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KNEWCO Please observe. In the space of one hundred and seventy-six years the Lower Mississippi has shortened itself two hundred and forty-two miles. This.

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Presentation on theme: "KNEWCO Please observe. In the space of one hundred and seventy-six years the Lower Mississippi has shortened itself two hundred and forty-two miles. This."— Presentation transcript:

1 KNEWCO Please observe. In the space of one hundred and seventy-six years the Lower Mississippi has shortened itself two hundred and forty-two miles. This is an average of a trifle over one mile and a third per year. Therefore, any calm person, who is not blind or idiotic, can see that in the Old Oolitic Silurian Period, just a million years ago next November, the Lower Mississippi River was upward of one million three hundred thousand miles long, and stuck out over the Gulf of Mexico like a fishing-rod. And by the same token any person can see that seven hundred and forty-two years from now the Lower Mississippi will be only a mile and three-quarters long, and Cairo and New Orleans will have joined their streets together, and be plodding comfortably along under a single mayor and a mutual board of aldermen. There is something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact. “ ”

2 KNEWCO Beyond Open Access Jan Velterop UKSG, Torquay, March 30, 2009

3 KNEWCO There is something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact. Mark Twain, Life on the Mississippi “ ”

4 KNEWCO What’s wrong? We have far too few returns in terms of actionable knowledge out of such overwhelming investment of fact! The reason is that a lot of fact is deeply hidden!

5 KNEWCO Current Knowledge Transfer Needle transport An analogy

6 KNEWCO Information overload? Too much knowledge? Stop acquiring it? Or organisation underload? Unprecedented opportunity? Just filtering it? Lack of conceptual structure?

7 KNEWCO Information ‘overload’ will increase

8 KNEWCO Analogy: What is the use of water? Analogy: What is the use of water?

9 KNEWCO H2OH2O H2OH2O Drink (take in)

10 KNEWCO What is the use of information?

11 KNEWCO Read (take in) Age to Know

12 KNEWCO Publish articles

13 KNEWCO Publish articles body composition obesity diabetes

14 KNEWCO Experienced in publishing articles e.g. providing author proofs with proposed triples and asking them to verify those

15 KNEWCO

16 Living not on detail alone Getting the big picture – too

17 KNEWCO Information silos MRS Index, virtual concepts Daily feed Uniprot PubMed Nextprot CALIPHO InWebWikiProSERMO BioBanks e.g. LOVD GEOGWA Community Annotation (a posteriori) Community Annotation (a posteriori) Triplet construction (unsupervised) Direct feed Blogs, etc. Community Annotation (a priori) Peregrine Concept Mapping Harmonized data Bio commontology Tools, RDF, OWL, OBO, Protégé

18 KNEWCO Database facts (multiple attributes) Community Annotations Co-occurrence sentence (abstracts e.g. PubMed) Co-occurrence Full Text (publisher e.g. Springer) Concept Profile Match Co-expression (gene expression Databases) Modelling hypothesis (e.g. Plectix, InWeb) Graph Building (e.g. WikiPathways) Multiple Triples F+ C+ A+ C+ A+ A+ Unique to Springer Unique to Plectix Unique to T-Cell Development Cancer Promoting Genes Interleukin-7 (node 1, unique ID)(node 2, unique ID) classdatevalueowner condition Etc. }

19 KNEWCO Unique to

20 KNEWCO curated Co-occ All Triples Remove Ambiguity and Redundancy Curated Observational Smart Triples Inferred Knowledge Space (node 1, unique ID)(node 2, unique ID) classdatevalueowner condition Etc.

21 KNEWCO Curated databases SwissProt Gene Ontology NCBO (ontologies) Peroxisome InWeb STRING HAPMAP LOVD Reactome IHop Literature (peer reviewed) Elsevier Springer Wiley BMC PubMed SciELO PLoS etc. ‘Grey’ literature Blogs SEED EURORDIS UPPMD (NORD) SPARC Research CR SOUHL Community-generated SIB-lab PatientsLikeMe Sermo Plectix NBIC WikiProfessional WikiPathways OWW Alert BioBanks Raw data GEO Express Many NBIC data Many NGI center data Many public data. sell sustainability

22 KNEWCO Download Concept Web Includes edges from: Pubmed (400,000,000 sentences, 5,000,000,000 concept co-occurrences) (from public data) Protein databases (UniProt, IntAct, PDB, HPRD – 75,000 human curated PPIs) (from public data) Private expression data (3000 extra edges, by Merck) (from proprietary data) InWeb edges (240,000 unique edges from 17 species) (from proprietary data) Plectix edges (5,000 extra edges (PPI modeling) (from proprietary data) Gene (co-expression databases (GEO, Express… – 25 square genes) (from public data) STRING edges (200,000 gene-gene edges) (from semi public data) Reactome edges (240,000 unique edges from 17 species) (from proprietary data) Chemspider edges (25,000,000 chemicals) (from semi public data) Wiki edges (WikEdge = WikiPathways, WikiProfessionals, Omegawiki, Wikigene) Et Cetera

23 KNEWCO What one can do to make scientific literature even more useful: Helping users find what is appropriate What one can do to make scientific literature even more useful: Helping users find what is appropriate

24 KNEWCO Slide by Carl Lagoze (Cornell) – from this presentation:

25 KNEWCO Using Knewco’s freely available functionality*, scientific publishers can add semantic functionality to their material by way of highlighting concepts and then linking to additional pertinent information about that concept as well as further search possibilities with automatic expansion of the search argument with synonyms. *Knewco is a Concept Web Alliance member Button changes when clicked An example ‘mash-up’: On the basis of Semantic Highlighting

26 KNEWCO Semantic highlighting

27 KNEWCO Semantic highlighting

28 KNEWCO Semantic highlighting

29 KNEWCO Semantic highlighting

30 KNEWCO Semantic highlighting

31 KNEWCO Semantic highlighting

32 KNEWCO Semantic highlighting

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35 KNEWCO Semantic highlighting

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38 KNEWCO Concept Web Alliance Inaugural Meeting May 8th, New York Hall of Science “…an important and critically necessary meeting” Info: Info:

39 KNEWCO Demo: Wikimore: Concept Web: Credits Thinking Neanderthal man (after Rodin) Needle transport Cupped hands Ship at sea Scientist Jungle (detail) Henri Rousseau Jungle (aerial – 2x) Triples etc. Barend Mons Fin


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