GNormPlus protocols

View GNormPlus computational protocol

GNormPlus statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Gene entity recognition chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

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

Download


Versioning


Add your version

Maintainer


  • person_outline Zhiyong Lu <>

Publication for GNormPlus

GNormPlus in pipeline

2016
PMCID: 5130168
PMID: 27902695
DOI: 10.1371/journal.pcbi.1005017

[…] between genes, variants, drugs, and cell lines from the full text of 108 articles []. finally, this proposed framework directly uses several state-of-the-art tools (like tmvar, dnorm and gnormplus). future advances in the respective domains of these tools would enable increased performance of the proposed approach. this study has been helpful to excavate several examples […]


To access a full list of citations, you will need to upgrade to our premium service.

GNormPlus in publications

 (6)
PMCID: 5691349
PMID: 29220476
DOI: 10.1093/database/bax081

[…] 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 […]

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

[…] sequence variants at the levels of both genes and proteins from biomedical literature; dnorm , which is a resource that is used to automatically identify disease names in biomedical text; and gnormplus , which identifies gene mentions and normalization in biological text. gene normalization, as described in , is the process of identifying and assigning biomedical database identifiers […]

PMCID: 5130168
PMID: 27902695
DOI: 10.1371/journal.pcbi.1005017

[…] 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 […]

PMCID: 4865327
PMID: 27173521
DOI: 10.1093/database/baw065

[…] our chemical ner system obtained 0.8752 precision and 0.9129 recall, for 0.8937 f-score on the cemp task. our gene/protein ner system is an extension of our previous work for gene and protein ner, gnormplus. this system obtained a performance of 0.8143 precision and 0.8141 recall, for 0.8137 f-score on the gpro task. both systems achieved the highest performance in their respective tasks […]

PMCID: 4783925
PMID: 26840308
DOI: 10.3390/ijms17020191

[…] within xml tag pairs. for each article, titles and abstract texts were fetched and transformed into the pubtator format [] using in-house perl scripts., text mining was performed by using the gnormplus pipeline []. gnormplus includes two modules: gene mention recognition and gene name normalization, respectively. gene mentions were detected by using the crf++ library []. gene name […]


To access a full list of publications, you will need to upgrade to our premium service.

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

GNormPlus reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GNormPlus