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 up-regulation of human leukocy te antigen (CD80, CD86, CD40 and CD54 and appearance of CD83. These A Proleptic View on Science Communication in the early 21 st century

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

Rejected Papers and Unpublished results Rejected proposals Knowledge generation Hypothesis generation 2006 Management of Science (work flow) proposal Peer Review manuscript Project Paper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

Believe it or not: In the early 21 st 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’

“Textmining” Writing: Legal Plagiarism Ambiguity Delay Future (hope) Papyrust

1,000,000 papers Meta-Analysis META-ANALYSIS 2005   292 Genes

Ambiguity 1 : Synonyms Facilitating networks of information. van Mulligen EM, Diwersy M, Schmidt M, Buurman H, Mons B Proceedings of AMIA Symposium 2000,

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 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:

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) SAP1PSAP proposin (variant Gaucher disease and variant metachromatic leukodystrophy) SAP1, GLBA Early this century

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.

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)

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

Text (free or structured) Resolving ambiguities (contextual reference concepts) Concept Tagging and inserting appropriate links 2005 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 KnowletsAggregation of Text Knowlets

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

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

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

REGISTRATION (1X) Unique Author ID 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

Dr. Johan den Dunnen Wiki-Authors OMIM NPOV DMD (Hs) MEI Wiki-Proteins DMD (Hs) AOI

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

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