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Open access - making the most of biomedical literature mining

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Lars Juhl Jensen
Lars Juhl Jensen

Berlin 4 Open Access - From Promise to Practice, Max-Planck-Institute for Gravitational Physics, Potsdam-Golm, Germany, March 29-31, 2006

TechnologyBusiness
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Open access – making the most of biomedical literature mining Lars Juhl Jensen EMBL Heidelberg
why open access?
why biomedicine?
why literature mining?
M EDLINE
Jensen et al., Nature Reviews Genetics, 2006
information retrieval
finding the papers
 
Mitotic cyclin (Clb2)-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5-dependent Swe1 hyperphosphorylation and degradation
entity recognition
identifying the substance(s)
Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation
 
 
information extraction
formalizing the facts
co-mentioning
 
NLP Natural Language Processing
Mitotic cyclin ( Clb2 )-bound Cdc28 (Cdk1 homolog) directly phosphorylated Swe1 and this modification served as a priming step to promote subsequent Cdc5 -dependent Swe1 hyperphosphorylation and degradation
[object Object],[object Object],[object Object],[object Object],[object Object]
Jensen et al., Nature Reviews Genetics, 2006
new discoveries
text mining
Jensen et al., Nature Reviews Genetics, 2006
integration of text and data
open access databases
von Mering et al., Nucleic Acids Research, 2005
 
network mining
genotype to phenotype
Korbel et al., PLoS Biology, 2005
Korbel et al., PLoS Biology, 2005
Korbel et al., PLoS Biology, 2005
where are we now?
Jensen et al., Nature Reviews Genetics, 2006
abstracts
complete papers
restricted access
open access
the tools are there
now we need the text!
Acknowledgments ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Thank you!

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