InfoTech for Pharma and Biotech - May 2008

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

11. Browse
Diabetes
Cancer
Cell Migration

12. Cell Migration Gateway

15. Chemical Blogspace
(PostGenomic: open source aggregator)

16. Increase the visibility of articles
Increased readership
Increased citations

17. Text mining
Abstracts
Full text
Access
OTMI

18. OTMI
opentextmining.org
Atom Entry elements
Metadata
Sentences
References

21. Extract

22. Garten, Niclas, Altman (Stanford University), in press

23. Metadata
Authors, Dates, Title, Journal, Abstract
PRISM, Dublin Core
References

24. Entities
People, Places, Companies
(Reuters OpenCalais)
Genes, Proteins, Molecules, Products

25. Full text
Sharable
NLM DTD Text mining
annotations

26. iHOP
Gene/protein entities
Interactions between proteins
MeSH
Gene Ontology

27. Interaction
Author/editor verification

29. 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

30. Possible shared
annotation formats
Atom
RDF
UIMA
Annotea
Zotero, Diigo

31. Atom
Extensible
Hierarchical content model
Atom Publishing Protocol

32. RDF
Completely extensible
Arbitrary attributes
Generic data storage
SPARQL queries

33. Licensing
Non-commercial (some rights reserved)
Attribution
Joint ownership
Facts vs creative arrangement
Redistribution (share-alike)
Preserve value

34. Participation
Vote annotations up/down
Highlight/suggest new annotations
Knowledge mapping (Mind Maps)

35. Semgine myMap

36. Communication
Bookmarks (Connotea)
Links to sections/paragraphs/figures/data
Blog posts

37. Structured HTML
Microformats
RDFa
Yahoo! search
Microcitation

38. APIs
Make content available to :
Researchers/scientists (desktop, mobile,
web)
Machines/indexers
Artists/visualizers
Integrate with data web