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?
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.
