Facts from Text—Is Text Mining Ready to Deliver 英文参考文献.docVIP

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Facts from Text—Is Text Mining Ready to Deliver 英文参考文献.doc

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Facts from Text—Is Text Mining Ready to Deliver 英文参考文献

Open access, freely available online Essay Facts from Text—Is Text Mining Ready to Deliver? Dietrich Rebholz-Schuhmann*, Harald Kirsch, Francisco Couto B iological databases offer access to formalized facts about many aspects of biology—genes and gene products, protein structure, metabolic pathways, diseases, organisms, and so on. These databases are becoming increasingly important to researchers. The information that populates databases is generated by research teams and is usually published in peer-reviewed journals. As part of the publication process, some authors deposit data into a database but, more often, it is extracted from the published literature and deposited into the databases by human curators, a painstaking process. Research literature and scienti?c databases ful?l different needs. Literature provides ideas and new hypotheses, but is not constrained to provide facts in formats suitable for use in databases. By contrast, databases ef?ciently provide large quantities of data and information in a standardised schema representing a prede?ned interpretation of the data. While the acceptance of a paper can enforce the submission of data to a central data repository, such as EMBL (http:??www. ebi.ac.uk/embl/) or ArrayExpress (http:??www.ebi.ac.uk/arrayexpress/), nobody receives credit for the submission of a fact to a database without an associated publication. As long as this practice continues, curation will be necessary to add the (re)formalised facts to biological databases. Given that publications are not about to be replaced with routine deposition of data into databases, is it possible to develop software tools to support the work of the curator? Could we automatically analyse new scienti?c publications routinely to extract facts, which could then be inserted into scienti?c databases? Could we tag gene and protein names, as well as other DOI: 10.1371/journal.pbio.0030065.g001 Figure 1. Medline Article Deluge This ?gure shows the exploding number