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The Ultralink – an expert system for contextual hyperlinking in knowledge management Manuel C. Peitsch Head of Systems Biology Novartis Institutes for Biomedical Research. A Knowledge Space. Connecting the Knowledge Bodies (requirements).

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The Ultralink – an expert system for contextual hyperlinking in knowledge managementManuel C. PeitschHead of Systems BiologyNovartis Institutes for Biomedical Research

connecting the knowledge bodies requirements
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
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

Searching a term in source A and B may lead to differentresults although the underlying concepts exists in both sources (false negatives in IR and IE)

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 constraints

Over 8 GB of cross-referencing information

  • Terminology Hub ensures coherent mapping
    • Between coding systems
    • Between different representation levels (e.g. ID vs. Concept)
    • Between local terms and global terms
what entities constitute our terminology
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
The UltraLink : a revolutionary tool to navigate the “Knowledge Space”
  • Zoning
      • This process uses our (meta-) knowledge about information structure, and tags the relevant contexts of the documents or database records.
  • 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
  • Extraction and normalization
  • Get list of rules to apply
      • Verifiers
      • Application of rules
  • Display
ultralink examples
UltraLink Examples
  • Treatment of ambiguities
  • WILMs TUMOR
  • DISEASE Wilms' tumor => nephroblastoma
  • GENE NAME WT1
  • TARGET Wilms' tumor
ultralink examples10
UltraLink Examples
  • Term extraction / Normalization -> Examples (mtor, mammalian target of rapamycin)
ultralink examples11
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, …
metacore map containing fzd4 frizzled 4
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
the ultralink can be call from the internet explorer

GPS Lexical Analysis Server Tools

Terminology

Zoning

DocStructures

Lexical Extraction

Tagging

Meta-Rules

The Ultralink can be call from the Internet Explorer

Internet Explorer Integration

GPS Add-in

1

User requests for analysis

4

Injection of specific HTML tags

Web Page

Tagged Document

3

Gets back tagged parts

Web Service (WSDL)

2

Sends the document for analysis

the ultralink is integrated with microsoft office

GPS Lexical Analysis Server Tools

Terminology

Zoning

DocStructures

Lexical Extraction

Tagging

Meta-Rules

The Ultralink is integrated with Microsoft Office

Microsoft Smart Tag

Extraction

1

User requests for analysis

Office Document

3

Gets back tagged parts

Tagged Document

Web Service (WSDL)

2

Sends the document for analysis

acknowledgements
Acknowledgements

Thérèse Vachon

Martin Romacker

Pierre Parisot

Nicolas Grandjean

Brigitte Charpiot

Jean-Marc von Allmen

Daniel Cronenberger

Olivier Kreim

what constitutes the knowledge space

Literature

Comp. Inf.

Bioinformatics

Biology

Other

Chemistry

Internet

ResearchDocumentation

What constitutes the Knowledge Space

Meta Data

K map

Defined

workflows

Ultralinker

Text

Mining

Analytics

SemanticSearch

Thesaurii

Ontologies

Rules

data analysis protease modulators in ci dbs july 2004 adis pharmaprojects

Univariate - Companies

Univariate - MOA

Univariate - Diseases conditionned by Companies

Clustering Diseases -MOAs

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