PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge

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Authors  : Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, Zhiyong Lu

PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer semantic and relation searches for key concepts like proteins, genetic variants, diseases and chemicals. It currently provides over one billion entity and relation annotations across approximately 36 million PubMed abstracts and 6 million full-text articles from the PMC open access subset, updated weekly.

PubTator 3.0’s online interface and API utilize these precomputed entity relations and synonyms to provide advanced search capabilities and enable large-scale analyses, streamlining many complex information needs. We showcase the retrieval quality of PubTator 3.0 using a series of entity pair queries, demonstrating that PubTator 3.0 retrieves a greater number of articles than either PubMed or Google Scholar, with higher precision in the top 20 results.

We further show that integrating ChatGPT (GPT-4) with PubTator APIs dramatically improves the factuality and verifiability of its responses. In summary, PubTator 3.0 offers a comprehensive set of features and tools that allow researchers to navigate the ever-expanding wealth of biomedical literature, expediting research and unlocking valuable insights for scientific discovery.

URL : PubTator 3.0: an AI-powered literature resource for unlocking biomedical knowledge

DOI : https://doi.org/10.1093/nar/gkae235

Text mining arXiv: a look through quantitative finance papers

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Author : Michele Leonardo Bianchi

This paper explores articles hosted on the arXiv preprint server with the aim to uncover valuable insights hidden in this vast collection of research. Employing text mining techniques and through the application of natural language processing methods, we examine the contents of quantitative finance papers posted in arXiv from 1997 to 2022.

We extract and analyze crucial information from the entire documents, including the references, to understand the topics trends over time and to find out the most cited researchers and journals on this domain. Additionally, we compare numerous algorithms to perform topic modeling, including state-of-the-art approaches.

Arxiv : https://arxiv.org/abs/2401.01751

Authorship conflicts in academia: an international cross‑discipline survey

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Authors : Elizaveta Savchenko, Ariel Rosenfeld

Collaboration among scholars has emerged as a significant characteristic of contemporary science. As a result, the number of authors listed in publications continues to rise steadily. Unfortunately, determining the authors to be included in the byline and their respective order entails multiple difficulties which often lead to conflicts. Despite the large volume of literature about conflicts in academia, it remains unclear how exactly these are distributed over the main socio-demographic properties, as well as the different types of interactions academics experience.

To address this gap, we conducted an international and cross-disciplinary survey answered by 752 academics from 41 fields of research and 93 countries that statistically well-represent the overall academic workforce. Our findings are concerning and suggest that conflicts over authorship credit arise very early in one’s academic career, even at the level of Master and Ph.D., and become increasingly common over time.

URL : Authorship conflicts in academia: an international cross‑discipline survey

DOI : https://doi.org/10.1007/s11192-024-04972-x

Le groupe Facebook La Bibliothèque Solidaire du confinement. Circulations et médiatisations numériques des contenus et des pratiques savantes en temps de pandémie

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Auteur.ices/Authors : Muriel Amar, Julien Hage

Le groupe Facebook La Bibliothèque Solidaire du confinement (Bsc) constitue un dispositif de production relationnelle qui couple une production de relation – courtage documentaire entre demandeurs de documents et propriétaires de documents – à une production par la relation : les échanges de fichiers donnent lieu à un écosystème de pratiques conversationnelles qui motive une présence dans le groupe nourrie par une constante attention médiatique comme à la volonté « d’en être » et de s’identifier à lui et à ses topoï.

En dehors de toute dimension marchande, la Bsc et ses échanges manifestent une valeur d’usage scientifique, une valeur de partage relationnelle et une valeur patrimoniale : c’est bien toute la dimension de bien « culturel » ou « symbolique » du livre que la plateforme met en mouvement, dans le cadre d’une économie morale de la science imposée par le contexte pandémique.

URL : https://intelligibilite-numerique.numerev.com/numeros/n-5-2024/2913-le-groupe-facebook-la-bibliotheque-solidaire-du-confinement-circulations-et-mediatisations-numeriques-des-contenus-et-des-pratiques-savantes-en-temps-de-pandemie

The impact of researchers’ perceived pressure on their publication strategies

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Authors : David Johann, Jorg Neufeld, Kathrin Thomas, Justus Rathmann, Heiko Rauhut

This article investigates researchers’ publication strategies and how their perceived pressure to publish and to obtain external funding are related to these strategies. The analyses rely on data from the Zurich Survey of Academics (ZSoA), an online survey representative of academics working at higher education institutions in Germany, Austria, and Switzerland. The results suggest that academics pursue both instrumental and normative publication strategies.

The main finding is that academics who perceive high pressure to publish tend to employ instrumental publication strategies rather than normative ones: they are more likely to focus on the journal’s reputation and the speed of publication when selecting an outlet for peer review. Publishing results in open-access outlets or in native languages other than English is less important for those under pressure.

However, the extent to which researchers’ perceived pressure affects publication strategies also depends on other factors, such as the discrepancy between the time available for research and the time actually desired for research.

URL : The impact of researchers’ perceived pressure on their publication strategies

DOI : https://doi.org/10.1093/reseval/rvae011

Evolution of Peer Review in Scientific Communication

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Author : Dmitry Kochetkov

It is traditionally believed that peer review is the backbone of an academic journal and scientific communication, ensuring high quality and trust in the published materials. However, peer review only became an institutionalized practice in the second half of the 20th century, although the first scientific journals appeared three centuries earlier. By the beginning of the 21st century, there emerged an opinion that the traditional model of peer review is in deep crisis.

The aim of this article is to formulate a perspective model of peer review for scientific communication. The article discusses the evolution of the institution of scientific peer review and the formation of the current crisis. The author analyzed the modern landscape of innovations in peer review and scientific communication. Based on this analysis, three main peer review models in relation to editorial workflow were identified: pre-publication peer review (traditional model),  registered reports, and post-publication (peer) review (including preprints (peer) review).

The author argues that the third model offers the best way to implement the main functions of scientific communication.

URL : Evolution of Peer Review in Scientific Communication

DOI : https://doi.org/10.31235/osf.io/b2ra3

On the Fast Track to Full Gold Open Access

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Author : Robert Kudelić

The world of scientific publishing is changing; the days of an old type of subscription-based earnings for publishers seem over, and we are entering a new era. It seems as if an ever-increasing number of journals from disparate publishers are going Gold, Open Access that is, yet have we rigorously ascertained the issue in its entirety, or are we touting the strengths and forgetting about constructive criticism and careful weighing of evidence?

We will therefore present the current state of the art, in a compact review/bibliometrics style, of this more relevant than ever hot topic and suggest solutions that are most likely to be acceptable to all parties–while the performed analysis also shows there seems to be a link between trends in scientific publishing and tumultuous world events, which in turn has a special significance for the publishing environment in the current world stage.

URL : On the Fast Track to Full Gold Open Access

Arxiv : https://arxiv.org/abs/2311.08313