Can bibliographic pointers for known biological data be found automatically? Protein interactions as a case study

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. Copyright (C) 2001 John Wiley & Sons, Ltd.