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AGRICULTURE #Theme 2

AGRICULTURE #Theme 2. Working sessions. Crop Trait ontology Biocuration in agrodatabases SPM III: Visual and textual standards for taxonomic identification Species-related databases, information systems and inventories of cultivated and useful plants

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AGRICULTURE #Theme 2

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  1. AGRICULTURE#Theme 2

  2. Working sessions • Crop Trait ontology • Biocuration in agrodatabases • SPM III: Visual and textual standards for taxonomic identification • Species-related databases, information systems and inventories of cultivated and useful plants • DarwinCore Germplasm Extension and GBIF IPT deployment • Standards for Plant traits (cultivated and wild) - expanding standards to include characterization and evaluation data, phenotypic descriptors • Ecosystem approach to genetic resources management • Herbarium digitization • Traditional knowledge

  3. Crop Trait ontology - propositions • Find mechanisms for the community can participate to the Crop Ontology activities • Use existing ontologies – cross products • Further use Terminizer (University of Manchester) • A brainstorming workshop with multidisciplinary group to define, agree and validate all concepts around the Plant Trait Ontology • Joint effort with TDWG Ontology

  4. Data quality (Biocuration) • A TDWG Interest group on Data quality management • Awareness to Decisions makers and donors • Define Incentives for providing data quality • Define DQI (data quality indicators), ‘validators’ , metadata, scoring • Differentiate the ‘interpreted’ and the ‘ original’ data from data source. Define what is ‘original’ data? • Develop generic tools that are simple to use – ‘electronic curators’ • Data quality control generating quality reports – structured, standardized • What quality control for evaluation/ phenotypic data ?

  5. Plant Traits • Core controlled vocabulary and a Trait ontology Provenance of the material: • Obtained from the wild or propagated • Get the data directly from the wild accession – data integration • Necessary metadata • Conservation trait - Is a taxon properly conserved from each ‘bioregion’ : total number of samples stored in ex situ  Darwin Core extension • IUCN indicators to focus on priority taxon Definition of Trait concept needed

  6. Plant Traits • Informing genebanks’ community about Darwin Core Extension and GBIF tools • Test IPT in genebanks • Look at light version of SDD • Existing databases: LEDA Trait base

  7. Traditional knowledge • real « action »--where biodiversity is being created, or is being destroyed—is in situ. • documenting information about the dynamics of biodiversity, in situ - Processes generating diversity • Indicators of change/erosion • Integration of in situ data is important for both wild and domesticated biodiversity.

  8. Traditional knowledge • Compiling and sharing data on local knowledge and integrating it into other biodiversity databases • Aid in management and conservation - “hotspots” of local knowledge about [agro]biodiversity, or of local creation • Revival of TDWG interest group on 'economic botany’

  9. Clear that collaboration between TDWG and genebank community is beneficial for both • Sharing infrastructure • Exchange tools, models, data

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