From Tools to Adoption: A Path to Modular and Interactive Scientific Publishing

Highlights of ICOR Public Meeting #9, 1 December 2025

Please see the video recording and chat record for rich details from speakers and meeting attendees.

Introduction

This ICOR meeting shared the findings from an in-person meeting called ‘From Tools to Adoption: A Path to Modular & Interactive Scientific Publishing’, hosted by openRxiv and the Continuous Science Foundation. The meeting provided dedicated time and space for invited participants to collaborate and work together on establishing a federated reference architecture using real bioRxiv content and connected authoring tools. The aim was to resolve critical technical gaps and demonstrate live interoperability, effectively laying the foundation for machine-readable research publishing.

Setting the Scene 

Tracy Teal, CEO, openRxiv [slides; streaming video 3-13 min]

Tracy began by explaining the core problem: scientific content remains trapped in static formats, severely hindering reuse, attribution, and machine readability, despite the availability of modern tools. Therefore, the meeting was strategically designed to address this challenge through practical, implementation-first development, prioritizing working software and demonstrable interoperability over abstract standardization.

Tracy also introduced the bedrock-soil-flowers metaphor that underpinned the meeting’s technical discussions.

  • The “bedrock” represents the fundamental, stable foundation: the schema or standard format that enables the linking, reuse, and interoperability of granular scientific content.
  • This content layer is supported by the “soil,” which represents the metadata and the connections it allows, nourishing the system.
  • The “flowers” are then the visible applications and services that exist in the presentation layer, built upon the nutrient-rich soil and stable bedrock.

The “Bedrock”

Rowan Cockett, Co-founder, Continuous Science Foundation:  [slides; streaming video 13-20 mins]

Rowan focused on the meeting’s work within the “bedrock,” which resulted in the creation of a new specification called the Open Exchange Architecture (OXA).

OXA is designed to represent scientific documents and their components as structured JSON objects. Its purpose is multifaceted: it enables exchange, interoperability, and long-term preservation of scientific knowledge while remaining fully compatible with modern web and data standards. Essentially, OXA is a bridge, connecting advanced, next-generation authoring systems (such as Stencila, MyST, and Quarto) with the established scientific publishing ecosystem that relies on tools like JATS.

Licensing Modular Research Outputs

Monica Granados, Director of Open Science, Creative Commons: [slides; streaming video 21-33 mins]

Monica described how a dedicated group worked on integrating licensing and attribution directly into the structure of research components. This new framework, which must support all research artifacts including traditional articles, modular elements like figures and datasets, and remixed compositions, led to the development of the “Paper Repo” concept. The Paper Repo is a core, shareable collection of claims supported by Panels of Evidence. Each Panel of Evidence, which includes text, figures, and tables, is linked to a Panel Dependency container holding all the necessary supporting assets such as code, datasets, and lab notes. This allows researchers to publish a standard PDF while ensuring all underlying dependencies are linked and accessible. 

Monica concluded by noting that Creative Commons is co-leading a working group to develop the formal recommendations for licensing each of these different levels and setting rules for remixing and reuse.

The “Soil”

Jason Priem, CEO, OpenAlex:  [streaming video 33-40 mins]

Jason provided a live demonstration of OpenAlex, using it to explain the concept of the “soil layer” within the scholarly research ecosystem. He described OpenAlex as analogous to the soil itself, which digests, organizes, and connects the hundreds of millions of existing works and the tens of thousands being created daily. 

Through OpenAlex’s dataset, Jason illustrated how the soil layer is crucial for linking research outputs together via robust metadata, graphs of relationships, citation networks, peer review, and other essential trust signals. He explained that a catalog of works linked in this way provides context, curation, and integration valuable to anyone interested in global research and scholarly communication. The soil layer also helps to moderate quality, effectively providing the “nutrients” that enrich the bedrock and enable the meaningful reuse of content.

The “Flowers”

Paul Shannon, Head of Technology and Innovation, eLife: [slides, streaming video 41-51 mins]

Paul’s presentation centered on the “Flowers” part of the metaphor, which are the applications, interfaces, and user experiences built directly atop the foundational, lower layers. These constitute the visible part of the scholarly communication ecosystem, the tools and products that educators, policymakers, and the public actually engage with, which blooms from the solid technical foundations and fertile connections beneath.

Paul went on to describe the group’s collaborative vibe-coding session, which aimed to produce working software for an exemplar flowering application, which was ‘Spotify for Science.’ This concept enabled the group to demonstrate how existing APIs and services could be composed to create a novel research browsing experience, one that elevates different trust signals and presents content in new ways. This working prototype validated the potential for significant value delivery, provided the underlying data and connection layers offer sufficient quality and structure.

Paul concluded that we are in an age where anyone can build useful, interesting applications, underscoring the need to focus on supporting and reinforcing the foundational layers on which to build from.

Summary

The goal of this ICOR meeting was to provide the wider open research community with a transparent view of the work that went on at the meeting and to enable engagement with the meeting participants as they move forward with some of their ideas.

For a full, detailed account of the meeting, please click here. Interested parties looking to find out more or wishing to contribute should reach out to the Continuous Science Foundation.

Please see the video recording for access to the full meeting.

ICOR Community members: please suggest topics or volunteer to host future public meetings on this Google Form.