The Modern Palimpsest


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A talk given at the Ingenta Publisher Forum, in November 2008.


For a detailed description of the talk.

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  • Introduction
  • The Modern Palimpsest

    1. 1. The Modern Palimpsest Leigh Dodds, Engineering Manager, IngentaConnect Ingenta Publisher Forum 28 th November 2005
    2. 2. Introduction <ul><li>An analogy: The Modern Palimpsest </li></ul><ul><li>What could we do with better data? </li></ul><ul><li>Reaching a new market? </li></ul>
    3. 3. Palimpsests A little history lesson
    4. 5. The Palimpsest <ul><li>Scriptio inferior (“underwriting”) </li></ul><ul><ul><li>Useful information just under the surface </li></ul></ul><ul><li>Reaction to high cost of publishing </li></ul><ul><li>A form of re-use? </li></ul><ul><ul><li>Certainly not was intended or hoped for! </li></ul></ul>
    5. 6. The Modern Palimpsest Lets take a look…
    6. 12. The Academic Paper as Palimpsest <ul><li>“ Loss” of data during authoring and publishing </li></ul><ul><ul><li>But useful information beneath the surface </li></ul></ul><ul><li>Limited Re-use </li></ul><ul><ul><li>Fixed data presentation </li></ul></ul><ul><ul><li>Non-web native format </li></ul></ul><ul><li>Limited Life time </li></ul><ul><ul><li>Once its been read, then what? </li></ul></ul>
    7. 13. … the times they are a-changin' Web 2.0
    8. 14. Current Trends <ul><li>Standardisation of data formats and identifiers </li></ul><ul><li>Maturation of browser technologies </li></ul><ul><ul><li>XML, CSS, Javascript </li></ul></ul><ul><li>The Two Way Web </li></ul><ul><ul><li>Users actively engaging with content AND data </li></ul></ul>
    9. 15. Example 1: Mapping New Ways to Explore Data Improved Browser Technologies
    10. 22. Example 2 - iSpecies New Ways to Find Data Composing Services (“Mashups”)
    11. 30. Aside: Author Identifiers <ul><li>Industry needs a unique identifier for Authors </li></ul><ul><ul><li>Why not use the DOI? </li></ul></ul><ul><li>More… </li></ul><ul><ul><li>By this author (accurately!), or co-authors </li></ul></ul><ul><ul><li>By research group/institution </li></ul></ul><ul><ul><li>By research interest </li></ul></ul><ul><li>Social Networking, Trust </li></ul>
    12. 31. Example 3 - HubMed Alternate User Interfaces Harvesting Collective Intelligence
    13. 36. Return of the Amateur? “… an amateur may be as competent as a paid professional, yet is motivated by a love or passion for the activity” wiki /Amateur
    14. 39. Summary <ul><li>Enable new markets by enabling new uses </li></ul><ul><li>Deconstruct the Academic Paper </li></ul><ul><li>Not just on the web, Part of the web </li></ul>
    15. 40. Publishing Richer Metadata
    16. 41. Publishing Richer Metadata <ul><li>Document Formats are Metadata Aware </li></ul><ul><ul><li>Office tools are XML based </li></ul></ul><ul><ul><li>Open Office Bibliographic project </li></ul></ul><ul><ul><li>Adobe XMP </li></ul></ul><ul><li>Post production enrichment </li></ul><ul><ul><li>Term extraction, e.g protein names, place names </li></ul></ul><ul><ul><li>Backfiles </li></ul></ul><ul><li>Supplementary Data </li></ul><ul><ul><li>Publish data separately from documents </li></ul></ul>
    17. 42. XML is Not Enough The Semantic Web
    18. 43. XML is Not Enough <ul><li>With the ongoing rapid increase in both volume and diversity of 'omic' data (genomics, transcriptomics, proteomics, and others), the development and adoption of data standards is of paramount importance to realize the promise of systems biology. A recent trend in data standard development has been to use extensible markup language (XML) as the preferred mechanism to define data representations. But as illustrated here with a few examples from proteomics data, the syntactic and document-centric XML cannot achieve the level of interoperability required by the highly dynamic and integrated bioinformatics applications </li></ul><ul><li>-- “From XML to RDF: how semantic web technologies will change the design of 'omic' standards” </li></ul><ul><li>Nature Biotechnology  23, 1099 - 1103 (2005) </li></ul>