Managing Ecological and Biodiversity

Data Using Ecoinformatics:

Taiwan Experience

Chau Chin Lin

Taiwan Forestry Research Institute

Dr. Bill Chang (US NSF)

Persons to Thank First for The

Following Presentation

Dr. Hen-biau King

(TFRI Director 2003-2007)

Ecology：Information of Biocomplexity

Biotic Abiotic Temporal Spatial

Vernacular (FR): Pyrale du maïs

Vernacular (ES): Piral del maíz

Vernacular (DE): Maiszünsler

Diagnosis: Wingspan 26-30mm;

sexually dimorphic;male:

forewings ochreous to dark

brown; female: forewings pale

yellow; …

Foodplant: Zea mais L. 1753

Species: Ostrinia nubilalis (Hübner, 1796)

Family: Pyralidae

Order: Lepidoptera

Class: Insecta

Genus: Ostrinia Hübner, 1825

Vernacular (EN): European Corn-borer

Family: Gramineae

Taxonomic Names

Collection: DGH Lepidoptera

Record id: DGHEUR_003217

Country: France

Coordinates: 03.047˚E 48.730˚N

Date: 28 June 2003

Collector: Donald Hobern

Individuals: 3

Richness:

Spatial /Temporal

Observations

Biotic Interactions

Locus: AAL35331

Definition: acyl-CoA Z/E11 desaturase 1 mvpyattadg hpekdecfed...

Sequence Data

Average Rainfall

Location: 48.82°N 2.29°E Jan Feb Mar Apr ...

182.3 120.6 158.1 204.9 ...

Abiotic

Taxonomic Descriptions

Pheromones of Ostrinia http://www.nysaes.cornell.edu/fst/faculty/acree

/pheronet/phlist/ostrinia.html

Digital Literature

and Web Resources

Synonym: Pyralis nubilalis Hübner, 1796

Biodiversity：Information of Life

All Based on Data

Why Data Management Is Important in

Ecological Research?

http://siliconangle.com/blog/2012/

Data Informs Impacts of Biodiversity Loss on

Ocean Ecosystem Services

Annual

Cumulative

Worm et al., Science 2006

Data Enhances Understanding of The Real World

Understanding this disease requires

knowledge of epidemiology,

genetics, and transmission modes,

along with their ecological contexts.

Integrating ecologically pertinent

data into the chain of information

from the gene to the biosphere will

significantly enhance our

understanding of the natural world.

Whitfield J. 2003 Ape populations decimated by hunting and

Ebola virus. Nature 422:551

However,

Observations/experiments

the real world

Data/Raw data/Dataset

information

Data Collection Is A Hard Work

Planning

Problem

Analysis

and

modeling

Traditional Way of Research

Doesn’t Care About Data

Data Collection

Raw Data

(Michener et al. 1997)

Data Entropy Occurs Without Managing In

form

ati

on

Co

nte

nt

Time

Time of publication

Specific details

General details

Accident

Retirement or

career change

Death

What Data We Have Collected

Slide from Dr. John Porter

For Example： Forest Dynamics Plot Data

Forest Dynamics Plots in Taiwan

16 Plots Around the Island

For Example ：

Biodiversity Data

For Example ：

Carbon Flux Towers

How Did We Do?

Planning Problem Definition

(Research Objectives)

Analysis

and

modeling

Collection

Original

Observations

Planning

Selection and

extraction

Secondary

Observations

Used

data

What Techniques We Need?

• A framework that enables scientists to

generate new knowledge through

innovative tools and approaches

• For management, archiving, curation,

discovering, retrieval, integrating, analyzing,

and visualization of biodiversity and

ecological data

• It is called “Ecoinformatics”

• Ecological Metadata Language, EML

• Morpho – metadata and data management software

• Metacat – distributed data system

– registries: KNB, UCNRS, OBFS, NCEAS, PISCO, LTER

• EcoGrid and Tool Kit – integrating distinct data systems and networks

• Kepler – grid-enabled scientific workflows

< EML>

Search and Adapt The Existing Tools

Assembling Tools As

An Information Management System

EML Driven IMS

Information

Synthesis

Senor Network

Information Management

QA/QC

ecogrid

Dealing with Data Flow Change

Slide from US LTER

Interpret a pattern

1,000 x daily

Interpret a

number

10 x daily

Dealing with Data Collecting Change

Dealing with Data Deluge

Providing Good Quality Data

Available Online

Capacity Building and Training

Helped from US LTER

International Collaborations

2006

U.S.

LTER

Taiwan TFRI

Malaysia (FRIM)

Kasetsart

University

Thailand

Help Each Other

within EAP!

Apart from software products there have also been a series of publications in both Asian and Western journals,

including TREE, Bioscience and Ecological Informatics

Management, Archiving (Creating Metadata)

Metadata?

Standard for Ecology/Biodiversity: EML

EML Modules

Metadata/Data Depository System

Data Curation Network

Metacat Catalog

Morpho clients

Key

Site metadata system

Web clients

AND

CAP

OBFS

XML output filter

TFRI

ECNU

LNO

SEV SEV?

PISCO

Replication

Harvester

Internet

User-1

User-2 User-3

National Science

Council

Database

Server

Forming A Decentralized National System

Authentication

National GIS

National Park

Agriculture

Forestry

Joining Data Observation Network for Earth

National Center for Ecological Analysis and Synthesis (NCEAS), U.S.A; ; http://www.dataone.org/what-dataone.

is a data repository for sharing and

preserving data

is capable of providing researchers to

access globally distributed, networked

data from a single point of discovery.

is a collaboration among many partner

organizations, and is funded by the

US-NSF.

DataONE

DataONE

DataONE

[Through the knowledge and infrastructure integrates information]

Data Integration Data integration refers to linking research & monitoring

data to the modeling community & vice versa.

Data integration also refers to archiving data from

monitoring, research, & modeling efforts, as well as

making the data easily available for others to access &

use.

http://www.clear.lsu.edu/data_integration/

Return

URL

Data Depository

Metadata

Shared

Data

Registry Data

Site 1

Data

Site 2

Query Data Grid to find

data

Get

Data

Compute grid

Simulation

Model

Algorithm

Service

Broker

(UDDI)

Web

Service

WSDL

Query Service broker to find

services Get Component

Return URL & call functions

Archive output data to

Depository

Archive workflow

Workflow

archive

Toward An Automation of Data Process

Scientific Workflow Approach to Analysis

C RESULTS:

Tables

Maps

Graphs

ASCII

Application-A Case

Luquillo,Puerdo Rico

Pasho,Malaysia

Lienhuachih,Taiwan

Ogawan,Japan

(LDAP)

WebServer

(Apache+PHP)

Data Retrieval

(SQL)

Raw

data

Upload

EML

Document

Metadata

Catalog EcoGrid

Scientific

Workflow

EML + Raw data

Download

Morpho

Metadata

CTFS

Data

Model

Other

Data

Models

Action Items for Individual Ecologists

• Organize, document, and preserve data

for posterity

• Share data

• Collaborate with networks of colleagues to

bring together heterogeneous datasets to

address larger scale questions

• Address data management issues with

students and peers

Data Sharing

• 1.Data policy

What are fair policies for providing access to data?

• 2.Agreements Specification

What controls, embargoes, usage constraints, or other

limitations are needed to assure fairness of access and use?

• 3.Policy Administration

What data publication models are appropriate?

Kaohsiung, Taiwan 2007

Experience Learned: Many hands truly do make "light work!"

THANK YOU FOR YOUR

ATTENTION!!

chin@tfri.gov.tw