The Ultralink – an expert system for contextual hyperlinking in knowledge management Manuel C....

The Ultralink – an expert system for contextual hyperlinking in knowledge management

Manuel C. Peitsch

Head of Systems BiologyNovartis Institutes for Biomedical Research

2 Ultralink/ M. Peitsch/ Bio-IT World April 2006

A Knowledge Space

0.5 1.50.5 1.50.5 1.5


Connecting the Knowledge Bodies (requirements)

Intelligent integration of heterogeneous data to enable “Seamless Navigation”:

One-stop shop.

Re-useable, in any Web and Office application.

Intelligent, i.e. knows about biology, medicine, chemistry, diseases, business, people, etc…

On demand and easy to use.

Configurable.


Connecting the Knowledge Bodies (Components)

Indexing of large heterogeneous data collections (databases, full texts) to enable semantic expansion.

Information Retrieval and Extraction, entity recognition, semantic enrichment.

Knowledge Map (navigating the conceptual network).

Terminology Hub (thesauri and ontologies).

Ontology-associated business rules.


Creating references (Terminology Hub)

Different knowledge repositories have different ways to encode a concept:

Registry Number

Unique Internal ID

Concept Identifier

Enumerating terms

Just using different terms without any constraintsSearching a term in source A and B may lead to different

results although the underlying concepts exists in both sources (false negatives in IR and IE)

Terminology Hub ensures coherent mapping

Between coding systems

Between different representation levels (e.g. ID vs. Concept)

Between local terms and global terms

Over 8 GB of cross-referencing information


What entities constitute our Terminology?

Chemical entities – IUPAC names, trivial names, trade names, INNs, compound codes, ligands.

Biological entities – targets, genes/protein, modes of actions…

Diseases, Indications, Side Effects, Contraindications

Institutions, Affiliations, People

Geographic locations

…


The UltraLink : a revolutionary tool to navigate the “Knowledge Space”

1. Zoning This process uses our (meta-) knowledge about information

structure, and tags the relevant contexts of the documents or database records.

2. Identification of terms based on the terminology or on regular expression

Term Identification: identify the lexical items in a text, relate them to a term and retrieve the corresponding reference term via thesaurus relations.

Concept Identification: identify the concept related to the reference term(s).

Type Assignment: Assign the concept type related to a concept identifier

3. Extraction and normalization

4. Get list of rules to apply Verifiers Application of rules

5. Display


Creating the Ultralink


UltraLink Examples

Treatment of ambiguities

WILMs TUMORDISEASE Wilms' tumor => nephroblastomaGENE NAME WT1TARGET Wilms' tumor


UltraLink Examples

Term extraction / Normalization -> Examples (mtor, mammalian target of rapamycin)


UltraLink Examples

Term to UltraLink:

granulocyte - macrophage colony stimulating factor

Concept Type: TARGET

Normalized term (non exhaustive):

Granulocyte-macrophage colony-stimulating factor

Synonyms:

colony stimulating factor 2

Colony-stimulating factor, CSF ,GCSF, GM-CSF

Granulocyte macrophage colony stimulating factor

Molgramostin, Sargramostim

Local terms (non exhaustive list of examples):

EMBL e.g. AC004511, AF373868, …

Pubmed e.g. 1569568, 1737041, …

NCBI e.g. 10090, 10116, 9606

GO e.g. GO:000512, GO:0019221, …

UniProt e.g. P01587, …


Link to Pathway information from TCF7L2


Further query, Genome/Proteome Information


Access to tools and reagents


MetaCore Map containing FZD4 (frizzled 4)

Proteins where

antibodies are available

are marked with

an additional icon

Mouse-over

shows

specificity

Hyperlink

to

Antibodies

Web Report


UltraLink Examples


UltraLink Examples


The Ultralink can be call from the Internet Explorer

Internet Explorer IntegrationGPS Add-in

Internet Explorer IntegrationGPS Add-in

Web Page Tagged Document

2

Sends the document for

analysis

3

Gets back tagged parts

1

User requests for analysis

4

Injection of specific HTML

tags

Web

Serv

ice (

WS

DL)

Web

Serv

ice (

WS

DL)

GPS Lexical Analysis Server ToolsGPS Lexical Analysis Server Tools

TerminologyTerminology

Lexical ExtractionLexical Extraction

ZoningZoning

TaggingTagging

DocStructuresDocStructures

Meta-RulesMeta-Rules


Activation UltraLink

Annotations on any web page


Web

Serv

ice (

WS

DL)

Web

Serv

ice (

WS

DL)

The Ultralink is integrated with Microsoft Office

Microsoft Smart TagExtraction

Microsoft Smart TagExtraction

Office Document

Tagged Document

2

Sends the document for

analysis

3

Gets back tagged parts

1

User requests for analysis

GPS Lexical Analysis Server ToolsGPS Lexical Analysis Server Tools

TerminologyTerminology

Lexical ExtractionLexical Extraction

ZoningZoning

TaggingTagging

DocStructuresDocStructures

Meta-RulesMeta-Rules


Annotations on full text in a Word document


Ultralinks can be coded into any application


Acknowledgements

Thérèse Vachon

Martin Romacker

Pierre Parisot

Nicolas Grandjean

Brigitte Charpiot

Jean-Marc von Allmen

Daniel Cronenberger

Olivier Kreim


Knowledge Space and GPS Navigator

Backup slides


What constitutes the Knowledge Space

Ultralinker

SemanticSearch

Text Mining

Analytics

Internet

Other ResearchDocumentation

Chemistry

Biology

Literature

Comp. Inf.

Bioinformatics

Meta Data K map

ThesauriiOntologies

Rules

Definedworkflows


Data Analysis – Protease modulators in CI DBs July 2004 - ADIS & Pharmaprojects

Univariate - Companies Univariate - MOA

Univariate - Diseases conditionned by Companies Clustering Diseases -MOAs


Graph Navigator – Protease modulators in CI DBs July 2004 - ADIS & Pharmaprojects


Clustering

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The Ultralink – an expert system for contextual hyperlinking in knowledge management Manuel C....

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