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NERsuite specifications

Information


Unique identifier OMICS_20493
Name NERsuite
Alternative name Named Entity Recognition Suite
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.2.1
Stability Stable
Requirements
libLBFGS, CRFsuite
Maintained Yes

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NERsuite citations

 (13)
call_split

Deep learning with word embeddings improves biomedical named entity recognition

2017
Bioinformatics
PMCID: 5870729
PMID: 28881963
DOI: 10.1093/bioinformatics/btx228
call_split See protocol

[…] bbreviation resolution.Cell Lines: we used a model presented in (), reported to outperform many other available systems in a cross-corpus setting. It is based on the domain-independent CRF-based tool NERsuite (http://nersuite.nlplab.org/). In addition to the pre-defined NERsuite features, it uses a comprehensive dictionary of cell line names from multiple sources.Chemicals: we employed tmChem (htt […]

library_books

Argo: enabling the development of bespoke workflows and services for disease annotation

2016
PMCID: 4869796
PMID: 27189607
DOI: 10.1093/database/baw066

[…] turn were decomposed into tokens by the OSCAR4 Tokeniser () which were then assigned lemmatised forms as well as part-of-speech (POS) and chunk tags by the GENIA Tagger (). Figure 4. We employed the NERsuite package (http://nersuite.nlplab.org), an implementation of conditional random fields (CRFs) (), to apply pre-trained models for sequence labelling. Each token was presented to the CRFs as a r […]

library_books

Text Mining the History of Medicine

2016
PLoS One
PMCID: 4703377
PMID: 26734936
DOI: 10.1371/journal.pone.0144717

[…] We have trained our NE recognition tool by applying an existing software package to the annotated HIMERA corpus. The package, called NERSuite (http://nersuite.nlplab.org/), is specifically designed to facilitate the development of ML-based NE recognition tools. Given the previously mentioned importance of various types of linguisti […]

call_split

Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013

2015
BMC Bioinformatics
PMCID: 4511510
PMID: 26202570
DOI: 10.1186/1471-2105-16-S10-S2
call_split See protocol

[…] ed the OSCAR4 system, which was trained on the chemical entity mention recognition corpus of Corbett and Copestake []. For GENE OR GENE PRODUCT mention detection, we used BANNER[] for the CG task and NERsuite [] for the PC task. Both of these systems were trained on the Gene Mention task corpus introduced in the BioCreative 2 evaluation []. NERsuite was also applied for anatomical entity mention d […]

call_split

Context based resolution of semantic conflicts in biological pathways

2015
BMC Med Inform Decis Mak
PMCID: 4461014
PMID: 26045143
DOI: 10.1186/1472-6947-15-S1-S3
call_split See protocol

[…] ected one best tool for each entity type. By this criterion, four NER tools were selected; Genia [] for tagging 'gene', 'protein' and 'cell type', BANNER [] for 'disease', LingPipe [] for 'organ' and NERSuite [] for 'metabolite', 'drug' and 'biological process'. According to the papers explaining the methods (see Table ), we chose tools to extract each type of biological entities. The performances […]

call_split

Supporting the annotation of chronic obstructive pulmonary disease (COPD) phenotypes with text mining workflows

2015
J Biomed Semantics
PMCID: 4364458
PMID: 25789153
DOI: 10.1186/s13326-015-0004-6
call_split See protocol

[…] e 2After running the syntactic tools, the workflow splits into four branches. The first branch performs joint annotation of concepts pertaining to Problem, Treatment and TestOrMeasure by means of the NERsuite [] component, a named entity recogniser (NER) based on an implementation of conditional random fields []. Supplied with a model trained on the 2010 i2b2/VA challenge training set [], this NER […]

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