Skip to content

Document new OWL generation ideas #2484

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
wants to merge 1 commit into
base: main
Choose a base branch
from
Draft

Document new OWL generation ideas #2484

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
35 changes: 35 additions & 0 deletions nmdc-schema.owl.Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
nmdc-schema.ols.owl.ttl: src/schema/nmdc.yaml
date && time poetry run linkml generate owl \
--add-ols-annotations \
--default-permissible-value-type "http://www.w3.org/2002/07/owl#Class" \
--enum-iri-separator "#" \
--format owl \
--log_level WARNING \
--mergeimports \
--metadata \
--metadata-profile ols \
--add-root-classes \
--no-assert-equivalent-classes \
--metaclasses \
--no-mixins-as-expressions \
--no-stacktrace \
--no-type-objects \
--ontology-uri-suffix .owl.ttl \
--use-native-uris \
--useuris $< > $@ && date

#Mon Jun 9 01:26:34 PM EDT 2025
#WARNING:linkml.generators.owlgen:ignoring equals_string=plate as unable to tell if literal
#WARNING:linkml.generators.owlgen:ignoring equals_string=plate as unable to tell if literal
#WARNING:linkml.generators.owlgen:ignoring equals_string=plate as unable to tell if literal
#WARNING:linkml.generators.owlgen:ignoring equals_string=plate as unable to tell if literal
#WARNING:linkml.generators.owlgen:ignoring equals_string=dataset_doi as unable to tell if literal
#WARNING:linkml.generators.owlgen:ignoring equals_string=award_doi as unable to tell if literal
#WARNING:linkml.generators.owlgen:ignoring equals_string=pass as unable to tell if literal
#WARNING:linkml.generators.owlgen:ignoring equals_string=gas_chromatography as unable to tell if literal
#WARNING:linkml.generators.owlgen:ignoring equals_string=liquid_chromatography as unable to tell if literal
#WARNING:linkml.generators.owlgen:ignoring equals_string=gas_chromatography as unable to tell if literal
#WARNING:linkml.generators.owlgen:ignoring equals_string=retention_index as unable to tell if literal
#8.86user 0.27system 0:07.43elapsed 122%CPU (0avgtext+0avgdata 204820maxresident)k
#46480inputs+2536outputs (5major+71342minor)pagefaults 0swaps
#Mon Jun 9 01:26:42 PM EDT 2025
Loading