SchemaLink: An Intelligent Web Editor for LinkML Schema Curation

Scientific processes are often described in heterogeneous article discourse, with details needed for comparison, reproducibility, reuse, and automation dispersed across prose, tables, figures, protocols, and supplementary files. We present the first release of SciSchema.org, a multidisciplinary collection of 16 expert-annotated schemas spanning Biology & Biotechnology, Materials & Chemistry, Imaging & Measurement, Physics, and Psychology. Each schema defines reusable fields for describing process instances, including inputs, outputs, materials, instruments or software, parameters, conditions, procedural steps, measurements, and provenance-related information. The schemas were created through a human-in-the-loop schema-mining workflow in which large language models generated candidate structures from process specifications, scientific articles, and expert feedback, followed by domain-expert construction of final master schemas. The dataset contains final schemas in JSON Schema and SHACL formats, intermediate model-generated schemas, expert-feedback records, source-paper metadata, community-development materials, and analysis scripts. Technical validation assessed schema structure, development provenance, expert review, and syntactic conformance. The collection supports structured annotation, metadata enrichment, scientific knowledge graphs, information extraction, semantic publishing, and cross-study comparison.

Many disciplines pose natural-language research questions over large document collections whose answers typically require structured evidence, traditionally obtained by manually designing an annotation schema and exhaustively labeling the corpus, a slow and error-prone process. We introduce ScheMatiQ, which leverages calls to a backbone LLM to take a question and a corpus to produce a schema and a grounded database, with a web interface that lets steer and revise the extraction. In collaboration with domain experts, we show that ScheMatiQ yields outputs that support real-world analysis in law and computational biology. We release ScheMatiQ as open source with a public web interface, and invite experts across disciplines to use it with their own data. All resources, including the website, source code, and demonstration video, are available at: www.ScheMatiQ-ai.com

Traditional Text-to-SQL research and benchmarks assume a known target database, overlooking settings in which a query must be routed within a large, heterogeneous database collection. We therefore study schema linking in a multi-database setting, where the system must first locate the target database and then construct a compact, SQL-relevant schema for generation. We propose MDB-Link, a hierarchical schema-linking framework that retrieves question-relevant columns from a global index, aggregates retrieval evidence to shortlist databases, and uses a budget-aware large language model (LLM) for database reranking, table selection, and column grounding. With Qwen2.5-14B, MDB-Link outperforms LinkAlign on MMQA, Spider2-Snow, and BIRD-dev in database localization and column selection while producing schema subsets close in size to the gold schemas. Exact match improves from 16.88 to 51.41 on MMQA, 2.50 to 9.17 on Spider2-Snow, and 12.52 to 38.01 on BIRD-dev. MDB-Link also runs faster than LinkAlign and AutoLink, demonstrating the effectiveness of hierarchical schema reduction for downstream SQL generation.