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E-BioSci

E-BioSci. Semantic networks of biological information. Les Grivell European Molecular Biology Organisation. “B iological research ha s reached a point where new generalizations and higher order biological laws are being approached, but may be obscured by the simple mass of data”.

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E-BioSci

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  1. E-BioSci Semantic networks of biological information Les Grivell European Molecular Biology Organisation

  2. “Biological research has reached a point where new generalizations and higher order biological laws are being approached, but may be obscured by the simple mass of data” Harold Morowitz, 1985 Report to the U.S. National Academy of Sciences

  3. One part of the information explosion …. Morowitz

  4. Sequences are not the only form of digital information

  5. The digital revolution is …. • driving dramatic changes in the way research is conducted and in the way knowledge is being generated • exposing limitations in current mechanisms for disseminating and sharing information • driving changes in publication strategies

  6. The knowledge cycle (traditional) Idea! Literature Hypothesis Publication Experiment Data

  7. The knowledge cycle (extended) Idea! Databases (e-)Literature Hypothesis Publication Experiment Data

  8. Biological information: current reality ….. • Hundreds of different databases, many in flat-file format • Non-uniform or lack of external identifiers • Lack of interoperability at the level of syntax and semantics • Knowledge scattered across the literature in many thousands of non-computer readable journal articles

  9. Information retrieval from text • There is increasing need for the use of literature as a computer-readable resource (intelligent search / retrieval) • There is a need to apply computational methods to text as well as data analysis (mining / analysis; literature as discovery resource) • There is a need for new methods of integration and visualization of this information • There is a need for a scale-up in the rate of curated database growth through integration with the literature

  10. Dealing with the data deluge: what do researchers need? • Intuitive interfaces to web resources • Advanced search / retrieval facilities • Smooth navigation from one resource to another • Immediate availability of authoritative information; free of charge at the point-of-use • Information that can be integrated / manipulated / visualized /output in another form

  11. E-BioSci A new information service for the life sciences that will interlink factual and image data repositories with the research literature EU Quality of Life research infrastructure: platform under construction Closely linked to ORIEL, an EU-funded research project in information technology

  12. The partnership The current E-BioSci - ORIEL partnership • Distributed network of information resources • Europe-based; world-wide role

  13. The platform • Services freely accessible to the academic research community • Set of distributed resources (literature, sequence- and image- databases) • Full-text search • across document repositories • using cross-language queries (e.g. English – French, - German etc) • 2-way navigation links between literature and molecular datasets via gene symbol recognition Features implemented via conceptual fingerprinting A discovery tool

  14. C198810.99 C929920.67 C020020.66 C992290.44 C003920.33 C939390.21 Index and link index terms to thesaurus Fingerprint database Full text document • 1 CFP = 400 bytes • Abstraction: 250.000 pages/PC/day • Matching: 500.000 CFP’s: 40 millisec. Conceptual fingerprints

  15. E-BioSci – distinguishing features • Is a free academic access to services • Places strong emphasis on concept searching of full text – a discovery tool • Uses conceptual fingerprints to semantically link text with different data types (in particular genomic and image data) • Links only to refereed material that meets criteria of editorial control • Welcomes principles of free access, but respects existing restrictions of (commercial) content providers

  16. Idea! Databases (e-)Literature Hypothesis Idea! Literature Hypothesis Publication Experiment Publication Experiment Data Data Community-driven e-science (1) • The growing importance of interactive databases Traditional Extended

  17. Idea! Databases (e-)Literature Hypothesis Ideas! Shared data resources Publication Experiment Experiments Data Community-driven e-science (2) • Large-scale projects will drive further changes in communication and publishing practice ‘Traditional’ Community ‘data-centric’ Hypotheses Community; quality control

  18. Shared data resources Shared data resources Shared data resources Shared data resources Shared data resources Community-driven e-science (3) • Proliferation of community knowledge networks raises new challenges of semantic interconnectivity

  19. Database annotations (sequences, images etc) Community resources Scientist profiles Literature Fingerprint collections Fingerprint Database(s) Open archive repositories E-BioSci and semantic interconnectionof searchable resources

  20. Acknowledgements • Frank Gannon, Executive Director EMBO • … and many others who contributed ideas to the concept of E-BioSci • The E-BioSci partners • European Commission(contracts QLRI-2001-30266 and IST-2001-32688)

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