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Hyung-Seon PARK Ph.D Biological diversity information flow in KBIF, and the role to GBIF Korea Institute of S&T Information (KISTI) 17 th CODATA/DSAO 21.

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Presentation on theme: "Hyung-Seon PARK Ph.D Biological diversity information flow in KBIF, and the role to GBIF Korea Institute of S&T Information (KISTI) 17 th CODATA/DSAO 21."— Presentation transcript:

1 Hyung-Seon PARK Ph.D Biological diversity information flow in KBIF, and the role to GBIF Korea Institute of S&T Information (KISTI) 17 th CODATA/DSAO 21 st October, 2006, China Global Biodiversity Information Facility

2 Biological information including Taxonomy data, Observation data, Geological data, Specimen data and, also in total concept in characteristics of molecular genetics, ecological and taxonomical systems. It assumed that the values in $$$ ’s, all around the world, particularly in biological industry. Biodiversity Information,

3 Specimens: Flowering Plants of Africa Specimens: Proteaceae of the World Taxon Names: Proteaceae of the World Observations: Birds of Central America Observations: Butterflies of Belize Checklist: Birds of Belize Specimens: Mammals of North Europe Taxon Names: Mammals of the World Specimens: Bacteria Cultures Taxon Names: Bacteria Further Links: Bacteria Further Links: Mammals Museum A Museum C University D Observer Network B GBIF Network A distributed network of Biodiversity web services

4 The Biodiversity and Ecosystems information domain is vast, complex, and critically important to society. However, most existing Biodiversity and Ecosystems information is not yet dynamically accessible and therefore not fully useful. Recent technological and political developments provide opportunity for the development of Global Biodiversity and Ecosystem Information Networks. Rationale For GBIF Global Biodiversity Information Facility

5 GBIF: chronological history First Meeting of OECD Working Group on Biological Informatics, 1996 Proposed by OECD Working Group on Biological Informatics in its final report, Jan. 1999 Basic operational aspects determined at meeting in March 99 Endorsed by OECD science ministers in June 99 GBIF Interim Steering Committee: first meeting (ISC1) in Sept. 99 GBIF Interim Steering Committee: second meeting (ISC2) in Feb. 00 GBIF Web page operational May 2000 CBD presentations at SBSTTA5 (January 2000) and COP5 (May 2000) Letter to all science ministers in June 2000 GBIF Interim Steering Committee: third meeting (ISC3) in Sept. 00 Fourth and final GBIF Interim Steering Committee, Dec 00. Invitation mailed to all countries, Dec 00. Global Biodiversity Information Facility

6 Voting Participants (26) Australia, Belgium, Canada, Costa Rica, Denmark, Estonia, Finland, France, Germany, Iceland, Japan, Republic of Korea May 2001, Mexico, Netherlands, New Zealand, Nicaragua, Norway, Peru, Portugal, Slovenia, South Africa, Spain, Sweden, United Kingdom, USA.. Associate Participants: Countries / Economies (21) Argentina, Austria, Bulgaria, Colombia, Czech, Ghana, India, Madagascar, Morocco, Pakistan, Papua New Guinea, Poland, Slovak Republic, Switzerland, Taiwan (Economy), Tanzania.. Associate Participants: Organizations (35) United Nations Environment Program (UNEP), World Federation for Culture Collections (WFCC), Species 2000, BIOSIS, BioNET-INTERNATIONAL, EASIANET, European Commission, IUCN, ITIS, OBIS, SAFRINET, Taxonomic Databases Working Group (TDWG), Man and the Biosphere Program (MAB), ASEANET, All Species Foundation … Cooperative activities with many others : CBD Clearing House Mechanism, UNEP-WCMC, CODATA (ICSU), NABIN, IABIN Many national-level organizations such as CONABIO (Mexico), ABIF (Australia), INBio (Costa Rica), etc. GBIF Communications (October 2006) Global Biodiversity Information Facility

7 What is GBIF? GBIF is an international scientific co-operative project based on a multilateral agreement (MoU) between countries and international organisations, dedicated to: establishing an interoperable, distributed network of databases containing scientific biodiversity information, in order to: - make the world’s scientific biodiversity data freely available to all, - with initial focus on species- and specimen-level data, - with links to molecular, genetic and ecosystems levels Global Biodiversity Information Facility

8 WWW.GBIF.ORG WWW.GBIF.ORG GBIF as a global Biodiversity Data Integrator Global Biodiversity Information Facility

9 Users and applications need data structured according to standards 2003-06-08 DGH DGH Lepidoptera DGHEUR_0002976 Dichomeris marginella (Fabricius, 1781) O Animalia Lepidoptera Gelechiidae Dichomeris marginella (Fabricius, 1781) Donald Hobern 2003 06 08 Europe Denmark Gentofte Amt Merianvej, Hellerup 12.538 55.737 100 1 1 in Skinner trap June 2003 S M T W T F S 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 Observation record formatted using the Darwin Core

10 GBIF as a global data Integrator Web services enable the aggregation of structured data Global Biodiversity Information Facility

11 Web services enable the aggregation of structured data HeterogeneousDatabases Web Service s Standardised Structured Data User … … … Global Biodiversity Information Facility

12 With GBIF’s components in place, data can be drawn directly from different sources with a single query. Compiled specimen, genetic, and ecological information GBIF contribution to interoperability Global Biodiversity Information Facility

13 biodiversity informatics True bioinformatics … “ bioinformatics ” ecoinformatics genomics proteomics Global Biodiversity Information Facility

14 Portal Data provider Provider Services Provider query Request Manager Query Engine Available providers UDDI Registry Institutions Services (Providers) AccessPoints Resource Metadat a Resource Metadata Index Metadata and name query Metadata response Data query Data response Metadata and logs Name provider Provider Services Resource Metadat a Resource Metadata Synonyms, GUIDs Publish availability Cache Metadata Accounting SOAP DiGIR HTTP Data Provider within GBIF Architecture Global Biodiversity Information Facility

15 The Protocol XML messaging on top of http Used for communication between data providers and data users More light-weight and specialised than SOAP Enables single point of access (portal/search) to distributed information resources Resource: a collection of data objects that conform to a common schema (DB records, XML documents) Distributed resources comply with a federation schema Enables search & retrieval of structured data Search for data values in context (semantics) Results are presented as a structured data set Makes location and technical characteristics of the native resource transparent to the user The Distributed Generic Information Retrieval protocol was created by the TDWG/CODATA subgroup on biological collection data

16 A simple DiGIR architecture DiGIR providers Databases Portals, search engines, and applications

17 data exchange format: Darwin Core2 Darwin Core2 is a model that allows data on individual spe cimens or observations to be structured and shared as XML documents that can be transmitted across the Internet. Suitable for collections and observations data. n2.xsd n2.xsd 48 Elements: DateLastModified *InstitutionCode *CollectionCode *CatalogNumber * ScientificName *BasisOfRecordKingdomPhylum ClassOrderFamilyGenus SpeciesSubspeciesScientificNameAuthorIdentifiedBy YearIdentifiedMonthIdentifiedDayIdentifiedTypeStatus CollectorNumberFieldNumberCollectorYearCollected MonthCollectedDayCollectedJulianDayTimeOfDay ContinentOceanCountryStateProvinceCounty LocalityLongitudeLatitudeCoordinatePrecision BoundingBoxMinimumElevationMaximumElevationMinimumDepth MaximumDepthSexPreparationTypeIndividualCount PreviousCatalogNumberRelationshipTypeRelatedCatalogItemNotes

18 DiGIR Provider Package Encompasses the DiGIR Provider software, Apache2 WEB s erver and PHP libraries. Requires from the user only basic knowledge of the operat ing system. Two available releases: ( ovider_package) ovider_package Linux (RedHat 7.3, 8, 9), MS Windows (2000, XP) Supported databases: MySQL, PostgreSQL, MS SQL Server, MS Access (only the MS Windows packag e) Offers automatic registration with GBIF UDDI Registry (http: // //

19 Data repository tool A tool to enable sharing of data Can upload and manage datasets in document format such as a) spreadsheet, b) embedded Darwin Core, or c) ABCD Can parse the data into embedded MySQL database that beco mes available to the public as a DiGIR resource Can revoke release (data is deleted from database) Stand-alone package or module of GBIF PTK For Linux and Windows Based on Python and Zope Includes automatic registration in GBIF registry

20 Governing Board -GB consisting of delegates from all countries and organizations that join GBIF -GB consisting of delegates from all countries and organizations that join GBIF Secretariat (Copenhagen, Denmark) consisting ofExecutive Office - Secretariat (Copenhagen, Denmark) consisting of Executive Secretary, Deputy Directors, Program Managers, technical and legal staff Executive Secretary, Deputy Directors, Program Managers, technical and legal staff Science Committee plus S& T Advisory GroupsScience Committee - Science Committee plus S& T Advisory Groups consisting of delegates from participants (+ other invited experts) consisting of delegates from participants (+ other invited experts) -DADI, -ECAT, -DIGIT, -OCB subcommittee Participant‘s Nodes that co-ordinate internalNODES Committee - Participant‘s Nodes that co-ordinate internal (national) activities with GBIF work programs (national) activities with GBIF work programs Budget Committee Review Committee - CODATA/KPMG GBIF Goverance Global Biodiversity Information Facility

21 The main GBIF work programs Data Access and Database Interoperability Data Access and Database Interoperability Electronic Catalogue of Names of Known Organisms Electronic Catalogue of Names of Known Organisms Digitisation of Natural History Collections Digitisation of Natural History Collections Outreach and Capacity Building Outreach and Capacity Building “Species Bank” Digital Biodiversity Literature Resources Global Biodiversity Information Facility

22 Why was GBIF established ? Both biodiversity and biodiversity data are unevenly distributed around the world: Developing World Biodiversity Biodiversity Data Developed World GBIF was established, in large part, to redress the inequality of data distribution Global Biodiversity Information Facility

23 Where is GBIF located ? Unlike CERN, the megascience instrumentation facility for particle physics that is located in Switzerland, GBIF is a megascience facility that is distributed all over the world, with its many parts connected by the Internet The small, non-bureaucratic GBIF Secretariat is hosted by the Zoological Museum of the University of Copenhagen, Denmark CERN Global Biodiversity Information Facility




27 U.S.A Denmark KOREA Germany

28 Korea, Opened GBIF Data portal Mirror Services Http://

29 GBIF Data Portal Statistics - ASIA.GBIF.NET

30 GBIF.NET log- User Statistics (Monthly)

31 GBIF.NET log- Statistics in Countries

32 12 th GBIF Governing Board Cape Town, South Africa 4 월 2-4 일, 2006 Report

33 ○ Strategic Plan ( 2007-2011) 5 parts18 modules Contents Known-organism data integration and Search available -Completion of ECAT 95% Service available 1 Billion data cases in GBIF Data Portal New data type search available; pictures and bibliography Informatics Improvement in current Data Portal Data available including molecular, ecological, biodiversity Participation 100% NODE operable by 2011 Online education and training GBIF Participation increase to 10% every year Governance Science Council Governing Board meeting once in a year Sustainable finance Campaign activity per year Secure finance level

34 ○ Funding for GBIF 2007-2011 <4 million Euros/year

35 8th NODES (node committee) Report

36 NODES Status Report - Data sharing is possible through 120,000 institutes within GBIF Korean Biodiversity Information Facility

37 Increment in data sharing

38 KBIF (Korean Biodiversity Information Facility)

39 Accessible Biodiversity Data in the globe Million 2.23% 97.77% 300 million species available (Museum, Herbarium, University …)


41 KBIF (Korea Biodiversity Information Facility) Korea national Node for GBIF IT Infrastructure and Web Services System Training and Disseminate the Key technology (S/W, Protocol etc.) Enlarge Data Provider, support biodiversity research and database

42 Role in GBIF NODES and KBIF Operation GBIF Portal CBIF Canada BeBIF Belgium JBIF Japan DanBIF Denmark GBIF 타 회원국 GBIF 타 회원국 GBIF 타 회원국 GBIF Other countries Participant Nodes DN1 Enviro nmenta l DN4 Agric ultura l DN2 Ocea nic DN3 Biores ource Data Node 특화 연구소 Data Node University Data Node Science, Natural History Museum KBIF Korea NODE Data Node Governm ental research Institute

43 KBIF Science Committee Aim to Work Program - DADI (Data Access and Data Interoperability ) - DIGIT (Digitization of Natural History Collections ) - ECAT (Electronic Catalogue of Names of Known Organisms) - OCB ( Outreach and Capacity Building) Korean NODE Act gateway to Integration of Biodiversity information - Build IT infra system and structure - Training and Disseminate the Key technology (S/W, Protocol etc.) - Develop data exchange Standard schema, metadata - Management and liaison Data Nodes (Enlarge Data Provider to GBIF) KBIF (Korean Biodiversity Information Facility) KBIF Committees (SC/NC/EC/BC/RC)

44 KISTI’s role in GBIF Acting Korea National Node for GBIF Network for Biodiversity information flow and Data Repository Training, disseminate and aids for the technological needed Act in GBIF Committee, NODES, Forum KBIF Operation Global Biodiversity Information Facility

45 Korean Biodiversity Information Facility (KBIF)

46 Korean Biodiversity Information Facility “Bio Diversity” + Genomics + Resources GBIF KBIF Data Sharing In GBIF GBIF Data Service Stable service 1 billion Data case services Activity in NODE committee Management and enlarge data registration to GBIF Training and disseminate key technology to Data Provider KBIF Stable operation Portal system KDR, NABIPOS 20062007 2008 < 100million data GBIF mirror Service Infra- setups Information Network Data Repository (KDR) KBIF Schema Web services Nat’l Science Museum 30 local museum, univ’s 1million cases to GBIF GBIF Data Service Asia Regional Hub Tech, help desk System development Data Exchange Standard and Protocol Develop retrieval system, Statistics, analyzing system Joining Government institutes Add 1million data case Enlarge data node Agricultural, Environ. Oceanic, Bioresources KOBIC National Data Service

47 National Biodiversity Information Portal System (NABIPOS) 1. NABIPOS(National Biodiversity Information Portal System) is integrated retrieval system to search the distributed biodiversity data of Korea. 2. It is currently providing the retrieval service and data provider state of Korea using the DarwinCore and DiGIR protocol. 3. It will provide retrieval service of various contents to extend a better understanding of the biodiversity.

48 KBIF Data Repository (KDR) 1. KDR(KBIF Data Repository) supports general user who can easily store, convert, and search their own biodiversity data within international standard. 2. It is designed to support Korean language and KBIF (Korea Biodiversity Information Facility) schema using the GBIF Data Repository Toolkit. 3. It is an effective tool to improve the accumulation of the biodiversity data and to enhance the data sharing.

49 The KBIF Value Chain Observer Taxonomist Collater Provider Indexer Portal GBIF Portal Nat’l GIS service Modelling service Scientist Policy maker Analytic service Mirror GENERATING - AGGREGATING - PROVIDING - INTEGRATING – DISCOVERING – ANALYSING - PRESENTING Archive Lit./ref. service Helpdesk service Public Usage service

50 Demonstration Google Earth- Korean Data

51 Synergetic Effects in Combining Data : 1+1 › 2 KBIF (Korean Biodiversity Information Facility) The value of data is in its use

52 Supercomputing, extending the Horizon of Science and Technology KISTI 感謝

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