1 / 28

A Knowledge Space

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).

johana
Download Presentation

A Knowledge Space

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

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

  2. A Knowledge Space

  3. 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.

  4. 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.

  5. 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

  6. 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 • …

  7. 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

  8. Creating the Ultralink

  9. UltraLink Examples • Treatment of ambiguities • WILMs TUMOR • DISEASE Wilms' tumor => nephroblastoma • GENE NAME WT1 • TARGET Wilms' tumor

  10. UltraLink Examples • Term extraction / Normalization -> Examples (mtor, mammalian target of rapamycin)

  11. 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, …

  12. Link to Pathway information from TCF7L2

  13. Further query, Genome/Proteome Information

  14. Access to tools and reagents

  15. 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

  16. UltraLink Examples

  17. UltraLink Examples

  18. 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

  19. Activation UltraLink Annotations on any web page

  20. 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

  21. Annotations on full text in a Word document

  22. Ultralinks can be coded into any application

  23. Acknowledgements Thérèse Vachon Martin Romacker Pierre Parisot Nicolas Grandjean Brigitte Charpiot Jean-Marc von Allmen Daniel Cronenberger Olivier Kreim

  24. Knowledge Space and GPS Navigator • Backup slides

  25. 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

  26. Univariate - Companies Univariate - MOA Univariate - Diseases conditionned by Companies Clustering Diseases -MOAs Data Analysis –Protease modulators in CI DBs July 2004 - ADIS & Pharmaprojects

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

  28. Clustering

More Related