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- Ontology release tooling (SHACL validation, Github Actions, automated release notes etc.) - Philip Strömert
- see also:
- What would need to be done, if VIVO were to be migrated to ODK?
- install requirements (ODK Docker container and Make)
- seed a new naked repo → https://docs.google.com/presentation/d/1TnLzIg_Y40I6hqbemmFOMHjwOmIOfuz2usKYZDxbgPY/
- build import modules for all existing VIVO ontology dependencies → probably the most time-hungry step as this might need some tweaking in the custom Makefile
- copy native VIVO terms into vivo-edit.owl, imported terms will be there via the import modules
- maybe think about, if you need/want a ROBOT tsv template pipeline as used in VIBSO
- activate documentation build pipeline and edit docs to entail what you need for your contributors
- make a release using the automated release build pipeline of ODK (
sh run.sh make
prepare_release) - publish new release
- Philip started a test migration in: https://github.com/vivo-ontologies/vivo-ontology-ODK
- all edits are made on the /src/ontology/vivo-edit.owl
- imports have to be declared via ODK in the src/ontology/vivo-odk.yaml then
sh run.sh make update_repo
has to be called in src/ontology to create- Philip already declared some standard OBO import: BFO, OMO, RO, IAO, OBI
- BFO and OMO should always be mirrored as we want all of what is defined in them
- possible parameters of this config yaml → https://github.com/INCATools/ontology-development-kit/blob/master/docs/project-schema.md
- Philip already declared some standard OBO import: BFO, OMO, RO, IAO, OBI
- already scraped all BFO declarations from the /src/ontology/vivo-edit.owl → BFO dependency is clean
- Problems noticed so far:
- first push led the CI/CD to fail because vivo is outside of the DL profile, which is considered a bad smell → some axioms somewhere that can hopefully be dropped, see also https://douroucouli.wordpress.com/2021/03/24/avoid-mixing-parthood-with-cardinality-constraints/
- owl:sameAs was declared as an OP → deleted
there was a weird blank node axiom → AnnotationAssertion(owl:minCardinality _:genid2147483649 "1"^^xsd:nonNegativeInteger) → deleted
owl:DeprecatedProperty was declared as an OP → deleted
owl:minCardinality was declared as an annotation property --> deleted
- http://purl.obolibrary.org/obo/ARG_ ← terms with this namespace only exist in VIVO ontology → why not mint it there instead then and not use these unresolvable IRIs?
- first push led the CI/CD to fail because vivo is outside of the DL profile, which is considered a bad smell → some axioms somewhere that can hopefully be dropped, see also https://douroucouli.wordpress.com/2021/03/24/avoid-mixing-parthood-with-cardinality-constraints/
- about version history
- this workflow depends on GitHub, so the better the PR and issue titles the easier it is to automatically let GH create a "what has changed" list from the merged PRs since the last tag, which will then be your release description
- Q by Egon Willighagen on Mastodon: https://mastodon.social/@egonw@social.edu.nl/111937329072554484 - Christian Hauschke
- Who is using CiTO in VIVO, in production?
- Could the data be parsed/queried/scraped for export to Wikidata?
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