.

Another campus-wide outcome was the creation of an action-oriented Data Management/Curation Task Force, led by the libraries and with participation from Research Computing and the Office of Research.

Conclusions

Initiating conversations with affected stakeholders and campus leadership about best practices in data management and implications for institutional policy shows the library’s proactive leadership and furthers our goal to provide concrete guidance to our users in this area.

URL : Assessment of and Response to Data Needs of Clinical and Translational Science Researchers and Beyond

Alternative location : http://escholarship.umassmed.edu/jeslib/vol5/iss1/2/

OpenTrials: towards a collaborative open database of all available information on all clinical trials

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OpenTrials is a collaborative and open database for all available structured data and documents on all clinical trials, threaded together by individual trial.

With a versatile and expandable data schema, it is initially designed to host and match the following documents and data for each trial: registry entries; links, abstracts, or texts of academic journal papers; portions of regulatory documents describing individual trials; structured data on methods and results extracted by systematic reviewers or other researchers; clinical study reports; and additional documents such as blank consent forms, blank case report forms, and protocols.

The intention is to create an open, freely re-usable index of all such information and to increase discoverability, facilitate research, identify inconsistent data, enable audits on the availability and completeness of this information, support advocacy for better data and drive up standards around open data in evidence-based medicine.

The project has phase I funding. This will allow us to create a practical data schema and populate the database initially through web-scraping, basic record linkage techniques, crowd-sourced curation around selected drug areas, and import of existing sources of structured and documents.

It will also allow us to create user-friendly web interfaces onto the data and conduct user engagement workshops to optimise the database and interface designs.

Where other projects have set out to manually and perfectly curate a narrow range of information on a smaller number of trials, we aim to use a broader range of techniques and attempt to match a very large quantity of information on all trials. We are currently seeking feedback and additional sources of structured data.

URL : OpenTrials: towards a collaborative open database of all available information on all clinical trials

Alternative location : http://trialsjournal.biomedcentral.com/articles/10.1186/s13063-016-1290-8