Comments (7)
it seems like we have some conflicts between whether this topic should be called library construction or library preparation
either is fine with me, but we should be consistent in the terms used in the schema and the terms we use in our discussions
from nmdc-schema.
I'm commenting out the "nested" protocol
entries in the example data files.
If we really want to use nesting, that means that the range of protocol
will be a class with name
and url
slots. That wouldn't be problematic, but we should see if there are any related patterns in the schema already that we can build off of.
from nmdc-schema.
As discussed at the squad meeting today we are using 'library preparation' in line with OBI ontology.
from nmdc-schema.
@turbomam is there a reason https://microbiomedata.github.io/nmdc-schema/LIBRARYTYPEENUM/ is all caps instead of camelcase like the other enums?
from nmdc-schema.
Last thing here is to update the date slots. example valid data
https://github.com/microbiomedata/nmdc-schema/blob/issue-917-neon-story/src/data/valid/Database-neon-story.yaml
from nmdc-schema.
One checkbox left, will move to new sprint to complete
from nmdc-schema.
The last slot that I wanted for Class LibraryPreparation isn't urgent for ESA so I made a separate issue, #1000, so we can close this one.
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Related Issues (20)
- 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- Docker Compose shows warning saying `version` (specifier) is obsolete
- extra leading caret in `structured_pattern`s HOT 3
- remove logic to repair curies HOT 1
- replace uses of `nmdc_schema_merged.yaml` with `nmdc_schema/nmdc_materialized_patterns.yaml` HOT 3
- force update of `urllib3` version HOT 2
- `berkeley-schema-fy24`: Schema version underlying `SchemaView` instance changes from one release to the next HOT 1
- Add PR template to `nmdc-schema`
- Finalize metatranscriptome modeling for nmdc HOT 1
- MIxS Environmental Context slot grouping
- `known_as` slot needs description and `structured_pattern` constraints
- `berkeley-schema-fy24`: id slot_usage resulting in badly minted IDs HOT 17
- `berkeley-schema-fy24`: Update `part_16` migrator to include `metatranscriptome_expression_analysis_set` collection
- document the fact that working on a PR template is the only case in which PRs don't require review HOT 1
- Fix PR template functionality HOT 1
- update range and pattern on metagenome_annotation_id to allow metatranscriptome workflow activities
- Draft: add details to `InstrumentModelEnum`
- `berkeley`: Fix range for `was_generated_by` slot
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