bioNerDS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool bioNerDS

Tool usage distribution map

This map represents all the scientific publications referring to bioNerDS per scientific context
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bioNerDS specifications


Unique identifier OMICS_04833
Name bioNerDS
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Robert Stevens

Publication for bioNerDS

bioNerDS citations


A Survey of Bioinformatics Database and Software Usage through Mining the Literature

PLoS One
PMCID: 4917176
PMID: 27331905
DOI: 10.1371/journal.pone.0157989

[…] t.Our medicine corpus shows a slightly different story—there are more mentions that may stem from false-positive mentions (e.g., healthcare, ECG, effective, etc.); this is likely to be an artefact of bioNerDS being trained on bioinformatics rather than medical text. That said, medicine shows a clear preference for SPSS and Stata over R for statistical processing (with double the mean number of SPS […]


Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature

PLoS One
PMCID: 5156472
PMID: 26730820
DOI: 10.1371/journal.pone.0146300

[…] expressions expressed as transition networks for resource naming, functionality detection and resource classification for resource inventory generation. BIRI is generated on 400 biomedical abstracts. BioNERDS [] is a named entity recognition (NER) system for detecting database and software names in the literature using extraction rules generated by examining 30 full text bioinformatics articles.In […]


Ambiguity and variability of database and software names in bioinformatics

J Biomed Semantics
PMCID: 4485340
PMID: 26131352
DOI: 10.1186/s13326-015-0026-0

[…] The datasets supporting the results of this article are available at: […]

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bioNerDS institution(s)
School of Computer Science, The University of Manchester, Manchester, UK

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