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AIIA-GMT specifications


Unique identifier OMICS_07927
Alternative name AIIA Gene Mention Tagger
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 0.05
Stability Stable
Maintained Yes


No version available


  • person_outline Cheng-Ju Kuo

Publication for AIIA Gene Mention Tagger

AIIA-GMT citations


Hybrid curation of gene–mutation relations combining automated extraction and crowdsourcing

PMCID: 4170591
PMID: 25246425
DOI: 10.1093/database/bau094
call_split See protocol

[…] odule of GenNorm such that only human genes were returned. Two additional steps were implemented to optimize results for this study:First, a second gene tagger was included. The original GenNorm uses AIIA-GMT () for recognizing GMs from a textual passage. To maximize recall, we added another system, GeneTuKit (), to the GM module of GenNorm. Based on the benchmarking results on the BioCreative II […]


The gene normalization task in BioCreative III

BMC Bioinformatics
PMCID: 3269937
PMID: 22151901
DOI: 10.1186/1471-2105-12-S8-S2

[…] efers to resolve an ambiguous gene name to an identifier already known to be connected to other genes mentioned in the document based on curated biological relations.Our system for BCIII:(1) used the AIIA-GMT gene mention tagger [] to identify gene mentions,(2) mapped each mention to candidate database identifiers using the BioThesaurus v.6.0 [],(3) applied abbreviation detection using the Schwart […]


Integrating text mining into the MGI biocuration workflow

PMCID: 2797454
PMID: 20157492
DOI: 10.1093/database/bap019

[…] the MGI GO curation team with a suite of tools they could start using immediately to help streamline gene indexing and GO annotation functions.Based on the results of this project, we recommended the AIIA gene mention tagger as a general, open-access resource for MGI curators. The MGI GO curation team is continuing to test OBA as tool for screening and prioritizing articles for curation. We have b […]


Incorporating rich background knowledge for gene named entity classification and recognition

BMC Bioinformatics
PMCID: 2725142
PMID: 19615051
DOI: 10.1186/1471-2105-10-223

[…] We would like to thank the anonymous reviewers for many useful suggestions, as well as Bob Leaman and Cheng-Ju Kuo for answering our questions about the BANNER and AIIA-GMT systems. This work was supported by grant from the Natural Science Foundation of China (No. 60373095 and 60673039) and the National High Tech Research and Development Plan of China (2006AA01Z […]


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AIIA-GMT institution(s)
Institute of Information Science, Academia Sinica and Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan

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