From Google’s English: “The beta version of the oa.atlas shows strategies and services related to Open Access at German universities and research institutions….”
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Category Archives: oa.tools
Project TARA | DORA
“Project TARA is supported by a generous three-year grant from Arcadia, a charitable fund of Lisbet Rausing and Peter Baldwin. It will help DORA identify, understand, and make visible the criteria and standards universities use to make hiring, promotion, and tenure decisions. This information will be used to create resources and practical guidance on research assessment reform for academic and scholarly institutions.”
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 (https://greenelab.github.io/word-lapse/). 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.
Economic analysis of antenatal screening for human T-cell lymphotropic virus type 1 in Brazil: an open access cost-utility model – The Lancet Global Health
“HTLV-1 antenatal screening is cost-effective in Brazil. An open-access model was developed, and this tool could be used to assess the cost-effectiveness of such policy globally, favouring the implementation of interventions to prevent HTLV-1 mother-to-child transmission worldwide….”
A high-quality cloned journal has duped hundreds of scholars, and has no reason to stop – Retraction Watch
“Have you heard about hijacked journals, which take over legitimate publications’ titles, ISSNs, and other metadata without their permission? We recently launched the Retraction Watch Hijacked Journal Checker, and will be publishing regular posts like this one to tell the stories of some of those cases….”
Bioinformatics, data and the value of open science
“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….”
OpCitance: Citation contexts identified from the PubMed Central open access articles | Scientific Data
Abstract: OpCitance contains all the sentences from 2 million PubMed Central open-access (PMCOA) articles, with 137 million inline citations annotated (i.e., the “citation contexts”). Parsing out the references and citation contexts from the PMCOA XML files was non-trivial due to the diversity of referencing style. Only 0.5% citation contexts remain unidentified due to technical or human issues, e.g., references unmentioned by the authors in the text or improper XML nesting, which is more common among older articles (pre-2000). PubMed IDs (PMIDs) linked to inline citations in the XML files compared to citations harvested using the NCBI E-Utilities differed for 70.96% of the articles. Using an in-house citation matcher, called Patci, 6.84% of the referenced PMIDs were supplemented and corrected. OpCitance includes fewer total number of articles than the Semantic Scholar Open Research Corpus, but OpCitance has 160 thousand unique articles, a higher inline citation identification rate, and a more accurate reference mapping to PMIDs. We hope that OpCitance will facilitate citation context studies in particular and benefit text-mining research more broadly.
New study shows OpenAlex is a good alternative to Scopus for demographic research – OurResearch blog
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Highlights
New research from the Max Planck Institute for Demographic Research analyzes global migration of scholars, using bibliometric data. They do a side-by-side comparison of this analysis between Scopus and OpenAlex data.
Counts of scholars by country are highly correlated between Scopus and OpenAlex.
Migration events are less correlated between the two, but trends in migration between top pairs of countries are consistent between them. There is higher correlation with Western countries, and OpenAlex has more coverage of non-Western countries.
OpenAlex is open. Scopus is not. This puts limits on how researchers can perform and share this type of analysis….”
DOAJ@20
Registration form for an event to celebrate the 20th birthday of the DOAJ.
DOAJ at 20 – DOAJ
“We are celebrating 20 years of being an important part of open infrastructure with a year-long campaign throughout 2023, and we want to invite you to be a part of our celebrations!
We are holding three events for our community around the themes: ‘Open’, ‘Global’, and ‘Trusted’. Details about these events and how you can join them will be available on this page. We will also share interviews with key individuals who have shaped DOAJ into what it is today.
Further down the page is a historical timeline to give you a full overview of DOAJ’s important milestones from 2003 to today….”
DeSci for Web3 Builders – The SCI’s Newsletter
“As various stakeholders recognize the importance of open science and as DeSci emerges as the leading movement to implement open science principles, it is reasonable to assume that DeSci’s success will contribute significantly to the validation of the entire web3 ecosystem….
DeSci tools are inclusive by nature, locking open participation to individuals from all backgrounds, socio-economic status, and geographies. Combining the open nature of DLT with science, DeSci promotes the development of cross-border standards and best practices for applying web3 technologies to scientific research….”
Experimental Publishing Compendium | Community-Led Open Publication Infrastructures for Monographs (COPIM)
The Experimental Publishing Compendium is a guide and reference for scholars, publishers, developers, librarians, and designers who want to challenge, push and redefine the shape, form and rationale of scholarly books. The compendium brings together tools, practices, and books to promote the publication of experimental scholarly works. Read more
Beta 1.0 (2023)
Version 1.0 has been curated by Janneke Adema, Julien McHardy, and Simon Bowie. Future versions will be overseen, curated, and maintained by an Editorial Board (members TBC).
Back-end coding by Simon Bowie, front-end coding by Joel Galvez, design by Joel Galvez & Martina Vanini.
Special thanks to Gary Hall, Rebekka Kiesewetter, Marcell Mars, Toby Steiner, and Samuel Moore, and everyone who has provided feedback on our research or shared suggestions of examples to feature, including the participants of COPIM’s experimental publishing workshop, and Nicolás Arata, Dominique Babini, Maria Fernanda Pampin, Sebastian Nordhoff, Abel Packer, and Armanda Ramalho, and Agatha Morka.
Our appreciation also goes out to the Next Generation Library Publishing Project for sharing an early catalogue-in-progress version of SComCat with us, which formed one of the inspirations behind the Compendium.
The compendium grew out of the following two reports:
Adema, J., Bowie, S., Mars, M., and T. Steiner (2022) Books Contain Multitudes: Exploring Experimental Publishing (2022 update). Community-Led Open Publication Infrastructures for Monographs (COPIM). doi: 10.21428/785a6451.1792b84f & 10.5281/zenodo.6545475.
Adema, J., Moore, S., and T. Steiner (2021) Promoting and Nurturing Interactions with Open Access Books: Strategies for Publishers and Authors. Community-Led Open Publication Infrastructures for Monographs (COPIM). doi: 10.21428/785a6451.2d6f4263 and 10.5281/zenodo.5572413
COPIM and the Experimental Publishing Compendium are supported by the Research England Development (RED) Fund and by Arcadia, a charitable fund of Lisbet Rausing and Peter Baldwin.
Omeka – Omeka is Celebrating Its 15th Anniversary and We have New Offerings for You
“When we released Omeka Classic fifteen years ago, I don’t know that any of us really thought we would still be working hard to provide open source web publishing platforms for stewards of cultural heritage and their communities. But, thankfully, here we are!
As the Omeka Team celebrates its fifteenth birthday, the project is sustainable and continues to provide software alternatives that serve the needs of our users as they endeavour to reach, engage, and collaborate with their communities. In part, this longevity can be attributed to the intelligence and dedication of the more than two dozen designers, developers, and digital humanists who have worked with Omeka over the years. In part, it can be attributed to our early decision to meet our users where they are. This commitment led to the launch of the Omeka.net hosted platform in 2010 to serve the needs of users who for a variety of reasons were unable or disinclined to host their own Omeka Classic sites. Then, in 2017, we launched Omeka S to serve the needs of institutional users and those who had an interest in working with more sophisticated approaches to digital pubishing such as using linked open data and embracing emerging standards such as the International Image Interoperability Framework.
In celebration of this milestone fifteenth year, the Omeka Team is launching a series of service offerings that demonstrate our commitment to continue meeting the needs of our wide range of users….”
Why open-source generative AI models are an ethical way forward for science
“From my perspective as a political and data scientist who is using and teaching about such models, scholars should be wary. The most widely touted LLMs are proprietary and closed: run by companies that do not disclose their underlying model for independent inspection or verification, so researchers and the public don’t know on which documents the model has been trained.
The rush to involve such artificial-intelligence (AI) models in research is a problem. Their use threatens hard-won progress on research ethics and the reproducibility of results.
Instead, researchers need to collaborate to develop open-source LLMs that are transparent and not dependent on a corporation’s favours.
It’s true that proprietary models are convenient and can be used out of the box. But it is imperative to invest in open-source LLMs, both by helping to build them and by using them for research. I’m optimistic that they will be adopted widely, just as open-source statistical software has been. Proprietary statistical programs were popular initially, but now most of my methodology community uses open-source platforms such as R or Python….”
Why open-source generative AI models are an ethical way forward for science
“From my perspective as a political and data scientist who is using and teaching about such models, scholars should be wary. The most widely touted LLMs are proprietary and closed: run by companies that do not disclose their underlying model for independent inspection or verification, so researchers and the public don’t know on which documents the model has been trained.
The rush to involve such artificial-intelligence (AI) models in research is a problem. Their use threatens hard-won progress on research ethics and the reproducibility of results.
Instead, researchers need to collaborate to develop open-source LLMs that are transparent and not dependent on a corporation’s favours.
It’s true that proprietary models are convenient and can be used out of the box. But it is imperative to invest in open-source LLMs, both by helping to build them and by using them for research. I’m optimistic that they will be adopted widely, just as open-source statistical software has been. Proprietary statistical programs were popular initially, but now most of my methodology community uses open-source platforms such as R or Python….”