Can Bibliographic Pointers for Known Biological Data Be Found Automatically Protein Interactions as a Case Study英文文献资料.docVIP

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Can Bibliographic Pointers for Known Biological Data Be Found Automatically Protein Interactions as a Case Study英文文献资料.doc

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Can Bibliographic Pointers for Known Biological Data Be Found Automatically Protein Interactions as a Case Study英文文献资料

ComparativeandFunctionalGenomics CompFunctGenom2001;2 :196–206. DOI:10.1002/cfg.91 ResearchArticle Canbibliographicpointersforknown biologicaldatabefoundautomatically? Proteininteractionsasacasestudy ChristianBlaschkeandAlfonsoValencia* ProteinDesignGroup,NationalCentreforBiotechnology,CNB-CSIC,Cantoblanco,MadridE-28049,Spain Abstract *Correspondenceto: A.Valencia,ProteinDesignGroup, NationalCentrefor Biotechnology,CNB-CSIC, Cantoblanco,MadridE-28049, Spain. TheDictionaryofInteractingProteins(DIP)(Xenariosetal.,2000)isalargerepository of protein interactions: its March 2000 release included 2379protein 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. E-mail:valencia@cnb.uam.es 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.Itisclearthatthelimitationofanalyzingabstractsratherthanfullpapersandthe lack of standard protein names are dif?culties of considerably more importance than the limitations of the IE methodology employed. A positive ?nding is the capacity of the IE system to identify new relations between proteins, even in a set of proteins previously characterizedbyhumanexperts.Theseidenti?cationsaremadewithaconsiderabledegree ofprecision. This is, to our knowledge, the ?rst large scale assessment of IE capacity to detect previouslyknowninteractions:wethusproposetheuseoftheDIPdataset