Category Archives: oa.biology

Paleontology journal adapts to open format with help from KU Libraries | The University of Kansas

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“Lieberman’s resume now includes something new: working with KU Libraries to evolve the distribution of knowledge and turn a prestigious subscription-based journal into a broadly accessible open access resource.

Lieberman is the editor of the Treatise on Invertebrate Paleontology, a resource of current and historical paleontology consisting of more than 50 volumes published since 1953 in an encyclopedic format. The journal accepts submissions from all over the world and is considered a foundational resource in paleontology, along with KU’s invertebrate fossil collection — one of the top-10 largest in the country with over 900,000 fossil invertebrate and microfossil specimens, which have been used in research for more than 125 years.

This spring, Lieberman worked with KU Libraries’ Marianne Reed, digital publishing and repository manager, to navigate the complexities of converting the journal to open access — scholarly literature that is digital, online and free of charge. Because the journal will be made fully available online, with reach beyond a printed book, printing the materials and the associated costs may eventually become unnecessary….”

ImmPRes

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“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

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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.

 

A Pilot Study to Locate Historic Scientific Data in a University Archive | Issues in Science and Technology Librarianship

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Abstract:  Historic data in analog (or print) format is a valuable resource that is utilized by scientists in many fields. This type of data may be found in various locations on university campuses including offices, labs, storage facilities, and archives. This study investigates whether biological data held in one institutional university archives could be identified, described, and thus made potentially useful for contemporary life scientists. Scientific data was located and approximately half of it was deemed to be of some value to current researchers and about 20% included enough information for the study to be repeated. Locating individual data sets in the collections at the University Archives at the University of Minnesota proved challenging. This preliminary work points to possible ways to move forward to make raw data in university archives collections more discoverable and likely to be reused. It raises questions that can help inform future work in this area.

 

JULAC consortia announcement – The Company of Biologists

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“The Company of Biologists is delighted to announce a new Read & Publish Open Access agreement with the Joint University Librarians Advisory Committee (JULAC) Consortium for 2023.

Corresponding authors at participating JULAC institutions in Hong Kong can publish an uncapped number of research articles immediately Open Access (OA) in our hybrid journals (Development, Journal of Cell Science and Journal of Experimental Biology) plus our fully Open Access journals (Disease Models & Mechanisms and Biology Open) without paying an article processing charge (APC). Researchers at participating institutions also benefit from unlimited access to our hybrid journals, including their full archives dating back to 1853….”

New Read & Publish Open Access agreement between The Company of Biologists and the IISER Consortium India | STM Publishing News

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“Corresponding authors at participating IISER institutions in India can publish an uncapped number of research articles immediately Open Access (OA) in our hybrid journals (Development, Journal of Cell Science and Journal of Experimental Biology) plus our fully Open Access journals (Disease Models & Mechanisms and Biology Open) without paying an article processing charge (APC). Researchers at participating institutions also benefit from unlimited access to our hybrid journals, including their full archives dating back to 1853….”

Beyond the Repository – ACM Queue

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“Open source is much more than a repository—it is a rich multilevel ecosystem of human contributors who collaboratively cooperate, in many capacities, to accomplish a shared creative endeavor. Consequently, when studying open source ecosystems, numerous interacting parts must be considered to understand the dynamics of the whole. Research on open source ecosystems is ultimately research about a sociotechnical ecosystem. Researchers should take care to retain the socio- element in research and understand how both their methods and results may impact entire open source ecosystems.

This article describes best practices for open source ecosystems research through multiple overarching best practices. It offers practical guidelines for conducting rigorous, ethical, respectful research that maintains the integrity of the open source ecosystem under consideration….”

A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences

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Abstract:  Data sharing and reuse are crucial to enhance scientific progress and maximize return of investments in science. Although attitudes are increasingly favorable, data reuse remains difficult due to lack of infrastructures, standards, and policies. The FAIR (findable, accessible, interoperable, reusable) principles aim to provide recommendations to increase data reuse. Because of the broad interpretation of the FAIR principles, maturity indicators are necessary to determine the FAIRness of a dataset. In this work, we propose a reproducible computational workflow to assess data FAIRness in the life sciences. Our implementation follows principles and guidelines recommended by the maturity indicator authoring group and integrates concepts from the literature. In addition, we propose a FAIR balloon plot to summarize and compare dataset FAIRness. We evaluated the feasibility of our method on three real use cases where researchers looked for six datasets to answer their scientific questions. We retrieved information from repositories (ArrayExpress, Gene Expression Omnibus, eNanoMapper, caNanoLab, NanoCommons and ChEMBL), a registry of repositories, and a searchable resource (Google Dataset Search) via application program interfaces (API) wherever possible. With our analysis, we found that the six datasets met the majority of the criteria defined by the maturity indicators, and we showed areas where improvements can easily be reached. We suggest that use of standard schema for metadata and the presence of specific attributes in registries of repositories could increase FAIRness of datasets.

 

Bioinformatics, data and the value of open science

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“Bioinformaticians were recently described as “hidden heroes of the Covid-19 pandemic” for the rate at which they adapted to the challenges of the crisis and came up with methods to “dramatically reduce experimental lab time and enabled the communication of key information”.

Doyle is UL’s community manager for Bioconductor, a global open-source software project that has more than 1,000 developers and is downloaded by more than 1m users every year. She works in Prof Aedín Culhane’s group and leads the Bioconductor global training programme, website redesign, community outreach and support….

Doyle is keen to emphasise the importance of open-source tools and resources in research. She mentions the Lero Open Source and Open Science Programme Office as an exciting recent initiative launched to promote and support open science. Earlier this year, Lero was awarded a European prize in recognition of its commitment to open science principles….”

[SPARC response to the NIH public access plan]

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“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

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“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]

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“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

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“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….”

Open Plant Pathology: How Much Do We (Plant Pathologists) Value Openness and Transparency?

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“We (Emerson Del Ponte and Adam Sparks) started this initiative (Open Plant Pathology) in early January 2018 with the idea that we would create a community in which plant pathologists could come together and share resources and ideas and encourage a freer exchange of information, code and data. One of the reasons for this was that a few years before that, we’d started working on analysis of randomly selected plant pathology papers, initially we looked at 300 published from 2012 until 2018, but it later grew to encompass 450 papers published from 2012 until 2021, with Kaique Alves, Zachary Foster and Nik Grünwald, which was published in Phytopathology® in January (Sparks et al. 2023b). What we were finding as we looked at papers across 21 journals that were dedicated to plant pathology research or published specialised sections or articles in the field of plant pathology was not surprising, but still disappointing. As a discipline, we simply do not make much, if any, effort to help ensure that others can easily reproduce our work after it is published (Sparks et al. 2023b).

We found that most articles were not reproducible according to our scoring system and failed to take advantage of open science and reproduciblity methods that would benefit both the authors and the readers. To wit, the vast majority of articles we looked at made no attempt to share code or data, scoring “0” in our system (Figure 1)….”

Citation pattern of open access and toll-based research articles in the field of biological and physical sciences: a comparative study | Emerald Insight

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Purpose

The purpose of this paper is to determine the relationship between the access mode of research articles [Open Access (OA) and Toll-Access (TA)] and their subsequent citation counts in Biological and Physical Sciences in three Impact factor zones (High, Medium and Low).

Design/methodology/approach

Three subjects each from Biological Sciences (Biochemistry, Cell Biology and Genetics) and Physical Sciences (Astronomy, Oceanography and Optics) were selected for the study. A comprehensive list of journals (TA and OA) in select subjects of Biological and Physical Sciences was prepared by consulting Journal Citation Report’s Master Journal List (for the compilation of both Open Access and Toll Access journal list) and Directory of Open Access Journals (for the compilation of Open Access journal list). For each journal, essential details like content language, format, year of publication, access mode (Open Access or Toll Access), etc. were obtained from Ulrich’s Periodical Directory. Web of Science (WoS) was used as citations indexing tool in this study. The data set was run on the WoS to collect the citation data.

Findings

The results of the study indicate that open mode of access is not a prerequisite for higher citation boost as in the majority of the cases in this study, TA articles have garnered a greater number of citations as compared to open access articles in different Impact factor zones in Biological and Physical Sciences.

Originality/value

A novel approach has been adopted to understand and compare the research impact of open access (OA) and toll access (TA) journal articles in the field of Biological and Physical Sciences at three Impact factor zone levels to reveal the citation metrics encompassing three parameters, i.e. citedness, average citation count and year wise distribution of citations in select subjects of Biological and Physical Sciences.