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BIOSEMANTICSSemantic Support Technology
For on-line Knowledge Tracking and Discovery
Second Order Semantic Enrichment
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
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Too much to read: major trends foreseen:
• From Reading to Consulting
• From Reading to Meta Analysis
• From Writing to Knowledge Representations
• To Central AND Distributed Annotation
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textminingWriting =ambiguity
Future (hope)
Papyrust
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What do we do ?
• Disambiguate Text and tag/link concepts– Pre-done for ‘own’ content– On the fly for selected web environments
• Meta-analyse at concept level
• Provide meta-analysed information
• Support Information Based Knowledge Discovery (especially new associations)
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Ambiguity 1: Synonyms
• Facilitating networks of information. van Mulligen EM, Diwersy M, Schmidt M, Buurman H, Mons BProceedings of AMIA Symposium 2000, 868-72
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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
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But…we have nomenclature committees now……
DEFB4DEFB4defensin, beta 4defensin, beta 4SAP1SAP1, HBD-2, DEFB-2, DEFB102, DEFB2, HBD-2, DEFB-2, DEFB102, DEFB2
ELK4ELK4ELK4, ETS-domain protein (SRF accessory protein 1)ELK4, ETS-domain protein (SRF accessory protein 1) SAP1SAP1
PSAPPSAPproposin (variant Gaucher disease and variant proposin (variant Gaucher disease and variant metachromatic leukodystrophy)metachromatic leukodystrophy)SAP1SAP1, GLBA, GLBA
PRESENT
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• 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
First order semantic enrichment
The Knowlet
2nd order S.E.
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Second Order Semantic Enrichment1: Creating Reference Knowlets
PSA Prostate Specific Antigen
PSA Psoriatic Arthritis
ReferenceKnowlet
ReferenceKnowlet
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2. 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
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Text (free or structured)
Resolving ambiguities (contextual reference concepts)
Concept Tagging and inserting appropriate links
Basic methodology:Concept Tagging, creation and systematic aggregation of Knowlets
Text Knowlet
Object Knowlets (people, diseases, drugs, genes)
Collection Knowlets ( category, pathway, Micro-array-gene-set )
Aggregation of Object Knowlets
Aggregation of Text Knowlets
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person organisation Object 1
gene
Object 2
disease
Object 3
drug
> 15 million Knowlets from PubMed etc.
3. Building an association matrix of large data sources
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1
0.16 1
0.30 0.03 1
0.28 0.35 0.20 1
0.188
0.004 0.15 0.13 1
A matrix of associative distances
meta-analysis
HierarchicalClusteringACSMDSEtc.
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4. Meta-analysis method 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
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Function unknow nChaperonesChromatin structureFibrous proteinsmRNA metabolismOthersRibosomal proteinsRibosome biogenesisTranslation
SRPPARN
l
• Assignment of protein function and discovery of new nucleolar proteins based on automatic analysis of MEDLINE. Martijn Schuemie, Christine Chichester, Frederique Lisaceck, Yohann Coute, Peter-Jan Roes, Jean Charles Sanchez, Barend MonsTo be Submitted
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Fingerprints
Knowlet
Association Matrix Meta-analysis
Expert Challenge
WikiZ/PExpert comments
Peer to Peer Review
Final Approval
U.W. Fingerprint
Update
Literature
Protein A
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0.1
0.4
0.9
New publications or annotations
Solid
Liquid
Gas
1st order Semantic enrichment
ReductionFalse Positives
DiscussionVoting in Wiki
Meta-analysisProximity measures
Proposals to Data bases ?
Central Annotation
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• REGISTRATION (1X)
• Unique Author ID• E-mail Adress• PHP/userpage• People Knowlets
• Unique concept ID• Language variants• Homonyms• Definitions (brief)• Object Knowlets
Science Wiki’s• UID from WiktionaryZ• Research information• Talk-page• Liquid Threads• Object Knowlets
• UID from WiktionaryZ• Articles about UID’s• Encyclopaedic/ NPOV• Anonymous allowed
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Dr. Johan den Dunnen
Wiki-Authors
OMIM
NPOV
DMD (Hs)
MEI
Wiki-Proteins
DMD (Hs)
AOI
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Freely provided by
• Original Source • WZ definition (choice)• Related concepts (Knowlet)• Experts (Wiki-Authors)• More about (Wiki-proteins)• Vote (Wiki-Proteins)• Wikipedia article• Browse (Knowlet Browser)• Google (e-vamp)
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