ArticleAdvances in bioinformatics2012
Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations.
Article in Advances in bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
18 citing papers in PubMed.
- Integrating Multi-Source Directed Gene Networks and Multi-Omics Data to Identify Cancer Driver Genes Based on Graph Neural Networks.International journal of molecular sciences · 2025Article
- Integration of multi-source gene interaction networks and omics data with graph attention networks to identify novel disease genes.Bioinformatics (Oxford, England) · 2025Article
- GePI: large-scale text mining, customized retrieval and flexible filtering of gene/protein interactions.Nucleic acids research · 2023Article
- A systematic evaluation of the computational tools for ligand-receptor-based cell-cell interaction inference.Briefings in functional genomics · 2022Article
- CellCall: integrating paired ligand-receptor and transcription factor activities for cell-cell communication.Nucleic acids research · 2021Article
- Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.Database : the journal of biological databases and curation · 2019Article
- BUSCA: an integrative web server to predict subcellular localization of proteins.Nucleic acids research · 2018Article
- Topological estimation of signal flow in complex signaling networks.Scientific reports · 2018Article
- The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.Nucleic acids research · 2017Article
- Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification.Journal of biomedical semantics · 2016Article
- Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes.Plant physiology · 2015Article
- Leaf responses to mild drought stress in natural variants of Arabidopsis.Plant physiology · 2015Article
- Application of the EVEX resource to event extraction and network construction: Shared Task entry and result analysis.BMC bioinformatics · 2015Article
- Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events.BMC systems biology · 2015Article
- OncoSearch: cancer gene search engine with literature evidence.Nucleic acids research · 2014Article
- Large-scale biomedical concept recognition: an evaluation of current automatic annotators and their parameters.BMC bioinformatics · 2014Article
- The potential of text mining in data integration and network biology for plant research: a case study on Arabidopsis.The Plant cell · 2013Article
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Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Technological advancements in the field of genetics have led not only to an abundance of experimental data, but also caused an exponential increase of the number of published biomolecular studies. Text mining is widely accepted as a promising technique to help researchers in the life sciences deal with the amount of available literature. This paper presents a freely available web application built on top of 21.3 million detailed biomolecular events extracted from all PubMed abstracts. These text mining results were generated by a state-of-the-art event extraction system and enriched with gene family associations and abstract generalizations, accounting for lexical variants and synonymy. The EVEX resource locates relevant literature on phosphorylation, regulation targets, binding partners, and several other biomolecular events and assigns confidence values to these events. The search function accepts official gene/protein symbols as well as common names from all species. Finally, the web application is a powerful tool for generating homology-based hypotheses as well as novel, indirect associations between genes and proteins such as coregulators.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.