GeneTUKit statistics

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GeneTUKit specifications


Unique identifier OMICS_05278
Name GeneTUKit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes


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  • person_outline Jingchen Liu <>

Publication for GeneTUKit

GeneTUKit in publications

PMCID: 4170591
PMID: 25246425
DOI: 10.1093/database/bau094

[…] 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 gene normalization task () test data, we observed ∼5% increase in recall., second, an abbreviation […]

PMCID: 3839972
PMID: 24282506
DOI: 10.1371/journal.pone.0079517

[…] entities is indeed an indispensable process. recently, some advanced retrieval systems, such as biocontext and evex , have begun to integrate entity normalization/disambiguation components e.g., genetukit and gennorm to deal with the ambiguity issues. entity normalization goes beyond the recognition task by linking a textual entity mention to a knowledge base entry. several preliminary […]

PMCID: 3662864
PMID: 23707966
DOI: 10.1093/database/bat033

[…] of the event chains that can be formed is provided in supplementary file 2., the genes, transcripts and proteins that form the themes and causes of each event were extracted using gnat () and genetukit (). where possible, each mention is then normalized to a species using linnaeus () and further normalized to an entrez gene id () and finally a homologene id ()., we took all event chains […]

PMCID: 3629873
PMID: 23599415
DOI: 10.1093/database/bat020

[…] regarding genes/proteins extraction, most of the missing annotations could have been recognized by gnat if we had used a lower threshold. other tools could also be combined with gnat, such as genetukit () or banner (). additionally, use of domain-specific post-processing, such as ‘whitelists’ of genes/proteins, would certainly help, and future work will concentrate on these two […]

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

[…] gn software and web tools have been developed and made publicly available to the research community by participating teams. for example, three top-performing teams respectively delivered gennorm [], genetukit [], and iasl-iisr gene mention/normalization tool []., each team agreed to contribute a brief summary of the most notable aspects of their system. the team summaries are given below ranked […]

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GeneTUKit institution(s)
Department of Computer Science and Technology, Tsinghua University, Beijing, China

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