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

AGRICULTURE#Theme 2


Working sessions

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

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

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

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 traits1

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

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 knowledge1

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

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

  • Sharing infrastructure

  • Exchange tools, models, data


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