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Bringing a publisher’s content to the Life Science researcher

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InfoTech for Pharma and Biotech - May 2008

InfoTech for Pharma and Biotech - May 2008

Published in: Education, Technology

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  • 1. Bringing a publisher’s content to the Life Science researcher Alf Eaton Nature Publishing Group
  • 2. Why? Find Browse Store
  • 3. Search
  • 4. HubMed Whatizit: GO, UniProt; Wikipedia
  • 5. GoPubMed
  • 6. GoPubMed
  • 7. Search Recognise entities, including synonyms. Discover and suggest connections between entities.
  • 8. NextBio
  • 9. Freebase
  • 10. Browse Diabetes Cancer Cell Migration
  • 11. Cell Migration Gateway
  • 12. Chemical Blogspace (PostGenomic: open source aggregator)
  • 13. Increase the visibility of articles Increased readership Increased citations
  • 14. Text mining Abstracts Full text Access OTMI
  • 15. OTMI opentextmining.org Atom Entry elements Metadata Sentences References
  • 16. Extract
  • 17. Garten, Niclas, Altman (Stanford University), in press
  • 18. Metadata Authors, Dates, Title, Journal, Abstract PRISM, Dublin Core References
  • 19. Entities People, Places, Companies (Reuters OpenCalais) Genes, Proteins, Molecules, Products
  • 20. Full text Sharable NLM DTD Text mining annotations
  • 21. iHOP Gene/protein entities Interactions between proteins MeSH Gene Ontology
  • 22. Interaction Author/editor verification
  • 23. Annotation formats Inline Stand-off Splice annotations into XML using PHP or Javascript XPath and character offsets for positioning Can store inline, eg in Marklogic, using start/ end markers
  • 24. Possible shared annotation formats Atom RDF UIMA Annotea Zotero, Diigo
  • 25. Atom Extensible Hierarchical content model Atom Publishing Protocol
  • 26. RDF Completely extensible Arbitrary attributes Generic data storage SPARQL queries
  • 27. Licensing Non-commercial (some rights reserved) Attribution Joint ownership Facts vs creative arrangement Redistribution (share-alike) Preserve value
  • 28. Participation Vote annotations up/down Highlight/suggest new annotations Knowledge mapping (Mind Maps)
  • 29. Semgine myMap
  • 30. Communication Bookmarks (Connotea) Links to sections/paragraphs/figures/data Blog posts
  • 31. Structured HTML Microformats RDFa Yahoo! search Microcitation
  • 32. APIs Make content available to : Researchers/scientists (desktop, mobile, web) Machines/indexers Artists/visualizers Integrate with data web