Centre for Genetic Resources, the Netherlands Information Standards for Plant Genebanks Theo van...
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Transcript of Centre for Genetic Resources, the Netherlands Information Standards for Plant Genebanks Theo van...
Centre for Genetic Resources, the Netherlands
Information Standards for Plant Genebanks
Theo van HintumCentre for Genetic Resources, The Netherlands
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks the context and big issues basis of further discussion in other sessions
plant genebanks in historical context the resulting documentation landscape
data structures in use in genebanks standardisation in plant genebank
documentation
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks plant genebanks in historical context farmers have been domesticating crops since
c. 10,000 years• selection adapted phenotypes from wild populations
• in ‘centers of origin’
• result: landraces
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks Vaviliov’s centres of origin
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks plant genebanks in historical context since c. 1850 crop genetic diversity disappears
due to monocultures and habitat destruction • scientific plant breeding based on Mendel and de Vries
• urbanization, desertification, climate change
• result: genetic erosion
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks plant genebanks in historical context to keep the diversity available it needs to be
conserved• ex situ: collections under controlled conditions (genebanks)
• in situ: protection wild species in nature
• on-farm: use and development of diversity in ‘traditional’ farming systems
genebanks are the ex situ component in the range of conservation approaches
• evolved from research and breeding collections
• estimated 500 in Europe
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks plant genebanks in historical context living collections
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks DB management in the documentation landscape local documentation systems of genebanks
• paper
• spreadsheets
• proper databases
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks the landscape is complex
holding institute
ex situ
PGR holding institute
ex situ
PGR holding institute
ex situ
PGR holding institute
ex situ
PGR holding institute
ex situ
PGR holding institute
ex situ
PGR holding institute
ex situ
PGR holding institute
ex situ
PGR holding institute
ex situ
PGR
Inventory
National Inventory
National Inventory
National
MCPD ex situ exchange format ex situ exchange format MCPD
ECCDB
ECCDB
ECCDB
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks data categories in plant genebanks genebank management data
• internal use only (data models vary) passport data
• broad external use (institute, national, European, incl. breeders) • fairly standardized (Multi-Crop Passport Descriptor (MCPD) list)
characterization & evaluation data • broad external use (breeders, researchers, others incl.
institutes)• limited availability• range of models varying level of detail
data about distribution and use of germplasm• institute (internal), national, international administration (e.g.
Treaty)
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks format or coding systems for plant genebanks passport data
• MCPD widely accepted descriptor list for data exchange
– simple
– incomplete and not expandable
• MCPD contains or refers to coding systems for a/o countries, origin types, population types
– institute codes remains a problem – attempt of World Information and Early Warning System on Plant Genetic Resources (WIEWS)
• no systems for taxonomy, or other descriptors (user type, coordinate type, etc.)
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks format or coding systems for plant genebanks characterization and evaluation data
• no accepted data structure for C&E exchange
– level of detail important due to GxE interaction
– some proposals have been developed now
• trait names not standardized
– several standards are available (Bioversity, UPOV) with rather low acceptance, incomplete crop coverage and not expandable
– ontologies are being developed
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks next steps facilitation information exchange change of MCPD
• to become more flexible• to accommodate new (ITPGRFA and AEGIS) requirements
development better standards for• institutions• taxonomy
development C&E exchange format introduction and use of life science identifiers
(LSID) allow exchange with data outside the plant
genebank community• compliance to Access to Biological Collection Data (ABCD 2.06)
Centre for Genetic Resources, the Netherlands
Information Standards for Plant
Genebanks summarizing remarks plant genebank documentation developed
locally• local solutions no standardization
passport data were exchanged• need further standardization
C&E data are the next major step• format for data exchange needed
• ontologies needed
part of TDWG community