A presentation to the biologically aware but totally TDWG uninitiated about the significance of sharing bio-data

1. Integrating Bio-Data
Lee Belbin
Manager, Infrastructure Project
TDWG
(Biodiversity Information Standards)

2. Who has heard of GBIF?

3. GBIF
The Global Biodiversity
Information Facility

4. GBIF
International organisation
established to share bio-data

5. GBIF
Supported by ~42 countries
(including Australia) and ~35
international organisations

6. GBIF
The Australian hub is through
ABRS (ABIF)

8. Who has heard of TDWG?

9. …that‟s what I figured

10. TDWG
Formerly: The Taxonomic
Database Working Group

11. …but more accurately
referred to as
Biodiversity Information
Standards

12. Biodiversity Information
Standards
International group responsible for
standards and protocols for
sharing bio-data

13. EOL?
Encyclopedia of Life

14. ALA?
Atlas of Living Australia

15. GBIF, EoL, ALA …
…are now or will be based on
TDWG standards

16. So what?
(…hence this talk…)

17. Science is getting more
collegiate
… a good thing.

18. The Project
US$2 million over 2.5 years
(Gordon & Betty Moore Foundation)

19. Aim
To improve the standards for
sharing 'bio-data'

20. Why?
The whole is (far) more than
the sum of the parts…

21. People
Lee Belbin (Hobart: Manager),
Roger Hyam (Edinburgh: Systems
Architect), Ricardo Pereira (Brasilia: Software
Engineer)
Donald Hobern (Copenhagen: GBIF & now
Manager of the ALA),
Stan Blum (San Francisco, TDWG old timer!)

22. Once … we had paper!

23. and calculators!

26. The attitude:
“It‟s Mine!”

27. Then..

31. … but we are moving to
…far more open sharing and
integration of data

32. This will enable
…more effective environmental and
species conservation / management
(among many other things)

33. To do this, we need
effective standards
…using „web 2.0‟ technologies

34. Video
„The web is us‟
http://www.youtube.com/watch?v=6gmP4nk0EOE

35. Standards?
…Good ones are transparent
to most who use them

36. But for your education…
I‟ll give you a little insight … it will be
good for you.
Promise

37. Standards to exchange bio-
data have three components-
1. An ontology
2. GUIDs
3. Transport protocols

38. 1. Ontology
Is a data model that represents a
formal set of concepts within a
domain and the relationships
between those concepts

39. Ontologies
…are the basis of the Semantic Web
where objects are given meaning
which computers and humans can
understand

40. Ontologies
…can be used by machines to
reason about the objects within
that domain

42. Resource Description
Framework …
RDF is the language of the
Semantic Web

44. ALL data can be stored in
the form of „RDF triples‟ …
subject – predicate (verb) – object
Wine – has vintage - 2005

46. 2. GUIDs
Globally Unique Identifiers

47. GUIDs
Assigned by authorities to their
(bio) objects

48. GUIDs
…Remain attached to data objects
(with attribution!)

49. GUIDs
… When „clicked‟ return
„semantic‟ metadata / data

50. GUID of Choice …
Life Science Identifiers
(LSIDs)

51. Transport Protocols
…Map local data to global standards

52. Transport Protocols
… Enable searching across
geographically separated data
repositories (based on different systems)

53. The transport protocol
of choice …
TAPIR
TDWG Access Protocol for
Information Retrieval

54. Transport Protocol
Video
http://www.youtube.com/watch?v=x9404is3RJ8

55. An Example
Antbase, Google, Genbank, Pu
bMed „skimmed‟ for RDF and
GUIDs using TAPIR

56. … Emergent Properties
…there are specimens that have been barcoded and which are
labelled in GenBank as unidentified (i.e., names like "Melissotarsus
sp. BLF m1"), but the same specimen has a proper name in AntWeb
(e.g., casent0107665-d01 is Melissotarsus insularis).
We can then use this information to add value to GenBank. For
example, a search of GenBank for sequences for Melissotarsus
insularis find nothing, but it does have sequences for this
taxon, albeit under the name "Melissotarsus sp. BLF m1".
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