Jonny L. Saunders | Searcharxiv

arXiv2026

LinkML: An Open Data Modeling Framework

Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, non-standardized spreadsheets, or data repositories. This lack of structure challenges interoperability, making data integration, validation, and reuse difficult. LinkML (Linked Data Modeling Language) is an open framework that simplifies the process of authoring, validating, and sharing data. LinkML can describe a range of data structures, from flat, list-based models to complex, interrelated, and normalized models that utilize polymorphism and compound inheritance. It offers an approachable syntax that is not tied to any one technical architecture and can be integrated seamlessly with many existing frameworks. The LinkML syntax provides a standard way to describe schemas, classes, and relationships, allowing modelers to build well-defined, stable, and optionally ontology-aligned data structures. Once defined, LinkML schemas may be imported into other LinkML schemas. These key features make LinkML an accessible platform for interdisciplinary collaboration and a reliable way to define and share data semantics. LinkML helps reduce heterogeneity, complexity, and the proliferation of single-use data models while simultaneously enabling compliance with FAIR data standards. LinkML has seen increasing adoption in various fields, including biology, chemistry, biomedicine, microbiome research, finance, electrical engineering, transportation, and commercial software development. In short, LinkML makes implicit models explicitly computable and allows data to be standardized at its origin. LinkML documentation and code are available at linkml.io.

cs.DB↗

arXiv2022

Decentralized Infrastructure for (Neuro)science

The most pressing problems in science are neither empirical nor theoretical, but infrastructural. Scientific practice is defined by coproductive, mutually reinforcing infrastructural deficits and incentive systems that everywhere constrain and contort our art of curiosity in service of profit and prestige. Our infrastructural problems are not unique to science, but reflective of the broader logic of digital enclosure where platformatized control of information production and extraction fuels some of the largest corporations in the world. I have taken lessons learned from decades of intertwined digital cultures within and beyond academia like wikis, pirates, and librarians in order to draft a path towards more liberatory infrastructures for both science and society. Based on a system of peer-to-peer linked data, I sketch interoperable systems for shared data, tools, and knowledge that map onto three domains of platform capture: storage, computation and communication. The challenge of infrastructure is not solely technical, but also social and cultural, and so I attempt to ground a practical development blueprint in an ethics for organizing and maintaining it. I intend this draft as a rallying call for organization, to be revised with the input of collaborators and through the challenges posed by its implementation. I argue that a more liberatory future for science is neither utopian nor impractical -- the truly impractical choice is to continue to organize science as prestige fiefdoms resting on a pyramid scheme of underpaid labor, playing out the clock as every part of our work is swallowed whole by circling information conglomerates. It was arguably scientists looking for a better way to communicate that created something as radical as the internet in the first place, and I believe we can do it again.

cs.GL↗