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ABNER specifications


Unique identifier OMICS_01168
Alternative name A Biomedical Named Entity Recognizer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Version 1.5
Stability Stable
Maintained Yes


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  • person_outline Burr Settles <>

Publication for A Biomedical Named Entity Recognizer

ABNER in publications

PMCID: 5753510
PMID: 29298665
DOI: 10.1186/s12885-017-3941-x

[…] and (“1980/01/01” [pdat]: “2015/05/25” [pdat]). all genes and proteins related to the key words were extracted and gathered in a list with the following of gene mention tagging by applying a biomedical named entity recognizer (abner, an open source tool for automatically tagging genes, proteins and other entity names in text, http://pages.cs.wisc.edu/bsettles/abner/) [] and conjunction […]

PMCID: 5704339
PMID: 29201171
DOI: 10.3892/etm.2017.5173

[…] myeloma’ and ‘resistance or prognosis or carcinogenesis or tumorigenesis’. all of the genes and proteins associated with these keywords were extracted, followed by gene mention tagging using a biomedical named entity recognizer software, version 1.5 (http://pages.cs.wisc.edu/~bsettles/abner). for the conditions, multiple genes were described in a word, such as ‘stat3/5 gene’, […]

PMCID: 5870729
PMID: 28881963
DOI: 10.1093/bioinformatics/btx228

[…] standard model, being the method of choice for essentially all tools winning recent ner competitions, such as biocreative iv () or i2b2 (). popular biomedical ner tools using crfs are, for instance, abner (a biomedical named entity recognizer) () and banner (). hybrid methods combine machine learning methods with dictionary- or rule-based techniques. for instance, chemspot () integrates results […]

PMCID: 5513884
PMID: 28744145
DOI: 10.2147/OTT.S138143

[…] keywords: 1) hepatocellular or liver or hepatic or hcc and 2) malignan* or cancer or tumor or tumour or neoplas* or carcinoma. in the published studies, the hcc-related genes were identified through a biomedical named entity recognizer (http://pages.cs.wisc.edu/~bsettles/abner/)., as for the nlp analysis, we computed the frequency of all the genes in the included studies in pubmed database. […]

PMCID: 5562079
PMID: 28627690
DOI: 10.3892/mmr.2017.6785

[…] were downloaded as. html text without images and converted into. xml documents. the genes and proteins reported were compiled into a data pool, and gene mention recognition was performed using a biomedical named entity recognizer version 1.5 tool (http://pages.cs.wisc.edu/~bsettles/abner/) (), and conjunction resolution was conducted to obtain specialized descriptions of the extracted […]

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ABNER institution(s)
Department of Computer Sciences and Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison Madison, WI, USA

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