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NERsuite specifications


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
libLBFGS, CRFsuite
Maintained Yes




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NERsuite citations


Deep learning with word embeddings improves biomedical named entity recognition

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 ( 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 […]


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

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 (, 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 […]


Text Mining the History of Medicine

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 (, is specifically designed to facilitate the development of ML-based NE recognition tools. Given the previously mentioned importance of various types of linguisti […]


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

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 […]


Context based resolution of semantic conflicts in biological pathways

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 […]


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

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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