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Vision Talk

Vision Talk. “If it is not in Wikipedia, it probably does not exist.” Jimmy Wales used to say that about Google when Google still existed. CD40 ligand and tumor necro sis factor alpha , the cells acquire a mature phenotype of dendritic cells that is characterized by

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Vision Talk

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  1. Vision Talk “If it is not in Wikipedia, it probably does not exist.” Jimmy Wales used to say that about Google when Google still existed.

  2. 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 A Proleptic View on Science Communication in the early 21st century

  3. In those days there was:Too much to read: so what happened ?a LANDSLIDE….. • From Reading to Consulting • From Reading to Meta Analysis • From Writing to Knowledge Representations • To Central AND Community Annotation

  4. 2006 Management of Science (work flow) = Text-semantic tagging = Semantic matching = currently heavily under-used Rough Experimental Data Rejected proposals Project Knowledge generation proposal Peer Review manuscript Hypothesis generation Paper Enriched (annotated) Knowledge Rejected Papers and Unpublished results

  5. Believe it or not:In the early 21st century • The ‘article’ was the unit of communication • There were centralised institutions calculating ‘impact’ • per article • or even per entire journal • Web sites were not counted • Some publishers still asked money for the reading of scientific articles • Articles did endlessly repeat already established knowledge • Hardly any of this mostly redundant information was interlinked semantically. • Web-publishing was still largely conceived as ‘putting dead PDFs of articles on the Internet’

  6. “Textmining” • Writing: • Legal Plagiarism • Ambiguity • Delay BRCA1 BRCA1 Future (hope) Papyrust

  7. META-ANALYSIS 1,000,000 papers 2005 292 Genes Meta-Analysis Enlightened Nonsense

  8. 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

  9. 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

  10. Early this century Then…we had nomenclature committees…… DEFB4 defensin, beta 4 SAP1, HBD-2, DEFB-2, DEFB102, DEFB2 ELK4 ELK4, ETS-domain protein (SRF accessory protein 1) SAP1 PSAP proposin (variant Gaucher disease and variant metachromatic leukodystrophy) SAP1, GLBA

  11. Some historic quotes from the nomenclature committee period (Most committees now extinct.) Biologists would rather share their toothbrush than their gene name unless it is the same name for a different gene. Now every-one is so convinced about the importance of standards that everyone creates their own. Craig Venter is fishing up more new protein sequences by himself every day than SwissProt can annotate with 70 people in a year.

  12. So……. • People started to try and recover things as simple as concepts from text, link them and use them for meta-analysis and annotation. • Imagine what you had to do to achieve this simple task in these days • (some companies even charged money for it)

  13. 2nd order S.E. The Knowlet 2002: First order semantic enrichment • 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

  14. Malaria is transmitted by Mosquitoes of the Genus Anopheles .Source: Wiki-diseases

  15. 2006 A matrix of associative distances meta-analysis Hierarchical Clustering ACS MDS Etc.

  16. An old picture from a publication by Schuemie and Supekar in 2007

  17. Science Wiki’s • UID from WiktionaryZ • Research information • Talk-page • Liquid Threads • Object Knowlets • REGISTRATION (1X) • Unique Author ID • E-mail Adress • PHP/userpage • People Knowlets Wiki-Authors Wiki-X • UID from WiktionaryZ • Articles about UID’s • Encyclopaedic/ NPOV • Anonymous allowed • Unique concept ID • Language variants • Homonyms • Definitions (brief) • Object Knowlets WiktionaryZ Wikipedia

  18. Association Matrix Meta-analysis old papers Knowlet Expert Challenge Protein A Update WikiZ/P Expert comments U.W. Fingerprint Peer to Peer Review Final Approval Fingerprints

  19. Solid Liquid Gas 0.1 0.9 0.4 Traditional publications or modern annotations Central Annotation Proposals to Data bases ? Discussion Voting in Wiki Reduction False Positives Meta-analysis Proximity measures 1st order Semantic enrichment

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