The methodology and validation behind BioMate, published openly. Organized by topic and month — newest first.
BioMate-KB: 15,641 real-execution-validated Bioconductor workflow steps. The public skill bundle is on GitHub for the community to clone, use, and build on.
A curated knowledge base of 15,641 workflow steps extracted across the Bioconductor 3.20 ecosystem — NAMESPACE-validated, EDAM-annotated, container-linked, and, for the validated head, confirmed by real end-to-end execution. Reframes executability as an empirical, reproducible property.
Bioconductor's formal structure (NAMESPACE, S4 types, BiocViews, vignettes) suppresses LLM hallucination — raising function-citation accuracy from 71.4% to 88.2% — but does not guarantee execution. Introduces execution-grounded validation as the strongest tier of a lexical ⊂ structural ⊂ executional grounding hierarchy.
Citations use the Zenodo concept DOIs (all versions). To pin v3 exactly: BioMate-KB 10.5281/zenodo.20616356 · Structure Grounding 10.5281/zenodo.20616544.
