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Event-based text mining for biology and functional genomics.

Ananiadou S, Thompson P, Nawaz R, McNaught J, Kell DB - Brief Funct Genomics (2014)

Bottom Line: This article provides an overview of recent research into event extraction.We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems.Finally, several concrete applications of event extraction are covered, together with emerging directions of research.

View Article: PubMed Central - PubMed

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PathText 2 Interface.
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elu015-F10: PathText 2 Interface.

Mentions: PathText 2 (http://www.nactem.ac.uk/pathtext2/demo/) [109] is an integrated search system that links biological pathways with supporting knowledge in the literature. It reads formal pathway models (represented in the Systems Biology Markup Language (SBML) [131] with CellDesigner [132]) and converts them into queries that are submitted to three semantic search systems operating over MEDLINE, i.e. KLEIO [6], which improves and expands on standard literature querying with semantic categories and facetted search, FACTA+ and MEDIE (both the original and GENIA event-based versions). The average hit ratio of each system (i.e. the fraction of queries generated by PathText 2 that retrieve a given document) is considered when ranking the documents. The GENIA event-based version of MEDIE was found to achieve the highest hit ratio, demonstrating the superiority of this search method. Accordingly, documents retrieved by this method are ranked first by the system. Figure 10 shows the PathText 2 interface. An SBML model is selected or uploaded, and a reaction is chosen. Textual evidence for the queried reaction in retrieved documents is displayed in the interface, along with a confidence score.Figure 10:


Event-based text mining for biology and functional genomics.

Ananiadou S, Thompson P, Nawaz R, McNaught J, Kell DB - Brief Funct Genomics (2014)

PathText 2 Interface.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4499874&req=5

elu015-F10: PathText 2 Interface.
Mentions: PathText 2 (http://www.nactem.ac.uk/pathtext2/demo/) [109] is an integrated search system that links biological pathways with supporting knowledge in the literature. It reads formal pathway models (represented in the Systems Biology Markup Language (SBML) [131] with CellDesigner [132]) and converts them into queries that are submitted to three semantic search systems operating over MEDLINE, i.e. KLEIO [6], which improves and expands on standard literature querying with semantic categories and facetted search, FACTA+ and MEDIE (both the original and GENIA event-based versions). The average hit ratio of each system (i.e. the fraction of queries generated by PathText 2 that retrieve a given document) is considered when ranking the documents. The GENIA event-based version of MEDIE was found to achieve the highest hit ratio, demonstrating the superiority of this search method. Accordingly, documents retrieved by this method are ranked first by the system. Figure 10 shows the PathText 2 interface. An SBML model is selected or uploaded, and a reaction is chosen. Textual evidence for the queried reaction in retrieved documents is displayed in the interface, along with a confidence score.Figure 10:

Bottom Line: This article provides an overview of recent research into event extraction.We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems.Finally, several concrete applications of event extraction are covered, together with emerging directions of research.

View Article: PubMed Central - PubMed

No MeSH data available.