Limits...
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

Visualization of a specific event occurrence by the stav text annotation visualiser. Genes and gene products (“GGPs”) are marked, as well as the trigger words that refer to specific event types. Finally, arrows denote the roles of each argument in the event (e.g. Theme or Cause). This visualization corresponds to the formal bracketed format of the event: Positive-regulation(C: Mec1, T:Phosphorylation(T:RAD9)).
© Copyright Policy - open-access
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3375141&req=5

fig6: Visualization of a specific event occurrence by the stav text annotation visualiser. Genes and gene products (“GGPs”) are marked, as well as the trigger words that refer to specific event types. Finally, arrows denote the roles of each argument in the event (e.g. Theme or Cause). This visualization corresponds to the formal bracketed format of the event: Positive-regulation(C: Mec1, T:Phosphorylation(T:RAD9)).

Mentions: Consider, for example, the phosphorylation of RAD9, regulated by Mec1 (Figure 4). To allow a detailed inspection of this event, the web application integrates the stav visualiser [26], which was developed as a supporting resource for the ST'11 [2] (Figure 6). This open-source tool provides a detailed and easily graspable presentation of the event structures and the associated textual spans. To any user interested in the text mining details, this visualization provides valuable insights into the automated event extraction process. Additionally, the web application provides the opportunity to visualise whole PubMed abstracts with the stav visualiser, allowing a fast overview of event information contained within an abstract.


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)

Visualization of a specific event occurrence by the stav text annotation visualiser. Genes and gene products (“GGPs”) are marked, as well as the trigger words that refer to specific event types. Finally, arrows denote the roles of each argument in the event (e.g. Theme or Cause). This visualization corresponds to the formal bracketed format of the event: Positive-regulation(C: Mec1, T:Phosphorylation(T:RAD9)).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig6: Visualization of a specific event occurrence by the stav text annotation visualiser. Genes and gene products (“GGPs”) are marked, as well as the trigger words that refer to specific event types. Finally, arrows denote the roles of each argument in the event (e.g. Theme or Cause). This visualization corresponds to the formal bracketed format of the event: Positive-regulation(C: Mec1, T:Phosphorylation(T:RAD9)).
Mentions: Consider, for example, the phosphorylation of RAD9, regulated by Mec1 (Figure 4). To allow a detailed inspection of this event, the web application integrates the stav visualiser [26], which was developed as a supporting resource for the ST'11 [2] (Figure 6). This open-source tool provides a detailed and easily graspable presentation of the event structures and the associated textual spans. To any user interested in the text mining details, this visualization provides valuable insights into the automated event extraction process. Additionally, the web application provides the opportunity to visualise whole PubMed abstracts with the stav visualiser, allowing a fast overview of event information contained within an abstract.

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