TY - JOUR T1 - Gilda: biomedical entity text normalization with machine-learned disambiguation as a service JF - bioRxiv DO - 10.1101/2021.09.10.459803 SP - 2021.09.10.459803 AU - Benjamin M. Gyori AU - Charles Tapley Hoyt AU - Albert Steppi Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/09/11/2021.09.10.459803.abstract N2 - Summary Gilda is a software tool and web service which 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 The Gilda web service is available at http://grounding.indra.bio with source code, documentation and tutorials are available via https://github.com/indralab/gilda.Contact benjamin_gyori{at}hms.harvard.eduCompeting Interest StatementThe authors have declared no competing interest. ER -