Comments (4)
poetry run linkml-lint --format tsv --output nmdc.yaml.lint.tsv src/schema/nmdc.yaml
does not catch those slots with whitespace in their names.
PS we could have a TSV liniting target in project.Makefile in addition to the basic one in Makefile
from nmdc-schema.
see also
from nmdc-schema.
@sujaypatil96 observed that it also appears in mixs.yaml
I think that once the slot assignment is deleted from Biosample
, its presence in mixs.yaml
won't re-inject the assignment back into Biosample.
But removing it form mixs.yaml
is preferable. Having said that, we will be switching to importing from GSC's mixs.yaml
(v6.2.0) soon, replacing our current practice of importing from our static mixs.yaml.
from nmdc-schema.
- removed the association between the
has ...
slots andBiosample
innmdc.yaml
- added deletion commands to
assets/yq-for-mixs_subset_modified.txt
so that thehas ...
slots won't get intosrc/schema/mixs.yaml
in the first place
from nmdc-schema.
Related Issues (20)
- remove build-datafile-from-api-requests usages and *filtered-request* from project.Makefile
- remove fuseki container shutdown and direct TDB2 writing from project.Makefile
- remove mixs regernation by introspetion
- remove legacy files from `assets/`
- move all Neon mapping files to a single path
- for visualizations, `slot_usages` over object properties should indicate narrowest range
- what to exclude from visualizastion?
- what predicates should be asserted in visualizations, esp for MIxS slots
- has_unit does not appear as a slot for QuantityValue in the online documentation ? HOT 1
- Split up MetatranscriptomeActivity like metaG was HOT 2
- `napa_compliance` branch: Make `insert_many_pymongo.py` more robust HOT 1
- Deprecate MetagenomeSequencingActivity
- `nmdc.owl` is being generated with URIs like `<https://w3id.org/mixs/depth>` not `<https://w3id.org/mixs/0000018>` HOT 3
- Update Code of conduct with staff feedback
- Update `extract_study` command to search Legacy IDs
- workarround: generate RDF joining element labels to id-based IRIs
- Check referential integrity of Napa squad's MongoDB database via SPARQL in Fuseki
- Add `associated_studies` onto Biosample and make part_of not required for Biosample
- Developer documentation and `Dockerfile` contradict one another HOT 3
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