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

Abstract

Abstract 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.