Knowledge Pixels Incubator #4: FAIRification of mass spectrometry workflows using FDOs
Project
📅 Date
ℹ About
Mass spectrometry research confronts challenges endemic to data-intensive science: vendor-specific proprietary formats from multiple Mass Spectrometry instruments, complex multi-consortium governance, and the near-impossibility of tracking provenance across thousands of heterogeneous digital objects spanning clinical samples, instrument logs, processing workflows, and publications. Traditional approaches that retrofit FAIR principles onto existing repositories fail at scale and perpetuate the research integrity and reproducibility crises. This project addresses this systemic failure by implementing nanopublication-based FAIR Digital Objects (FDOs) as minimal, but precise metadata tags at the source, combining automated and human curated machine-actionable assertions that establish unambiguous provenance chains before data enters any workflow. This source-level FAIRification demonstrates that trusted AI in biomedicine requires fundamentally reliable data infrastructure where agentic AI can automatically assess the quality, context, and trustworthiness of every datum from its moment of creation.
Roles:
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Admins
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Observers
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Project Leads
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📌 Relevant resources
- https://github.com/easchultes/mac-fdt-staging/ Mac-fdt-staging GitHub Repo · Staging materials for minting the 38 nanopublication-based FAIR Digital Twins of SARS-CoV-2 Spike RBD variants (Alpha, Epsilon, Eta) reported in Schultes et al. (in preparation). MAC / Leiden University LACDR. Project StayAhead (LSHM22038). · https://w3id.org/np/RAEH40u-6b... ^
📢 Our news
- Incubator #4 extended · We are extending our incubator #4 "FAIRification of mass spectrometry workflows using FDOs" by three more months to have more time to work on its promising developments. · 2026-04-28 · https://w3id.org/np/RALR5RDD0g... ^
- Incubator #4 launched · We have launched our fourth incubator project: FAIRification of mass spectrometry workflows using FDOs · 2025-10-29 · https://w3id.org/np/RAG0vWE1m7... ^
- FAIR Digital Twins of COVID Spike variants · The MAC FDT demonstration is complete and fully version-controlled all live on the nanopub network : 3 FDTs for COVID Spike protein variants are realized using nanopub-based FDOs representing 45 vocabulary terms + 11 templates --> 38 instances · https://w3id.org/np/RAlBaZCdmk... ^
MAC FDT — Alpha variant digital twin
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Alpha AgMata = 0.7004717948717948 — Bio2Byte
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Alpha pLDDT = 23.673561732385306 — ESM2
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Alpha pLDDT = 93.74392833444035 — AlphaFold 2
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Alpha RMSD = 13.378861773140596 Å — ESM2
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Alpha RMSD = 2.277628683231952 Å — AlphaFold 2
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Alpha SASA = 10141.236988525969 Ų — AlphaFold 2
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Alpha SASA = 16494.878394358453 Ų — ESM2
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Alpha DMS observation — Bloom Lab (bind=9.81374, expr=10.05266)
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Alpha real-world occurrence — England (late 2020-2021)
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Alpha — WHO Variant of Concern (2020-12-18)
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📋 Pinned templates
- Template: Declaring a WHO Variant Classification (MAC FDT Type 8) · https://w3id.org/np/RACUcWRMyh... ^
- Template: Declaring a Deep Mutational Scanning Observation (MAC FDT Type 7) · https://w3id.org/np/RAuAWYd-Nm... ^
- Template: Declaring a Computational Prediction — AgMata (MAC FDT Type 6) · https://w3id.org/np/RALWZvGntZ... ^
- Template: Declaring a Computational Prediction — pLDDT (MAC FDT Type 5) · https://w3id.org/np/RAy82yN6QK... ^
- Template: Declaring a Computational Prediction — SASA (MAC FDT Type 4) · https://w3id.org/np/RALkWB__ft... ^