open access – making the most of biomedical literature...
TRANSCRIPT
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Open access – making the mostof biomedical literature mining
Lars Juhl JensenEMBL Heidelberg
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why open access?
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why biomedicine?
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why literature mining?
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MEDLINE
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Jensen et al., Nature Reviews Genetics, 2006
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information retrieval
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finding the papers
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Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1homolog) directly phosphorylated Swe1 andthis modification served as a priming step topromote subsequent Cdc5-dependent Swe1
hyperphosphorylation and degradation
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entity recognition
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identifying the substance(s)
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Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1homolog) directly phosphorylated Swe1 andthis modification served as a priming step topromote subsequent Cdc5-dependent Swe1
hyperphosphorylation and degradation
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information extraction
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formalizing the facts
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co-mentioning
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NLPNatural Language Processing
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Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1homolog) directly phosphorylated Swe1 andthis modification served as a priming step topromote subsequent Cdc5-dependent Swe1
hyperphosphorylation and degradation
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Gene and protein namesCue words for entity recognitionVerbs for relation extraction
[nxgene The GAL4 gene]
[nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]]is controlled by[nxpg HAP1]
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Jensen et al., Nature Reviews Genetics, 2006
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new discoveries
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text mining
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Jensen et al., Nature Reviews Genetics, 2006
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integration of text and data
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open access databases
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von Mering et al., Nucleic Acids Research, 2005
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network mining
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genotype to phenotype
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Korbel et al., PLoS Biology, 2005
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Korbel et al., PLoS Biology, 2005
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Korbel et al., PLoS Biology, 2005
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where are we now?
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Jensen et al., Nature Reviews Genetics, 2006
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abstracts
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complete papers
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restricted access
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open access
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the tools are there
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now we need the text!
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Acknowledgments
Work done in collaboration withPeer Bork
Jasmin SaricRossitza Ouzounova
Michael KuhnIsabel Rojas
Presentation style stolen fromLawrence Lessig
Dick Clarence Hardt
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Thank you!