Agriculture theme 2
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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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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

  • 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


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


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 ?


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


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


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.


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’


Clear that collaboration between TDWG and genebank community is beneficial for both

  • Sharing infrastructure

  • Exchange tools, models, data


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