Comments (3)
We will need special handling for host_taxid in NMDC.
Example:
host_tax_id: {
{
"has_raw_value": "Homo sapiens [NCBITaxon:9606]",
"term": {
"id": "NCBITaxon:9606",
"name": "Homo sapiens"
}
}
In MIxS and NCBI, we will need to map host_taxid to host_tax_id.term.id
and split it up to get only the integer part, i.e., 9606. The other term host
(MIxS 6.0 term) will need to be retrieved from host_tax_id.term.name
.
from nmdc-schema.
We will need special handling for host_tax_id in NMDC.
I was expecting that this would be a common pattern. Is host_tax_id
the only place you've see it so far?
from nmdc-schema.
Yup, host_taxid
is the only slot I've noticed this inconsistency on so far. Perhaps you can help me look through the results of automated exact matching and see if I'm missing something? I will have a PR out soon.
from nmdc-schema.
Related Issues (20)
- 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 19
- `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
- delete `assets/yq-for-nmdc_schema_accepting_legacy_ids.txt`
- resume efforts to detect examples coverage HOT 1
- range constraint for gene_function_id on Class FunctionalAnnotationAggMember
- `berkeley`: Fix range for `has_calibration` slot
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from nmdc-schema.