Embed Size (px)
DESCRIPTION
Data exchange for germplasm data sets with PyWrapper/BioCASE. TDWG 2006 conference, 16th October 2006, St. Louis. Dag Endresen, Johan Bäckman, Helmut Knupffer, Samy Gaiji.
Citation preview
TDWG 2006, Missouri, U.S.A.TDWG 2006, Missouri, U.S.A.
Exchange of germplasm datasets with PyWrapper/BioCASE
October 16, 2006TDWG annual Meeting 2006Missouri Botanical GardenSt. Louis, Missouri, U.S.A.
Dag Endresen, Nordic Gene BankJohan Bäckman, Nordic Gene BankHelmut Knüpffer, IPK GaterslebenSamy Gaiji, IPGRI, Bioversity International
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 2
TOPICSTOPICS
Genetic resources:
Data standards Data exchange Information network Outlook
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 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.
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 4
Germplasm Data Standards
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 5
IPGRI Crop DescriptorsIPGRI Crop Descriptors
The IPGRI crop descriptors are developed to standardize characterization and evaluation data – called “descriptive data” in TDWG context.
The MCPD (Multi Crop Passport Descriptors) is designed to standardize "passport data" across crops. It enables compatibility with the IPGRI crop specific descriptor lists and the FAO World Information and Early Warning System (WIEWS) and serves as a basis for data exchange.
The MCPD descriptor list was made fully compatible with ABCD 2.06
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 6
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, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 7
GCP_Passport Upgrade to ABCDGCP_Passport Upgrade to ABCD
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 8
PGR sub-unit of ABCD 2.06PGR sub-unit of ABCD 2.06
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 9
Germplasm Data Catalogues
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 10
Germplasm cataloguesGermplasm catalogues
Most genebank datasets are indexed by three major germplasm catalogues
EURISCO is the data catalogue of the European genebanks (836 725 accessions)
SINGER is the portal to the international CGIAR collections (442 635 accessions)
USDA-GRIN is the portal to the USDA ARS National Germplasm Repositories of the USA (464 586 accessions)
All three catalogues are published in GBIF
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 11
Data warehouse modelData warehouse model
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 12
Decentralized data network with web services
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 13
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, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 14
Germplasm BioCASE entry pointsGermplasm BioCASE entry points
[http://chm.grinfo.net/index.php?app=data_providers]
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 15
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 Data Portal) USER
chm.grinfo.net(Global germplasmData Portal)
Internet
MCPD
MCPDMCPD MCPD MCPD
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 16
Germplasm data indexingGermplasm data indexing
The genebanks are building data indexing methodologies for access to global germplasm data.
It is planned to build a “Clearing House Mechanism” for germplasm.
This data portal is developed in cooperation with GBIF, which is also harvesting global biodiversity data using a similar approach.
[http://chm.grinfo.net]
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 17
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, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 18
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, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 19
Special thanks toSpecial thanks to
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]
GCP, The Generation Challenge Programme [http://www.generationcp.org/]
Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006Exchange of germplasm datasets with PyWrapper/BioCASE, October 16, 2006, TDWG 2006 20
Thanks for listening!
