pizza example

I managed to convert the pizza ontology https://protege.stanford.edu/ontologies/pizza/pizza.owl to linkml using

https://www.researchgate.net/profile/Marjan-Mernik/publication/228408042/figure/fig1/AS:301805855625217@1448967532277/Class-hierarchy-of-Pizza-Ontology.png

schemauto import-owl pizza.ofn -o pizza.yaml

using

docker run  -v $PWD:/work -w /work -ti linkml/schema-automator

after having run

docker run -v $PWD/:/work -w /work --rm -ti obolibrary/robot robot convert pizza.owl --output pizza.ofn

(all following the instructions on https://linkml.io/schema-automator/packages/importers.html)

this exersise resulted in a valid linkml definition in yaml.

idea: work on dissamination+outreach example that simulates what we try do achieve e.g. for techniques just for the pizza example

I propose to start a pizza_toy_example (or similar) folder that mimics the structure of the repo internally again. (or should it be included in the main stucture? ... to be discussed)

Main thoughts:

• use the imported results from pizza to map them to our scicat strurture

  • All NamedPizza become datasets in SciCat with a tag pizza

• we should start with the same SciCat Dataset as we do always

• helps to explore the use of is_a, has_a, meanings...

• document all such that it can be used for dissamination

• helps us to learn what we can do and how we should structure things

• exploit and document the full cycle from owl to linkml-yml to scicat and potentially export from scicat to tripple store

• create jupyter notebook that populates scicat accordingly using pyscicat

Rogh idea of analogies

• One dataset is one NamedPizza
• In ScientificMetadata we could have Topping and Base as containers that would have multivalued attributes refleccting the sub-categories

pizza.ofnpizza.yaml