Bringing a publisher’s
     content to the
Life Science researcher

            Alf Eaton
     Nature Publishing Group
Why?

 Find
Browse
 Store
Search
HubMed




Whatizit: GO, UniProt; Wikipedia
GoPubMed
GoPubMed
Search
Recognise entities, including synonyms.
Discover and suggest connections
between entities.
NextBio
Freebase
Browse

Diabetes
Cancer
Cell Migration
Cell Migration Gateway
Chemical Blogspace




   (PostGenomic: open source aggregator)
Increase the visibility of articles
Increased readership
Increased citations
Text mining

   Abstracts
   Full text
    Access
    OTMI
OTMI

opentextmining.org
Atom Entry elements
     Metadata
    Sentences
    References
Extract
Garten, Niclas, Altman (Stanford University), in press
Metadata

Authors, Dates, Title, Journal, Abstract


          PRISM, Dublin Core


              References
Entities

     People, Places, Companies
       (Reuters OpenCalais)
Genes, Proteins, Molecules, Products
Full text

                          Sharable
NLM DTD     Text mining
                          annotations
iHOP

    Gene/protein entities
Interactions between proteins
           MeSH
       Gene Ontology
Interaction

Author/editor verification
Annotation formats
                     Inline
                   Stand-off


Splice annotations into XML using PHP or
Jav...
Possible shared
annotation formats
        Atom
         RDF
        UIMA
       Annotea
     Zotero, Diigo
Atom

        Extensible
Hierarchical content model
Atom Publishing Protocol
RDF

Completely extensible
 Arbitrary attributes
Generic data storage
   SPARQL queries
Licensing
Non-commercial (some rights reserved)
Attribution
Joint ownership
Facts vs creative arrangement
Redistribution (...
Participation

   Vote annotations up/down
Highlight/suggest new annotations



Knowledge mapping (Mind Maps)
Semgine myMap
Communication

         Bookmarks (Connotea)
Links to sections/paragraphs/figures/data
               Blog posts
Structured HTML

    Microformats
        RDFa
    Yahoo! search
    Microcitation
APIs
Make content available to :

Researchers/scientists (desktop, mobile,
web)
Machines/indexers
Artists/visualizers
Inte...
Bringing a publisher’s content to the Life Science researcher
Bringing a publisher’s content to the Life Science researcher
Bringing a publisher’s content to the Life Science researcher
Bringing a publisher’s content to the Life Science researcher
Bringing a publisher’s content to the Life Science researcher
Bringing a publisher’s content to the Life Science researcher
Bringing a publisher’s content to the Life Science researcher
Bringing a publisher’s content to the Life Science researcher
Upcoming SlideShare
Loading in …5
×

Bringing a publisher’s content to the Life Science researcher

1,351 views

Published on

InfoTech for Pharma and Biotech - May 2008

Published in: Education, Technology
0 Comments
1 Like
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total views
1,351
On SlideShare
0
From Embeds
0
Number of Embeds
17
Actions
Shares
0
Downloads
10
Comments
0
Likes
1
Embeds 0
No embeds

No notes for slide

Bringing a publisher’s content to the Life Science researcher

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

×