The Importance and Future Trends of Sharing Biodiversity Data

Chau Chin LinTaiwan Forestry Research Institute

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Chris King 2011 Genotype 1.1.9

Biodiersity: Tree of Life on the Planet

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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 LepidopteraRecord id: DGHEUR_003217Country: FranceCoordinates: 03.047˚E 48.730˚NDate: 28 June 2003Collector: Donald HobernIndividuals: 3Richness:

Spatial /Temporal Observations

Biotic Interactions

Locus: AAL35331Definition: acyl-CoA Z/E11 desaturase

1 mvpyattadg hpekdecfed...

Sequence Data

Average RainfallLocation: 48.82°N 2.29°E Jan Feb Mar Apr ...182.3 120.6 158.1 204.9 ...

Abiotic

Taxonomic Descriptions

Pheromones of Ostriniahttp://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

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Challenges and OpportunitiesScientific innovation has been called on to spur economic recovery and to inform sustainability.Data collection,curation, and access are central to all of these issues

Science 311:692-694, 2011

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Annual

Cumulative

Worm et al., Science 2006

Data Informs the Lost of Biodiviersity

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Data Provides Actions Making

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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

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All about Data

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Observations/experimentsObservations/experiments

the real worldthe real world

Data/Raw data/DatasetData/Raw data/Dataset

informationinformation

Data Comes from Research of the Real World

http://taibif.twPlanning

Problem

Analysisand

modeling

The Traditional Paradigm of Data

Data Collection

Publications

Raw Data

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(Michener et al. 1997)

Data EntropyIn

form

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t

Time

Time of publication

Specific details

General details

Accident

Retirement or career change

Death

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Planning Problem Definition(Research Objectives)

Analysisand

modeling

Collection

OriginalObservations

Publications

Planning

Selection andextraction

SecondaryObservations

used data

New Paradigm of Data

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Data CyberinstrstructureData Cyberinstrstructure

The Real WorldThe Real World

Synthesis Hubsand Nodes

Fundamental Research

ObservatoryNetworks

Collaboratories

A Data-intensive ApproachA Data-intensive Approach

InformationResources

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Breaking Spatial and Temporal Barriers

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Integrating Heterogeneous Data

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Data collecting

Data Preserving and managing

Adapting Cutting Edge Technologies

Data transferring

Data discovering,Integrating,analyzing,visualizing

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Providing Good Quality Data Available Online

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Dealing with Data Flow Change

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Interpret a pattern1,000 x daily

Interpret a number10 x daily

Dealing with Data Collecting Change

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Dealing with Data Deluge

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Raw data

InformationKnowledge

Management,Archiving,

&Curation

Discovery,Retrieval

Integrating,Analysis

&Visualization

Towards Automation of Data Processing

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Metadata?

Metadata Is the Key to New Paradigm

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Metadata

Date(YYYYMMDD)

Temp(°C)

Precip.(mm)

Obs. #1

Obs. #2

Obs. #3

20040928 29.4 18.4

20040929 29.7 4.2

20040930 28.9 21.3

Data

What Is Metadata-An Example

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Metadata Is Data about Data

… and All Other Facet of Dataset!

Who?

What?

Wh

en?

Where?

How?

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Standards for Metadata• ISO 19115 is a geo-spatial metadata standard developed by ISO/TC 211. ISO 19115 defines a comprehensive metadata model for geographic objects. ISO/TC 211also defined a smaller set of core metadata elements (shown on example slide.) This core contains the minimum elements that satisfy the requirements of an ISO conformant metadata record. The ISO 19115 standard does not specify storage format, but XML schemas are under development for an XML encoding of it (in full or for specialized profiles).

• CSDGM/FGDC (Content Standard for Digital Geospatial Metadata) is a standard for metadata for geographic objects developed by FGDC (Federal Geographic Data Committee). However, this standard is not limited to spatial data. FGDC enables development of profiles, i.e. customization of the standard to suit the needs of a particular application domain (while staying within the framework of the standard).

SPOT imagery FGDC examplehttp://gcmd.nasa.gov/servlets/md/getdif.py?entry_id=[GCMD]CANEMRCCRSSPOT&xsl=dif_to_fgdc-html.xsl&currentTab=&currentItem=&portal=gcmd

• EML (Ecological Metadata Language) http://knb.ecoinformatics.org/data.html

•Darwin CoreThe Darwin Core (sometimes abbreviated as DwC) is a standard designed to facilitate the exchange of information about the geographic occurrence of species and the existence of specimens in collections.

Many Standards Can be Chosen

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Ecological Metadata Language is…• an ecological metadata standard• very extensible; it can be used to describe

many different types of data• comprehensive and supports a rich set of

constructs to fully describe data• XML and is defined by an XML Schema• exploitable by different computer

applications

What Is EML?

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1990 1995 2000 2005

Early ecological metadata work in LTER and elsewhere

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EML History

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EML Modules

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Darwin Core Ratified in the Year of Darwin!!

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taxonRank

higherClassification

taxonConceptIDassociatedSequences

geodeticDatumspecificEpithet

coordinatePosition

associatedSequences: A list (concatenated and separated) of identifiers (publication, global unique identifier, URI) of genetic sequence information associated with the Occurrence.

Darwin Core – a glossary of terms

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Data Archiving Provides Opportunities for Auto Analysis

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Species Distribution Prediction

(Abies Kawakamii)

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Metadata list

Key words query

Metadata provides data source

Retrieval of dataset

Data analysis

An Example of Biodiversity and Ecological Data

Thank You!

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