On our way toto

Information Overload ?

Or to prevent it by Or to prevent it by Appropriate use of Technology ?Appropriate use of Technology ?

C19881 0.99C92992 0.67C02002 0.66C99229 0.44C00392 0.33C93939 0.21

consolidated knowledge

Collexis Fingerprints (CFP’s)

English

French

Spanish

Peoplemedical researchersaround the world

Activitiesin elect. text like projects, publicationsMedline abstracts...

Disease: #12674

MultilingualThesaurus IndexerMatches keywords, translatesthem to identical numbers and ranks them by their relevance

Maladie: #12674

Enfermedad: #12674

Malaria: #24530

Hospital: #19994

Paludisme: #24530

Paludismo: #24530

Hôpital : #19994

Hospital: #19994

...

...

...

The CommonLanguageEach activity is representedas a set of keyword numbersranked by their relevance

#4256 : 1.0#3627 : 0.8#19994 : 0.5#28746 : 0.3#32874 : 0.1#32874 : 0.1#32874 : 0.1

#14325 : 1.0#3627 : 0.8#19994 : 0.5#28746 : 0.3#32874 : 0.1#32874 : 0.1#32874 : 0.1

#85643 : 1.0#3627 : 0.8#19994 : 0.5#28746 : 0.3#32874 : 0.1#32874 : 0.1#32874 : 0.1

#17345 : 1.0#3627 : 0.8#19994 : 0.5#28746 : 0.3#32874 : 0.1#1c8456 : 0.1#00356 : 0.1

„Collexion“ of activities

You:

#17345:1.0#3627 :0.8#19994:0.5#28746:0.3#32874:0.1

Your activity as text

Submit and indexed to keyword numbers

Find similaractivities andthe peoplebehind

Cross-language networking

The Early evolution of Fingerprint Manipulation

contents fingerprints

addadd

people fingerprints

addadd

organization fingerprint

JobsCV’s, Skills

Articles,books

Emails,Word RFP’s

BIOSEMANTICS• “Cellese”: the language that cells use to communicate

internally and externally.

• The Molecular Language and its biological MEANING• The Group

– Jan Kors PhD.– Erik van Mulligen PhD– Bob Schijvenaars PhD– Marc Weeber PhD– Christiaan v.d. Eyck MsC– Rob Jelier PhD – Barend Mons PhD– Johan van der Lei PhD

SERENDIP

Beyond PublicationBeyond PublicationSemantic metaSemantic meta--analysis of massive data and information sources for discoveryanalysis of massive data and information sources for discovery

Bsik 2003Bsik 2003

A consortium to combine State-of-the-art Information and Knowledge Mining Technologies

To support:

•Thesaurus and ontology enrichment

•Disambiguation of concepts

•Semantic meta-analysis of massive information

To enable:

•Information-based discovery

•Evidence based policy making

Thesaurus and Ontology Enrichment

• New concepts• Synonyms• Homonyms• Genes, Proteins • Pictures

Valida

tion 3

Freetext

UnexplainedText (XML)

Potential concepts

Thesauri:•Mesh•HUGO•SwissProt•SAGE•Others

FUA

4

1Fingerprints(known concepts)

partners

E-BioSci

EMBOElsevier

NLP

2

TNO

LUMC

HUGONC

Genebio

AMC

EUR

UVA

SERENDIP

Too much to read: major trends foreseen:

• From Reading to Consulting• From Reading to Meta-analysis• From Text to Knowledge

Representations

C19881 0.99C92992 0.67C02002 0.66C99229 0.44C00392 0.33C93939 0.21

Semantic typesSemantic typesCo-occurrence dataCo-occurrence data

The first step: to the Conceptual Semantic Network

Calcium deposition Pleocytosis Basal Ganglia EncephalopathyCerebrospinal Fluid Tomography, X-Ray Computed Parents FamilyAicardi Goutieres syndrome Ferrocalcinotic deposition Spastic quadraplegia Fahr disease Microcephaly AGS1

xG-protein coupled receptors G-substrate Lipoid dermatoarthritis Receptors Complement Factor B RNA, Complementary Xenopus oocyte AGS1

SwissProt: Activator of G-protein signaling 1 (AGS1)

*225750

AICARDI-GOUTIERES SYNDROME 1; (AGS1) : OMIM

Aicardi Goutieres syndrome 1Heterogeneity Linkage (Genetics) Clinical diagnosis Family 2 AGS1 **Lod Score Genetic Heterogeneity analysis Toxoplasmosis Calcium deposition 3 Encephalopathy 4 Cadmium Genus: Human cytomegalovir... Cerebrospinal fluid abnorm. 5.. Interferon-alpha Chromosomes Viral Child Head Tricuspid Valve Stenosis

Fingerprinting

disambiguatio

n

ACS

META-ANALYSIS

Applications

• Cross-language, jargon and cross-system matching (implemented): www.sharingpoint.shared-global.org

• Information-based discovery (Research)

• Community building (Experts,Policy Making)

• Trendwatching and Indicators (Policy Making)

Seed-Term based Conceptual Semantic Networks

??

Clustering of genes on-the-fly

Predicting new knowledge ?

III= Distribution over distance categories of concept-pairs without co-occurrence in the learning set.

IV= Distance categories of concept pairs related to the probability that there is no explicit relationship or co-occurrence in Medline (zero ratio) . A ratio of 0 means that an automatic Query in Medline with the concept pair with “AND” in between does lead to 0 hits in Medline.

New Drug discovery ?

Semantic Filtering

Knowledge Maps, Nature Biotechnology Map

Knowledge Maps: Medline Bioterrorism Map 1997

Knowledge Maps: Medline Bioterrorism Map 2001

Private Research

DC

Public

E-BioSciPharma etc.

ORIELSERENDIPFP6 etc.

I-ResearchMinistiesWHO, FAOetc.

SHAREDBIREME/VHLEDCTPOxford intiative etc.