ArticleBioinformatics advances2022
Gilda: biomedical entity text normalization with machine-learned disambiguation as a service.
Article in Bioinformatics advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
11 citing papers in PubMed.
- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- textToKnowledgeGraph: generation of molecular interaction knowledge graphs using large language models for exploration in Cytoscape.Bioinformatics (Oxford, England) · 2026Article
- Assembly and reasoning over semantic mappings at scale for biomedical data integration.Bioinformatics (Oxford, England) · 2025Article
- Chemical entity normalization for successful translational development of Alzheimer's disease and dementia therapeutics.Journal of biomedical semantics · 2024Article
- preon: Fast and accurate entity normalization for drug names and cancer types in precision oncology.Bioinformatics (Oxford, England) · 2024Article
- Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.Bioinformatics (Oxford, England) · 2024Article
- Automated assembly of molecular mechanisms at scale from text mining and curated databases.Molecular systems biology · 2023Article
- Prediction and curation of missing biomedical identifier mappings with Biomappings.Bioinformatics (Oxford, England) · 2023Article
- Unifying the identification of biomedical entities with the Bioregistry.Scientific data · 2022Article
- A roadmap for the functional annotation of protein families: a community perspective.Database : the journal of biological databases and curation · 2022Article
- A Simple Standard for Sharing Ontological Mappings (SSSOM).Database : the journal of biological databases and curation · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
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
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.