“The Immunological Proteomic Resource (ImmPRes) originated from a collaboration between the Laboratory for Quantitative Proteomics and the Division of Cell Signalling & Immunology within the School of Life Sciences at the University of Dundee. ImmPRes is an open access public resource created with the aim to provide an in-depth, high quality, quantitative map of the immuno proteome. It integrates proteomic data generated by large-scale quantitative mass-spectrometry of murine immune cell populations….”

Biomedical supervisors’ role modeling of open science practices | eLife

Abstract:  Supervision is one important way to socialize Ph.D. candidates into open and responsible research. We hypothesized that one should be more likely to identify open science practices (here publishing open access and sharing data) in empirical publications that were part of a Ph.D. thesis when the Ph.D. candidates’ supervisors engaged in these practices compared to those whose supervisors did not or less often did. Departing from thesis repositories at four Dutch University Medical centers, we included 211 pairs of supervisors and Ph.D. candidates, resulting in a sample of 2062 publications. We determined open access status using UnpaywallR and Open Data using Oddpub, where we also manually screened publications with potential open data statements. Eighty-three percent of our sample was published openly, and 9% had open data statements. Having a supervisor who published open access more often than the national average was associated with an odds of 1.99 to publish open access. However, this effect became nonsignificant when correcting for institutions. Having a supervisor who shared data was associated with 2.22 (CI:1.19–4.12) times the odds to share data compared to having a supervisor that did not. This odds ratio increased to 4.6 (CI:1.86–11.35) after removing false positives. The prevalence of open data in our sample was comparable to international studies; open access rates were higher. Whilst Ph.D. candidates spearhead initiatives to promote open science, this study adds value by investigating the role of supervisors in promoting open science.


Changing word meanings in biomedical literature reveal pandemics and new technologies | BioData Mining | Full Text

Abstract:  While we often think of words as having a fixed meaning that we use to describe a changing world, words are also dynamic and changing. Scientific research can also be remarkably fast-moving, with new concepts or approaches rapidly gaining mind share. We examined scientific writing, both preprint and pre-publication peer-reviewed text, to identify terms that have changed and examine their use. One particular challenge that we faced was that the shift from closed to open access publishing meant that the size of available corpora changed by over an order of magnitude in the last two decades. We developed an approach to evaluate semantic shift by accounting for both intra- and inter-year variability using multiple integrated models. This analysis revealed thousands of change points in both corpora, including for terms such as ‘cas9’, ‘pandemic’, and ‘sars’. We found that the consistent change-points between pre-publication peer-reviewed and preprinted text are largely related to the COVID-19 pandemic. We also created a web app for exploration that allows users to investigate individual terms ( To our knowledge, our research is the first to examine semantic shift in biomedical preprints and pre-publication peer-reviewed text, and provides a foundation for future work to understand how terms acquire new meanings and how peer review affects this process.

[SPARC response to the NIH public access plan]

“SPARC strongly supports the OSTP Memorandum’s emphasis on ensuring equity in contributing to, accessing, and benefitting from the results of federally funded research, and we appreciate NIH’s specific attention on how to ensure equity in publication opportunities for its funded investigators. As the research process has shifted to the digital environment, a wide variety of channels designed to support more rapid, frequent, and iterative communication of research findings have emerged. It is vital that researchers have compliance options that do not present them with financial barriers. To that end, NIH should make it clear that investigators can fully comply with its public access policy by depositing their author’s accepted manuscripts into PubMed Central (PMC) or any other agency-approved repository—and that there is no charge to do so. In its guidance, it is important for NIH to make clear that any fee that investigators may be asked to pay is a publication fee, and not a fee required by NIH to comply with its policy. It is critical that investigators do not conflate compliance with article processing charges (APCs), which create significant barriers for less-well-resourced investigators and institutions to make their research available….”

OASPA response to NIH RFI 2023 – OASPA

“This is OASPA’s response to the Request for Information based on this policy (with revisions) from the NIH as released on 21 Feb 2023.

OASPA (the Open Access Scholarly Publishing Association) represents a diverse community of organizations engaged in open scholarship and encourages and enables open access as the predominant model for scholarly outputs. 

OASPA wishes to ensure that open access is equitable and inclusive and is keen to explore with its publisher members and library stakeholders ways to increase equity in open access publishing. Why? Because the inclusion of all researchers, including authors from developing and transition countries, and indeed from all backgrounds and life stages, is essential for advancing human knowledge and also for a successful transition to open access. Without the development of new and more equitable approaches to open access, we will not benefit from its full potential….”

[COGR comments on the NIH public access plan]

“COGR is an association of over 200 public and private U.S. research universities and affiliated academic medical centers and research institutes. COGR concerns itself with the impact of federal regulations, policies, and practices on the performance of research conducted at our member institutions. As recipients of a significant portion of NIH extramural research programs, COGR’s member institutions value the opportunity to respond to this request. The White House Office of Science and Technology Policy (OSTP) memo1 sets forth requirements to increase access to publications and data resulting from federally funded research, and the NIH RFI NOT-OD-23-091 outlines NIH’s plans to address this directive. As recipients of federally funded research, ensuring public access to publications and research data resulting from supported research is core to our mission as research institutions and a responsibility we take seriously. COGR looks forward to continuing to engage with the community and the agencies on this important topic and offer the following comments….”

ARL Comments on NIH Plan to Enhance Public Access to Results of NIH-Supported Research – Association of Research Libraries

“On February 21, 2023, the US National Institutes of Health (NIH) released “Request for Information on the NIH Plan to Enhance Public Access to the Results of NIH-Supported Research.” The Association of Research Libraries (ARL) is pleased to offer the following comments in response to this request….”

Sample Partnering Agreement Template | Ombudsman

Sample template for a deliberative approach by team members to assess and plan for key issues — e.g., collaboration rationale and readiness, inter- and intra-team communication, investigators’ technologies & resources, conflict management, budget issues, publication — that influence both scientific and collaborative success.

The Rapid Growth of Mega-Journals: Threats and Opportunities | Medical Journals and Publishing | JAMA | JAMA Network

“Mega-journals, those that publish large numbers of articles per year,1 are growing rapidly across science and especially in biomedicine. Although 11 Scopus-indexed journals published more than 2000 biomedical full papers (articles or reviews) in 2015 and accounted for 6% of that year’s literature, in 2022 there were 55 journals publishing more than 2000 full articles, totaling more than 300?000 articles (almost a quarter of the biomedical literature that year). In 2015, 2 biomedical research journals (PLoS One and Scientific Reports) published more than 3500 full articles. In 2022, there were 26 such prolific journals (Table). The accelerating growth of mega-journals creates both threats and opportunities for biomedical science….”


Characterization and Reach of Orthopaedic Research Posted to Preprint Servers: Are We “Undercooking” Our Science?

Abstract:  Background 

Although biomedical preprint servers have grown rapidly over the past several years, the harm to patient health and safety remains a major concern among several scientific communities. Despite previous studies examining the role of preprints during the Coronavirus-19 pandemic, there is limited information characterizing their impact on scientific communication in orthopaedic surgery.


(1) What are the characteristics (subspecialty, study design, geographic origin, and proportion of publications) of orthopaedic articles on three preprint servers? (2) What are the citation counts, abstract views, tweets, and Altmetric score per preprinted article and per corresponding publication?


Three of the largest preprint servers (medRxiv, bioRxiv, and Research Square) with a focus on biomedical topics were queried for all preprinted articles published between July 26, 2014, and September 1, 2021, using the following search terms: “orthopaedic,” “orthopedic,” “bone,” “cartilage,” “ligament,” “tendon,” “fracture,” “dislocation,” “hand,” “wrist,” “elbow,” “shoulder,” “spine,” “spinal,” “hip,” “knee,” “ankle,” and “foot.” Full-text articles in English related to orthopaedic surgery were included, while nonclinical studies, animal studies, duplicate studies, editorials, abstracts from conferences, and commentaries were excluded. A total of 1471 unique preprints were included and further characterized in terms of the orthopaedic subspecialty, study design, date posted, and geographic factors. Citation counts, abstract views, tweets, and Altmetric scores were collected for each preprinted article and the corresponding publication of that preprint in an accepting journal. We ascertained whether a preprinted article was published by searching title keywords and the corresponding author in three peer-reviewed article databases (PubMed, Google Scholar, and Dimensions) and confirming that the study design and research question matched.


The number of orthopaedic preprints increased from four in 2017 to 838 in 2020. The most common orthopaedic subspecialties represented were spine, knee, and hip. From 2017 to 2020, the cumulative counts of preprinted article citations, abstract views, and Altmetric scores increased. A corresponding publication was identified in 52% (762 of 1471) of preprints. As would be expected, because preprinting is a form of redundant publication, published articles that are also preprinted saw greater abstract views, citations, and Altmetric scores on a per-article basis.


Although preprints remain an extremely small proportion of all orthopaedic research, our findings suggest that nonpeer-reviewed, preprinted orthopaedic articles are being increasingly disseminated. These preprinted articles have a smaller academic and public footprint than their published counterparts, but they still reach a substantial audience through infrequent and superficial online interactions, which are far from equivalent to the engagement facilitated by peer review. Furthermore, the sequence of preprint posting and journal submission, acceptance, and publication is unclear based on the information available on these preprint servers. Thus, it is difficult to determine whether the metrics of preprinted articles are attributable to preprinting, and studies such as the present analysis will tend to overestimate the apparent impact of preprinting. Despite the potential for preprint servers to function as a venue for thoughtful feedback on research ideas, the available metrics data for these preprinted articles do not demonstrate the meaningful engagement that is achieved by peer review in terms of the frequency or depth of audience feedback.

Clinical Relevance 

Our findings highlight the need for safeguards to regulate research dissemination through preprint media, which has never been shown to benefit patients and should not be considered as evidence by clinicians. Clinician-scientists and researchers have the most important responsibility of protecting patients from the harm of potentially inaccurate biomedical science and therefore must prioritize patient needs first by uncovering scientific truths through the evidence-based processes of peer review, not preprinting. We recommend all journals publishing clinical research adopt the same policy as Clinical Orthopaedics and Related Research®, The Bone & Joint Journal, The Journal of Bone and Joint Surgery, and the Journal of Orthopaedic Research, removing any papers posted to preprint servers from consideration.

Community consensus on core open science practices to monitor in biomedicine | PLOS Biology

Abstract:  The state of open science needs to be monitored to track changes over time and identify areas to create interventions to drive improvements. In order to monitor open science practices, they first need to be well defined and operationalized. To reach consensus on what open science practices to monitor at biomedical research institutions, we conducted a modified 3-round Delphi study. Participants were research administrators, researchers, specialists in dedicated open science roles, and librarians. In rounds 1 and 2, participants completed an online survey evaluating a set of potential open science practices, and for round 3, we hosted two half-day virtual meetings to discuss and vote on items that had not reached consensus. Ultimately, participants reached consensus on 19 open science practices. This core set of open science practices will form the foundation for institutional dashboards and may also be of value for the development of policy, education, and interventions.


Introducing Jot — a new open-source tool that help researchers with journal selection < Yale School of Public Health

“Say hello to Jot: a free, open-source web application that matches manuscripts in the fields of biomedicine and life sciences with suitable journals, based on a manuscript’s title, abstract, and (optionally) citations.

Developed by the Townsend Lab at the Yale School of Public Health, Jot gathers a wealth of data on journal quality, impact, fit, and open access options that can be explored through a dashboard of linked, interactive visualizations….”

FAIR service investigation survey

“The FAIR principles and “making data FAIR” have become common buzzwords in the biomedical field in recent years. Many organizations are striving to create fully FAIR data or to FAIRify existing data. In that process they often find themselves hindered by a range of challenges. To address those challenges, the FAIRplus consortium and other organizations have developed FAIR products and services in recent years. Now the question is: what is the need for new FAIR services or for improvement of the existing ones, in order to better serve life science organizations in their quest to accelerate biomedical research? To answer this, The Hyve run a survey to collect experience with the FAIR principles, main challenges and the products or services that help (or might have helped) to overcome those challenges….”

Introducing Jot — a new open-source tool that help researchers with journal selection < Yale School of Medicine

“Say hello to Jot: a free, open-source web application that matches manuscripts in the fields of biomedicine and life sciences with suitable journals, based on a manuscript’s title, abstract, and (optionally) citations….”

Public Access to Scientific Research Findings and Principles of Biomedical Research—A New Policy for the JAMA Network | Medical Journals and Publishing | JAMA Internal Medicine | JAMA Network

“Beginning in 2023, JAMA and all of the journals in the JAMA Network will adopt a new policy that permits authors of original research investigations to deposit their accepted manuscript in a public repository of their choosing immediately on the day that the manuscript is published by the JAMA Network….

With these and future policies, JAMA and the JAMA Network look forward to working collaboratively with scientists, research institutions, policy makers, funders, and other journals to lean in on first principles that support a thriving, robust scientific enterprise. Stakeholders have a shared responsibility to craft solutions that balance equity, accessibility, and sustainability. Together, we will continue to collegially debate and advance the steps to safeguard and evolve the growth and health of our ecosystem, which manifestly includes timely public access to biomedical research.”