Data exchange alternativesGlobal Information on Germplasm Accessions (GIGA, ALIS)2nd GIGA Technical Advisory Group MeetingDag Terje Filip Endresen, Nordic Genetic Resources Center, NordGen (Sweden)

Data exchange2Cartoon by Sasha Kopf (Creative Commons)

Data Exchange FormatMCPD (1997)Multi Crop Passport DescriptorsDarwin Core (2001) **New version up for revision at TDWG2009http://rs.tdwg.org/dwc/index.htmABCD (2001) Access to Biological Collections Datahttp://wiki.tdwg.org/twiki/bin/view/ABCDGCP Passport (2005)http://www.generationcp.orgOntology (including all above)perhaps develop a new GIGA ontology3

Data Provider SoftwareBioMOBY (2001)http://biomoby.orgDiGIR (2002, not active)http://digir.sourceforge.netBioCASE (2003, PyWrapper v2)http://www.biocase.orgEURISCO (2003, tab delimited text)http://eurisco.ecpgr.orgPyWrapper 3 (2006, not active)http://trac.pywrapper.orgTapirLink (2007)http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLinkGBIF Provider Toolkit (2009) **http://code.google.com/p/gbif-providertoolkit4

Data Harvest InfrastructureGIGA Registry (UDDI)New GIGA registry for germplasm dataset?ICIS and CropForge toolshttp://cropwiki.irri.org/icis/https://cropforge.org/GBIF data portal and registry**http://data.gbif.orggbrds.gbif.org (registry)GBIF Indexing Toolkit (2009)http://code.google.com/p/gbif-indexingtoolkit/5

Data Provider Software6

EURISCO tab delimited uploadhttp://eurisco.ecpgr.org7

8BioMOBYThe BioMOBY project was initiated in 2001 (in Saskatchewan, Canada). Two branches, web service and semantic (MOBY-S).MOBY ontology-aware registry for discovery of both data and services.Works well with TAPIR and BioCASE.GCP have selected BioMOBY as the main web service technology.http://biomoby.org

BioCASE 2.59The BioCASE provider software is a product of the EU funded BioCASE project (2001-2004). Developed at BGBM in Berlin. Last updated in April 2008, with support for Python version 2.5Data formats include: ABCD 2.06, Darwin Core, GCP_Passport, MCPD.http://www.biocase.org

BioCASE 2.5Configuration Add datasource (dsa) Database connection Database table structure Mapping of data model to standard schema10

Add datasource (dsa)

Database connection

Database table structure

Mapping of data model to standard schema

TAPIRTAPIR - TDWG Access Protocol for Information Retrieval. During the 2004 TDWG meeting in Christchurch, NZ, work started on a unified protocol and named TAPIR.TAPIR is based on the protocol from the two data provider software, BioCASE and DiGIR. 11

PyWrapper3Home:http://trac.pywrapper.org/Primary developers: Markus Döring, Javier de la TorreSource code: Python14/07/2008 - Development stalledWe are sorry to inform you that development of the TAPIR branch of PyWrapper has been stalled. The latest 3.1 alpha version is not stable and not recommended for production! (Message from the home page)PyWrapper is tested and verified to work fine with Windows, Mac OS X and Linux.12

Web configuration toolPyWrapper graphical web based configuration tool13

TapirLink 0.6.1Home: http://wiki.tdwg.org/twiki/bin/view/TAPIR/TapirLinkPrimary developers: Renato De Giovanni, Dave VieglaisDownload: http://sourceforge.net/project/showfiles.php?group_id=38190Source code: PHP14Test resource with client form:http://localhost/tapirlink/tapir_client.phpThe XML Client form is very illustrative for understanding exactly how the wrapper software works!

GBIF IPTHome: http://code.google.com/p/gbif-providertoolkit/Primary developers: Markus Döring, Tim RobertsonDownload: http://code.google.com/p/gbif-providertoolkit/downloads/listSource code: Java15DEMO at http://atlas.nordgen.org/ipt/

GBIF IPT The GBIF IPT is an open source, Java (TM) based web application that connects and serves three types of biodiversity data: taxon primary occurrence data, taxon checklists and general resource metadata. The data registered in the IPT is connected to the GBIF distributed network and made available for public consultation and use. Designed to transfer big amounts of records. Decentralize and speed up the process of indexing biodiversity occurrence datasets. IPT also provides a local tool for data quality assessment to data publishers. The data publisher will easily monitor data access and use.16

The GBIF IPT is an open source, Java (TM) based web application that connects and serves three types of biodiversity data: taxon primary occurrence data, taxon checklists and general resource metadata.

The data registered in the IPT is connected to the GBIF distributed network and made available for public consultation and use.

Designed to transfer big amounts of records. Decentralize and speed up the process of indexing biodiversity occurrence datasets.

IPT also provides a local tool for data quality assessment to data publishers.

The data publisher will easily monitor data access and use.

GBIF IPT17

GBIF IPT18

IPT19

GBIF IPT20

Web service interface21

Example TAPIR service SEARCH request22

Example TAPIR service Search response23

Example of OAI-PMH service requestRequest types:IdentifyListMetadataFormatsListSetsGetRecordListIdentifiersListRecordshttp://an.oa.org/OAI-script?verb=GetRecord &identifier=oai:arXiv.org:hep-th/9901001 &metadataPrefix=oai_dc24OAI-PMH requests are submitted using either the HTTP GET or POST methods.

Example of OAI-PMH service RESPONSE25OAI-PMH responses formatted as HTTP.With The Content-Type as text/xml.

GBIF PGR Network 2[http://data.gbif.org/datasets/network/2]26

27Darwin CoreA new version of Darwin Core is up for public review.http://rs.tdwg.org/dwc/terms/index.htmTDWG 2009, Montpellier, November 9 -13DRAFT Germplasm extensionhttp://code.google.com/p/darwincore/source/browse/#svn/trunk/xsd/profiles/germplasmRDF, LSID, ontology friendly

28OutlookThe compatibility of data standards between PGR and biodiversity collections made it possible to integrate the worldwide germplasm collections into the biodiversity community (GBIF, TDWG).Using GBIF technology (and contributing to its development), the PGR community can easily establish specific PGR networks without duplicating GBIF's work.Use of GBIF technology and integration of PGR collection data into GBIF allows PGR users to simultaneously search PGR collections and other biodiversity collections, and to get access to the data (and possibly the material) of relevant biodiversity collections.The establishment of new data portals and tools on a specific crop, a regional thematic network or similar subset of the total global biodiversity datasets; can be done with rather few efforts! Adopted from a slide by Helmut Knüpffer (IPK Gatersleben)

Special thanks to29Bioversity International http://www.bioversityinternational.orgGBIF, Global Biodiversity Information Facility http://www.gbif.orgBioCASE, The Biological Collection Access Service for Europe. http://www.biocase.orgTDWG, Biodiversity Information Standards http://www.tdwg.org

Bioversity International

GBIF, Global Biodiversity Information Facility http://www.gbif.org

BioCASE, The Biological Collection Access Service for Europe.

TDWG, Biodiversity Information Standards http://www.tdwg.org

Data portal example (2006)30

31http://wwwdev.ngb.se/portal/index.php?scope=demo

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Data Harvest36

GBIF GBRDShttp://gbrds.gbif.org37

GBIF GBRDShttp://gbrds.gbif.org38

Fallacies of Distributed ComputingThe network is reliable.Latency is zero.Bandwidth is infinite.The network is secure.Topology doesn't change.There is one administrator.Transport cost is zero.The network is homogeneous.This list of fallacies came about at Sun Microsystems around 1994.39