Streamlined peer review and PubMed-ready XML: How Spartan Medical Research Journal is using Scholastica to grow

“When SMRJ was started, the editors used email and Word docs to track peer review, and they published all articles in PDF format. However, with the journal continuing to expand, the editors realized they were in need of an easier way to track submissions and a new publishing system to improve the journal’s online reading experience and chances of being added to relevant indexes. As a result, Chief Editor William Corser and Assistant Editor Sam Wisniewski began searching for publishing tools and services, focused on three key areas: streamlining peer review, modernizing the journal’s website, and producing XML for all articles.

After considering different options, Corser and Wisniewski chose to use Scholastica’s peer review and open access publishing software, as well as Scholastica’s typesetting service to produce PDF, HTML, and XML article files. Since making the switch, they’ve found that peer review is smoother for editors and authors and they’re making strides towards reaching their article discovery and indexing goals….”

NIH Preprint Pilot Update. NLM Technical Bulletin. 2021 Mar–Apr

“Ten months into the NIH Preprint Pilot, more than 2,100 preprints reporting NIH-supported research on COVID-19 are now discoverable in PubMed Central (PMC) and PubMed. Through early April 2021, these records have been viewed more than 1 million times in each of these databases (1.4 million in PMC; 1 million in PubMed). Of the preprints included in the pilot, ~60% are currently discoverable only as a preprint version, having not yet been linked to a published article. All articles are clearly identified as preprints. Preprints may be selected or excluded in searches by using the preprint filter.

The pilot launched in June 2020 with preprint records from medRxiv, bioRxiv, arXiv, ChemRxiv, Research Square, and SSRN. Phase 1 has focused on improving the discoverability of preprints relating to the ongoing public health emergency and accelerating dissemination of NIH-supported research on the SARS-CoV-2 virus and COVID-19. This narrowly scoped first phase has allowed the National Library of Medicine (NLM) to streamline curation and ingest workflows for NIH-supported preprints and refine the details of implementation with a set of articles for which there has been high demand for accelerated access and discovery. Since launching the pilot, NLM has made display of preprint records in PubMed search results more transparent. We have also automated checks for new preprint versions and preprint withdrawals, and reduced the steps required to report preprints as products of awards in My Bibliography….”

Broader reach in searching for adverse events articles – a case study with DOAJ and Crossref

“An efficient strategy for searching for adverse events in scientific literature should find as many relevant events as possible and maintain screening effort within reasonable levels.

 

Naturally, finding more adverse events is directly related to the question of where to search. Past studies suggest results do improve when searching multiple established proprietary global literature databases. We decided to investigate databases that favor open models of scholarly publications, now gaining traction in the academic world. Can they be a cost-effective way to more adverse events results from the literature?

 

In this post, we investigate the use of alternative scientific literature sources to complement searching for adverse events on a mainstream index (PubMed). In particular we explored:

The Directory of Open Access Journals (DOAJ) indexes academic literature with an open access license from publishers worldwide. It currently hosts over 5 million records.

Crossref: a community organization dedicated to supporting scholarly communication by generating metadata and providing services for content discoverability. The Crossref metadata spans over 120 million records, with a growing proportion being published as open abstracts….”

CORE and PubMed collaborate for further full text dissemination – Research

“CORE provides access to freely available full text papers which were previously  unavailable in PubMed to enhance the experience of PubMed users. This is delivered via the LinkOut service. 

PubMed is maintained by the US National Library of Medicine at the National Institutes of Health. It constitutes the largest citations database in health sciences and is one of the most widely used scholarly infrastructure services with millions of monthly active users.

We are happy to announce that hundreds of thousands of relevant articles hosted in CORE are now linked from PubMed, taking  more  available content directly to the researchers.   

Currently, many PubMed records offer metadata information and the full text may not be available. This development now enables PubMed users to access full text links to articles hosted in CORE via its LinkOut service, providing researchers with a direct route to the research. The linking of CORE papers directly from PubMed resources and other related databases further increases the discoverability of content aggregated by CORE, providing a valuable service to our repositories.  …”

A detailed open access model of the PubMed literature | Scientific Data

Abstract:  Portfolio analysis is a fundamental practice of organizational leadership and is a necessary precursor of strategic planning. Successful application requires a highly detailed model of research options. We have constructed a model, the first of its kind, that accurately characterizes these options for the biomedical literature. The model comprises over 18 million PubMed documents from 1996–2019. Document relatedness was measured using a hybrid citation analysis?+?text similarity approach. The resulting 606.6 million document-to-document links were used to create 28,743 document clusters and an associated visual map. Clusters are characterized using metadata (e.g., phrases, MeSH) and over 20 indicators (e.g., funding, patent activity). The map and cluster-level data are embedded in Tableau to provide an interactive model enabling in-depth exploration of a research portfolio. Two example usage cases are provided, one to identify specific research opportunities related to coronavirus, and the second to identify research strengths of a large cohort of African American and Native American researchers at the University of Michigan Medical School.

 

LitCovid – NCBI – NLM – NIH

“LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus. It is the most comprehensive resource on the subject, providing a central access to 1121 (and growing) research articles in PubMed. The articles are updated daily and are further categorized by different research topics and geographic locations for improved access….”

LitCovid – NCBI – NLM – NIH

“LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus. It is the most comprehensive resource on the subject, providing a central access to 1121 (and growing) research articles in PubMed. The articles are updated daily and are further categorized by different research topics and geographic locations for improved access….”

Keep up with the latest coronavirus research

“An open-resource literature hub known as LitCovid curates the most comprehensive collection of international research papers so far on the new coronavirus disease COVID-19 (see go.nature.com/3almd5p). Developed with the support of the US National Institutes of Health’s intramural research programme, LitCovid is updated daily with newly published articles. The aim is to provide timely insight from the scientific literature into the biology of the virus and the diagnosis and management of those who have been infected.

LitCovid has a more sophisticated search function than existing resources. It identifies roughly 35% more relevant articles than do conventional keyword-based searches for entries such as ‘COVID-19’ or ‘nCOV’. Furthermore, the articles are categorized by topic — overview, disease mechanism, transmission dynamics, treatment, case report and epidemic forecasting — as well as by geographic location for visualization on a world map…..”

Keep up with the latest coronavirus research

“An open-resource literature hub known as LitCovid curates the most comprehensive collection of international research papers so far on the new coronavirus disease COVID-19 (see go.nature.com/3almd5p). Developed with the support of the US National Institutes of Health’s intramural research programme, LitCovid is updated daily with newly published articles. The aim is to provide timely insight from the scientific literature into the biology of the virus and the diagnosis and management of those who have been infected.

LitCovid has a more sophisticated search function than existing resources. It identifies roughly 35% more relevant articles than do conventional keyword-based searches for entries such as ‘COVID-19’ or ‘nCOV’. Furthermore, the articles are categorized by topic — overview, disease mechanism, transmission dynamics, treatment, case report and epidemic forecasting — as well as by geographic location for visualization on a world map…..”

2019 Was Big for Academic Publishing. Here’s Our Year in Review | The Scientist Magazine®

“The global push to make the scholarly literature open access continued in 2019. Some publishers and libraries forged new licensing deals, while in other cases contract negotiations came to halt, and a radical open access plan made some adjustments. Here are some of the most notable developments in the publishing world in 2019:…”

How to add academic journal articles to PubMed: An overview for publishers

“If you work with journals in the biomedical or life sciences, getting the articles you publish added to PubMed to make them more discoverable is likely one of your top goals. But, you may be wondering how to go about it.

We caught up with PubMed Central (PMC) Program Manager Kathryn Funk to get answers to some of the most common questions that we hear from journal publishers about PubMed and the related literature databases at the National Library of Medicine (NLM), MEDLINE and PMC. Read on to learn more about how the PubMed database works and how to apply to have a journal included in MEDLINE or PMC in order to make its articles searchable via PubMed….”

Frequency and format of clinical trial results dissemination to patients: a survey of authors of trials indexed in PubMed

Abstract:  Objective Dissemination of research findings is central to research integrity and promoting discussion of new knowledge and its potential for translation into practice and policy. We investigated the frequency and format of dissemination to trial participants and patient groups. Design Survey of authors of clinical trials indexed in PubMed in 2014–2015. Results Questionnaire emailed to 19 321 authors; 3127 responses received (16%). Of these 3127 trials, 2690 had human participants and 1818 enrolled individual patients. Among the 1818, 498 authors (27%) reported having disseminated results to participants, 238 (13%) planned to do so, 600 (33%) did not plan to, 176 (10%) were unsure and 306 (17%) indicated ‘other’ or did not answer. Of the 498 authors who had disseminated, 198 (40%) shared academic reports, 252 (51%) shared lay reports, 111 (22%) shared both and 164 (33%) provided individualised study results. Of the 1818 trials, 577 authors (32%) shared/planned to share results with patients outside their trial by direct contact with charities/patient groups, 401 (22%) via patient communities, 845 (46%) via presentations at conferences with patient representation, 494 (27%) via mainstream media and 708 (39%) by online lay summaries. Relatively few of the 1818 authors reported dissemination was suggested by institutional bodies: 314 (17%) of funders reportedly suggested dissemination to trial participants, 252 (14%) to patient groups; 333 (18%) of ethical review boards reportedly suggested dissemination to trial participants, 148 (8%) to patient groups. Authors described many barriers to dissemination. Conclusion Fewer than half the respondents had disseminated to participants (or planned to) and only half of those who had disseminated shared lay reports. Motivation to disseminate results to participants appears to arise within research teams rather than being incentivised by institutional bodies. Multiple factors need to be considered and various steps taken to facilitate wide dissemination of research to participants.

Which Academic Search Systems are Suitable for Systematic Reviews or Meta?Analyses? Evaluating Retrieval Qualities of Google Scholar, PubMed and 26 other Resources – Gusenbauer – – Research Synthesis Methods – Wiley Online Library

Abstract:  Rigorous evidence identification is essential for systematic reviews and meta?analyses (evidence syntheses), because the sample selection of relevant studies determines a review’s outcome, validity, and explanatory power. Yet, the search systems allowing access to this evidence provide varying levels of precision, recall, and reproducibility and also demand different levels of effort. To date, it remains unclear which search systems are most appropriate for evidence synthesis and why. Advice on which search engines and bibliographic databases to choose for systematic searches is limited and lacking systematic, empirical performance assessments.

This study investigates and compares the systematic search qualities of 28 widely used academic search systems, including Google Scholar, PubMed and Web of Science. A novel, query?based method tests how well users are able to interact and retrieve records with each system. The study is the first to show the extent to which search systems can effectively and efficiently perform (Boolean) searches with regards to precision, recall and reproducibility. We found substantial differences in the performance of search systems, meaning that their usability in systematic searches varies. Indeed, only half of the search systems analysed and only a few Open Access databases can be recommended for evidence syntheses without adding substantial caveats. Particularly, our findings demonstrate why Google Scholar is inappropriate as principal search system.

We call for database owners to recognise the requirements of evidence synthesis, and for academic journals to re?assess quality requirements for systematic reviews. Our findings aim to support researchers in conducting better searches for better evidence synthesis.

Academics Raise Concerns About Predatory Journals on PubMed | The Scientist Magazine®

“PubMed, the National Library of Medicine’s repository of millions of abstracts and citations, has long been one of the most highly regarded sources for searching biomedical literature. For some members of the scientific community, the presence of predatory journals, publications that tend to churn out low-quality content and engage in unethical publishing practices—has been a pressing concern….

In 2017, Manca, Franca Deriu, a professor of physiology at the University of Sassari, and their colleagues conducted two studies that pinpointed more than 200 predatory journals across the disciplines of neuroscience, neurology, and rehabilitation, and discovered that several of those also appeared on PubMed….

According to Manca, content from predatory publishers likely seeps into PubMed via PMC, where he and his colleagues have been able to find papers from several predatory journals….”

Exploring PubMed as a reliable resource for scholarly communications services | Ossom Williamson | Journal of the Medical Library Association

“Abstract

Objective: PubMed’s provision of MEDLINE and other National Library of Medicine (NLM) resources has made it one of the most widely accessible biomedical resources globally. The growth of PubMed Central (PMC) and public access mandates have affected PubMed’s composition. The authors tested recent claims that content in PMC is of low quality and affects PubMed’s reliability, while exploring PubMed’s role in the current scholarly communications landscape.

Methods: The percentage of MEDLINE-indexed records was assessed in PubMed and various subsets of records from PMC. Data were retrieved via the National Center for Biotechnology Information (NCBI) interface, and follow-up interviews with a PMC external reviewer and staff at NLM were conducted.

Results: Almost all PubMed content (91%) is indexed in MEDLINE; however, since the launch of PMC, the percentage of PubMed records indexed in MEDLINE has slowly decreased. This trend is the result of an increase in PMC content from journals that are not indexed in MEDLINE and not a result of author manuscripts submitted to PMC in compliance with public access policies. Author manuscripts in PMC continue to be published in MEDLINE-indexed journals at a high rate (85%). The interviewees clarified the difference between the sources, with MEDLINE serving as a highly selective index of journals in biomedical literature and PMC serving as an open archive of quality biomedical and life sciences literature and a repository of funded research.

Conclusion: The differing scopes of PMC and MEDLINE will likely continue to affect their overlap; however, quality control exists in the maintenance and facilitation of both resources, and funding from major grantors is a major component of quality assurance in PMC….”