Can LLMs Reliably Annotate Bioassay Metadata to Improve Data Readiness?

תקציר מקורי באנגליתarXiv:2610.01616v1 Announce Type: cross Abstract: The emergence of foundation models for molecular property prediction requires a high degree of AI data readiness, including reliable metadata annotation. However, both public repositories and industrial screening databases suffer from missing, inconsistent, or conflated assay annotations. In this work, we quantify the extent of missing annotations in PubChem for the BioAssay Ontology (BAO) assay format and physical detection method fields and investigate whether open-source and proprietary large language models (LLMs) can reliably predict and audit metadata annotations directly from the assay text. In our assessment, we found that the annotation coverage across PubChem's $\sim$2 million bioassays is critically sparse, 36\% lacking an assay