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GENIA Tagger specifications


Unique identifier OMICS_05279
Name GENIA Tagger
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes


No version available

GENIA Tagger citations


Classification and analysis of a large collection of in vivo bioassay descriptions

PLoS Comput Biol
PMCID: 5517062
PMID: 28678787
DOI: 10.1371/journal.pcbi.1005641

[…] based on their semantic similarity., we begin with preprocessing and grammatical analysis of the assay descriptions extracted from chembl (the overview of this step is illustrated by ). we use the genia tagger to tokenize the sentences and to annotate the words with part-of-speech (pos) tags and other linguistic features. next, we use custom grammatical patterns to chunk the descriptions […]


Disease named entity recognition by combining conditional random fields and bidirectional recurrent neural networks

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

[…] corpus: we use a sentence boundary detection tool called ‘splitta’ ( to split each pubmed abstract into sentences which are subsequently tagged using the genia tagger (); (ii) feature extraction: this component extracts the features from the preprocessed pubmed text, including words, part-of-speech tags, chunking information, word shape features […]


Building a glaucoma interaction network using a text mining approach

BioData Min
PMCID: 4857381
PMID: 27152122
DOI: 10.1186/s13040-016-0096-2

[…] the text retrieval step performance metrics and values are listed in table  and table . for the entity extraction step performance, the genia tagger targets a broader domain. hence, it can be expected to tag varied entities (including localization, cell type, dna, etc.), but possibly less genes/proteins than the gentag tagger. […]


Exploiting syntactic and semantics information for chemical–disease relation extraction

PMCID: 4831723
PMID: 27081156
DOI: 10.1093/database/baw048

[…] cdr task, we ignore cdr across sentences and only identify cdr in a sentence. each chemical–disease pair in a sentence is regarded as a candidate instance. the cdr corpus is preprocessed with genia tagger (, berkeley parser ( and gdep parser ( to get lexical […]


Text Mining the History of Medicine

PLoS One
PMCID: 4703377
PMID: 26734936
DOI: 10.1371/journal.pone.0144717

[…] types of linguistic information in the accurate prediction of semantic information, nersuite comes with built-in functionality to carry out linguistic pre-processing, using the biomedically-tuned genia tagger []. the suitability of nersuite for application in our scenario is reinforced by its previous use in the development of a number of other medically-relevant ne tools, which achieved high […]


A Relation Extraction Framework for Biomedical Text Using Hybrid Feature Set

PMCID: 4546954
PMID: 26347797
DOI: 10.1155/2015/910423

[…] (nlp) information is the second representation. it has noun phrases and verb phrases that are very important for relation classification. we consider these phrasal features with the unigrams. genia tagger [] is used to extract the syntactical information from the data. genia tagger is specially designed for biomedical text, such as, medline abstracts. the tagger takes an english sentence […]

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