The best way for humankind to benefit from research is to prioritize machines over people when sharing data. Here’s why.
We push out the lines that academic research needs to be Findable, Accessible, Interoperable and Re-usable (FAIR) for humans and machines. This suggests humans and machines should get equal priority when it comes to FAIR. This is not the case, we should prioritize the machines. Machine-generated new knowledge will accelerate knowledge discovery.
While humans can infer insights from sparse information in academic literature and datasets – due to our ability to find more context online – the machines currently cannot. To go further, faster in knowledge discovery we need to move past human-powered knowledge discovery. To do this, the machines need structure and pattern. Every research-generating organization should be prioritizing this.
Academia is Ignoring Decades of Advancement
Academic research generates more than 6.5 million papers annually, and over 20 million datasets, each representing potential training signals for the artificial intelligence systems reshaping discovery. Yet most institutional data remains locked in formats optimized for human consumption rather than computational processing.
While most stakeholders know the theoretical merits of making data FAIR (Findable, Accessible, Interoperable, Reusable) for both humans and machines, the practical reality is starker: in an era where language models can process orders of magnitude more literature than any human researcher, we are still organizing our most valuable research assets for the wrong consumer.
The economic implications are substantial. Organizations like the Chan Zuckerberg Initiative (CZI) have committed over $3.4 billion toward AI-powered biology, funding projects ranging from their 1,024 GPU DGX SuperPOD cluster for computational biology research to the Virtual Cell Platform that aims to create predictive models of cellular behavior. The Navigation Fund, with its $1.3 billion endowment, has invested in AI infrastructure through their Voltage Park subsidiary, while simultaneously funding open science initiatives focused on machine-actionable intelligence and metadata enhancement. Astera Institute has deployed portions of its $2.5 billion endowment to support projects like their $200 million investment in Imbue’s AI agent research and their Science Entrepreneur-in-Residence program specifically targeting scientific publishing infrastructure. Meanwhile, the Allen Institute for AI demonstrates the practical returns on machine-first approaches through projects like their OLMo series of fully open language models, where complete training datasets, code, and methodologies are published in computational formats, and their Semantic Scholar platform, which processes millions of academic papers to extract structured, machine-readable knowledge graphs.
Yet the vast majority of academic institutions continue to publish their findings in PDFs or as poorly described datasets. While LLMs are getting better at ingesting multi-modal content, PDF is a format that remains surprisingly resistant to reliable automated extraction, despite decades of advancement in natural language processing. This is not merely a technical limitation. Modern large language models struggle with PDFs because these documents prioritize visual presentation over semantic structure. Critical information becomes trapped in figures, tables, and formatting that computational systems cannot reliably parse. A reaction scheme embedded as an image, a dataset described in paragraph form, or experimental parameters scattered across multiple tables represent precisely the kind of structured knowledge that could accelerate discovery if only machines could access it consistently.
The Architecture of Computational Research Infrastructure
The solution requires a fundamental reorientation toward machine-first data architecture. Rather than retrofitting human-readable outputs for computational consumption, we can take inspiration from pharma and industry writ large, who are designing their data flows to serve algorithms from the ground up, with human-friendly interfaces emerging as downstream products of this computational foundation.
Consider the transformation pathway implemented by teams working with Digital Science’s suite of computational research tools. We’re building workflows in our tools for automated knowledge extraction at scale. The extracted knowledge gains semantic coherence through integration into domain-specific knowledge graphs. Platforms like metaphacts (metaphactory) provide the infrastructure to align these signals with established ontologies while enforcing quality constraints through SHACL validation integrated into continuous deployment pipelines. The result is not merely a database of facts, but a queryable intelligence system that can answer novel questions through automated reasoning over validated relationships.
Simultaneously, the operational requirements of research continue through dedicated literature management systems. Tools like ReadCube maintain the audit trails and conflict resolution workflows that regulatory environments demand, while ensuring that every screening decision and data extraction connects to persistent identifiers. The curated evidence flows directly into the computational infrastructure rather than terminating in isolated spreadsheets.
The critical innovation lies in packaging. While human researchers expect PDFs and narrative summaries, machine learning pipelines require structured metadata that specifies exactly what each dataset contains, where to retrieve it, and how to interpret every field.
The Metadata Multiplier Effect on Repository Platforms
Academic data repositories like Figshare occupy a unique position in the machine-first FAIR ecosystem. We serve as the critical junction between human research practices and computational discovery. When researchers publish datasets with comprehensive, structured metadata, these platforms transform from simple storage services into computational assets that can feed directly into AI research pipelines. The difference lies entirely in how authors describe their work at the point of deposit.
Consider two datasets published on the same platform: one uploaded with a generic title like “experiment_data_final.xlsx” and minimal description, the other with machine-readable field descriptions, standardized vocabulary terms, and explicit links to ontologies and methodologies. The first requires human interpretation before any computational system can make sense of its contents. The second can be discovered, validated, and integrated into training pipelines automatically. Figshare’s API can surface the rich metadata to computational systems, but only if researchers have provided it in the first place.
The platform infrastructure already supports the technical requirements for machine-first FAIR. Persistent DOIs ensure stable identifiers, while structured metadata fields can accommodate everything from ORCID researcher identifiers to detailed provenance information. When authors invest time in describing their data using controlled vocabularies, specifying units of measurement, documenting collection methodologies, and linking to relevant publications, they create computational assets rather than digital archives. The same dataset that might languish undiscovered with poor metadata becomes a valuable training resource when described with machine-readable precision.
This creates a powerful feedback loop. Datasets with excellent metadata get discovered and reused more frequently, driving citation counts and demonstrating impact. Meanwhile, poorly described data remains computationally invisible regardless of its scientific value. Platforms like Figshare could amplify this effect by providing better authoring tools that encourage structured metadata entry, perhaps even using AI to suggest appropriate ontology terms or validate metadata completeness before publication. The infrastructure for machine-first FAIR already exists, it simply requires researchers to embrace metadata as a first-class research output rather than an administrative afterthought. But this is an evolving field, new standards are emerging that repositories need to engage with.
The Croissant format, a lightweight JSON-LD descriptor based on schema.org, provides this computational bridge. A single Croissant file enables any training pipeline to hydrate datasets without custom loaders while simultaneously supporting discovery through standard web infrastructure.
Practical Implementation in Institutional Contexts
The transition to machine-first FAIR follows a predictable arc when properly resourced. Initial implementations focus on proving the fundamental workflow with narrowly scoped pilot projects. A team might select a single dataset and one sharply defined outcome, perhaps drug-target interaction prediction or materials property modeling and implement the complete pipeline from literature extraction through validated knowledge graph construction to machine-readable packaging.
The critical insight from successful implementations is the importance of automation as the second phase. Manual processes that work for pilot projects become bottlenecks at scale. The most effective teams invest heavily in converting their proven workflows into tested, continuous integration pipelines that enforce quality gates automatically. This includes SHACL validation for knowledge graphs, automated license checking, and provenance tracking.
Production deployment requires infrastructure investments that many academic institutions are not yet considering. Successful implementations provide stable, resolvable URLs for every dataset and descriptor, enable content negotiation so that both machines and humans receive appropriate formats, and implement comprehensive monitoring of data quality trends and usage patterns. This is the stack that Digital Science can provide.
Quantifying Institutional Success
Organizations can assess their progress toward machine-first FAIR through several concrete indicators. Successful implementations demonstrate that every significant dataset resolves to a persistent identifier that returns structured JSON-LD for computational consumers while maintaining readable landing pages for human users. Knowledge graphs pass automated validation, maintain stable URI schemes, and support catalogued query patterns rather than requiring ad hoc exploration.
Literature workflows leave complete audit trails with PRISMA-compliant reporting that can be generated automatically rather than assembled manually. Licensing and provenance information becomes verifiable through computational means rather than requiring human interpretation. Most importantly, the time taken from initial hypothesis to trained model decreases as institutional infrastructure matures and teams spend more of their time on discovery rather than data preparation.
The research organizations that define the next decade will not necessarily be those with the largest datasets, but rather those whose data infrastructure works most effectively at computational scale. Every day spent optimizing publishing workflows for human-readable reports while leaving data computationally inaccessible represents lost ground in an increasingly competitive landscape.
The funders backing this transformation, from CZI’s investments in computational biology to Astera’s focus on AI-native research infrastructure, are betting that machine-first approaches will determine which institutions can effectively leverage artificial intelligence for discovery. The technical architecture exists today. The standards are stable. The remaining barrier is institutional commitment to prioritizing computational accessibility over familiar but inefficient human-centered workflows.
Academic research stands at yet another technology-driven inflection point. The institutions that embrace machine-first FAIR will find themselves having more impact for their research and researchers.
The post Machine-First FAIR: Realigning Academic Data for the AI Research Revolution appeared first on Digital Science.
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