prototype germplasm data portal (2006)
DESCRIPTION
Prototype Germplasm Data Portal, predecessor for the ALIS-Global of the GIGA project. Presentation for the Nordic Gene Bank board meeting on 4th December 2006.TRANSCRIPT
NGB Board Meeting December 4, 2006NGB Board Meeting December 4, 2006
Exchange of germplasm datasets with PyWrapper/BioCASE
GAINGlobal Accession Information Network
December 4, 2006NGB Board Meeting 2006Alnarp, Sweden
Dag Endresen, Nordic Gene Bank
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 2
TOPICSTOPICS
Genetic resources:
Data exchange Information network Outlook
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 3
Germplasm data, seed Germplasm data, seed genebanksgenebanks
Germplasm genebanks are biodiversity collections.
Collection level dataMetadata about genebank institutes and the germplasm collections they hold.
Unit level dataThe unit level data for germplasm collections are the accessions. Genebank accessions share many properties and attributes with other biodiversity specimens.
Descriptive data (phenotype)The germplasm accessions are further described by descriptive characterization and evaluation data.
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 4
Germplasm cataloguesGermplasm catalogues
Most genebank datasets are indexed by three major germplasm catalogues
EURISCO is the data catalogue of the European genebanks (997 631 accessions)
SINGER is the portal to the international CGIAR collections (689 349 accessions)
USDA-GRIN is the portal to the USDA ARS National Germplasm Repositories of the USA (475 178 accessions)
All three catalogues are now published in GBIF
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 5
Data warehouse modelData warehouse model
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 6
The present data flow from genebanks to EURISCO and The present data flow from genebanks to EURISCO and
ECCDBsECCDBs
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 7
Decentralized modelDecentralized model
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 8
Decentralized modelDecentralized model
EURISCO(Data Portal
Europe)
Nordic Gene Bank(Northern Europe)
IPK Gatersleben(Germany)
IHAR(Poland)
(Other European gene banks...)
SINGER(Data Portal for
CGIAR) (CGIARInternationalFuture Harvest gene banks...)
USDA GRIN(Data Portal USA)
(USDA ARSNational Germplasm Repositories...)
WUR CGN(Netherlands)
GBIF(Global BiodiversityData Portal)USER
GAIN(Global germplasmData Portal)[chm.grinfo.net]
Internet
MCPD
MCPDMCPD MCPD MCPD
Svalbard International Seed Vault(Safe Backup)
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 9
Germplasm data indexing toolsGermplasm data indexing tools
We have recently built data indexing methodologies for access to germplasm data with BioCASE/PyWrapper.
This is planned to build a Germplasm Clearing House Mechanism (GAIN).
Development in close cooperation with GBIF, which themselves index basic biodiversity data from a similar approach.
[http://chm.grinfo.net/index.php]
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 10
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 11
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 12
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 13
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 14
Decentralized data network with web services
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 15
Germplasm data exchange with Germplasm data exchange with PyWrapper/BioCASEPyWrapper/BioCASE
GBIF technology demonstrated to IPGRI, FAO, CGIAR centres and genebanks (2005) and widely adopted for PGR information networks
In the spring of 2004 the first European genebanks joined GBIF as data providers.
In 2005 USDA-GRIN joined GBIF. In 2006 both SINGER and EURISCO joined GBIF.
The germplasm datasets worldwide are compatible with the MCPD data standard.
Sharing of germplasm datasets with GBIF was rather straight forward after mapping of the MCPD data standard to ABCD 2.06
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 16
Germplasm BioCASE entry pointsGermplasm BioCASE entry points
[http://chm.grinfo.net/index.php?app=data_providers]
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 17
Taxonomic Database Working GroupTaxonomic Database Working Group
Darwin Core 2 - Element definitions designed to support the sharing and integration of primary biodiversity data". [http://darwincore.calacademy.org/]
Access to Biological Collection Data (ABCD) 2.06 - An evolving comprehensive standard for the access to and exchange of data about specimens and observations (a.k.a. primary biodiversity data)“.[http://www.bgbm.org/TDWG/CODATA/Schema/]
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 18
PGR sub-unit of ABCD 2.06PGR sub-unit of ABCD 2.06
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 19
Generation Challenge Programme, Generation Challenge Programme, GCP_Passport_1.03GCP_Passport_1.03
The Generation Challenge Programme is a research and capacity building network that uses plant genetic diversity to produce better crop varieties for resource-poor farmers.
In the context of the GCP (Generation Challenge Programme), the GCP Passport data exchange schema was developed.
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 20
GCP_Passport Upgrade to ABCDGCP_Passport Upgrade to ABCD
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 21
Global Unique Identifiers, GUID (LSID, Life Science Identifiers) [http://lsid.sourceforge.net/]
Biodiversity informatics workflow tools (BioMOBY and Taverna)
Work in progressWork in progress
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 22
OutlookOutlook
The compatibility of data standards between PGR and biodiversity collections made it possible to integrate the worldwide germplasm collections into the biodiversity community.
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.
Users from the biodiversity community (who may not be aware of the existence of relevant material in genebanks) will find in GBIF genebank material of, e.g. crop wild relatives, along with data of the same species from herbaria, botanical gardens and floristic observations.
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 23
Special thanks toSpecial thanks to
IPGRI (Bioversity International) [http://www.bioversityinternational.org]
GCP, The Generation Challenge Programme [http://www.generationcp.org/]
GBIF, Global Biodiversity Information Facility [http://www.gbif.org]
BioCASE, The Biological Collection Access Service for Europe. [http://www.biocase.org]
TDWG, Taxonomic Database Working Group [http://www.tdwg.org]
Exchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board MeetingExchange of germplasm datasets with PyWrapper/BioCASE, December 4, 2006, NGB Board Meeting 24
Thank you for listening!