Managing Ecological and Biodiversity Data Using Ecoinformatics: Taiwan Experience. Chau Chin Lin Taiwan Forestry Research Institute

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1 Managing Ecological and Biodiversity Data Using Ecoinformatics: Taiwan Experience Chau Chin Lin Taiwan Forestry Research Institute

2 Persons to Thank First for The Following Presentation Dr. Hen-biau King (TFRI Director ) Dr. Bill Chang (US NSF)

3 Ecology:Information of Biocomplexity Biotic Abiotic Temporal Spatial

4 Biodiversity:Information of Life Class: Insecta Order: Lepidoptera Family: Pyralidae Genus: Ostrinia Hübner, 1825 Taxonomic Names Synonym: Pyralis nubilalis Hübner, 1796 Sequence Data Locus: AAL35331 Definition: acyl-coa Z/E11 desaturase 1 mvpyattadg hpekdecfed... Species: Ostrinia nubilalis (Hübner, 1796) Vernacular (EN): European Corn-borer Vernacular (DE): Maiszünsler Vernacular (ES): Piral del maíz Vernacular (FR): Pyrale du maïs Family: Gramineae Taxonomic Descriptions Diagnosis: Wingspan 26-30mm; sexually dimorphic;male: forewings ochreous to dark brown; female: forewings pale yellow; Digital Literature and Web Resources Foodplant: Zea mais L Biotic Interactions Spatial /Temporal Observations Collection: DGH Lepidoptera Record id: DGHEUR_ Country: France Coordinates: E N Date: 28 June 2003 Collector: Donald Hobern Individuals: 3 Richness: Pheromones of Ostrinia /pheronet/phlist/ostrinia.html Abiotic Average Rainfall Location: N 2.29 E Jan Feb Mar Apr

5 All Based on Data Why Data Management Is Important in Ecological Research?

6 Data Informs Impacts of Biodiversity Loss on Ocean Ecosystem Services Annual Cumulative Worm et al., Science 2006

7 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 Ape populations decimated by hunting and Ebola virus. Nature 422:551

8 However,

9 Data Collection Is A Hard Work information Data/Raw data/dataset Observations/experiments the real world

10 Traditional Way of Research Doesn t Care About Data Analysis and modeling Raw Data Data Collection Problem Planning

11 Information Content Data Entropy Occurs Without Managing Time of publication Specific details General details Accident Retirement or career change Death Time (Michener et al. 1997)

12 What Data We Have Collected Slide from Dr. John Porter

13 For Example: Forest Dynamics Plot Data

14 Forest Dynamics Plots in Taiwan 16 Plots Around the Island

15 For Example : Biodiversity Data

16 For Example : Carbon Flux Towers

17 How Did We Do? Used data Collection Original Observations Analysis and modeling Selection and extraction Secondary Observations Planning Problem Definition (Research Objectives) Planning

18 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

19 Search and Adapt The Existing Tools < EML> 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

20 Assembling Tools As An Information Management System

21 EML Driven IMS Senor Network ecogrid QA/QC Information Management Information Synthesis

22 Dealing with Data Flow Change Slide from US LTER

23 Dealing with Data Collecting Change Interpret a number 10 x daily Interpret a pattern 1,000 x daily

24 Dealing with Data Deluge

25 Providing Good Quality Data Available Online

26 Capacity Building and Training Helped from US LTER

27 International Collaborations 2006

28 Help Each Other within EAP! U.S. LTER Taiwan TFRI Malaysia (FRIM) Kasetsart University Thailand

29 Apart from software products there have also been a series of publications in both Asian and Western journals, including TREE, Bioscience and Ecological Informatics

30 Management, Archiving (Creating Metadata) Metadata?

31 Standard for Ecology/Biodiversity: EML

32 EML Modules

33 Metadata/Data Depository System

34 Data Curation Network SEV SEV? AND OBFS TFRI Harvester CAP Replication ECNU Key Metacat Catalog LNO Morpho clients Web clients Site metadata system XML output filter PISCO

35 Forming A Decentralized National System Internet User-2 User-3 Forestry User-1 Agriculture Authentication National GIS National Park Database Server National Science Council

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38 Joining Data Observation Network for Earth DataONE DataONE 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. [Through the knowledge and infrastructure integrates information] National Center for Ecological Analysis and Synthesis (NCEAS), U.S.A; ;

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40 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.

41 Toward An Automation of Data Process Workflow archive Data Site 1 Data Site 2 Data Depository Metadata Shared Data Registry Compute grid Service Broker (UDDI) Web Service WSDL Algorithm Simulation Model Get Data Query Data Grid to find data Return URL Query Service broker to find services Return URL & call functions Get Component Archive output data to Depository Archive workflow

42 Scientific Workflow Approach to Analysis ASCII C RESULTS: Tables Maps Graphs

43 Application-A Case

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45 Ogawan,Japan Luquillo,Puerdo Rico Lienhuachih,Taiwan Pasho,Malaysia

46 Metadata Upload EML Document Metadata Catalog EcoGrid Scientific Workflow Morpho EML + Raw data Download Raw data CTFS Data Model Data Retrieval (SQL) Other Data Models (LDAP) WebServer (Apache+PHP)

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49 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

50 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?

51 Experience Learned: Many hands truly do make "light work!" Kaohsiung, Taiwan 2007

52 THANK YOU FOR YOUR ATTENTION!!