4. BACKGROUND
• The project to develop the ontology for beans
was initially lead by Dr. Matthew Blair and Juana
Cordoba was in charge of this. With the
departure of Dr. Blair and Juana, Dr. Steve Beebe
is leading this activity and I have been responsible
to coordinate for the past one year.
• Until December 2011,a total of 140 traits were
described by the bean team. The process
included the scientists in the disciplines of
breeding, pathology, entomology, virology and
physiology.
5. RANKING
• In December 2011, GCP decided to rank the 140
traits and based on this ranking to establish a list
of 50 most commonly used traits that will be
included initially in the IB-Fieldbook.
• Fernando Rojas (data manager consultant) helped
in this process. Members of the bean community
of practice created in October-2011 in Malawi
participated in the ranking process.
• Ranking of traits was based on the frequency of
use in breeding (1 = always used, 2 = sometimes
used, 3 = seldom used, and 4 = never used so far)
6. RANKING
BEAN TRAITS RANKING SUMMARY
TOT-
TRAITS MORPHOLOGICAL AGRONOMIC BIOTIC STRESS ABIOTIC STRESS QUALITY PASSPORT RANKING
23 7 3 7 4 0 2 1
60 20 1 5 22 2 10 2
57 20 1 14 10 6 6 3, 4
140 47 5 26 36 8 18 140
• According to the ranking, 23 were classified as the
traits most used, 60 traits as sometimes used and
57 traits as seldom used. Of the first 2 groups (83
in total) were further prioritized to 60 by the bean
team for the IB-Fieldbook.
7. Crop Ontology CoP Workshop
• In March of this year we had a meeting in
Rome "Crop Ontology Community of Practice
Workshop", where the traits were classified in
two categories. The traits most used were
called Primary Traits that will be used in
Fieldbook (60 traits) and the rest were called
secondary Traits. The full documentation for
the primary traits should be completed in May.
8. Some traits divided
• After this meeting, it was decided by the bean
team to subdivide some traits. For example, all
disease traits were divided into greenhouse and
field evaluations; and each of them for their
reaction in leaves and pods.
• Anthracnose was divided in Anthracnose on leaves
in greenhouse, Anthracnose on leaves in field,
Anthracnose on pods in field, given the
importance of maintaining the origin of data and
the plant organ, to set the context of the data.
9. Traits subdivided
OLD TRAIT NEW TRAIT
Angular Leaf Spot on leaves in field
Angular Leaf Spot Angular Leaf Spot on leaves in greenhouse
Angular Leaf Spot on pods in field
Anthracnose on leaves in field
Anthracnose Anthracnose on leaves in greenhouse
Anthracnose on pods in field
Common Bacterial Blight on leaves in field
Common Bacterial Blight on leaves in
Common Bacterial Blight
greenhouse
Common Bacterial Blight on pods in field
Fusarium solani in field
Fusarium solani
Fusarium solani in greenhouse
Halo blight on leaves in field
Halo blight Halo blight on leaves in greenhouse
Halo blight on pods in field
Pythium spp. in field
Pythium spp
Pythium spp. in greenhouse
•The above disease traits were subdivided
10. 70 primary traits
• In total 70 primary traits were defined
(before it was 60).
Trait Class Number
Morphological 10
Agronomic 4
Biotic stress 22
Abiotic stress 25
Quality 3
Passport 6
Total 70
• The template for Fieldbook with these 70
traits (description, scale, method) was
provided to GCP in April.
11. Other tasks defined in Rome Workshop:
May:
• In parallel with the English version of the primary traits (70), we are
working on a Spanish version, which will be delivered.
October:
• Translation into French – Primary Traits
• Translation into Portuguese - Primary Traits
• Complete documentation of all methods and scales (English and
Spanish) – Secondary Traits
December:
• Translation into French – Secondary Traits
• Translation into Portuguese - Secondary Traits
13. Phenotypic Data
• Phenotypic Data are present in activities 1,4 and 5 (28 datasets).
• We have focused in the curation of these Excel files. All our
phenotypic datasets include primary and secondary traits. As was
mentioned previously, our priority has been to have the 70 primary
traits in English and Spanish. At present, these traits are fully
documented (unit, method, synonym, references) and will be
delivered to GCP in May.
• Other traits (secondary traits) have not been fully reviewed in detail
by the bean team and these will be ready for October as was decided
in Rome. It is extremely important to have completely revised trait
dictionary-ontology (primary and secondary traits), before uploading
information to the database.
14. Phenotypic Data
Some problems encountered
•Checking file by file, we have found that the majority
of these traits are not documented adequately. Many
trait names are not fully defined, lacking unit and plot
area that are important for conversions, etc.
•Also, we found that investigators use different units
for some traits. These need to be standardized.
•Many new traits (up to 20) will be added to the trait
dictionary and these will be fully defined.
15. Phenotypic Data
• As mentioned before, we renamed variables, done
conversions for many traits to synchronize with the
ontology (units), added traits to the ontology.
• To complete this work and have all files fully curated,
it is essential for bean team to complete the task of
fully defining the secondary traits.
• For all the above reasons, it was decided to
postpone the uploading of the information to the
IPHIS database.
16. Next steps for Phenotypic Data
• Upload all the datasets completed from Bean trials by
December, after completing trait dictionary.
17. Genotypic Data
• Genotypic datasets (23) are assembled from activities 2
and 3.
• We are curating these files.
Next steps
• Upload all the datasets in status completed in GDMS by
February 2013
