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About

EVEX is a text mining resource built on top of PubMed abstracts and PubMed Central full text articles. It contains over 40 million bio-molecular events among more than 76 million automatically extracted gene/protein name mentions. The text mining data further has been enriched with gene identifiers and gene families from Ensembl and HomoloGene, providing homology-based event generalizations. EVEX presents both direct and indirect associations between genes and proteins, enabling explorative browsing of relevant literature.

Community collaboration:

The EVEX resource is made possible thanks to collaborative efforts within the BioNLP community, specifically by the BioNLP group at the University of Turku (Finland), the Tsujii lab at Tokyo University (Japan), the Bioinformatics group at Ghent University (Belgium), the NaCTeM text mining center at the University of Manchester (UK) and the Intelligent Knowledge Management Laboratory at the National Cheng Kung University of Tainan (Taiwan).

Software components:

EVEX is primarily built upon the NER package BANNER, the TEES event extraction system and the NEN system GenNorm. Further, events are visualised on the website using the stav visualiser.

Support and funding:

The development of EVEX is possible thanks to funding granted by University of Turku, Turku Centre for Computer Science (TUCS), Academy of Finland, the Belgian Research Foundation Flanders (FWO-Vlaanderen), the Intramural Research Program of NIH, NLM and the UK Biotechnology and Biological Sciences Research Council (BBSRC). Computational resources are provided by CSC - IT Center for Science.

Terms of use:

EVEX is provided as a free service to anybody interested, on an "as is" basis with no warranty whatsoever. We disallow scripted access via the web interface, as bulk downloads will be made publicly available for each major upgrade. Further, we are always happy to discuss possible collaborations on the extension of data or functionality within EVEX. If you use EVEX in research, please consult the FAQ page for citation details. The textual data underlying EVEX are PubMed abstracts and PubMed Central full text articles, which are covered by the Terms of use of PubMed.

Contact:

Filip Ginter
Sofie Van Landeghem
All interactions mentioned for the specific gene symbol in text. The results are not restricted to any specific organism.
All interactions for genes that have these gene symbols as official name or synonym. The results are restricted to specific organisms and synonyms are taken into account.
All interactions for families that contain genes with these gene symbols as official name or synonym. The results group interologs and regulogs together, and synonyms are taken into account for each gene in the gene family.
All interactions mentioned between these specific gene symbols in text. The results are not restricted to any specific organism.
All interactions between genes that have these gene symbols as official name or synonym. The results are restricted to specific organisms and synonyms are taken into account.
All interactions between families that contain genes with these gene symbols as official name or synonym. The results group interologs and regulogs together, and synonyms are taken into account for each gene in the gene family.
We recommend the latest versions of Google Chrome or Mozilla Firefox browsers for the best visualization experience. Internet Explorer versions 9 and 10 have been tested as well and should show the visualization correctly. However, older Internet Explorer versions are not capable of showing the graphics format used in these visualizations.