2001 CanBiblioPointersProteinInteractionsAsACaseStudy

(Blaschke & Valencia, 2001) ⇒ Christian Blaschke, Alfonso Valencia. (2001). “Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study.” In: Comparative and Functional Genomics, 2.

Subject Headings: Relation Recognition, Protein-Protein Interaction

Notes

Cited By

~58 http://scholar.google.com/scholar?cites=16070970677626548266

Quotes

Abstract

The Dictionary of Interacting Proteins (DIP) (Xenarios et al., [2000]) is a large repository of protein interactions: its March 2000 release included 2379 protein pairs whose interactions have been detected by experimental methods. Even if many of these correspond to poorly characterized proteins, the result of massive yeast two-hybrid screenings, as many as 851 correspond to interactions detected using direct biochemical methods.

We used information retrieval technology to search automatically for sentences in Medline abstracts that support these 851 DIP interactions. Surprisingly, we found correspondence between DIP protein pairs and Medline sentences describing their interactions in only 30% of the cases. This low coverage has interesting consequences regarding the quality of annotations (references) introduced in the database and the limitations of the application of information extraction (IE) technology to Molecular Biology. It is clear that the limitation of analyzing abstracts rather than full papers and the lack of standard protein names are difficulties of considerably more importance than the limitations of the IE methodology employed. A positive finding is the capacity of the IE system to identify new relations between proteins, even in a set of proteins previously characterized by human experts. These identifications are made with a considerable degree of precision.

This is, to our knowledge, the first large scale assessment of IE capacity to detect previously known interactions: we thus propose the use of the DIP data set as a biological reference to benchmark IE systems.

References

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	Author	volume	Date Value	title	type	journal	titleUrl	doi	note	year
2001 CanBiblioPointersProteinInteractionsAsACaseStudy	Alfonso Valencia Christian Blaschke			Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study			http://doi.wiley.com/10.1002/cfg.91	10.1002/cfg.91