Workshop Presentations and Notes

NOTES FROM THE WORKSHOP


Develop Trait dictionary  

use the version 3.0 of the template 

field to indicate the default IB fieldbook list

Use the field for language version 


Upload the Trait dictionary

Add a CO unique identifier  for each : Trait, method and scale 

Always add the version of the TD and the ontology

Ability to sort on field values (e.g. categorical values)

System should enforce formatting rules when uploading

Avoid the null column

Fieldbook

        Fieldbook needs trait names, methods names and scales names with IDs – where the details about the scales should reside?

        Where is the load of the default list done? At the Central crop database level?

        Shall we have a online  dictionary for constants measured at field ? What can we ask Glenn?

        Instead of “primary” traits refer to these sets as “ Default IB Fieldbook list”.

        Default fieldbook traits are a development tool and have no biological significance.  They should not be part of the ontology

        How do we make the synchronization of the fieldbook  with the CO?

Trait Dictionaries vs Ontology

        Distinguish role of Trait dictionaries from Ontology

        Trait dictionaries are used as a starter for the ontology but:

  - Trait dictionaries are classified by ICIS trait categories : agronomical, biotic stress, abiotic stress

  -  Ontology is organize around the botanical, physiological, etc  classes

Define sub-lists by objective, functions?

Add sub Lists

a. Per breeding objective ADD a DROUGHT Tolerance 

b. For variety botanical identification

c. UPOV lists

Distinction between:

    VCU traits = value for cultivation and use - formal traits used by breeders, map, QTL analysis 

    DUS traits = distinctiveness , uniformity and stability traits - Varieties needs to pass DUS to be ‘marketable

ideas

Put a weight on the relation between traits based on the genetic results and correlation so the list of traits contributing to the expression of phenotype are immediatly  proposed

ADD a DROUGHT Tolerance breeding objective and check of we have all traits for it /crop – e.g. cassava


GDMS and the CO API

The GDMS will be linked to the Crop Ontology using the API that has been provided. The ‘trait names’ in the QTL information will be hyperlinked to the cropontology in a two step process: If the cropontology id exists in the database (IBDB) it will directly display the ontology page for a specific term, in case it does not exist then it will use the search term function of the API.

For linking from the Ontology to the GDMS, we are looking at implementing a similar solution (using JSON) to what has been used for the crop ontology database.

 

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