Comments (5)
Nice work, @brynnz22 and @bmeluch
Are you requesting that dna_concentration
and dna_absorb1
should be attributes of the Extraction
process? I suggest associating those slots with the ProcessedSample
that actually has those characteristics. Maybe we should relocate sample_mass
too.
Think about it this way: if a schema had a Cooking
processes, and a served_to
slot that pointed to a Person
, then a satisfaction
slot should be associated with the Person
, not the Cooking
.
It doesn't matter how our data source models the data, especially if it's coming form relational tables, which are notorious for mixing concerns. It's our responsibility to determine what entities have what qualities, and the nmdc-schema supports doing that in a way that reflects reality better than most relational databases.
Sometimes you can double check your intentions by looking at the other things that use those slots. dna_concentration and dna_absorb1 are only associated with Biosample, which is a MaterialEntity
, not a PlannedProcess
from nmdc-schema.
@turbomam We were discussing which ones it belongs to, and ProcessedSample
makes a lot of sense. I think since sample_mass
was in the Extraction
class, we thought those should go in there too. But it makes sense to move those slots into ProcessedSample
!
from nmdc-schema.
Are we done with this?
from nmdc-schema.
@turbomam are we done with this?
from nmdc-schema.
Might want to revisit this some day
from nmdc-schema.
Related Issues (20)
- Remodel class that aggregates steps of `WorkflowExecution` for easier schema traversal HOT 1
- `has_input`, `has_output`, and `has_process_parts` slots on `ProtocolExecution` need pattern constraints
- `berkeley-schema-fy24`: Facilitate access to `nmdc_materialized_patterns` schema via PyPI package HOT 2
- Delete Class WorkflowChain in Berkeley schema HOT 2
- `berkeley-schema-fy24`: Implement super migrator that runs all partial migrators in correct order HOT 1
- Find a home for these comments taken from `src/scripts/report_biosamples_per_study.py`
- check if classes associated with `alternative_identifiers` can use ANY `alternative_identifiers` HOT 5
- Migrations: Make it easier to test migrators against a Mongo database
- `berkeley-schema-fy24`: Update migrators to account for `WorkflowChain` class being removed
- Publish schema to PyPI via GitHub Release `v10.5.4` HOT 1
- Migrations: Implement "no op" migrator from `v10.4.0` to `v10.5.4`
- `berkeley-schema-fy24`: Some migrators use incorrect collection name (instead of `mags_set`)
- Rename branches to eliminate Berkeley commits from `main` HOT 6
- 2024-06-18 `id` pattern validation summaries and SPARQL-based referential integrity checks on MongoDB contents with and without migration HOT 6
- Facilitate access to `nmdc_materialized_patterns` schema variant via PyPI package HOT 2
- produce a nmdc-schema YAML artifact with deprecated elements included HOT 1
- Remove WorkflowExeuctionActivity as a range for Database slot activity_set
- tighter pattern constraint on was_generated_by
- Migrator: Update `migrator_from_10_3_0_to_10_4_0.py` so it also updates `was_generated_by` values HOT 1
- Docker Compose shows warning saying `version` (specifier) is obsolete
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