My presentation at APAN 45 in the joint session with agGateway

1. eROSA has received funding from the European
Union’s Horizon 2020 research and innovation
programme under grant agreement No 730988
goFAIR
The Agrisemantics Project
Johannes Keizer, GODAN Secretariat, eROSA project

2. Horizon 2020 research and innovation programme - grant agreement No 730988
Johannes Keizer APAN 45, 2018-03-28

3. ......but there are nitty gritty problems
Compound Species Concentration
(mg/l)
Mortality
(%)
Observations
Diazinon Danio rerio 20 10
Diazinon Danio rerio 40 40 Mortality occurs
within 30 minutes
Example: Research on fish toxicity of Pesticides
Active
Ingredient
Species Concentration
(ppm)
Dead fish (%) Remarks
二嗪磷 Zebrafish 10 5
二嗪磷 Zebrafish 30 40 Mortality occurs
within 30 minutes
Lab 1
Lab 2

4. Horizon 2020 research and innovation programme - grant agreement No 730988
Johannes Keizer APAN 45, 2018-03-28
How to resolve
Unifying data schemes and back
ends
Single data processing for any
front end with mapping

5. Horizon 2020 research and innovation programme - grant agreement No 730988
Johannes Keizer APAN 45, 2018-03-28
Unifying data schemes and back ends
....for ever lasting discussions

6. Mapping at the front end level
DB1
DB2
DB3
DB4

7. The solution
https://www.go-fair.org/

8. The FAIR principles

9. An Architecture based on FAIR data
Multiple
Frontends
- Galaxy
- R
- Portals
- D4Science
- Excel
- PDF
- CMS
Whatever
people want to
do
Multiple
Backends
• SQL
• Dataverse
• CKAN
• Text
Whatever
people want to
do
Temporary
and
permanent
triple stores
Shared Semantics
Agroportal - GACS- Maps of Standards - RING
APIs to link
to all kind of
backends
APIs to link
to all kind
of front
ends

10. What we need
• Extensive and powerful shared semantics
• Performant and scalable triple stores
• An API factory that produces APIs which
link to any back end and any front end
• A powerful dataset/information source
discover/registration mechanism

11. ......solution to the problem
Compound
(1)
Species
(1)
Concentration
(mg/l) (1)
Mortality
(%) (1)
Observations
(1)
Diazinon (3) Danio rerio
(3)
20 10
Diazinon Danio rerio 40 40 Mortality occurs
within 30 minutes
Example: Research on fish toxicity of Pesticides
Lab 1
1) http://agroportal.lirmm.fr/ontologies/toxtestont
2) http://browser.agrisemantics.org/gacs/en/page/C15291
3) http://browser.agrisemantics.org/gacs/en/page/C9983
http://bioportal.bioontology.org/ontologies/NCBITAXON?p=classes&conceptid=
7955

12. http://browser.agrisemantics.org/gacs
/en/page/C15291

13. ......the problem is resolvable
Compound Species Concentration
(mg/l)
Mortality
(%)
Observations
Diazinon Danio rerio 20 10
Diazinon Danio rerio 40 40 Mortality occurs
within 30 minutes
Example: Research on fish toxicity of Pesticides
Active
Ingredient
Species Concentration
(ppm)
Dead fish (%) Remarks
二嗪磷 Zebrafish 10 5
二嗪磷 Zebrafish 30 40 Mortality occurs
within 30 minutes
Lab 1
Lab 2

14. A global attempt

15. Metada passport from fairshairing

16. Our contribution http://agrisemantics.org/

18. GACS http://browser.agrisemantics.org/gacs/en/

19. Agroportal http://agroportal.lirmm.fr/

20. The CIARD RING

21. A record from the RING

22. Horizon 2020 research and innovation programme - grant agreement No 730988
Johannes Keizer APAN 45, 2018-03-28
What is the GACS?
Global Agricultural Concept Space
Stable URIs with as little semantic
determination as possible
Interoperability Switchboard
Reusable concepts
Mapping on low level

23. GACS – born from merging 3 thesauri

24. service
2
GACS
Thes
etc.
thes1
Onto1
Onto2
Onto3
Onto
An interoperability Switchboard
Yes, very much
oversimplified,
but....

25. Horizon 2020 research and innovation programme - grant agreement No 730988
Johannes Keizer APAN 45, 2018-03-28
A vision of the process
A community needs a new
Ontology/Taxonomy/Thesaurus/...........
It consults GACS vocabularies for an informed decison
It constructs it’s own KOS
It checks, where classes/concept/terms have a related
instance in GACS
If yes, it creates the appropriate semantic relationship
If no, it evaluates if the new concept is of common interest
If yes, it adds the concept to GACS

26. But.....
The existing GACS module is already able to crosslink
different KOS,
link your concepts and classes to GACS concepts
add your URIs to GACS

27. AgroPortal an
ontology repository for
agronomy, food, plant sciences
& biodiversity
Publish, search,
download
Browse,
visualize
Peer review
Versioning
Annotation
Recommendati
on
Mapping
Notes
Projects
77 ontologies, 95
candidates
5 driving use cases
~90 registered users
http://agroportal.
lirmm.fr

29. Conclusion: state of Infrastructure