Report slots, as used by some class, that have another class in their range, when that range class has a strcutred pattern

microbiomedata / nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

https://microbiomedata.github.io/nmdc-schema/

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Report slots, as used by some class, that have another class in their range, when that range class has a strcutred pattern #1990

Closed turbomam closed 4 months ago

turbomam commented 4 months ago

see also

https://github.com/microbiomedata/nmdc-schema/pull/1989

turbomam commented 4 months ago

Some of this could have gone in a separate PR, although it all makes the output from src/scripts/project_id_patterns.py briefer

assets/yq-for-mixs_subset_modified.txt: do customization of MIxS slots here, not in Biosample slot_usage (no now there's no difference between the global range and the Biosample range)
src/schema/annotation.yaml
- remove as many slot_usages ranges as possible especially if they are redundant to the global range
- type has a non-monotonic slot_usage in OntologyClass. Remove the slot assignment.
src/schema/core.yaml: remove all false assertions
src/schema/external_identifiers.yaml: seems like ranges isn't begin inherited. May need to do some more resrach for a global solution.
src/schema/mixs.yaml regenerated from new assets/yq-for-mixs_subset_modified.txt:
src/schema/nmdc.yaml and src/schema/workflow_execution_activity.yamlremoval of reiterated slot_usage ranges

turbomam commented 4 months ago

QuantityValue.has_numeric_value global_range = 'float' usage.range = 'double'

turbomam commented 4 months ago

ChromatographicSeparationProcess.has_input
    global_range = 'NamedThing'
    any_of.range = 'Biosample'
    any_of.range = 'ProcessedSample'
    prioritized_range = {'range': 'Biosample', 'range_types': 'linkml:ClassDefinition'}
    prioritized_range = {'range': 'ProcessedSample', 'range_types': 'linkml:ClassDefinition'}
DataObject.was_generated_by
    global_range = 'Activity'
    any_of.range = 'Activity'
    any_of.range = 'OmicsProcessing'
    prioritized_range = {'range': 'Activity', 'range_types': 'linkml:ClassDefinition'}
    prioritized_range = {'range': 'OmicsProcessing', 'range_types': 'linkml:ClassDefinition'}
Extraction.has_input
    global_range = 'NamedThing'
    any_of.range = 'Biosample'
    any_of.range = 'ProcessedSample'
    prioritized_range = {'range': 'Biosample', 'range_types': 'linkml:ClassDefinition'}
    prioritized_range = {'range': 'ProcessedSample', 'range_types': 'linkml:ClassDefinition'}
MixingProcess.has_input
    global_range = 'NamedThing'
    any_of.range = 'Biosample'
    any_of.range = 'ProcessedSample'
    prioritized_range = {'range': 'Biosample', 'range_types': 'linkml:ClassDefinition'}
    prioritized_range = {'range': 'ProcessedSample', 'range_types': 'linkml:ClassDefinition'}
SubSamplingProcess.has_input
    global_range = 'NamedThing'
    any_of.range = 'Biosample'
    any_of.range = 'ProcessedSample'
    prioritized_range = {'range': 'Biosample', 'range_types': 'linkml:ClassDefinition'}
    prioritized_range = {'range': 'ProcessedSample', 'range_types': 'linkml:ClassDefinition'}

turbomam commented 4 months ago

Results have already been filtered to only include classes with an identifying slot, which is always id
we probably don't want to project the NamedThing pattern
will need to traverse though subclasses
will need to find all structured patterns (what about literal patterns?)

then

merge patterns for consensus over typecodes and then assign the merged pattern as a constraint on the relevant class/slot pair.

turbomam commented 4 months ago

Merging this. Will address projecting the asserted patterns onto mentioning slots separately.