NegEx specifications


Unique identifier OMICS_17597
Name NegEx
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Other
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes



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Publications for NegEx

NegEx in publications

PMCID: 5568290
PMID: 28830409
DOI: 10.1186/s12911-017-0518-1

[…] list of acr criteria seen in table . what is unknown however is whether positive antinuclear antibody or negative antinuclear antibody is what is being found as it is not believed that ctakes/ytex’s negex would function as negative counts for negative antinuclear antibody and positive counts for positive antinuclear antibody. lupus nephritis, as indicated by slicc to be indicative of a positive […]

PMCID: 5519723
PMID: 28729710
DOI: 10.1038/s41598-017-05778-z

[…] (umls) for diseases where the mapping was known. similarly, if a link to an icd-9 code was provided, we searched for that code in the record’s structured administrative data. a modified version of negex was used to find negation scopes in the clinical text, . mentions that occured within a negation scope were not counted. figure  illustrates the data extraction and processing pipeline.figure 1 […]

PMCID: 5467704
PMID: 28634427
DOI: 10.1177/1178222617713018

[…] including negation should also be analyzed. methods for identifying negation expressions have been developed in recent years.– chapman et al, developed a regular expression-based algorithm, negex, to search specific expressions (eg, not, without, and absence of) around a phrase to identify negated phrases. by evaluating different methods for negation detection, goryachev et al concluded […]

PMCID: 5383046
PMID: 28384212
DOI: 10.1371/journal.pone.0174708

[…] terms. for example, “no chest-pain” and “no fever, chills” would be substituted with “chest-pain_neg” and “fever_neg, _neg chills_neg”. we used a custom negation detection algorithm that is based on negex [], but has additional negation termination words that are optimized for ed triage nursing assessments. see for implementation details of the tokenization, bigram, and negation detection […]

PMCID: 4874549
PMID: 27203858
DOI: 10.1371/journal.pone.0156031

[…] mining concepts. nevertheless, metamap can eliminate the problems of term variants and synonymy by mapping clinical terms with terms in the umls database, those of negations by using the negation (negex) list, and those of word meaning ambiguity by using the word sense disambiguation (wsd) server [–]. here, all 4,515 journal articles were imported to the batch metamap 2014 server [] […]

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NegEx institution(s)
Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA; Departement of Computer and Systems Sciences (DSV), Stockholm University, Stockholm, Sweden; Department of clinical immunology and transfusion medicine, Karolinska University Hospital, Sweden; The Computer Sciences Laboratory for Mechanics and Engineering Sciences, CNRS, Orsay, France
NegEx funding source(s)
Supported by NIGMS-5R01GM090187, NLM-1R01LM010964, U54HL108460, and the Stockholm University Academic Initiative.

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