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Identifying germplasm samples in multi-user databases

Identifying germplasm samples in multi-user databases. Ruaraidh Sackville Hamilton. Identifying your own samples: you do what you want!.  in ICIS as a name You may create an ID to identify the sample uniquely in your collection  ICIS name NSTAT=8 (“preferred ID”)

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Identifying germplasm samples in multi-user databases

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  1. Identifying germplasm samples in multi-user databases Ruaraidh Sackville Hamilton

  2. Identifying your own samples:you do what you want!  in ICIS as a name • You may create an ID to identify the sample uniquely in your collection ICIS name NSTAT=8 (“preferred ID”) • Collector: collected sample ID • Genebank: accession ID, seed increase ID • Breeder: cross ID, selection ID • Others, e.g. nurseries, labs: line ID • National authority for variety release • You may just use pre-existing names • Breeders & researchers using lines created by others • Farmers  ICIS assigns a unique ID ICIS developers' workshop

  3. Sharing among similar partnerse.g. genebank accession database • GID doesn’t help identify • To identify the sample, must also know the holder / manager of the sample • In ICIS as Germplasm Location (GLOCN) • GLOCN= “Identifier of the location where the germplasm was created as a distinct unit of management with a new GID”  works if location where it is managed = location where it was created • Cf past confusion ICIS developers' workshop

  4. Sharing dissimilar types of germplasm • To identify the sample, must also know the type of germplasm • In ICIS as Germplasm Creation Method (METHN) • Shawn Yates 2010 • METHN = “Number that identifies the method of genesis for the germplasm”  works if method of genesis type of germplasm ICIS developers' workshop

  5. Conclusion:3-level sample identification • Type of germplasm : METHN • Needs ontology of types • Location : GLOCN • Preferred ID : NSTAT=8 • N.B. preferred name (NSTAT=1) is not part of the sample ID • Cf past confusion between a name and an ID • GIDs with single names should often have NSTAT=8 • E.g. breeders’ selections • Genebank seed increases ICIS developers' workshop

  6. ICIS developers' workshop

  7. ICIS developers' workshop

  8. Genebank’s view of passport data:Multi-crop passport descriptors ICIS developers' workshop

  9. ICIS view of MCPD What? Who? Where? When? Genebank accession Acquired by donation from What? Who? Where? When? Donor’s sample Originating from What? Who? Where? When? Original material(collection or cross) ICIS developers' workshop

  10. Types, methods, locations ICIS developers' workshop

  11. Reviewing methods for an ontology of germplasm types SF / CF is a property of the parents, not the method Interspecific or not is a property of the parents, not the method ICIS developers' workshop

  12. Reviewing methods Applied to accessions:Historical confusion between method of collecting from fieldand method of accessing into genebank ICIS developers' workshop

  13. Reviewing methods Shouldn’t have methods specific to a project ICIS developers' workshop

  14. Other problems with methods? • No distinction between reproduction and taking a sub-sample • Is a greater hierarchy needed? • Top level for identifying type of germplasm? • Lower level for finer distinction e.g. betweendifferent methods of seed increase? ICIS developers' workshop

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