the importance and future trends of sharing biodiversity data chau chin lin taiwan forestry research...
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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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n C
on
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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¤tTab=¤tItem=&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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