Addressing challenges in agentic retrieval of structured data from biomedical databases

Biomedical research increasingly relies on expert-curated databases to connect diseases, genes, variants, phenotypes, pathways and therapeutics. Incomplete or irreproducible retrieval can distort interpretation, mechanistic inference, variant assessment or therapeutic prioritization despite an unchanged evidence base. Agentic natural-language-to-SQL (NL2SQL) systems and Model Context Protocol-enabled agents can autonomously retrieve evidence from biomedical databases, including Open Targets and the Highly Confident Drug-Target Database, in response to natural-language questions. However, they may truncate large result sets, miss records when terminology differs from database vocabulary and return different outputs across runs. We systematically quantify these failures and introduce BioChirp, a goal-directed autonomous system for reliable retrieval from structured biomedical databases, built on interpretation-execution separation. A coordinated language-model layer interprets intent and resolves database-field assignments, after which entity resolution maps user terms to database terminology. A deterministic Steiner-tree planner and executor then retrieve matching records without further language-model involvement. Across curated biomedical databases spanning more than one million associations, BioChirp retrieved thousands of records for exhaustive queries, whereas baseline agents returned at most a few hundred or failed. Across 70 queries, five runs and three BioChirp database backends, BioChirp achieved a median cross-run Jaccard similarity of 1.0. Across 910 database-question evaluations derived from expert-written BioASQ questions and spanning ten databases, BioChirp retrieved at least one database record in 85.4% of cases and produced a fully correct answer in 51.1% of cases, compared with 44.6% and 17.4% for agentic NL2SQL. BioChirp is publicly available at https://biochirp.iiitd.edu.in.