2018 03 apan

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Johannes Keizer

My presentation at APAN 45 in the joint session with agGateway

Science

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

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

......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

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

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

Mapping at the front end level
DB1
DB2
DB3
DB4

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

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

......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

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

......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

Our contribution http://agrisemantics.org/

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

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

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

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

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

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

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Jupiter’s moon Io hosts extensive volcanism, driven by tidal heating. The isotopic composition of Io's inventory of volatile chemical elements, including sulfur and chlorine, reflects its outgassing and mass loss history, and thus records information about its evolution. We used millimeter observations of Io’s atmosphere to measure sulfur isotopes in gaseous SO2 and SO, and chlorine isotopes in gaseous NaCl and KCl. We find 34S/32S = 0.0595 ± 0.0038 (equivalent to δ34S = +347 ± 86‰), which is highly enriched compared to average Solar System values and indicates that Io has lost 94 to 99% of its available sulfur. Our measurement of 37Cl/35Cl = 0.403 ± 0.028 (δ37Cl = +263 ± 88‰) shows that chlorine is similarly enriched. These results indicate that Io has been volcanically active for most (or all) of its history, with potentially higher outgassing and mass-loss rates at earlier times.

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Mustard, as a crop, is susceptible to a variety of pests that can affect its growth and yield. Here’s a rundown of some common pests that target mustard plants: Aphids: These small, sap-sucking insects can cause significant damage by feeding on the leaves and stems. Aphids also excrete a sticky substance known as honeydew, which can lead to the growth of sooty mold on the plants. Flea Beetles: These tiny beetles jump like fleas when disturbed and chew small holes in the leaves. They are particularly damaging in the early growth stages of the plant. Cabbage Loopers: The larvae of a type of moth, these caterpillars are known for their distinctive looping movement. They chew large holes in the leaves and can defoliate plants if present in large numbers. Diamondback Moth Larvae: Another caterpillar pest, these larvae chew small holes in the leaves and can cause extensive damage, especially when infestations are heavy. Whiteflies: These are tiny, winged insects that feed on plant sap and can quickly become a problem in greenhouse or close planting conditions. Like aphids, they also secrete honeydew. Cutworms: These are the larvae of certain types of moths and are known for cutting young plants at the stem base at ground level. They are most destructive during the night. Root Maggots: The larvae of root maggot flies, these pests attack the roots of mustard plants, causing wilting and potentially killing young plants. Harlequin Bugs: These are colorful stink bugs that suck the sap from mustard plant stems and leaves, causing the leaves to become stippled, wilt, and eventually die if the infestation is severe. Mustard Sawfly: The larvae of the mustard sawfly can cause considerable defoliation, as they feed voraciously on the leaves. Clubroot: Caused by a fungus-like organism, clubroot affects the roots, causing them to swell and distort. While technically a disease, it is often associated with pest management because controlling it involves similar preventative strategies. Control Measures: Managing pests in mustard involves a combination of cultural, biological, and chemical methods. Crop rotation, resistant varieties, timely sowing, maintaining plant health, and using natural predators like ladybugs and parasitic wasps can help keep pest populations under control. Chemical pesticides should be used as a last resort due to their potential impact on the environment and non-target species.

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Bollworms are among the most damaging pests in cotton cultivation, affecting the bolls where the cotton fibers are formed. There are several species of bollworms, each capable of causing significant yield loss and quality degradation if not effectively managed. Here’s a detailed look at the primary bollworm species affecting cotton: Cotton Bollworm (Helicoverpa armigera): Also known as the corn earworm or the Old World bollworm, this pest is found in many regions around the world. It is highly polyphagous (feeds on many different plants) and poses a threat not only to cotton but also to maize, tomatoes, and legumes. The larvae bore into the cotton bolls, feeding on the developing seeds and fibers, which can lead to boll rot. Pink Bollworm (Pectinophora gossypiella): A significant pest of cotton, the pink bollworm larvae infest the cotton bolls, feeding on the seeds and lint. This can severely damage or destroy the bolls. In regions where pink bollworms are prevalent, they have been a major driver for the adoption of genetically engineered Bt cotton, which expresses a bacterium gene toxic to certain insects. Tobacco Budworm (Heliothis virescens): Closely related to the cotton bollworm, the tobacco budworm primarily attacks tobacco but is also a common pest in cotton. It primarily damages the flowers and bolls of the cotton plant. Differentiating between the tobacco budworm and the cotton bollworm based on appearance can be challenging, but it is crucial for effective management. American Bollworm (Helicoverpa zea): Known in some regions as the corn earworm, it is similar in behavior to Helicoverpa armigera and poses a threat to a variety of crops, including cotton. The larvae attack the cotton bolls, leading to direct damage to the cotton lint and seeds. Management Strategies: Cultural Controls: Crop rotation, destruction of crop residues, and deep plowing can help break the pest’s life cycle. Timing of planting can also be adjusted to avoid peak pest infestation. Biological Controls: Natural enemies like Trichogramma wasps, which parasitize bollworm eggs, and predators such as lacewings and ladybugs can be encouraged. Bacillus thuringiensis (Bt) products can also be sprayed, which are particularly effective against young larvae. Chemical Controls: Insecticides may be required when infestation levels exceed economic thresholds. However, resistance management must be considered, alternating modes of action to avoid developing resistance. Genetic Approaches: Bt cotton, genetically modified to express Bacillus thuringiensis toxin, has been highly effective in controlling bollworms and has dramatically reduced the reliance on chemical insecticides. Monitoring and Scouting: Regular field scouting and using pheromone traps to monitor adult populations can help in timely and targeted application of control measures. The effective management of bollworms often requires an integrated approach

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Context. WASP-76 b has been a recurrent subject of study since the detection of a signature in high-resolution transit spectroscopy data indicating an asymmetry between the two limbs of the planet. The existence of this asymmetric signature has been confirmed by multiple studies, but its physical origin is still under debate. In addition, it contrasts with the absence of asymmetry reported in the infrared (IR) phase curve. Aims. We provide a more comprehensive dataset of WASP-76 b with the goal of drawing a complete view of the physical processes at work in this atmosphere. In particular, we attempt to reconcile visible high-resolution transit spectroscopy data and IR broadband phase curves. Methods. We gathered 3 phase curves, 20 occultations, and 6 transits for WASP-76 b in the visible with the CHEOPS space telescope. We also report the analysis of three unpublished sectors observed by the TESS space telescope (also in the visible), which represents 34 phase curves. Results. WASP-76 b displays an occultation of 260±11 and 152±10 ppm in TESS and CHEOPS bandpasses respectively. Depending on the composition assumed for the atmosphere and the data reduction used for the IR data, we derived geometric albedo estimates that range from 0.05 ± 0.023 to 0.146 ± 0.013 and from <0.13 to 0.189 ± 0.017 in the CHEOPS and TESS bandpasses, respectively. As expected from the IR phase curves, a low-order model of the phase curves does not yield any detectable asymmetry in the visible either. However, an empirical model allowing for sharper phase curve variations offers a hint of a flux excess before the occultation, with an amplitude of ∼40 ppm, an orbital offset of ∼−30◦ , and a width of ∼20◦ . We also constrained the orbital eccentricity of WASP-76 b to a value lower than 0.0067, with a 99.7% confidence level. This result contradicts earlier proposed scenarios aimed at explaining the asymmetry observed in high-resolution transit spectroscopy. Conclusions. In light of these findings, we hypothesise that WASP-76 b could have night-side clouds that extend predominantly towards its eastern limb. At this limb, the clouds would be associated with spherical droplets or spherically shaped aerosols of an unknown species, which would be responsible for a glory effect in the visible phase curves.

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2018 03 apan

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/

17.

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

28.

29. Conclusion: state of Infrastructure

Editor's Notes

Before oversimplified statement, telling the story of dc author, foaf name, biblio.type

2018 03 apan

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Editor's Notes