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EVEX specifications


Unique identifier OMICS_12912
Alternative name EVent EXtraction
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes



  • person_outline Filip Ginter

Publication for EVent EXtraction

EVEX citations


New hairworm (Nematomorpha, Gordiida) species described from the Arizona Madrean Sky Islands

PMCID: 5806596
PMID: 29434487
DOI: 10.3897/zookeys.733.22798

[…] nally, specimens were dried using HDMS, mounted on aluminum stubs, coated with gold palladium, and examined with a FEI Quanta 600 field emission gun ESEM (ThermoFisher Scientific, Hillsboro, OR) with Evex EDS and HKL EBSD as described previously (). The following morphological surface characteristics were recorded for at least 30 individual larvae: number of terminal spines on the postseptum, the […]


SciLite: a platform for displaying text mined annotations as a means to link research articles with biological data

Wellcome Open Res
PMCID: 5527546
PMID: 28948232
DOI: 10.21956/wellcomeopenres.10999.r18949

[…] er of text-mining based tools that have been developed to facilitate automated extraction of various article types and biological concepts, such as Textpresso ( ), iHOP ( ), Whatizit ( ), EAGLi ( ; ) EVEX ( ), PubTator ( ) and Argo ( ). Among these tools, Textpresso has been significantly adapted by data providers and the curation community to triage articles for curation ( ; ). Collaboration betw […]


Role of activating transcription factor 4 in the hepatic response to amino acid depletion by asparaginase

Sci Rep
PMCID: 5430736
PMID: 28455513
DOI: 10.1038/s41598-017-01041-7

[…] ome P450-mediated reactions and activation of cytoplasmic nuclear receptors (e.g., FXR, RXR, PXR, LXR, VDR) stood out as shared among categories E, F, G. Interestingly, biomolecular data mining using EVEX (evexdb.org) indicated that ATF4 binds LXR, PXR and RXR and coregulates multiple gene families; many of these encode transcriptional and translational responses to ER and oxidative stress in addi […]


Gene expression changes in damaged osteoarthritic cartilage identify a signature of non chondrogenic and mechanical responses

PMCID: 4989048
PMID: 26973327
DOI: 10.1016/j.joca.2016.03.007

[…] Chip-seq data from ENCODE and ReMap was used to produce ranked lists of target genes for each TF by the enrichment score, . Text-mining based TF to gene regulatory interactions were derived from the EVEX database. Coexpression data was taken from CoExpressDB for human experiments across GEO and genes were ranked for each TF by correlation. The differentially expressed upregulated or down-regulate […]


Defined enzyme cocktail from the anaerobic fungus Orpinomyces sp. strain C1A effectively releases sugars from pretreated corn stover and switchgrass

Sci Rep
PMCID: 4933900
PMID: 27381262
DOI: 10.1038/srep29217

[…] -sided tape and gold-palladium-coated (Balzers Union MED 010 Au-Pd Sputter Coater, Liechtenstein). Samples were viewed with a Scanning Electron Microscope (FEI Quanta 600 field emission gun ESEM with Evex EDS and HKL EBSD). For each sample, (Swol-treated and control), five random images were taken at 1500 x magnification. Images were analyzed using ImageJ. For each of the images, ten cotton fibers […]


Filtering large scale event collections using a combination of supervised and unsupervised learning for event trigger classification

J Biomed Semantics
PMCID: 4864999
PMID: 27175227
DOI: 10.1186/s13326-016-0070-4

[…] nd all of their parts, using the BioLemmatizer tool [] which is specifically developed for the biomedical domain, and record all the produced lemmas for each trigger word.After the preprocessing, 977 EVEX trigger words that can directly be found in the ST-set are regarded as safe. The rest of the triggers are regarded as safe if their exact form, or one of their parts, or one of the lemmas of thei […]


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EVEX institution(s)
Department of Plant Systems Biology, VIB, Gent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium; Department of Information Technology, University of Turku, Turku, Finland; Turku BioNLP Group, Turku Centre for Computer Science (TUCS), Turku, Finland
EVEX funding source(s)
This work was partly funded by the Academy of Finland, and the computational resources were provided by CSC-IT Center for Science Ltd., Espoo, Finland and the Department of IT, University of Turku, Finland.

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