Open access - making the most of biomedical literature mining
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Open access - making the most of biomedical literature mining

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Open Access indenfor naturvidenskaberne, Copenhagen University Library, Copenhagen, Denmark, September 8, 2006

Open Access indenfor naturvidenskaberne, Copenhagen University Library, Copenhagen, Denmark, September 8, 2006

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Open access - making the most of biomedical literature mining Open access - making the most of biomedical literature mining Presentation Transcript

  • Open access – making the most of biomedical literature mining Lars Juhl Jensen EMBL Heidelberg
  • why open access?
  • why biomedicine?
  • why literature mining?
  • M EDLINE
  •  
  • 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 retrieval
  • finding the papers
  • if you can’t find them …
  • … they don’t exist!
  • ad hoc retrieval
  • users-specified query
  • “ yeast AND cell cycle”
  • 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
  •  
  •  
  • M EDLINE
  • abstracts
  • complete papers
  •  
  •  
  • tricks
  • stemming
  • yeast / yeasts
  • synonyms
  • yeast / S. cerevisiae
  • dynamic query expansion
  • next logical step
  • ontologies
  • annotation
  • Cdc28  yeast gene
  • Cdc28  cell cycle
  • 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
  • “ yeast AND cell cycle”
  • 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
  • if you can’t find them …
  • … they don’t exist!
  •  
  •  
  •  
  • abstracts
  • M EDLINE
  • tricks
  • good synonyms list
  • manual curation
  • orthographic variation
  • CDC28
  • Cdc28p
  • disambiguation
  • hairy
  • SDS
  • Cdc2
  • information extraction
  • formalizing the facts
  • co-mentioning
  • 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
  •  
  • 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
    • Gene and protein names
    • Cue words for entity recognition
    • Verbs for relation extraction
    • [ nxexpr T he expression of [ nxgene the cytochrome genes [ nxpg CYC1 and CYC7 ]]] is controlled by [ nxpg HAP1 ]
  •  
  • new discoveries
  • text mining
  •  
  •  
  • temporal trends
  •  
  • buzzwords
  •  
  • grant applications
  • global correlations
  • 32 79 83 3592 Regulates Regulated P < 9  10 -9
  • transcriptional networks
  • 11 27 44 3704 Phosphorylates Phosphorylated P < 2  10 -7
  • signal cascades
  • 8 107 47 3625 Expression Phosphorylation P < 5  10 -4
  •  
  • integration of text and data
  •  
  •  
  •  
  •  
  • network mining
  • linking genes to diseases
  •  
  •  
  •  
  •  
  • multifactorial diseases
  • genotype to phenotype
  •  
  •  
  •  
  • where are we now?
  •  
  • abstracts
  • complete papers
  • restricted access
  • open access
  • the tools are there
  • now we need the text!
  • Acknowledgments
    • Jasmin Saric
    • Rossitza Ouzounova
    • Michael Kuhn
    • Isabel Rojas
    • Miguel Andrade
    • Peer Bork