Open turbomam opened 2 days ago
The structured_pattern
in https://microbiomedata.github.io/berkeley-schema-fy24/MetaproteomicsAnalysis/#induced
seems to imply that '{id_nmdc_prefix}:(dobj)-{id_shoulder}-{id_blade}$'
is expected
now that we are aggregating all workflows into the workflow_execution_set
, I can't exclude MetaproteomicsAnalysis instances!
does rdf not use the structured_pattern?
does rdf not use the structured_pattern?
Good question. For the record, nothing uses structured_pattern
directly at this point in time. To benefit from a structured_pattern
, one has to re-generate the schema with something like gen-linkml --materialize-patterns
, which the kind of process that generates nmdc_schema/nmdc_materialized_patterns.yaml
. It's the pattern
s that are utilized.
I still think that this problem may be due to LinkML tooling rater than the nmdc-schema, though.
If it helps debug the only Classes that has a pattern match of (bsm|procsm) is DataGeneration and subclasses. Not sure how or where it is confusing a WorkflowExecution subclass for a DataGeneration subclass.
I did
make squeaky-clean all test make-rdf
in berkeley-schema-fy24. I haven't doen that in a while and added some collection that I may have never run throughmake-rdf
before.passes, but
emits
corresponding to this fragment:
Traceback
> File "/home/mark/.cache/pypoetry/virtualenvs/nmdc-schema-gXr5ogK9-py3.10/bin/linkml-convert", line 8, in