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Updated: Aug 12, 2025

Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
Published on: June 13, 2025
Gilda: biomedical entity text normalization with machine-learned disambiguation as a service
Benjamin M Gyori1, Charles Tapley Hoyt1, Albert Steppi1
1Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
Summary:
Gilda is a software tool and web service that implements a scored string matching algorithm for names and synonyms across entries in biomedical ontologies covering genes, proteins (and their families and complexes), small molecules, biological processes and diseases. Gilda integrates machine-learned disambiguation models to choose between ambiguous strings given relevant surrounding text as context, and supports species-prioritization in case of ambiguity.
Availability And Implementation:
The Gilda web service is available at http://grounding.indra.bio with source code, documentation and tutorials available via https://github.com/indralab/gilda.
Supplementary Information:
Supplementary data are available at Bioinformatics Advances online.
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