Day-to-day discovery of preprint–publication links | SpringerLink

Abstract:  Preprints promote the open and fast communication of non-peer reviewed work. Once a preprint is published in a peer-reviewed venue, the preprint server updates its web page: a prominent hyperlink leading to the newly published work is added. Linking preprints to publications is of utmost importance as it provides readers with the latest version of a now certified work. Yet leading preprint servers fail to identify all existing preprint–publication links. This limitation calls for a more thorough approach to this critical information retrieval task: overlooking published evidence translates into partial and even inaccurate systematic reviews on health-related issues, for instance. We designed an algorithm leveraging the Crossref public and free source of bibliographic metadata to comb the literature for preprint–publication links. We tested it on a reference preprint set identified and curated for a living systematic review on interventions for preventing and treating COVID-19 performed by international collaboration: the COVID-NMA initiative (covid-nma.com). The reference set comprised 343 preprints, 121 of which appeared as a publication in a peer-reviewed journal. While the preprint servers identified 39.7% of the preprint–publication links, our linker identified 90.9% of the expected links with no clues taken from the preprint servers. The accuracy of the proposed linker is 91.5% on this reference set, with 90.9% sensitivity and 91.9% specificity. This is a 16.26% increase in accuracy compared to that of preprint servers. We release this software as supplementary material to foster its integration into preprint servers’ workflows and enhance a daily preprint–publication chase that is useful to all readers, including systematic reviewers. This preprint–publication linker currently provides day-to-day updates to the biomedical experts of the COVID-NMA initiative.

 

[2104.05891] Science-Software Linkage: The Challenges of Traceability between Scientific Knowledge and Software Artifacts

Abstract:  Although computer science papers are often accompanied by software artifacts, connecting research papers to their software artifacts and vice versa is not always trivial. First of all, there is a lack of well-accepted standards for how such links should be provided. Furthermore, the provided links, if any, often become outdated: they are affected by link rot when pre-prints are removed, when repositories are migrated, or when papers and repositories evolve independently. In this paper, we summarize the state of the practice of linking research papers and associated source code, highlighting the recent efforts towards creating and maintaining such links. We also report on the results of several empirical studies focusing on the relationship between scientific papers and associated software artifacts, and we outline challenges related to traceability and opportunities for overcoming these challenges.

 

Why researchers created a database of half a million journal editors | Nature Index

“In an attempt to capture that information, Pacher and his colleagues created Open Editors, a database containing information such as names, affiliations and editorial roles of just under half a million editors working for more than 6,000 journals run by 17 scholarly publishers.

They outline their initiative in a SocArXiv preprint paper published on 11 March.

Although Open Editors already includes editor data from publishing heavyweights such as Elsevier and Cambridge University Press, Pacher says, other major players such as Springer Nature, John Wiley & Sons, and Taylor and Francis are so far missing.

Pacher has made the data and code freely available to encourage other academics to help build the database….”

A Giant Medieval Puzzle – Library Matters

““Fragmentology” is a new approach to the visual gathering of such dispersed fragments in order to re-assemble the pieces of a codex.  A digital platform is now available to apply collective energy into fitting the pieces of the puzzle back together again, which has an enormous potential for research.  Fragmentarium is the name of a partnership of institutions gathered to develop the technologies needed to build “a common laboratory for fragments” and conduct research.  It promises to yield digital versions from the original fragments, constituted from various holdings. This process will enable provenance research, the study of the circulation of manuscripts, and generate connections among researchers and curators. Thus a leaf holding comparable visual cues may be further investigated as a originating from the same or similar source. …”

Towards open science: what we know and what we need to know

“Open science presents itself as a set of policies and actions to disseminate research results in an accessible, free and reusable and reproducible way through public digital repositories. As a movement, it uses three basic elements: open access to publications; data opening (whether raw, models, specifications, or documentation); computational process opening (software and algorithms)(1).

Although it is not a new phenomenon, the term can still cause strangeness even to experienced researchers. Open access to articles, as the first element, encountered (and still finds) great resistance to becoming unanimous, although pressure from the scientific society and funding agencies has accelerated the progress of this stage. On the other hand, data opening seems to have been better received, at least in its interface related to the deposit of scientific manuscripts in the preprint format, however this is only the beginning.

Concerning the Brazilian experience, SciELO and the Brazilian Institute of Information in Science and Technology (IBICT – Instituto Brasileiro de Informação em Ciência e Tecnologia) have been leading the opening process and for some time have designed guidelines and strategies to guide their journals towards open science: TOP (Transparency and Openness Promotion)(2). This system interestingly presents levels of openness experimentation that range from pointing out what is a certain item to making it conditional on it being expressly fulfilled for the manuscript to be published.

Although it has existed since 2017, it was only in 2020 that the alignment of Brazilian journals to TOP was indeed accelerated, and significant changes will be adopted in the journals in the coming months and years to adapt to such principles.

Having this information and basing ourselves on the fact that historically changes have been the target of resistance, especially when they happen in an ancient system, like the scientific publication system, we use our privilege to take on multiple roles (author, reviewer, and editor) among the scientific publication process in Brazilian journals to reflect and point out in this editorial four central issues related to editorial management that should be recurrent among the actors involved in the publication process in the coming years months: …”

Pilot Program Offers NYU Students and Faculty Instant Access to 150,000 Ebooks Via App

“NYU Libraries and ProQuest have launched a pilot project that will make over 150,000 scholarly titles available to students and faculty via their mobile devices. NYU users can access coursebooks, ebooks, and reference works from major publishers through an e-reader app called SimplyE….”

Collaborating with our community to increase code sharing

“Given how essential newly developed code can be to computational biology research we have been collaborating with the Editorial Board of PLOS Computational Biology and consulting with computational biology researchers to develop a new more-rigorous code policy that is intended to increase code sharing on publication of articles….”

The Open Library Foundation Names New Board President and Two New Board Members

“The Open Library Foundation, which enables the development, accessibility and sustainability of open source projects for and by libraries, is making changes to its Board. 

Tom Cramer, the Associate University Librarian and Director of Digital Library Systems and Services at Stanford University will replace David Carlson as Board President. Carlson, Dean of Libraries at Texas A&M University, will maintain his seat on the Board. The Board is also welcoming Chris Keene and Paula Sullenger. …”

Open Source is Everywhere, but So Is Fake Open Source | Hacker Noon

“Tristan Louis gives weight to new term that I like a lot: fauxpen. Faux in French means “false” or “fake”. So fauxpen means fake open. There has always been a lot of that going around, but since the world of tech inevitably contains more of everything, there’s more fauxpen stuff than ever….”