20110222 behesty monitoring and measuring biodiversity

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.

With my best thanks!

Donat Agosti

agosti@amnh.org

http://plazi.org

http://antbase.org