Understanding the Changing Roles of Scientific Publications via Citation Embeddings

Authors : Jiangen He, Chaomei Chen

Researchers may describe different aspects of past scientific publications in their publications and the descriptions may keep changing in the evolution of science. The diverse and changing descriptions (i.e., citation context) on a publication characterize the impact and contributions of the past publication.

In this article, we aim to provide an approach to understanding the changing and complex roles of a publication characterized by its citation context. We described a method to represent the publications’ dynamic roles in science community in different periods as a sequence of vectors by training temporal embedding models.

The temporal representations can be used to quantify how much the roles of publications changed and interpret how they changed.

Our study in the biomedical domain shows that our metric on the changes of publications’ roles is stable over time at the population level but significantly distinguish individuals. We also show the interpretability of our methods by a concrete example.

URL : https://arxiv.org/abs/1711.05822

A review of data sharing statements in observational studies published in the BMJ: A cross-sectional study

Authors : Laura McDonald, Anna Schultze, Alex Simpson, Sophie Graham, Radek Wasiak, Sreeram V. Ramagopalan

In order to understand the current state of data sharing in observational research studies, we reviewed data sharing statements of observational studies published in a general medical journal, the British Medical Journal.

We found that the majority (63%) of observational studies published between 2015 and 2017 included a statement that implied that data used in the study could not be shared. If the findings of our exploratory study are confirmed, room for improvement in the sharing of real-world or observational research data exists.

URL : A review of data sharing statements in observational studies published in the BMJ: A cross-sectional study

DOI : http://dx.doi.org/10.12688/f1000research.12673.2

Publications en libre accès en biologie–médecine : historique et état des lieux en 2016

Auteurs/Authors : Christophe Boudry, Manuel Durand-Barthez

L’apparition du mouvement « open access » (libre accès, LA) et des archives ouvertes a bouleversé (et bouleverse encore) l’économie et l’accès aux publications scientifiques. L’objectif de cet article est de réactualiser et compléter les résultats des études antérieures qui ont tenté de quantifier l’importance du LA dans le domaine de la biologie/médecine, par le biais d’un focus sur la base de données bibliographiques PubMed.

Une analyse des publications en LA dans PubMed en fonction de l’origine géographique des auteurs a également été menée (pays et continents) et un certain nombre de paramètres liés au LA (évolution du nombre de journaux en LA, nombre de mandats et d’archives ouvertes par pays et continents) ont également été étudiés et mis en perspective. Les résultats mettent en évidence que les pourcentages d’articles dont le texte intégral et disponible en LA ne cessent de progresser et concernent en 2015, 39,1 % des articles disponibles dans PubMed.

L’analyse géographique des 25 pays les plus productifs et des continents montre une grande variabilité concernant le pourcentage d’articles en LA (de 21,9 % pour l’Italie à 42,08 % pour les États-Unis et de 22,80 % pour l’Océanie à 40,84 % pour l’Amérique du Nord).

Par ailleurs, nos données montrent que le nombre de mandats et d’archives ouvertes n’est pas corrélé de manière significative au pourcentage d’articles en LA au niveau national et continental, confirmant ainsi que les politiques publiques successives ou les mandats relatifs au LA n’ont eu qu’une influence, sinon secondaire, du moins inférieure aux attentes.

La mise en place de mandats plus coercitifs parviendra peut-être à obtenir des effets plus significatifs à plus ou moins long terme. L’augmentation régulière du nombre de journaux en LA, concomitante à l’augmentation avérée du nombre de citations des articles en LA, amplifiera certainement encore l’attrait des auteurs pour le LA.

DOI : https://doi.org/10.1016/j.jemep.2017.02.021

 

 

How to responsibly acknowledge research work in the era of big data and biobanks: ethical aspects of the Bioresource Research Impact Factor (BRIF)

Authors : Heidi Carmen Howard, Deborah Mascalzoni, Laurence Mabile, Gry Houeland, Emmanuelle Rial-Sebbag, Anne Cambon-Thomsen

Currently, a great deal of biomedical research in fields such as epidemiology, clinical trials and genetics is reliant on vast amounts of biological and phenotypic information collected and assembled in biobanks.

While many resources are being invested to ensure that comprehensive and well-organised biobanks are able to provide increased access to, and sharing of biomedical samples and information, many barriers and challenges remain to such responsible and extensive sharing.

Germane to the discussion herein is the barrier to collecting and sharing bioresources related to the lack of proper recognition of researchers and clinicians who developed the bioresource. Indeed, the efforts and resources invested to set up and sustain a bioresource can be enormous and such work should be easily traced and properly recognised.

However, there is currently no such system that systematically and accurately traces and attributes recognition to those doing this work or the bioresource institution itself. As a beginning of a solution to the “recognition problem”, the Bioresource Research Impact Factor/Framework (BRIF) initiative was proposed almost a decade and a half ago and is currently under further development.

With the ultimate aim of increasing awareness and understanding of the BRIF, in this article, we contribute the following: (1) a review of the objectives and functions of the BRIF including the description of two tools that will help in the deployment of the BRIF, the CoBRA (Citation of BioResources in journal Articles) guideline, and the Open Journal of Bioresources (OJB); (2) the results of a small empirical study on stakeholder awareness of the BRIF and (3) a brief analysis of the ethical dimensions of the BRIF which allow it to be a positive contribution to responsible biobanking.

URL : How to responsibly acknowledge research work in the era of big data and biobanks: ethical aspects of the Bioresource Research Impact Factor (BRIF)

Alternative locaton : https://link.springer.com/article/10.1007/s12687-017-0332-6

The rise of the middle author: Investigating collaboration and division of labor in biomedical research using partial alphabetical authorship

Authors : Philippe Mongeon, Elise Smith, Bruno Joyal, Vincent Larivière

Contemporary biomedical research is performed by increasingly large teams. Consequently, an increasingly large number of individuals are being listed as authors in the bylines, which complicates the proper attribution of credit and responsibility to individual authors.

Typically, more importance is given to the first and last authors, while it is assumed that the others (the middle authors) have made smaller contributions. However, this may not properly reflect the actual division of labor because some authors other than the first and last may have made major contributions.

In practice, research teams may differentiate the main contributors from the rest by using partial alphabetical authorship (i.e., by listing middle authors alphabetically, while maintaining a contribution-based order for more substantial contributions). In this paper, we use partial alphabetical authorship to divide the authors of all biomedical articles in the Web of Science published over the 1980–2015 period in three groups: primary authors, middle authors, and supervisory authors.

We operationalize the concept of middle author as those who are listed in alphabetical order in the middle of an authors’ list. Primary and supervisory authors are those listed before and after the alphabetical sequence, respectively.

We show that alphabetical ordering of middle authors is frequent in biomedical research, and that the prevalence of this practice is positively correlated with the number of authors in the bylines. We also find that, for articles with 7 or more authors, the average proportion of primary, middle and supervisory authors is independent of the team size, more than half of the authors being middle authors.

This suggests that growth in authors lists are not due to an increase in secondary contributions (or middle authors) but, rather, in equivalent increases of all types of roles and contributions (including many primary authors and many supervisory authors).

Nevertheless, we show that the relative contribution of alphabetically ordered middle authors to the overall production of knowledge in the biomedical field has greatly increased over the last 35 years.

URL : The rise of the middle author: Investigating collaboration and division of labor in biomedical research using partial alphabetical authorship

DOI : https://doi.org/10.1371/journal.pone.0184601

 

 

Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

Authors : Julie A. McMurry, Nick Juty, Niklas Blomberg, Tony Burdett, Tom Conlin, Nathalie Conte, Mélanie Courtot, John Deck, Michel Dumontier, Donal K. Fellows, Alejandra Gonzalez-Beltran, Philipp Gormanns, Jeffrey Grethe, Janna Hastings, Jean-Karim Hériché, Henning Hermjakob, Jon C. Ison, Rafael C. Jimenez, Simon Jupp, John Kunze, Camille Laibe, Nicolas Le Novère, James Malone, Maria Jesus Martin, Johanna R. McEntyre, Chris Morris, Juha Muilu, Wolfgang Müller, Philippe Rocca-Serra, Susanna-Assunta Sansone, Murat Sariyar, Jacky L. Snoep, Stian Soiland-Reyes, Natalie J. Stanford, Neil Swainston, Nicole Washington, Alan R. Williams, Sarala M. Wimalaratne, Lilly M. Winfree, Katherine Wolstencroft, Carole Goble, Christopher J. Mungall, Melissa A. Haendel, Helen Parkinson

In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from such databases depends on the discipline of data science and on the humble bricks and mortar that make integration possible; identifiers are a core component of this integration infrastructure.

Drawing on our experience and on work by other groups, we outline 10 lessons we have learned about the identifier qualities and best practices that facilitate large-scale data integration. Specifically, we propose actions that identifier practitioners (database providers) should take in the design, provision and reuse of identifiers.

We also outline the important considerations for those referencing identifiers in various circumstances, including by authors and data generators. While the importance and relevance of each lesson will vary by context, there is a need for increased awareness about how to avoid and manage common identifier problems, especially those related to persistence and web-accessibility/resolvability.

We focus strongly on web-based identifiers in the life sciences; however, the principles are broadly relevant to other disciplines.

URL : Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data

DOI : https://doi.org/10.1371/journal.pbio.2001414