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BANNER specifications

Information


Unique identifier OMICS_05251
Name BANNER
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for BANNER

BANNER in pipelines

 (2)
2009
PMCID: 2723093
PMID: 19635172
DOI: 10.1186/1471-2105-10-233

[…] here. it is not possible to use pre-tagged entities with the pipeline, be they the gold-standard corpus entities used in our evaluation, or those generated by a state-of-the-art tagger such as banner. moreover, in the case where the same protein name occurs more than once in a single sentence, the pipeline does not specify which of the names it has identified as providing evidence […]

2009
PMCID: 2723093
PMID: 19635172
DOI: 10.1186/1471-2105-10-233

[…] install akaneppi locally at birkbeck, william baumgartner for supplying us with custom-written code that enabled us to evaluate opendmap, and nigel ferguson at birkbeck for tagging our corpora using banner. the research of r.k. was supported by the european commission under fp6-2004-ist-4 contract no. 028069 (the immunogrid project) and the uk orsas […]


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BANNER in publications

 (25)
PMCID: 5130168
PMID: 27902695
DOI: 10.1371/journal.pcbi.1005017

[…] a curated tmvar corpus. some additional rare mutation mentions are handled in the post-processing module., dnorm. dnorm segments the given text into sentences and identifies disease mentions using banner []. the mentions are then normalized to disease concepts in mesh by finding the best match using a learning-to-rank technique []. finally the disambiguation related to primary disease […]

PMCID: 5088735
PMID: 27777244
DOI: 10.1093/database/baw140

[…] klinger et al. () employed conditional random fields (crfs) to find the international union of pure and applied chemistry (iupac) and iupac-like chemical names; leaman and gonzalez () presented banner, which is an open-source biomedical named entity recognition system implemented using crfs; leaman et al. () developed a high performance chemical named entity recognizer created by combining […]

PMCID: 4930833
PMID: 27374122
DOI: 10.1093/database/baw076

[…] texts are tokenised and syntactically parsed using the stanford parser (), and biomedical entities such as genes and proteins are identified using a biomedical named entity recognition (ner) module, banner (). then, anaphoric mentions such as pronouns, e.g. ‘it’, ‘its’ and ‘they’, and definite noun phrases containing domain-specific nouns, such as ‘the protein’ and ‘these genes’ are identified […]

PMCID: 4852402
PMID: 27141091
DOI: 10.1093/database/baw061

[…] systems in the previous biocreative chemdner challenge (). the tmchem system is an ensemble system that combines the output of two crf-based systems. the first system is a modified version of the banner system (), the second is based on the tmvar system (), which employs crf ++ libraries (https://taku910.github.io/crfpp/). previous results of tmchem showed that the second system outperformed […]

PMCID: 4806637
PMID: 27019783
DOI: 10.7717/peerj.1811

[…] superpathway of pyridoxal 5′-phosphate biosynthesis and salvage. the recall showed less than 70%, and the f-score showed less than 80%. these results seem to indicate that the entity tagger (i.e., banner) has a weakness in detecting metabolite entities in an abbreviated form (e.g., pyridoxine (pn), pyridoxal (pl), and 4-hydroxy-l-threonine phosphate (htp))., we evaluated the performance […]


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BANNER institution(s)
Department of Computer Science and Engineering, Arizona State University and Department of Biomedical Informatics, Arizona State University, AZ, USA

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