The community blog for all things Open Research.

Esha Datta

Traditionally, journal subject classification was done manually at varying levels of granularity, depending on the use case for the institution. Subject classification is done to help collate resources by subject enabling the user to discover publications based on different levels of subject specificity.

Attempts at automating journal subject classification

PIDs in scholarly communications and research infrastructure have garnered government attention lately. By aligning with frameworks such as FAIR and POSI and incorporating insights from global initiatives, we present some desirable characteristics of PID infrastructures to guide them.

University of California Office of the President

John Chodacki

Todd Carpenter

Considerations in the context of open scholarship and open infrastructure

Persistent identifiers (PIDs) in scholarly communications and research infrastructure have garnered growing attention over the last several years, especially from governments who are recognizing the vital role PIDs play in creating a more efficient and trustworthy research ecosystem.

Desirable Characteristics of Persistent Identifiers

Metadata Game Changers

Ted Habermann

Jamaica Jones

Howard Ratner

Tara Packer

Argo float data and metadata from Global Data Assembly Centre (Argo GDAC)

Publications

WhatCameFirst: The Paper Or the Data

INFORMATE: Where Are the Data?

Journal Production Guidance for Software and Data Citations

In a recent Upstream blog post we explored where data connected to papers funded by several U.S. Federal Agencies are published. Different data sharing practices across these agencies led to very different distributions of datasets across various repositories. We used CHORUS reports that combine linked article and dataset metadata as input for that work.

INFORMATE: When Are the Data?

By embracing DataCite and Crossref DOIs, the global scholarly community is empowered, reducing financial barriers and fostering broad creation, dissemination, and recognition of research outputs and resources.

Ginny Hendricks

Matt Buys

Persistent Identifiers, or “PIDs”, have become a popular topic for anyone involved in the research communications world. PIDs play a crucial role in the scholarly ecosystem by providing long-lasting references to and between all kinds of digital resources. PIDs usually consist of a unique identifier and a service that resolves resource references over time.

Working for Global Equity through Digital Object Identifiers

Amalia Raquel Pérez-Nebra

Coming from the Global South, I have frequently experienced the cucaracha (cockroach) syndrome, where I feel like what I do is not interesting. This is the phrase that I give to the feeling of my research and perspective being routinely undervalued and underappreciated due to my local context and language abilities.

Experiences of scholarly marginalization

How comprehensive are bibliographic databases when it comes to preprints? Ludo Waltman and Nees Jan van Eck provide six recommendations for improvement.

Leiden University

Ludo Waltman

Nees Jan van Eck

Scholarly publishing is going through an exciting transition. Researchers are increasingly publishing their work on preprint servers before submitting it to journals. Some researchers have even decided not to submit to journals at all. On top of this, new forms of peer review are emerging, organized around preprints and operating independently from traditional journal peer review.

The preprint revolution - Implications for bibliographic databases

Saikiran Chandha

Sucheth R

Tirthankar Ghosal

Since its release towards the end of 2022, ChatGPT has been dominating the majority of AI-related conversations on social media. One could almost say it has made AI more mainstream and accessible than ever. AI is quickly revolutionizing the modern-day research landscape. According to a CSIRO report, nearly 98% of scientific fields use AI in some way.

Setting the Scene: How Artificial Intelligence is reshaping how we consume and deliver research

Ashley Farley

Since 2015 I’ve been steeped in the world of open access, academic publishing, and funder policies. This is a blip of time compared to many other experts and advocates in this space. I’ve often sardonically joked that if I had received a dollar for every time I’ve heard that open access will become the norm once the United States changes its policy I could retire early.

Hot memo summer: How OSTP’s recommendations will lead to a large-scale transformation of the research ecosystem

Bianca Kramer

Bianca Kramer has been scholarly communication/open science librarian at Utrecht University Library for 15 years, and recently moved to an independent consulting/research analyst role as Sesame Open Science, with a focus on open science, open metadata and open infrastructure.

Being encouraged to keep “open tabs”, has been an interesting experience - turning something that’s usually guilt-inducing (“I really should be reading this…!”)

Bianca Kramer is Keeping Tabs on Open Research

Alexis-Michel Mugabushaka

Worldwide, governments have started to ease or end the Covid-19 restrictions, signaling the beginning of the end of a pandemic which, according to the WHO, infected over 400 million people and caused 5.8 million deaths, not to speak of the devastating disruptions it caused to public and economic life.

Funding Covid-19 research: Insights from an open data infrastructure

Christine Ferguson

Front Matter

Martin Fenner

Today we are announcing

 Upstream

. And if you’re reading this, you’re already a part of it! Upstream is a community blogging platform designed for Open enthusiasts to discuss… you guessed it: all things Open. It’s a space for the whole community to voice opinions, discuss open approaches to scholarly communication, and showcase research.

Welcome to Upstream: the new space for scholarly community discussion on all things open

Adam Hyde

Paul Shannon

Although advances in artificial intelligence (AI)

 1

have been unfolding for over decades, the progress in the last six months has come faster than anyone expected. The public release of ChatGPT in November 2022, in particular, has opened up new possibilities and heightened awareness of AI's potential role in various aspects of our work and life.

An Initial Scholarly AI Taxonomy

Cameron Neylon

Academic Observatory Workflows

Comparison of language identification models

COKI Language Dataset

COKI Language Detection

Data Processing and production: Jamie Diprose


 Cross-posted from the COKI blog.

There is a lot of lip service paid to the idea of diversity in scholarly publishing and often diversity of language is used as an example.

Language Diversity in Scholarly Publishing

Carolina Tanigushi

DataCite

Gabi Mejias

Infrastructure: what’s at stake {#infrastructure-what%E2%80%99s-at-stake}   Infrastructure often is perceived as a “given”, as something that was always there, as “natural”. In the digital age, infrastructure seems more “natural” than ever (it's hard to imagine there was a time without internet connectivity in our mobile phones or even a time when phone lines were a luxury item) and the social and economic dimension of infrastructure tend to be

Scholarly Infrastructure: a Latin American perspective

Jennifer Gibson

This post is the last in a four-part series by Jennifer Gibson. The first post, on the shape and impact of research communication is available here. Reactions from readers are very welcome. Please use the commenting function.

A modern take on research communication, Part IV: Commitment and call to action

Scholarly publishing at times seems to want to hold on to some outdated processes. At the top of my list is the dreaded RFP (Request for Proposals) process. In the scholarly comms world, consultants send these out on behalf of publishers that are seeking solutions or services. My career involves designing and building publishing technology and so I have been on the receiving end of many RFPs for developing new platforms.

Can we do away with RFPs?

Iratxe Puebla

Researchers spend a lot of time doing peer review, and by a lot we are talking about over 100 million hours per year (estimate for 2020 by Aczel et al.). It is a complex and time consuming process that is often presented as a pillar to science dissemination, because of its function to scrutinize research papers to check whether they contain any flaws, oversights, or they meet certain criteria for novelty or advance, before the article appears in

Let's make our reviews open, starting now

University of Illinois Urbana-Champaign

Daniel S. Katz

Michelle Barker

Track 1 Paper: Surveying the U.S. National Postdoctoral Association Regarding Software Use and Training in Research

Defining the roles of research software

Amsterdam Declaration on Funding Research Software Sustainability

Report on Vive la différence - research software engineers

The Research Software Community Landscape in the Global South

Evidence for the importance of research software

Final release: COVID-19 guidelines

FAIR Principles for Research Software (FAIR4RS Principles)

FAIR4RS Roadmap Report

The Research Software Alliance (ReSA) and the community landscape

Research software is a key part of most research today.

The Research Software Alliance (ReSA)

Jeff Pooley

The New York Times

ushered in the New Year with a lawsuit against OpenAI and Microsoft. The paper covered the suit, fittingly, as a major business story.

Large Language Publishing

Adopters of the POSI principles have met several times over the last few years to discuss the challenges and the improvements they’ve made in the transparency and longevity of their operations and governance. Hear from those involved in introducing the latest version - v1.1.

The Upstream platform was created in order to discuss all things open. Open scholarly infrastructure and the need for the community to assess such infrastructures are surely at the heart of enabling the open research movement.

Principles of Open Scholarly Infrastructure (POSI) version 1.1: Reflections from adopters

Dylan Roskams-Edris

I help Canadian neuroscience research institutes create and adopt an institute-level approach to open science. Inevitably, I end up talking to researchers, administrators, academic commercialization offices, and businesses about open science, intellectual property (IP), and technology transfer.

Opening New Paths to Technology Transfer: Open Science, Intellectual Property, and Technology Transfer

Stephan Druskat

Kristi Holmes

Jose Benito Gonzalez Lopez

Lars Holm Nielsen

Stefano Iacus

Adam Shepherd

Danie Kinkade

Gustavo Durand

Research data and software rely heavily on the technical and social infrastructure to disseminate, cultivate, and coordinate projects, priorities, and activities. The groups that have stepped forward to support these activities are often segmented by aspects of their identity - facets like discipline, for-profit versus academic orientation, and others.

Interoperable infrastructure for software and data publishing

Rob van Nieuwpoort

In November of 2022, the Research Software Alliance (ReSA) and the Netherlands eScience Center organized a two-day international workshop titled “The Future of Research Software.” In the workshop, funding organizations joined forces to explore how they could effectively contribute to making research software sustainable. The workshop had many participants from all continents and was a huge success.

Digital object identifiers (DOIs) and relevant metadata have been used for 20 years to help preserve the scholarly record by maintaining stable links to scholarly publications and other important scholarly resources, combined with long-term archiving by publishers and libraries. Lots and tools and services have been built around this infrastructure to make it easier for scholars to consume and contribute to this scholarly record.

The Rogue Scholar: An Archive for Scholarly blogs

Jeroen Sondervan

Jeroen Bosman

Researchers, librarians, policy makers, and practitioners often complain about the scholarly publishing system, but the system also offers exciting opportunities to contribute to innovations in the way academic findings are disseminated and evaluated.

Preprints and open preprint review: a workshop on innovations in scholarly publishing

A journey started with the INArxiv hosted by The Center of Open Science to RINarxiv hosted by BRIN Indonesia.

Dasapta Erwin Irawan

Preprint as a Way to Universal Open Access

Cathleen Berger

Chris Hartgerink

In 2021 the UNESCO agreed on their Recommendation on Open Science, a consensus document of 193 countries highlighting values such as equity in open research, alongside principles of sustainability. Improving sustainability is critical from a social, economic, and ecological perspective given the global climate crisis.

The Environmental Impact of Research Infrastructures: Publishers, Open Science, and the Climate Crisis

Monica Gonzalez-Marquez

Anouschka Foltz

Jeffrey K. Bye

Ali Fulsher

Take a look at the picture below. What do you see? Think for a moment and write down your observations or say them out loud. Did you see tracks in the snow and the shadow of trees in the background? Maybe you were more specific, noting there are different kinds of tracks going in different directions, and at least two trees casting shadows.

Science Reading: Cognitive narrative helps us understand science better

Inspired by a conversation on Twitter, Upstream is publishing a new blog series. Each month (ish) one person will post their reading wishlists based on the browser tabs they have open. We'll learn the articles they're most keen to read - and why.

Cameron Neylon is Keeping Tabs on Open Research

What if we could start all over again? Knowing what we know now, about the needs for research and the opportunities to improve the human condition, about the power of the Internet, and about the importance of the global village, what would we want publishing to look like? How would we use instant online sharing? How would we tap into experts in other corners of the globe?

A modern take on research communication, Part I

This post is the third in a four-part series by Jennifer Gibson. The first post, on the shape and impact of research communication is available here. Reactions from readers are very welcome. Please use the commenting function. Before I dive into this part of the discussion, I’d like to credit Damian Pattinson and Stuart King at eLife, with whom I worked to develop the three first tenets below in 2020 and 2021, as eLife's core values.

A modern take on research communication, Part III: Tenets of a modern system

This post is second in a four-part series on a modern system for research communication, by Jennifer Gibson. The first post, on the shape and impact of research communication is available here. Reactions from readers are very welcome. Please use the commenting function. ________________  Now, as I wrote a moment ago, I have some strong ideas about how research communication should work, which you might guess based on my work to date.

A modern take on research communication, Part II: Changing perspectives

Gimena del Rio

Gimena del Rio Riande is Associate Researcher at the Instituto de Investigaciones Bibliográficas y Crítica Textual (IIBICRIT-CONICET, Argentina) (https://orcid.org/0000-0002-8997-5415). Her main academic interests deal with digital humanities, digital scholarly edition and publishing, and Open Research Practices in the Humanities.

Gimena del Rio Riande is Keeping Tabs on Open Research

Uttkarsha Bhosale

Gayatri Phadke

Anupama Kapadia

As we witness the ever-evolving landscape of technology, we realize that artificial intelligence (AI) is not just a buzzword anymore; it's a reality that is already leading to transformation in how scholarly research is published and disseminated.

Need for Consistent and Uniform Guidelines Regarding the Use and Disclosure of AI-generated Scholarly Content

Guiding principles for implementing persistent identification and metadata features on research tools to boost interoperability of research data and support sample management workflows

Introduction   A recent blog post described a new partnership between Metadata Game Changers and CHORUS aimed at understanding how CHORUS data can help federal agencies, other funders, and other users access and use information from the global research infrastructure to measure this infrastructure and understand connections between research objects.

In order to deliver on the 2030 Agenda and its 17 Sustainable Development Goals (SDGs), all sectors must urgently intensify fair and equitable transformations to sustainability. Scientific publishing must reform if it is to play its part.

Moumita Koley

Megha Sud

Opening the record of science: making scholarly publishing work for science in the digital era

Business Models and Market Structure within the Scholarly Communications Sector

The normalization of preprints

The International Science Council is a non-government organization that brings together 45 international scientific Unions and Associations, over 140 national and regional scientific organizations, including Academies and Research Councils, 60 international Federations and Societies, and Young Academies and Associations.


 The ISC is charting a path toward the mission to advance human development within sustainable planetary and

The Imperative of Reforming Scientific Publishing

We analyse samples of DataCite metadata from ten repositories that have already created &gt;100k project IDs. The FAIR Island Project will provide working examples that demonstrate how DataCite and other existing infrastructure are being used and can be leveraged to support project-level metadata.

Erin Robinson

Project identifiers have been used in DataCite for nearly a decade. While this adoption has been inconsistent, the consistent adoption of Project IDs could aid with the tracking of provenance of data and other project assets, ensuring transparency and compliance with data management practices.

Building a Community of Practice: Observations of the Current Use of DataCite DOIs as Project IDs

Andrea Chiarelli

The exponential surge in research data, coupled with the advent of cutting-edge computational tools, is ushering in an era of unprecedented opportunities for research performing organisations. However, with many still in the process of adopting basic research data management practices and support mechanisms, the current state of play is concerning.

Navigating data-intensive innovation: The transition from research data management to research data governance

Recognizing the need for dialogue on best practices around ethical challenges in data publication, the FORCE11 Research Data Publication Ethics Working Group started in early 2021 as a multi-stakeholder community effort involving representatives of data repositories, journals, researchers, institutional research integrity officers and libraries.

Announcing new resources from the FORCE11-COPE Research Data Publishing Ethics Working Group: flowcharts!

Bruce Caron guides us through their  open browser tabs. What are some of the must-reads at the moment?

Bruce Caron

Like the rest of you, I’ve been deluged with opinions and advice about recent advances in AI. So, I hopped into the AI mosh-pit. Last fall, I grabbed an account on DALL-E and spun up intricate artwork in my spare time. I jumped on Chat GPT 3.5 when it arrived, and this week, on GPT-4.  I have an open tab that takes me to my account with Openai.

Bruce Caron is Keeping Tabs on AI

Ginny Barbour

If anyone thought that 2022 was going to be a time of peace and harmony in open access, some of the last salvos of 2021 will surely have put that to rest.

Words matter

Gisela Govaart

Simon M. Hofmannn

The climate crisis is affecting us all, and it seems like there is a role for open research to play.

The sustainability argument for open science? In conversation with the authors.

Joanna Ball

Lars Bjørnshauge is the visionary founder of the Directory of Open Access Journals (DOAJ). His transformation of a simple idea into a globally trusted directory revolutionized the accessibility and credibility of open access publishing. Under his leadership, DOAJ became a critical resource, supporting the dissemination of scholarly work worldwide and setting high standards for transparency in publishing.

Open Publishing Fest Lifetime Achievement Award: Interview with Lars Bjørnshauge

Aaron Tay

Several weeks ago, Cameron Neylon kicked off a good idea to list a few articles he was keen to read and tell us why.


 Based on 'open tabs' in their browser, approximately every month one person will share their reading wishlists so we can curate some of the 'must-read' posts of the moment.


 Each author concludes by tagging the next;

Aaron Tay is Keeping Tabs on Open Research

Explore limitations, concerns, and proposed solutions in this thought-provoking piece based on a global survey. Join the discussion with Enago Academy on sustainable and equitable access to knowledge.

Riya Thomas

The open access (OA) movement has undoubtedly revolutionized the accessibility of scholarly research, aiming to make knowledge freely available to all. While many countries have embraced OA publishing with supportive policies, a persistent obstacle remains—article processing charges (APCs). These charges/fees have led to a debate within the academic community, questioning whether they align with the best interests of open science.

A Fairer Future for Open Science: Choosing community over commercialization with equitable article processing charges

Mohammad Hosseini

Violeta Ilik

Nicole Vasilevsky

The FORCE11 attribution working group held a workshop during the 2021 FORCE conference to explore some ethical aspects of using Contributor Roles (CRs). This workshop provided an overview of various CRs and their practical values in terms of providing a better recognition of the wide range of scholarly contributions.

Deep dive into ethics of Contributor Roles: report of a FORCE11 workshop

Fiona Hutton

In October, the journal eLife announced that it will change how it handles peer review starting January 2023:  To better understand what this change means for authors and reviewers, Upstream editor Martin Fenner asked Fiona Hutton, eLife's Head of Publishing, a few questions.

eLife Reviewed Preprints: Interview with Fiona Hutton

Patricio Pantaleo guides us through their open browser tabs. Recommends readings on Open Journal Systems, Open Access and Creative Commons licenses.

Patricio Pantaleo

Patricio Pantaleo is a freelance open science advisor and web developer in Latin America with expertise in Open Journal Systems, Open Monograph Press, and Crossref.