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Biological diversity information flow in KBIF , a nd the role to GBIF

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

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Biological diversity information flow in KBIF , a nd the role to GBIF

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

  2. Biodiversity Information, 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.

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

  4. Rationale For GBIF Global Biodiversity Information Facility • 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.

  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 www.gbif.org • 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. GBIF Communications (October 2006) 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. 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 GBIFas a global Biodiversity Data Integrator Global Biodiversity Information Facility WWW.GBIF.ORG

  9. 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 Users and applications need data structured according to standards <?xml version="1.0" encoding="UTF-8"?> <response> <record> <darwin:DateLastModified>2003-06-08</darwin:DateLastModified> <darwin:InstitutionCode>DGH</darwin:InstitutionCode> <darwin:CollectionCode>DGH Lepidoptera</darwin:CollectionCode> <darwin:CatalogNumber>DGHEUR_0002976</darwin:CatalogNumber> <darwin:ScientificName>Dichomeris marginella (Fabricius, 1781)</darwin:ScientificName> <darwin:BasisOfRecord>O</darwin:BasisOfRecord> <darwin:Kingdom>Animalia</darwin:Kingdom> <darwin:Order>Lepidoptera</darwin:Order> <darwin:Family>Gelechiidae</darwin:Family> <darwin:Genus>Dichomeris</darwin:Genus> <darwin:Species>marginella</darwin:Species> <darwin:ScientificNameAuthor>(Fabricius, 1781)</darwin:ScientificNameAuthor> <darwin:IdentifiedBy>Donald Hobern</darwin:IdentifiedBy> <darwin:Collector>Donald Hobern</darwin:Collector> <darwin:YearCollected>2003</darwin:YearCollected> <darwin:MonthCollected>06</darwin:MonthCollected> <darwin:DayCollected>08</darwin:DayCollected> <darwin:ContinentOcean>Europe</darwin:ContinentOcean> <darwin:Country>Denmark</darwin:Country> <darwin:County>Gentofte Amt</darwin:County> <darwin:Locality>Merianvej, Hellerup</darwin:Locality> <darwin:Longitude>12.538</darwin:Longitude> <darwin:Latitude>55.737</darwin:Latitude> <darwin:CoordinatePrecision>100</darwin:CoordinatePrecision> <darwin:IndividualCount>1</darwin:IndividualCount> <darwin:Notes>1 in Skinner trap</darwin:Notes> </record> </response> Observation record formatted using the Darwin Core

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

  11. <request> <response> <record> … User <response> <record> … <request> <response> <record> … <request> Web services enable the aggregation of structured data Web Services Heterogeneous Databases Global Biodiversity Information Facility Standardised Structured Data

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

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

  14. Data Provider within GBIF Architecture Metadata and name query Provider query Index Portal UDDI Registry Request Manager Metadata Cache Institutions Services (Providers) AccessPoints Available providers Query Engine Metadata response Accounting Publish availability Metadata and logs Data query Data response Synonyms, GUIDs Name provider Data provider Provider Services Provider Services DiGIR Metadata Resource Metadata SOAP Resource Metadata Resource Metadata Resource HTTP 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. Portals, search engines, and applications DiGIR providers Databases A simple DiGIR architecture

  17. data exchange format:Darwin Core2 • Darwin Core2 is a model that allows data on individual specimens or observations to be structured and shared as XML documents that can be transmitted across the Internet. • Suitable for collections and observations data. • http://digir.net/schema/conceptual/darwin/2003/1.0/darwin2.xsd • 48 Elements:

  18. DiGIR Provider Package • Encompasses the DiGIR Provider software, Apache2 WEB server and PHP libraries. • Requires from the user only basic knowledge of the operating system. • Two available releases:(http://circa.gbif.net/Public/irc/gbif/ict/library?l=/digir_provider_package) • Linux (RedHat 7.3, 8, 9), MS Windows (2000, XP) • Supported databases: • MySQL, PostgreSQL, MS SQL Server, MS Access (only the MS Windows package) • Offers automatic registration with GBIF UDDI Registry (http://registry.gbif.net)

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

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

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

  23. CERN 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 Global Biodiversity Information Facility • The small, non-bureaucratic GBIF Secretariat is hosted by the Zoological Museum of the University of Copenhagen, Denmark

  24. Denmark KOREA U.S.A Germany

  25. Http://www.asia.gbif.net Korea, Opened GBIF Data portal Mirror Services Http://www.asia.gbif.net

  26. GBIF Data Portal Statistics - ASIA.GBIF.NET

  27. GBIF.NET log- User Statistics (Monthly)

  28. GBIF.NET log- Statistics in Countries

  29. 12th GBIF Governing Board Cape Town, South Africa 4월 2-4일, 2006 Report

  30. ○ Strategic Plan(2007-2011)

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

  32. 8th NODES (node committee) Report

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

  34. Increment in data sharing

  35. KBIF (Korean Biodiversity Information Facility)

  36. 2.23% 97.77% Accessible Biodiversity Data in the globe Million • 300 million species available • (Museum, Herbarium, University …)

  37. 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

  38. BeBIF Belgium www.be.gbif.net CBIF Canada Participant Nodes www.cbif.gc.ca JBIF Japan DanBIF Denmark GBIF Portal www.jbif.go.jp www.danbif.dk GBIF 타 회원국 Data Node 특화 연구소 www.gbif.net Data Node University GBIF 타 회원국 KBIF Korea GBIF 타 회원국 GBIF Other countries NODE Data Node Science, Natural History Museum www.kbif.re.kr DN1 Environmental Data Node Governmental research Institute DN2 Oceanic DN3 Bioresource DN4 Agricultural Role in GBIF NODES and KBIF Operation

  39. KBIF (Korean Biodiversity Information Facility) KBIF Committees (SC/NC/EC/BC/RC) • 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)

  40. 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 http://www.kbif.re.kr

  41. Korean Biodiversity Information Facility (KBIF)

  42. GBIF “Bio Diversity” + Genomics + Resources • KOBIC • National • Data Service Data Sharing In GBIF KBIF 2008 < 2006 2007 GBIF Data Service Asia Regional Hub Tech, help desk System development GBIF Data Service Stable service 1 billion Data case services 100million data GBIF mirror Service Infra- setups • Activity in NODE committee • Management and enlarge data registration to GBIF • Training and disseminate key technology to Data Provider Korean Biodiversity Information Facility Data Exchange Standard and Protocol Develop retrieval system, Statistics, analyzing system Information Network Data Repository (KDR) KBIF Schema Web services KBIF Stable operation Portal system KDR, NABIPOS Joining Government institutes Add 1million data case Nat’l Science Museum 30 local museum, univ’s 1million cases to GBIF Enlarge data node Agricultural, Environ. Oceanic, Bioresources

  43. 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.

  44. 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.

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

  46. http://www.kbif.re.kr Demonstration Google Earth- Korean Data

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