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.
© The Author(s) 2022. Published by Oxford University Press.