Next generation semantic support technology
CD40 ligand and tumor necrosis factor alpha, the cells acquire a mature phenotype of dendritic cells that is characterized by up-regulation of human leukocy
te antigen (CD80, CD86, CD40and CD54 and appearance of CD83. These
What we are NOT
• A Search Engine
• A Pathway Tool
• An Annotated Database
What do we do ?
• Disambiguate Text
• Meta-analyse at concept level
• Provide meta-analysed information
• Support Information Based Knowledge Discovery (especially new associations)
Ambiguity 1: Synonyms
• Facilitating networks of information. van Mulligen EM, Diwersy M, Schmidt M, Buurman H, Mons BProceedings of AMIA Symposium 2000, 868-72
Ambiguity 2: Homonyms
PSAProstate Specific AntigenPSoriatic Arthritisalpha-2,8-PolySialic AcidPolySubstance AbusePicryl Sulfonic AcidPolymeric Silicic AcidPartial Sensory AgnosiaPoultry Science Association
• 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 2004 Nov 1, 20:2597-604
The Knowlet
• 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
Creating Reference Knowlets
PSA Prostate Specific Antigen
PSA Psoriatic Arthritis
ReferenceKnowlet
ReferenceKnowlet
Context matching
PSA ??
Prostate Specific Antigen
Psoriatic Arthritis
ReferenceKnowlet
ReferenceKnowlet
New text
93 % correct in ‘Worst Case Scenario’98 % overall….
• Thesaurus-based disambiguation of gene symbols. Schijvenaars BJ, Mons B, Weeber M, Schuemie MJ, van Mulligen EM, Wain HM, Kors JABMC Bioinformatics 2005 Jun 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
x
person organisation Object 1
gene
Object 2
disease
Object 3
drug
> 15 million Knowlets from PubMed etc.
Building an association matrix of large data sources
0
16 0
30 3 0
28 35 20 0
188 4 15 13 0
A matrix of associative distances
meta-analysis
HierarchicalClusteringACSMDSEtc.
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 JJournal 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 Bioinformatics 2005 May 1, 21:2049-58
Meta Analysis 2: Multidimensional Scaling (MDS)
• Paper in co-authorship with SIB and GeneBio/SwissProt in preparation by M. Scheumie and Christine Chicester.
> 700 proteins from the Nucleolus, re-annotated……….and more…..
Meta Analysis 2: Hierarchical Clustering
200779_at200799_at200800_s_at201000_at201427_s_at201939_at202022_at202887_s_at203355_s_at203574_at203622_s_at204026_s_at204033_at204146_at204285_s_at204415_at205047_s_at205239_at208763_s_at208813_at208949_s_at209230_s_at209608_s_at210338_s_at212063_at212501_at212971_at213040_s_at213075_at213703_at217999_s_at218145_at218180_s_at218585_s_at218986_s_at219588_s_at219961_s_at221731_x_at222039_at222111_at35820_at
Q-norm
Q-norm
Q-norm
Physiology Phosphorylation Lymphocyte Transformation Cell Cycle
Anatomy Cells T-Lymphocytes Dendritic Cells Monocytes Lymph Nodes Cell Line
Blood Platelets
Anatomy T-Lymphocytes Macrophages Cells Cell Line Fibroblasts Monocytes Neutrophils
Immunity, Natural Genotype Transfection Antigen Presentation Genetic Predisposition to Disease Fibrinolysis
2004----2005
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textmining
PLEASE !
Writing =ambiguity
Future (hope)
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