beyond open access

KNEWCO

Please observe. In the space of one hundred and seventy-six years the Please observe. In the space of one hundred and seventy-six years the Lower Mississippi has shortened itself two hundred and forty-two miles. 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. 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 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 Old Oolitic Silurian Period, just a million years ago next November, the Lower Mississippi River was upward of one million three hundred the Lower Mississippi River was upward of one million three hundred thousand miles long, and stuck out over the Gulf of Mexico like a 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 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 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 only a mile and three-quarters long, and Cairo and New Orleans will have joined their streets together, and be plodding comfortably along have joined their streets together, and be plodding comfortably along under a single mayor and a mutual board of aldermen. There is under a single mayor and a mutual board of aldermen. There is something fascinating about science. One gets such wholesale returns of something fascinating about science. One gets such wholesale returns of conjecture out of such a trifling investment of fact.conjecture out of such a trifling investment of fact.

“

”

KNEWCO

Beyond Open AccessBeyond Open Access

Jan VelteropJan VelteropUKSG, Torquay, March 30, 2009

KNEWCO

There is something fascinating about science.There is something fascinating about science.One gets such wholesale returns of conjecture out of One gets such wholesale returns of conjecture out of such a trifling investment of fact.such a trifling investment of fact.

Mark Twain, Mark Twain, Life on the MississippiLife on the Mississippi

“”

KNEWCO

What’s wrong?What’s wrong?

We have far too We have far too fewfew returns in terms of actionable returns in terms of actionable knowledge out of such overwhelming investment of knowledge out of such overwhelming investment of fact!fact!

The reason is that a lot of fact is deeply hidden!The reason is that a lot of fact is deeply hidden!

KNEWCO

Current Knowledge Transfer Current Knowledge Transfer

Needle transportNeedle transport

An analogyAn analogy

KNEWCO

Information overload?Information overload?

Too much knowledge?Too much knowledge?

Stop acquiring it?Stop acquiring it?

Or organisation underload?Or organisation underload?

Unprecedented opportunity?Unprecedented opportunity?

Just filtering it?Just filtering it?

Lack of conceptual structure?Lack of conceptual structure?

KNEWCO

Information ‘overload’ will increaseInformation ‘overload’ will increase

KNEWCO

Analogy:

What is the use of water?

Analogy:

What is the use of water?

KNEWCO

H2OH2O

Drink(take in)

KNEWCO

What is the use of information?What is the use of information?

KNEWCO

Read(take in)

Age to KnowAge to Know

KNEWCO

Publish articles

KNEWCO

Publish articles

body composition

obesity

diabetes

QuickTime™ and a decompressor

are needed to see this picture.

KNEWCO

Experienced in publishing articles

e.g. providing author proofs e.g. providing author proofs with proposed triples and with proposed triples and asking them to verify thoseasking them to verify those

e.g. providing author proofs e.g. providing author proofs with proposed triples and with proposed triples and asking them to verify thoseasking them to verify those

KNEWCO

KNEWCO

Living not on detail aloneLiving not on detail alone

Getting the big picture – too Getting the big picture – too

KNEWCOInformation silos

MRSIndex, virtual concepts

Daily feed

UniprotPubMed

NextprotCALIPHO InWeb WikiPro SERMO

BioBankse.g. LOVD GEO GWA

CommunityAnnotation(a posteriori)

CommunityAnnotation(a posteriori)

<ID1><edge><ID2>

Triplet construction(unsupervised)

Direct feedBlogs, etc.

CommunityAnnotation(a priori)

Peregrine

Concept Mapping

Harmonized data

Biocommontology

Tools, RDF, OWL, OBO, Protégé

KNEWCO

<Type F1> Database facts (multiple attributes) <Type F2> Community Annotations

<Type C1> Co-occurrence sentence (abstracts e.g. PubMed) <Type C2> Co-occurrence Full Text (publisher e.g. Springer)

<Type A1> Concept Profile Match <Type A3> Co-expression (gene expression Databases) <Type A4> Modelling hypothesis (e.g. Plectix, InWeb)

Graph Building (e.g. WikiPathways)

Multiple Triples

F+ C+ A+F+ C+ A+

C+ A+C+ A+

A+A+

Unique to Springer

Unique to Plectix

Unique to 101668678

T-Cell Development

Cancer Promoting GenesInterleukin-7

(node 1, unique ID) (node 2, unique ID)

< Source concept > < Target Concept > < Relations (edge) >

class date value owner condition Etc.

}

KNEWCO

Unique to 101668678

KNEWCO

curatedcuratedcurated



Co-occ



All Triples

Remove

Ambiguity

and

Redundancy

Curated

Observational

Smart Triples

Inferred

Knowledge Space

(node 1, unique ID) (node 2, unique ID)

< Source concept > < Target Concept > < Relations (edge) >

class date value owner condition Etc.

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

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

KNEWCO

What one can do to make scientific literature What one can do to make scientific literature even more useful: even more useful:

Helping users find what is appropriateHelping users find what is appropriate

What one can do to make scientific literature What one can do to make scientific literature even more useful: even more useful:

Helping users find what is appropriateHelping users find what is appropriate

KNEWCO

Slide by Carl Lagoze (Cornell) – from this presentation:http://journal.webscience.org/112/3/orechem.pdf

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 memberButton changes

when clicked

An example ‘mash-up’: On the basis of Semantic Highlighting

KNEWCO

Semantic highlighting

KNEWCO

Concept Web AllianceInaugural Meeting

May 8th, New York Hall of Science

“…an important and critically necessary meeting”

Info: http://conceptweblog.wordpress.comInfo: http://conceptweblog.wordpress.com

KNEWCO

Demo:Demo:http://demo.knewco.comhttp://demo.knewco.com

Wikimore:Wikimore:http://wikimore.orghttp://wikimore.org

Concept Web:Concept Web:http://conceptweblog.wordpress.comhttp://conceptweblog.wordpress.com

Credits

Thinking Neanderthal man (after Rodin)http://blogs.sundaymercury.net/weirdscience

Needle transporthttp://fisherwy.blogspot.com

Cupped handswww.goldcoast.qld.gov.au

Ship at seahttp://vikingeskibsmuseet.dk

Scientistwww.drugdevelopment-technology.com

Jungle (detail)Henri Rousseau

Jungle (aerial – 2x)http://passporttoknowledge.com

Triples etc.Barend Mons

FinFin

beyond open access

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