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bioRxiv · 10.1101/2021.09.10.459803

Gilda: biomedical entity text normalization with machine-learned disambiguation as a service

Gyori, B. M.·Hoyt, C. T.·Steppi, A.
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Abstract

SummaryGilda 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. AvailabilityThe Gilda web service is available at http://grounding.indra.bio with source code, documentation and tutorials are available via https://github.com/indralab/gilda. Contactbenjamin_gyori@hms.harvard.edu

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Gyori, B. M., Hoyt, C. T., Steppi, A.. 2021-09-11. Gilda: biomedical entity text normalization with machine-learned disambiguation as a service. https://doi.org/10.1101/2021.09.10.459803

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