ArticleBioinformatics (Oxford, England)2011
The GNAT library for local and remote gene mention normalization.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- Assessing Artificial Intelligence (AI) Implementation for Assisting Gene Linking (at the National Library of Medicine).JAMIA open · 2025Article
- GNorm2: an improved gene name recognition and normalization system.Bioinformatics (Oxford, England) · 2023Article
- Edge Weight Updating Neural Network for Named Entity Normalization.Neural processing letters · 2022Article
- Assigning species information to corresponding genes by a sequence labeling framework.Database : the journal of biological databases and curation · 2022Article
- Joint Learning for Biomedical NER and Entity Normalization: Encoding Schemes, Counterfactual Examples, and Zero-Shot Evaluation.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2021Article
- Large-scale literature mining to assess the relation between anti-cancer drugs and cancer types.Journal of translational medicine · 2021Article
- NLM-Gene, a richly annotated gold standard dataset for gene entities that addresses ambiguity and multi-species gene recognition.Journal of biomedical informatics · 2021Article
- Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature.Briefings in bioinformatics · 2021Review
- OGER++: hybrid multi-type entity recognition.Journal of cheminformatics · 2019Article
- A method for named entity normalization in biomedical articles: application to diseases and plants.BMC bioinformatics · 2017Article
- Beyond accuracy: creating interoperable and scalable text-mining web services.Bioinformatics (Oxford, England) · 2016Article
- Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts.BMC bioinformatics · 2016Article
- AuDis: an automatic CRF-enhanced disease normalization in biomedical text.Database : the journal of biological databases and curation · 2016Article
- Recent Advances and Emerging Applications in Text and Data Mining for Biomedical Discovery.Briefings in bioinformatics · 2016Review
- PALM-IST: Pathway Assembly from Literature Mining--an Information Search Tool.Scientific reports · 2015Article
- DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions.Nucleic acids research · 2015Article
- Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.Database : the journal of biological databases and curation · 2015Article
- Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events.BMC systems biology · 2015Article
- Assembly of a comprehensive regulatory network for the mammalian circadian clock: a bioinformatics approach.PloS one · 2015Article
- GNormPlus: An Integrative Approach for Tagging Genes, Gene Families, and Protein Domains.BioMed research international · 2015Article
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9 authors.
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Abstract
summaryIdentifying mentions of named entities, such as genes or diseases, and normalizing them to database identifiers have become an important step in many text and data mining pipelines. Despite this need, very few entity normalization systems are publicly available as source code or web services for biomedical text mining. Here we present the Gnat Java library for text retrieval, named entity recognition, and normalization of gene and protein mentions in biomedical text. The library can be used as a component to be integrated with other text-mining systems, as a framework to add user-specific extensions, and as an efficient stand-alone application for the identification of gene and protein names for data analysis. On the BioCreative III test data, the current version of Gnat achieves a Tap-20 score of 0.1987. AVAILABILITY: The library and web services are implemented in Java and the sources are available from http://gnat.sourceforge.net. CONTACT: jorg.hakenberg@roche.com.
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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.