ArticlePloS one2015
pGenN, a gene normalization tool for plant genes and proteins in scientific literature.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- GeneReL: a large language model-powered platform for gene regulatory relationship extraction with community curation.Database : the journal of biological databases and curation · 2026Article
- Extracting knowledge networks from plant scientific literature: potato tuber flesh color as an exemplary trait.BMC plant biology · 2021Article
- Automatic gene annotation using GO terms from cellular component domain.BMC medical informatics and decision making · 2018Article
- Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling.Database : the journal of biological databases and curation · 2018Article
- eGARD: Extracting associations between genomic anomalies and drug responses from text.PloS one · 2017Article
- Analysis of Protein Phosphorylation and Its Functional Impact on Protein-Protein Interactions via Text Mining of the Scientific Literature.Methods in molecular biology (Clifton, N.J.) · 2017Article
- eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality.Database : the journal of biological databases and curation · 2017Article
- Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over.Frontiers in genetics · 2016Article
- NTTMUNSW BioC modules for recognizing and normalizing species and gene/protein mentions.Database : the journal of biological databases and curation · 2016Article
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Authors and funding
5 authors.
Funding
Abstract
backgroundAutomatically detecting gene/protein names in the literature and connecting them to databases records, also known as gene normalization, provides a means to structure the information buried in free-text literature. Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines.
methodsIn this manuscript, we describe a gene normalization system specifically tailored for plant species, called pGenN (pivot-based Gene Normalization). The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases.
resultsWe evaluated the performance of pGenN on an in-house expertly annotated corpus consisting of 104 plant relevant abstracts. Our system achieved an F-value of 88.9% (Precision 90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in BioCreative III. We have processed over 440,000 plant-related Medline abstracts using pGenN. The gene normalization results are stored in a local database for direct query from the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature corpus is also publicly available through the PIR text mining portal (proteininformationresource.org/iprolink/).
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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.