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Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations.

Van Landeghem S, Hakala K, Rönnqvist S, Salakoski T, Van de Peer Y, Ginter F - Adv Bioinformatics (2012)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium.

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.

No MeSH data available.


Related in: MedlinePlus

Detailed representation of all evidence supporting the regulation of RAD9 by Mec1. Regulatory mechanisms can have a certain polarity (positive/negative) and may involve physical events such as phosphorylation or protein-DNA binding.
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fig4: Detailed representation of all evidence supporting the regulation of RAD9 by Mec1. Regulatory mechanisms can have a certain polarity (positive/negative) and may involve physical events such as phosphorylation or protein-DNA binding.

Mentions: Selecting the target RAD9, the web application visualises all event structures expressing regulation of RAD9 by Mec1 (Figure 4). This enables a quick overview of the mechanisms through which the regulation is established, which can have a certain polarity (positive/negative) and may involve physical events such as phosphorylation or protein-DNA binding. The different types of event structures are coarsely grouped into categories of similar events and presented from most to least reliable using the confidence scores.


Exploring Biomolecular Literature with EVEX: Connecting Genes through Events, Homology, and Indirect Associations.

Van Landeghem S, Hakala K, Rönnqvist S, Salakoski T, Van de Peer Y, Ginter F - Adv Bioinformatics (2012)

Detailed representation of all evidence supporting the regulation of RAD9 by Mec1. Regulatory mechanisms can have a certain polarity (positive/negative) and may involve physical events such as phosphorylation or protein-DNA binding.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3375141&req=5

fig4: Detailed representation of all evidence supporting the regulation of RAD9 by Mec1. Regulatory mechanisms can have a certain polarity (positive/negative) and may involve physical events such as phosphorylation or protein-DNA binding.
Mentions: Selecting the target RAD9, the web application visualises all event structures expressing regulation of RAD9 by Mec1 (Figure 4). This enables a quick overview of the mechanisms through which the regulation is established, which can have a certain polarity (positive/negative) and may involve physical events such as phosphorylation or protein-DNA binding. The different types of event structures are coarsely grouped into categories of similar events and presented from most to least reliable using the confidence scores.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Systems Biology, VIB, Technologiepark 927, 9052 Gent, Belgium.

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.

No MeSH data available.


Related in: MedlinePlus