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Biological literature mining - from information retrieval to biological discovery

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Lars Juhl Jensen
Lars Juhl Jensen

14th International Conference on Intelligent Systems for Molecular Biology, Tutorial, Fortaleza Conference Center, Fortaleza, Brazil, August 6-10, 2006

TechnologieFormation
1  sur  72
Biological literature mining from information retrieval to biological discovery Lars Juhl Jensen EMBL, Germany [email_address]
Why do we need it?
Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Status ,[object Object],[object Object],[object Object]
Example ,[object Object]
Information Retrieval and Entity Recognition Lars Juhl Jensen EMBL, Germany [email_address]
Information retrieval ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Example ,[object Object],[object Object],[object Object],[object Object]
Ad hoc IR ,[object Object],[object Object],[object Object],[object Object],[object Object]
 
 
 
 
Automatic query expansion ,[object Object],[object Object],[object Object],[object Object],[object Object]
 
Document similarity ,[object Object],[object Object],[object Object],[object Object],[object Object]
Document clustering ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Text categorization ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Machine learning ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Entity recognition ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Example ,[object Object],[object Object],[object Object]
Recognition ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Identification ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Disambiguation ,[object Object],[object Object],[object Object],[object Object],[object Object]
 
 
 
Summary ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Information Extraction and Text/Data Mining Lars Juhl Jensen , EMBL, Germany [email_address]
Overview ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
IE by co-occurrence ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Example ,[object Object],[object Object],[object Object]
 
Categorization ,[object Object],[object Object],[object Object],[object Object],[object Object]
 
NLP ,[object Object],[object Object],[object Object],[object Object]
Example ,[object Object],[object Object],[object Object],[object Object]
An NLP architecture ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
[ phosphorylation_active Lyn , [ negation but not Jak2 ] phosphorylated CrkL ] [ phosphorylation_active Lyn also participates in [ phosphorylation the tyrosine phosphorylation and activation of syk ]] [ phosphorylation_nominal the phosphorylation of the adapter protein SHC by the Src-related kinase Lyn ] [ phosphorylation_nominal phosphorylation of Shc by the hematopoietic cell-specific tyrosine kinase Syk ] [ dephosphorylation_nominal Dephosphorylation of Syk and Btk mediated by SHP-1 ] [ expression_activation_passive [ expression IL-13 expression ] induced by IL-2 + IL-18 ] [ expression_repression_active IL-10 also decreased [ expression mRNA expression of IL-2 and IL-18 cytokine receptors ] [ expression_repression_active Btk regulates the IL-2 gene ]
 
Mining text for nuggets ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
 
Trends ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Time
Successful genes
Buzzwords
Correlations ,[object Object],[object Object],[object Object],[object Object],[object Object]
Transcriptional networks 32 79 83 3592 Regulates Regulated P < 9  10 -9
Signaling pathways 11 27 44 3704 Phosphorylates Phosphorylated P < 2  10 -7
Multiple regulation 8 107 47 3625 Expression Phosphorylation P < 5  10 -4
Integration ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Annotation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
 
 
 
Disease candidate genes ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
G2D
 
 
 
Genotype–phenotype ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
 
 
Summary ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Outlook Lars Juhl Jensen EMBL, Germany [email_address]
Necessity ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Permission ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Innovation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Acknowledgments ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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En vedette

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En vedette (7)

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Biological literature mining - from information retrieval to biological discovery

  • 1. Biological literature mining from information retrieval to biological discovery Lars Juhl Jensen EMBL, Germany [email_address]
  • 2. Why do we need it?
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  • 6. Information Retrieval and Entity Recognition Lars Juhl Jensen EMBL, Germany [email_address]
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  • 29. Information Extraction and Text/Data Mining Lars Juhl Jensen , EMBL, Germany [email_address]
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  • 40. [ phosphorylation_active Lyn , [ negation but not Jak2 ] phosphorylated CrkL ] [ phosphorylation_active Lyn also participates in [ phosphorylation the tyrosine phosphorylation and activation of syk ]] [ phosphorylation_nominal the phosphorylation of the adapter protein SHC by the Src-related kinase Lyn ] [ phosphorylation_nominal phosphorylation of Shc by the hematopoietic cell-specific tyrosine kinase Syk ] [ dephosphorylation_nominal Dephosphorylation of Syk and Btk mediated by SHP-1 ] [ expression_activation_passive [ expression IL-13 expression ] induced by IL-2 + IL-18 ] [ expression_repression_active IL-10 also decreased [ expression mRNA expression of IL-2 and IL-18 cytokine receptors ] [ expression_repression_active Btk regulates the IL-2 gene ]
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  • 50. Transcriptional networks 32 79 83 3592 Regulates Regulated P < 9  10 -9
  • 51. Signaling pathways 11 27 44 3704 Phosphorylates Phosphorylated P < 2  10 -7
  • 52. Multiple regulation 8 107 47 3625 Expression Phosphorylation P < 5  10 -4
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  • 68. Outlook Lars Juhl Jensen EMBL, Germany [email_address]
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