GNormPlus statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GNormPlus
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Tool usage distribution map

This map represents all the scientific publications referring to GNormPlus per scientific context
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Associated diseases

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Protocols

GNormPlus specifications

Information


Unique identifier OMICS_12927
Name GNormPlus
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Zhiyong Lu

Publication for GNormPlus

GNormPlus citations

 (9)
library_books

How Artificial Intelligence Can Improve Our Understanding of the Genes Associated with Endometriosis: Natural Language Processing of the PubMed Database

2018
Biomed Res Int
PMCID: 5884286
PMID: 29750165
DOI: 10.1155/2018/6217812

[…] re precise, with content enclosed within XML tag pairs []. The titles and abstracts of each article were converted into the PubTator format [] through a custom Perl script.For the TM, we employed the GNormPlus system [], which contains two modules (gene mention recognition and gene normalization) essential for understanding the specific and complex nature of TM when focusing on genes. […]

call_split

eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality

2017
PMCID: 5691349
PMID: 29220476
DOI: 10.1093/database/bax081
call_split See protocol

[…] discussed in our previous paper, most of the existing gene normalization tools are either designed for non-plant species or not publicly accessible. Thus, we are only able to compare our results with GNormPlus (), an updated version of GenNorm (). Results of GNormPlus were retrieved via PubTator (). Since GNormPlus normalizes genes to EntrezGene () identifiers, we used the ID mapping tool provided […]

library_books

Semantic annotation in biomedicine: the current landscape

2017
J Biomed Semantics
PMCID: 5610427
PMID: 28938912
DOI: 10.1186/s13326-017-0153-x

[…] EUS [], which is a tool for the same purpose built using a dictionary-based approach for mention detection and a set of heuristics for ambiguity resolution. The authors of SR4GN subsequently proposed GNormPlus that focuses on the identification of gene names and their identifiers. The distinguishing aspect of this tool is that it is able to distinguish gene, gene family, and protein domains by tra […]

library_books

Recent advances in predicting gene–disease associations

2017
F1000Res
PMCID: 5414807
PMID: 28529714
DOI: 10.12688/f1000research.10788.1

[…] ease association can be implemented by performing a PubMed-like keyword search using PubTator, using normalisation and annotation tools to retrieve relationships between concepts (tmVar for mutation, GNormPlus for genes, and DNorm for diseases), and then presenting the results for visual inspection or integration into other analysis pipelines. […]

call_split

nala: text mining natural language mutation mentions

2017
Bioinformatics
PMCID: 5870606
PMID: 28200120
DOI: 10.1093/bioinformatics/btx083
call_split See protocol

[…] orpus was the annotation of genetic markers. To limit the workload, for the nala corpus we refrained from annotating organisms or GGP terms. Only to ease the reading of mutation mentions, we used the GNormPlus tagger () to automatically annotate gene/protein terms.Three experts annotated nala; their agreement over 30 documents was F_IAA = 95 for all mutation mentions and F_IAA = 89 for NL. The nal […]

call_split

Text Mining Genotype Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine

2016
PLoS Comput Biol
PMCID: 5130168
PMID: 27902695
DOI: 10.1371/journal.pcbi.1005017
call_split See protocol

[…] rpus, we collected the PubMed title, abstract and annotation results for gene, mutation and disease mentions via PubTator []. In PubTator, the gene, mutation and disease annotations were extracted by GNormPlus [], tmVar [] and DNorm [], respectively.Our approach for identifying gene-disease-mutation relationships is portrayed schematically in and can be summarized as follows: Step 1: Identify all […]


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GNormPlus institution(s)
National Center for Biotechnology Information (NCBI), Bethesda, MD, USA; Department of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan

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