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Next generation semantic support technology

Next generation semantic support technology. CD40 ligand and tumor necro sis factor alpha , the cells acquire a mature phenotype of dendritic cells that is characterized by up - regulation of human leukocy te antigen ( CD80 , CD86 , CD40

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Next generation semantic support technology

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  1. Next generation semantic support technology CD40ligand and tumornecro sisfactoralpha, the cells acquire a mature phenotype of dendriticcells that is characterized by up-regulation of humanleukocy teantigen (CD80, CD86, CD40 and CD54 and appearance of CD83. These

  2. What we are NOT • A Search Engine • A Pathway Tool • An Annotated Database

  3. What do we do ? • Disambiguate Text • Meta-analyse at concept level • Provide meta-analysed information • Support Information Based Knowledge Discovery (especially new associations)

  4. Ambiguity 1: Synonyms Relatively straightforward: Thesaurus • Facilitating networks of information. van Mulligen EM, Diwersy M, Schmidt M, Buurman H, Mons B • Proceedings of AMIA Symposium 2000, 868-72

  5. Ambiguity 2: Homonyms PSA Prostate Specific Antigen PSoriatic Arthritis alpha-2,8-PolySialic Acid PolySubstance Abuse Picryl Sulfonic Acid Polymeric Silicic Acid Partial Sensory Agnosia Poultry Science Association Not so easy: context needed • Distribution of information in biomedical abstracts and full-text publications, Schuemie MJ, Weeber M, Schijvenaars BJ, van Mulligen EM, • van der Eijk CC, Jelier R, Mons B, Kors JA, Bioinformatics 2004Nov 1, 20:2597-604

  6. Contextual annotation of web pages for interactive browsing, van Mulligen E, Diwersy M, Schijvenaars B, Weeber M, van der Eijk CC, Jelier R, Schuemie M, Kors J, Mons B, Medinfo 2004, 11:94-8 • Which gene did you mean?, Mons B, BMC Bioinformatics 2005 Jun 7, 6:142 The Knowlet

  7. Creating Reference Knowlets PSA Prostate Specific Antigen Reference Knowlet PSA Psoriatic Arthritis Reference Knowlet

  8. Reference Knowlet Reference Knowlet Context matching New text Prostate Specific Antigen • 93 % correct in • ‘Worst Case Scenario’ • 98 % overall…. PSA ?? x Psoriatic Arthritis • Thesaurus-based disambiguation of gene symbols. Schijvenaars BJ, Mons B, Weeber M, Schuemie MJ, van Mulligen EM, Wain HM, Kors JA • BMC Bioinformatics 2005Jun 16, 6:149 • Word sense disambiguation in the biomedical domain: an overview. Schuemie MJ, Kors JA, Mons B, Journal of Computational Biology 2005 Jun, 12:554-65

  9. person organisation Object 1 Object 2 Object 3 drug disease Building an association matrix of large data sources gene > 15 million Knowlets from PubMed etc.

  10. A matrix of associative distances meta-analysis Hierarchical Clustering ACS MDS Etc.

  11. Meta-analysis 1: ACS • Constructing an Associative Concept Space for Literature-based Discovery, van der Eijk CC, van Mulligen EM, Kors JA, Mons B, van den Berg J • Journal of the American Society for Information Science and Technology 2004, 55(5): 436-444 • Co-occurrence based meta-analysis of scientific texts: retrieving biological relationships between genes. Jelier R, Jenster G, Dorssers LC, van der Eijk CC, • van Mulligen EM, Mons B, Kors JA Bioinformatics2005 May 1, 21:2049-58

  12. Meta Analysis 2: Multidimensional Scaling (MDS) > 700 proteins from the Nucleolus, re-annotated……….and more….. • Paper in co-authorship with SIB and GeneBio/SwissProt in preparation by M. Scheumie and Christine Chicester.

  13. Meta Analysis 2: Hierarchical Clustering

  14. 200779_at 200799_at 200800_s_at2 01000_at 201427_s_at 201939_at 202022_at 202887_s_at 203355_s_at 203574_at 203622_s_at 204026_s_at 204033_at 204146_at 204285_s_at 204415_at 205047_s_a t205239_at 208763_s_at 208813_at 208949_s_at 209230_s_at 209608_s_at 210338_s_at 212063_at 212501_at 212971_at 213040_s_at 213075_at 213703_at2 17999_s_at 218145_at 218180_s_at 218585_s_at 218986_s_at 219588_s_at 219961_s_at 221731_x_at 222039_at 222111_at 35820_at Q-norm

  15. Q-norm

  16. Q-norm

  17. PhysiologyPhosphorylationLymphocyte TransformationCell Cycle AnatomyCellsT-LymphocytesDendritic CellsMonocytesLymph NodesCell LineBlood Platelets AnatomyT-LymphocytesMacrophagesCellsCell LineFibroblastsMonocytesNeutrophils Immunity, NaturalGenotypeTransfectionAntigen PresentationGenetic Predisposition to DiseaseFibrinolysis

  18. 2004----2005

  19. 1996

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  25. 2002

  26. 2003

  27. 2004

  28. 2005

  29. Writing = ambiguity textmining BRCA1 BRCA1 Future (hope) PLEASE ! Papyrust But….. journal editors who publish scientific studies and grant institutions that fund them very often see less value in efforts to build and analyze scientific databases than in old-fashioned experiments

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