lecture presented at Shahid Beheshti University, Tehran, Iran. Feb 22, 2011

1. Monitoring and Measuring
Biodiversity: Some Thoughts
Donat Agosti
Beheshty University, Tehran
February 21, 2011

2. Do you know ...

3. Earth Summit

4. IPBES

5. NCBI

6. GBIF

7. TDWG

8. Darwin Core

9. They all have to do with
global biodiversity issues

10. Earth Summit
Rio Earth Summit 1992:
Global Biodiversity Crisis
Convention on Biological Diversity

11. IPBES
Intergovernmental Platform on
Biodiversity and Ecoystem
Services
Tool to assess global biodiversity
patterns and change

12. NCBI
National Center for Biotechnology
Information
Global resource for molecular
biology information (eg GenBank)

13. GBIF
Global Biodiversity Information
Facility
Access point to specimen data

14. http://data.gbif.org/countries/IR

15. TDWG
Taxonomic Data Working Group
Body to create standards to
exchange data to build highly
distributed global information
systems

16. Darwin Core
Global standard to describe specimen
data needed for exchange

18. An example from the Neurocommons text mining
pilot:
• PubMed abstracts: > 16,000,000
• CNS classified abstracts: 874,727
• text mining recognized: 368,688
• text mining processed: 94,381
• extracted graph of 30,000+ relationships and 5,500
genes and proteins
“protein-protein
interaction networks”
John Wilbanks,
Neurocommons

19. “protein-protein
interaction networks”
John Wilbanks,
Neurocommons

20. This is the world we live in:
A truly global community where
machines can do an unimaginable
amount of work.

21. It has its dangers:
We are not all the same

22. It has its dangers:
We are not all the same
It has its advantages:
All events can be put in context.

26. Is something a local, regional or
global event?

28. Is something a local, regional or
global event?
Connecting time series (local) with
spatial data

29. Is something a local, regional or
global event?
Or is it just a fluctuation or
artifact?

30. Monitoring as a comparative
science

31. Monitoring as a comparative
science
Change over time
Change over land use

32. What kind of and
how many ants?
Δt ?
Δt ? What is the impact of
Δt ? land use change?
Δ? Δt ?
What happens over
time?
Δt ?
What happens over
Forest Urban areas space and time?
Pasture Campus
Cacao / Cabruca

33. What does it mean?
Science
Standard sampling

34. Standard repetitive samples

35. What does it mean?
Science
Standard sampling
Quality control

36. What does it mean?
Science
Standard sampling
Quality control
Standards for data description
Exchange protocols

37. What does it mean?
Science
Standard sampling
Quality control
Standards for data description

38. http://www.sciencemag.org/content/331/6018/703.full.html

39. selamat
bonjour
ciao
salam
helo

40. What does it mean?
Science
Standard sampling
Quality control
Standards for data description
Exchange protocols

41. Plazi Search and Retrieval
Server: Access to data
TAPIR, SPM
You
You human
machine
You

42. What do we need?
Access

43. Before antbase.org, Harvard„s Museum of
Comparative Zoology could claim to be the only
location with a complete set of ant systematics
publications from 1758 - present.
Through antbase.org„s
digital library, access
to this body of
literature is worldwide,
and it is actively used
(>10,000 visits in one
month only).

44. What do we need for monitoring?
Access
Identification aids

45. Who are you?
What do you do?
Who is this? Where are you
from?
What do I know about her?
Where does she live?

46. What do we need for monitoring?
Access
Identification aids
What species is it?

49. Semantic, enhanced treatments do
the job ...

50. What do we need monitoring?
Access
Identification aids
What species is it?
What do I know about the species?

52. What do we need for monitoring?
Access
Identification aids
What species is it?
What do I know about the species?
Where does it live?

54. What do we need for monitoring?
Access
Metadata

55. What do we need for monitoring?
Access
Metadata
Describing the data; also to
discover it

56. Linnaeus, C., 1758, Systema naturae. Regnum Animale. 10 th ed., W. Engelmann, Lipsiae,
<tax:taxonx xsi:schemaLocation="http://www.taxonx.org/schema/v1
http://www.taxonx.org/schema/v1/taxonx1.xsd http://www.loc.gov/mods/v3
http://www.loc.gov/mods/v3/mods-3-1.xsd
http://digir.net/schema/conceptual/darwin/2003/1.0
http://digir.net/schema/conceptual/darwin/2003/1.0/darwin2.xsd">
<tax:taxonxHeader>
<mods:mods>
<mods:titleInfo>
<mods:title>Systema naturae. Regnum Animale. 10 th ed.</mods:title>
</mods:titleInfo>
<mods:name type="personal">
<mods:role>
<mods:roleTerm>Author</mods:roleTerm>
</mods:role>
<mods:namePart>Linnaeus, C.</mods:namePart>
</mods:name>
<mods:originInfo>
<mods:dateIssued>1758</mods:dateIssued>
<mods:publisher>W. Engelmann</mods:publisher>
<mods:place>
<mods:placeTerm type="text">Lipsiae</mods:placeTerm>
</mods:place>

57. What do we need monitoring?
Access
Metadata
Networks
get info – provide info

59. What do we need for monitoring?
Access
Metadata
Networks
get info – provide info
use standards

60. What kind of ants live in Iran?

61. Standards
„Iran ants“:
Use iran ants in google 495,000 records
Show iran ants in plazi.org

64. Semantic, XML enhanced
treatments do the job ...

65. This can also be applied to entire sections of text, such as
the treatment of a species and its parts.
<tax:treatment>
<tax:nomenclature>
<tax:name>
<tax:xid source="HNS" identifier="19
<tax:xmldata>
<dc:Genus>Mystrium</dc:Genus>
<dc:Species>leonie</dc:Species>
</tax:xmldata>
Mystrium leonie
</tax:name>
<tax:status>n. sp.</tax:status>
Fig 1 D - F
</tax:nomenclature>
<tax:div type="description">
<tax:p>HOLOTYPE WORKER: TL 3.95, H
1.30, SI 137, PW 0.73, ML 0.38. Mand

66. What do we need for monitoring?
Networks
get info – provide info
use standards
use open access / open source

67. What do we need monitoring?
Social networks
Information is not free in the
sense of „it doesn‘t cost anything“

68. What do we need?
Social networks
Information is not free in the
sense of „it doesn‘t cost anything“
Information depends on you!

69. Monitoring biodiversity depends
foremost on science...

70. Monitoring biodiversity depends
foremost on science (and good
scientists)...
... technology makes it just more
relevant and powerful.

71. Biodiversity data at work:
The use of our monitoring data by
IPBES is an indication that we
deliver data and information that
can be used beyond our own work
to save planet earth.

72. With my best thanks!
Donat Agosti
agosti@amnh.org
http://plazi.org
http://antbase.org