20110222 behesty monitoring and measuring biodiversity
DESCRIPTION
lecture presented at Shahid Beheshti University, Tehran, Iran. Feb 22, 2011TRANSCRIPT
Monitoring and Measuring Biodiversity: Some Thoughts
Donat Agosti
Beheshty University, Tehran
February 21, 2011
Do you know ...
Earth Summit
IPBES
NCBI
GBIF
TDWG
Darwin Core
They all have to do with
global biodiversity issues
Earth Summit
Rio Earth Summit 1992:
Global Biodiversity Crisis
Convention on Biological Diversity
IPBES
Intergovernmental Platform on Biodiversity and Ecoystem Services
Tool to assess global biodiversity patterns and change
NCBI
National Center for Biotechnology Information
Global resource for molecular biology information (eg GenBank)
GBIF
Global Biodiversity Information Facility
Access point to specimen data
http://data.gbif.org/countries/IR
TDWG
Taxonomic Data Working Group
Body to create standards to exchange data to build highly distributed global information systems
Darwin Core
Global standard to describe specimen data needed for exchange
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
“protein-protein interaction networks”
John Wilbanks,
Neurocommons
This is the world we live in:
A truly global community where machines can do an unimaginable amount of work.
It has its dangers:
We are not all the same
It has its dangers:
We are not all the same
It has its advantages:
All events can be put in context.
Is something a local, regional or global event?
Is something a local, regional or global event?
Connecting time series (local) with spatial data
Is something a local, regional or global event?
Or is it just a fluctuation or artifact?
Monitoring as a comparative science
Monitoring as a comparative science
Change over time
Change over land use
What kind of and how many ants?
What is the impact of land use change?
What happens over time?
What happens over space and time?Forest
Pasture
Cacao / Cabruca
Urban areas
Campus
Δt ?
Δt ?
Δt ?Δt ?
Δt ?
Δ ?
What does it mean?
Science
Standard sampling
Standard repetitive samples
What does it mean?
Science
Standard sampling
Quality control
What does it mean?
Science
Standard sampling
Quality control
Standards for data description
Exchange protocols
What does it mean?
Science
Standard sampling
Quality control
Standards for data description
http://www.sciencemag.org/content/331/6018/703.full.html
bonjour
salam
helo
ciao
selamat
What does it mean?
Science
Standard sampling
Quality control
Standards for data description
Exchange protocols
Plazi Search and Retrieval Server: Access to data
TAPIR, SPM
You
You
You
human
machine
What do we need?
Access
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).
What do we need for monitoring?
Access
Identification aids
Who is this?What do I know about her?
Where does she live?
Who are you?What do you do?
Where are you from?
What do we need for monitoring?
Access
Identification aids
What species is it?
Semantic, enhanced treatments do the job ...
What do we need monitoring?
Access
Identification aids
What species is it?
What do I know about the species?
What do we need for monitoring?
Access
Identification aids
What species is it?
What do I know about the species?
Where does it live?
What do we need for monitoring?
Access
Metadata
What do we need for monitoring?
Access
Metadata
Describing the data; also to discover it
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>
</mods:originInfo>
What do we need monitoring?
Access
Metadata
Networks
get info – provide info
What do we need for monitoring?
Access
Metadata
Networks
get info – provide info
use standards
What kind of ants live in Iran?
Standards
Use iran ants in google
Show iran ants in plazi.org
„Iran ants“:495,000 records
Semantic, XML enhanced treatments do the job ...
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="193329"/><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, HL 1.02, HW 0.95, CI 93, SL 1.30, SI 137, PW 0.73, ML 0.38. Mandible outer margin strongly curving to a sharp apical tooth, the apex parallel to the anterior clypeal margin.
What do we need for monitoring?
Networks
get info – provide info
use standards
use open access / open source
What do we need monitoring?
Social networks
Information is not free in the sense of „it doesn‘t cost anything“
What do we need?
Social networks
Information is not free in the sense of „it doesn‘t cost anything“
Information depends on you!
Monitoring biodiversity depends foremost on science...
Monitoring biodiversity depends foremost on science (and good scientists)...
... technology makes it just more relevant and powerful.
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.
