biological diversity information flow in kbif , a nd the role to gbif

Hyung-Seon PARK Ph.D

Biological diversity information flow in KBIF, and the role to GBIF

Korea Institute of S&T Information (KISTI)

17th CODATA/DSAO 21st October, 2006, China

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http://www.kbif.re.kr

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,


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

GBIFNetwork

A distributed network of Biodiversity web services


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

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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.

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Voting Participants (26) Australia, Belgium, Canada, Costa Rica, Denmark, Estonia, Finland, France, Germany, Iceland, J

apan, 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, P

apua New Guinea, Poland, Slovak Republic, Switzerland, Taiwan (Economy), Tanzania ..

Associate Participants: Organizations (35) United Nations Environment Program (UNEP), World Federation for Culture Collections (WFC

C), 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)

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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

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WWW.GBIF.ORGWWW.GBIF.ORGWWW.GBIF.ORGWWW.GBIF.ORG

GBIF as a global Biodiversity Data Integrator

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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>

June 2003 S M T W T F S 1 2 3 4 5 6 7 8 9 10 11 12 13 1415 16 17 18 19 20 2122 23 24 25 26 27 2829 30

Observation record formatted using the Darwin Core


GBIF as a global data Integrator

Web services enable the aggregation of structured dataG

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Web servicesWeb services enable the aggregation of enable the aggregation of structured datastructured data

HeterogeneouHeterogeneous s DatabasesDatabases

Web Web ServicServic

eses

StandardisStandardiseded

Structured Structured DataData

UserUser<response> <record> …

<response> <record> …

<response> <record> …

<request>

<request>

<request>

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With GBIF’s components inplace, data can be drawn directly from different sources with a single query.Compiled specimen, genetic, and

ecological information

GBIF contribution to interoperability

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biodiversity informatics

True bioinformatics …True bioinformatics …

“bioinformatics”

ecoinformatics genomics

proteomics

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Portal

Data providerProvider Services

Providerquery

RequestManager

QueryEngine

Availableproviders

UDDI RegistryInstitutions

Services (Providers)AccessPoints

ResourceMetadat

aResourceMetadata

Index

Metadataand name

query

Metadataresponse

Dataquery

Dataresponse

Metadata and logs

Name providerProvider Services

ResourceMetadat

aResourceMetadata

Synonyms, GUIDs

Publishavailability

CacheMetadata

Accounting

SOAP

DiGIR

HTTP

Data Provider within GBIF Architecture

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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 (D

B 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


A simple DiGIR architecture

DiGIR providers

Databases

Portals, search engines, andapplications


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/dar

win2.xsd• 48 Elements:DateLastModified * InstitutionCode * CollectionCode * CatalogNumber *

ScientificName * BasisOfRecord Kingdom Phylum

Class Order Family Genus

Species Subspecies ScientificNameAuthor IdentifiedBy

YearIdentified MonthIdentified DayIdentified TypeStatus

CollectorNumber FieldNumber Collector YearCollected

MonthCollected DayCollected JulianDay TimeOfDay

ContinentOcean Country StateProvince County

Locality Longitude Latitude CoordinatePrecision

BoundingBox MinimumElevation MaximumElevation MinimumDepth

MaximumDepth Sex PreparationType IndividualCount

PreviousCatalogNumber RelationshipType RelatedCatalogItem Notes


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)


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


Governing Board --GBGB con consisting of delegates from all countries and organizations that join GBIFsisting of delegates from all countries and organizations that join GBIF

• Executive Office -Secretariat (Copenhagen, Denmark) consisting of Secretariat (Copenhagen, Denmark) consisting of

Executive Secretary, Deputy Directors, Program Managers, technical and legal staffExecutive Secretary, Deputy Directors, Program Managers, technical and legal staff

• Science Committee -Science Committee plus S& TScience Committee plus S& T Advisory Groups Advisory Groups

consisting of delegates from pconsisting of delegates from participantsarticipants (+ other invited experts) (+ other invited experts)

-DADI, -ECAT, -DIGIT, -OCB subcommittee

• NODES Committee -Participant‘s Nodes that co-ordinate internal 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 GoveranceGBIF Goverance

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The main GBIF work programsThe main GBIF work programs

Data Access and Database InteroperabilityData Access and Database Interoperability Electronic Catalogue of Names of Electronic Catalogue of Names of

Known Organisms Known Organisms Digitisation of Natural History CollectionsDigitisation of Natural History Collections Outreach and Capacity BuildingOutreach and Capacity Building “Species Bank” Digital Biodiversity Literature Resources

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Why was GBIF established ?Why was GBIF established ?

Both biodiversity and biodiversity data are unevenly distributed around the world:

Developing WorldDeveloping World

BiodiversityBiodiversity

Biodiversity Biodiversity DataData

Developed WorldDeveloped World

GBIF was established, in large part, to redress the inequality of data distribution

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Where is GBIF located ?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

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U.S.A

Denmark

KOREAGermany


Korea, Opened GBIF Data portal Mirror Services

Http://www.asia.gbif.netHttp://www.asia.gbif.net


GBIF Data Portal Statistics - ASIA.GBIF.NET


GBIF.NET log- User Statistics (Monthly)


GBIF.NET log- Statistics in Countries


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

Report


○ Strategic Plan (2007-2011)

5 parts 18 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

Sustainablefinance

Campaign activity per year

Secure finance level


○ Funding for GBIF 2007-2011

<4 million Euros/year


8th NODES (node committee) Report


NODES NODES Status ReportStatus Report

- Data sharing is possible through 120,000 institutes within GBIF

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Increment in data sharing


KBIF (Korean Biodiversity Information Facility)


Accessible Biodiversity Data in the globe

0

10

20

30

40

50

60

70

80

Sep.2003

Dec.2003

Mar.2004

J un.2004

Sep.2004

Dec.2004

Mar.2005

# of

dat

a re

cord

s

Million

Sleepingrecords

sharedrecords 2.23%

97.77%

• 300 million species available(Museum, Herbarium, University …)


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


Role in GBIF NODES and KBIF Operation

GBIFPortal

www.gbif.net

www.cbif.gc.ca

www.danbif.dk

CBIFCanada

BeBIFBelgium

JBIFJapan

DanBIFDenmark

www.be.gbif.net

GBIF타 회원국GBIF

타 회원국GBIF타 회원국GBIFOther countries

Participant Nodes

www.jbif.go.jp

DN1Environmenta

l

DN4Agricultura

l

DN2Oceanic DN3

Bioresource

Data Node

특화 연구소 Data

Node University

Data Node

Science,Natural History

Museum

www.kbif.re.kr

KBIFKorea

NODE

Data Node

Governmental

research Institute


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 Committees (SC/NC/EC/BC/RC)


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

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Korean Biodiversity Information Facility (KBIF)


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“BioDiversity”

+Genomics

+Resources

GBIF

KBIF

Data SharingIn GBIF

GBIF Data Service Stable service

1 billionData 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 systemKDR, NABIPOS

2006 2007 2008 <

100million dataGBIF mirror Service

Infra- setups

Information NetworkData Repository (KDR)

KBIF SchemaWeb services

Nat’l Science Museum 30 local museum, univ’s

1million cases to GBIF

GBIF Data Service Asia Regional Hub

Tech, help deskSystem 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


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.


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.


The KBIF Value Chain

Observer

Taxonomist

Collater

Provider

Indexer

Portal GBIF

PortalNat’l

GISservice Modelling

service

Scientist

Policymaker

Analyticservice

Mirror

GENERATING - AGGREGATING - PROVIDING - INTEGRATING – DISCOVERING – ANALYSING - PRESENTING

Archive Lit./ref.service

Helpdeskservice

Public

Usageservice



Demonstration

Google Earth- Korean Data


Synergetic Effects in Combining Data

: 1+1 › 2


The value of data is in its use


Supercomputing, extending the HorizonSupercomputing, extending the Horizon

of Science and Technologyof Science and Technology

KISTI KISTI

感謝

biological diversity information flow in kbif , a nd the role to gbif

Documents

existing biodiversity

ecosystems information

ecosystem information

gbif communications

meeting of oecd

gbif web page operational

meeting isc2

meeting isc1