Potential Predatory and Legitimate Biomedical Journals
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Stephen P. Lock on "Journalology"
INSTITUTE FOn SCIENTl FICl NF0F4MAT10N8 3501 MARKET ST PHILADELPHIA PA 19104 Stephen P. Lock on “Journalology” Number 3 January 15, 1990 I don’t remember exactly how long I have Lock: Editor and Scholar known Stephen P. Lock. Our first encounter was probably at a meeting of the Council of Biology Editors (CBE) some 20 years Stephen P. Lock was born in 1929 and re- ago. It is somewhat unsettling to realize that ceived his education at Queen’s College, so much time has gone by. Equally disquiet- Cambridge University, UK, and the Medical ing is the notion that Steve will soon retire College of St. Bartholomew’s Hospital. as editor of the venerable British Medical Trained as a hematologist, he served on the Journal (BMJ). But in the near future Steve staffs of various London teaching hospitals, will indeed step down, having helped train including St. Bartholomew’s and the Hos- his successor, due to be appointed in the fall pital for Sick Children, before being ap- of 1990. pointed assistant editor of BMJ in 1964. It seems odd to refer to Lock as an elder After serving as senior assistant editor and statesman of biomedical editing-however deputy editor, Lock became editor in 1975. accurate that description might be. The word I am amused that Steve opened his talk that comes to mind when I think of Steve with the traditional, mythical reminder about is youth. This youthfidness is reflected in the estimates of the number of extant jour- his writing and in his approach to problems. nals. -
Bioinformatics
Bioinformatics Bioinformatics is the combination of biology and information technology. The discipline encompasses any computational tools and methods used to manage, analyze and manipulate large sets of biological data. Essentially, bioinformatics has three components: The creation of databases allowing the storage and management of large biological data sets. The development of algorithms and statistics to determine relationships among members of large data sets. The use of these tools for the analysis and interpretation of various types of biological data, including DNA, RNA and protein sequences, protein structures, gene expression profiles, and biochemical pathways. The term bioinformatics first came into use in the 1990s and was originally synonymous with the management and analysis of DNA, RNA and protein sequence data. Computational tools for sequence analysis had been available since the 1960s, but this was a minority interest until advances in sequencing technology led to a rapid expansion in the number of stored sequences in databases such as GenBank. Now, the term has expanded to incorporate many other types of biological data, for example protein structures, gene expression profiles and protein interactions. Each of these areas requires its own set of databases, algorithms and statistical methods. Bioinformatics is largely, although not exclusively, a computer-based discipline. Computers are important in bioinformatics for two reasons: First, many bioinformatics problems require the same task to be repeated millions of times. For example, comparing a new sequence to every other sequence stored in a database or comparing a group of sequences systematically to determine evolutionary relationships. In such cases, the ability of computers to process information and test alternative solutions rapidly is indispensable. -
Assessing the Utility of an Institutional Publications Officer: a Pilot Assessment
Assessing the utility of an institutional publications officer: a pilot assessment Kelly D. Cobey1,2,3, James Galipeau1, Larissa Shamseer1,2 and David Moher1,2 1 Centre for Journalology, Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Canada 2 School of Epidemiology, Public Health, and Preventative Medicine, University of Ottawa, Ottawa, Canada 3 School of Natural Sciences, Department of Psychology, University of Stirling, Stirling, United Kingdom ABSTRACT Background. The scholarly publication landscape is changing rapidly. We investigated whether the introduction of an institutional publications officer might help facilitate better knowledge of publication topics and related resources, and effectively support researchers to publish. Methods. In September 2015, a purpose-built survey about researchers' knowledge and perceptions of publication practices was administered at five Ottawa area research institutions. Subsequently, we publicly announced a newly hired publications officer (KDC) who then began conducting outreach at two of the institutions. Specifically, the publications officer gave presentations, held one-to-one consultations, developed electronic newsletter content, and generated and maintained a webpage of resources. In March 2016, we re-surveyed our participants regarding their knowledge and perceptions of publishing. Mean scores to the perception questions, and the percent of correct responses to the knowledge questions, pre and post survey, were computed for each item. The difference between these means or calculated percentages was then examined across the survey measures. Results. 82 participants completed both surveys. Of this group, 29 indicated that they had exposure to the publications officer, while the remaining 53 indicated they did not. Interaction with the publications officer led to improvements in half of the knowledge items (7/14 variables). -
Core Competencies for Scientific Editors Of
Moher et al. BMC Medicine (2017) 15:167 DOI 10.1186/s12916-017-0927-0 CORRESPONDENCE Open Access Core competencies for scientific editors of biomedical journals: consensus statement David Moher1,2* , James Galipeau3, Sabina Alam4, Virginia Barbour5, Kidist Bartolomeos6, Patricia Baskin7,8, Sally Bell-Syer9,10, Kelly D. Cobey1,2,11, Leighton Chan12, Jocalyn Clark13, Jonathan Deeks14, Annette Flanagin15, Paul Garner16, Anne-Marie Glenny17, Trish Groves18, Kurinchi Gurusamy19, Farrokh Habibzadeh20,21,22, Stefanie Jewell-Thomas23, Diane Kelsall24, José Florencio Lapeña Jr22,25,26,27, Harriet MacLehose28, Ana Marusic29,30, Joanne E. McKenzie31, Jay Shah32,33,34, Larissa Shamseer1,2, Sharon Straus35, Peter Tugwell2,36,37, Elizabeth Wager38,39, Margaret Winker22 and Getu Zhaori40 Abstract Background: Scientific editors are responsible for deciding which articles to publish in their journals. However, we have not found documentation of their required knowledge, skills, and characteristics, or the existence of any formal core competencies for this role. Methods: We describe the development of a minimum set of core competencies for scientific editors of biomedical journals. Results: The 14 key core competencies are divided into three major areas, and each competency has a list of associated elements or descriptions of more specific knowledge, skills, and characteristics that contribute to its fulfillment. Conclusions: We believe that these core competencies are a baseline of the knowledge, skills, and characteristics needed to perform competently the duties of a scientific editor at a biomedical journal. Keywords: Core competencies, Scientific editor, Biomedical journal, Delphi, Expert consensus, Editor role Introduction and in guidance for members of editor organizations Scientific editors (editors are responsible for the content [3–8]. -
Downloads Presented on the Abstract Page
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.063578; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. A systematic examination of preprint platforms for use in the medical and biomedical sciences setting Jamie J Kirkham1*, Naomi Penfold2, Fiona Murphy3, Isabelle Boutron4, John PA Ioannidis5, Jessica K Polka2, David Moher6,7 1Centre for Biostatistics, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom. 2ASAPbio, San Francisco, CA, USA. 3Murphy Mitchell Consulting Ltd. 4Université de Paris, Centre of Research in Epidemiology and Statistics (CRESS), Inserm, Paris, F-75004 France. 5Meta-Research Innovation Center at Stanford (METRICS) and Departments of Medicine, of Epidemiology and Population Health, of Biomedical Data Science, and of Statistics, Stanford University, Stanford, CA, USA. 6Centre for Journalology, Clinical Epidemiology Program, Ottawa Hospital Research Institute, Ottawa, Canada. 7School of Epidemiology and Public Health, Faculty of Medicine, University of Ottawa, Ottawa, Canada. *Corresponding Author: Professor Jamie Kirkham Centre for Biostatistics Faculty of Biology, Medicine and Health The University of Manchester Jean McFarlane Building Oxford Road Manchester, M13 9PL, UK Email: [email protected] Tel: +44 (0)161 275 1135 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.27.063578; this version posted April 28, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. -
Cancer Informatics (A)
Cancer Open Access: Full open access to this and thousands of other papers at Informatics http://www.la-press.com. Computational Advances in Cancer Informatics (A) §§Xiaoqian Jiang §§Bairong Shen Assistant Professor of Biomedical Informatics, University Professor of Systems Biology, Soochow University, of California San Diego, La Jolla, CA, USA. Suzhou, Jiangsu, China. §§Rui Chen §§Rong Xu Research Assistant Professor of Computer Science, Hong Assistant Professor, Division of Medical Informatics, Case Kong Baptist University, Kowloon Tong, China. Western Reserve University, Cleveland, OH, USA. §§Samuel Cheng §§Song Yi Associate Professor of Electrical and Computing Research Fellow of Genetics, Harvard Medical School, Engineering, University of Oklahoma, Norman, OK, USA. Boston, MA, USA. §§Xia Jiang Assistant Professor of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA. Supplement Aims and Scope C a n c e r I n f o r m a t i c s r e p r e s e nt s a h y b r i d d i s c i p l i n e e n c o m p a s s i n g §§ Gene Set Enrichment Analysis the fields of oncology, computer science, bioinformatics, sta- §§ Hybrid Computing tistics, computational biology, genomics, proteomics, metabo- §§ Efficient Cloud Storage and Retrieval lomics, pharmacology, and quantitative epidemiology. The §§ Matching of Expression Patterns common bond or challenge that unifies the various disciplines §§ Multi-Modal Analysis is the need to bring order to the massive amounts of data gen- §§ Splice Variations and Chip Seq System Algorithms erated by researchers and clinicians attempting to find the §§ Rapid High-Throughput Analysis underlying causes and effective means of treating cancer. -
Developing PRISMA-RR, a Reporting Guideline for Rapid Reviews of Primary Studies (Protocol)
Developing PRISMA-RR, a reporting guideline for rapid reviews of primary studies (Protocol) Adrienne Stevens1,2, Chantelle Garritty1,2, Mona Hersi1, David Moher1,3,4 1Ottawa Methods Centre, Clinical Epidemiology Program, Ottawa Hospital Research Institute, Canada; 2TRIBE Graduate Program, University of Split School of Medicine, Croatia; 3Centre for Journalology, Clinical Epidemiology Program, Ottawa Hospital Research Institute, Canada; 4School of Epidemiology and Public Health, University of Ottawa, Canada; Funding: The development of PRISMA-RR is supported by a grant from the Canadian Institutes of Health Research (CIHR FRN-142310). The funder had no role in the development of this protocol and will not have a role in the data collection, analyses, interpretation of the data, and publication of the findings. Funding will be sought to develop the Explanation and Elaboration manuscript. Developing PRISMA-RR, a reporting guideline for rapid reviews of primary studies February 2018 INTRODUCTION Systematic reviews are known to be the best evidence upon which to make healthcare decisions, but can take years to complete (1). Rapid reviews have emerged as accelerated and/or abbreviated versions of systematic reviews with certain concessions made in the systematic review process to accommodate decision-making situations that require an expedited compilation of the evidence (2). Rapid reviews are usually conducted for a specific requestor and are typically understood to take 6 months or less to complete. Rapid reviews may differ from systematic reviews in a number of ways, such as the number of abbreviated methods or shortcuts employed and the breadth or scope of the question(s) posed (2–4). Some rapid reviews involve accelerated data mining processes and targeted screening of studies. -
Bioinformatics and Biology Insights Structural and Functional Insights
Bioinformatics and Biology Insights OPEN ACCESS Full open access to this and thousands of other papers at REVIEW http://www.la-press.com. Structural and Functional Insights on the Myosin Superfamily Divya P. Syamaladevi1,2, James A. Spudich1,3,* and R. Sowdhamini1,* 1National Centre for Biological Sciences (NCBS-TIFR), GKVK Campus, Bellary Road, Bangalore, India. 2Sugarcane Breeding Institute (SBI-ICAR), Coimbatore, Tamilnadu, India. 3Department of Biochemistry, Stanford University, Stanford, California. *Corresponding authors email: [email protected]; [email protected] Abstract: The myosin superfamily is a versatile group of molecular motors involved in the transport of specific biomolecules, vesicles and organelles in eukaryotic cells. The processivity of myosins along an actin filament and transport of intracellular ‘cargo’ are achieved by generating physical force from chemical energy of ATP followed by appropriate conformational changes. The typical myosin has a head domain, which harbors an ATP binding site, an actin binding site, and a light-chain bound ‘lever arm’, followed often by a coiled coil domain and a cargo binding domain. Evolution of myosins started at the point of evolution of eukaryotes, S. cerevisiae being the simplest one known to contain these molecular motors. The coiled coil domain of the myosin classes II, V and VI in whole genomes of several model organisms display differences in the length and the strength of interactions at the coiled coil interface. Myosin II sequences have long-length coiled coil regions that are predicted to have a highly stable dimeric interface. These are interrupted, how- ever, by regions that are predicted to be unstable, indicating possibilities of alternate conformations, associations to make thick fila- ments, and interactions with other molecules. -
The Evolution of the Science Citation Index Search Engine to the Web of Science, Scientometric Evaluation and Historiography
The Evolution of the Science Citation Index Search Engine to the Web of Science, Scientometric Evaluation and Historiography Eugene Garfield Chairman Emeritus, Thomson ISI 3501 Market Street, Philadelphia PA 19104 Fax: 215-387-1266 Tel. 215-243-2205 [email protected] www.eugenegarfield.org Presented at the University of Barcelona January 24, 2007 _________________________________ The Science Citation Index was proposed over fifty years ago to facilitate the dissemination and retrieval of scientific literature. Its unique search engine based on citation searching was not widely adopted until it was made available online in 1972. Its by product Journal Citation Reports became available in 1975 including its rankings by impact factor. Impact factors were not widely adopted until about a decade ago when they began to be used as surrogates for expected citation frequencies for recently published papers--a highly controversial application of scientometrics in evaluating scientists and institutions. The inventor of the SCI and its companion Social Sciences Citation Index will review its history and discuss their more recent use in graphically visualizing micro-histories of scholarly topics. Using the patented HistCite software for algorithmic historiographic analysis, the genealogy of the Watson-Crick discovery of the double helix structure of DNA and its relationship to the work of Heidelberger, Avery, and others will be discussed. ____________________________________ It is now over fifty years since the idea of the Science Citation Index (SCI) was first promulgated in Science magazine in 1955.i However, as the older generation of scientists will remember Current Contents is the information service that proved to be the primordial revolutionary “idea” which made the practical realization of the SCI possible. -
Where to Publish?
Where (Not) to Publish? B. Mohan Kumar Outline • What factors decide choice of journals • Journal impact factors • Predatory journals WHERE TO REPORT Choosing a journal -- international or local International journals: More prestigious (than local ones); Wider readerships Higher standards and rejection rates; Publishing in international journals requires more efforts, but is more rewarding in the long run. How do you choose a journal for publishing the paper? • Whoever will accept my article • Has friends on the editorial board • Has good artwork • Has (does not have) ads • Has fast turnaround time • Highest Journal Impact Factor • Impact factors are used to rank and, therefore, identify the so-called best journal to publish one’s work. • Journal most relevant to my field • Journal likely to be read by colleagues • Journal with reputation for timely, helpful review • Journal affiliated with professional society • Other factors : Intuitively - prestige? Past experience • Ask a librarian or respected colleague Journal Impact Factor: the central dogma of scholarly publishing Journal Impact Factor: Historical Aspects • Eugene Garfield, the founder of the Institute for Scientific Information (ISI, now the Thomson Scientific) in 1955 envisioned creating a metric to evaluate journal performance. • Over the next 20 years, Garfield and the late Irving H. Sher, worked to refine the Journal Impact Factor concept. • Science Citation Index in the 1960s, subsequently published in 1975 the Journal Citation Reports (JCR). • Calculated each year for those journals which Thomson Reuters indexes and are published in JCR. • A highly influential ranking tool used by participants in all phases of the research publishing cycle — librarians, publishers, editors, authors and information analysts. -
The Journal Impact Factor Is Under Attack – Use the CAPCI Factor Instead Eleftherios P
Diamandis BMC Medicine (2017) 15:9 DOI 10.1186/s12916-016-0773-5 EDITORIAL Open Access The Journal Impact Factor is under attack – use the CAPCI factor instead Eleftherios P. Diamandis1,2 Abstract The uses and misuses of the Journal Impact Factor (JIF) have been thoroughly discussed in the literature. A few years ago, I predicted that JIF would soon be replaced, while another colleague argued the opposite. Over the past few months, attacks on JIF have intensified, with some publishing organizations gradually removing the indicator from their journals’ websites. Here, I argue that most, if not all of the misuses of JIF are related to its name. The word “impact” should be removed, since it implies an influential attribute, either for the journals, their published papers, or their authors. I propose instead the use of a new name, the “CAPCI factor”, standing for Citation Average Per Citable Item, which accurately describes what is represented by this measure. Keywords: Journal impact factor, CAPCI factor, Scientific impact, Journal quality Editorial for a metric that could separate, with a glimpse of eye, More than 50 years ago, information scientist Eugene published gold from published mediocrity. But, is the JIF Garfield and colleagues described a simple publication really telling you this? indicator, known as the Journal Impact Factor (JIF) [1]. Now, please allow me to divert, to make an analogy The JIF indicates the average number of citations which has many similarities with the issue at hand. received by papers published in a specific journal over a Many know that my favorite sport is tennis. -
FMCH Departmental Policy on Funding Open Access Journal Publication Fees
Feb 8, 2016 FMCH Departmental Policy on Funding Open Access Journal Publication Fees The department is interested in supporting wide dissemination of scholarship by faculty, residents, and medical students. Increasingly, many journals, known as Open Access Journals, are aggressively soliciting manuscripts. These journals are available online to the reader. Open Access (OA) Journals charge processing fees to the submitting author that can range from $500-$5000. As of October 2015, the number of open access journals exceeded 10,000. There are several varieties of open access journals, including full open access journals with all content open access and hybrid open access journals where only some of the content is open access. Many open access journals lack a rigorous peer review process, diminishing the overall quality of publishing. Many open access journals also lack the reputation of their subscription counterparts. Other problems with these journals include: Notifying academics of article fees only after papers are accepted. Aggressively campaigning for academics to submit articles or serve on editorial boards. Listing academics as members of editorial boards without their permission. Appointing fake academics to editorial boards. Fake or non-existent impact factors. Recently however, there is an emerging group of higher quality professional open access publishers such as PLOS and BioMedCentral so there may be times when publication in this type of journal is warranted. For information on specific journals, you can check: “Think, Check, Submit” at: http://thinkchecksubmit.org/. While the Department will make available limited funds to support publications within these journals, given the poor quality of many of these journals (and their predatory publishing practices), the following guidelines have been established: The journal must have a peer-review process for all manuscripts submitted.