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The `env_package` slot in the schema should have the range of an Enum, with the list of permissible values constructed using the value of `` in https://www.ncbi.nlm.nih.gov/biosample/docs/packages/?fo…
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I was trying to use `efetch ` to obtain the Attributes of a BioSample record, but I found that for some BioSample records, the Attributes reported in the xml are completely different from those disp…
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This misbehavior happens with fasterq-dump 3.0.7 on the following accession and a few others, at a rate of about 7% of biosample-based accessions. **SAMN08049698** and some other biosample-based acces…
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- `depth2` is being deprecated in https://github.com/microbiomedata/nmdc-schema/blob/issue-486-data-to-7-0 (which will actually result in a new version of the schema, greater than 7.0.0)
- the releas…
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## To move from https://github.com/turbomam/biosample-xmldb-sqldb/issues/42
@ssarrafan @emileyfadrosh and others from NMDC went through milestones and priorities and wanted to follow up something t…
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Discussed during squad-lead call 2020-07-09:
ongoing discussion about biobanks dealing with stem cell and deposition process to Biosample.
Biosample serves Bioschema based JSON-LD
Purpose of recipe…
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Our current MiAIRR submission pipeline is not able to deal with BioSample updates. If a given biosample identifier is already in the NCBI systems and a user needs to update the metadata for that biosa…
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This corresponds to sampled_tissue in the [GA4GH Biosample](https://phenopacket-schema.readthedocs.io/en/latest/biosample.html).
Add it using the cda_biosample_factory class.
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I thought I was missing some metadata in one of our own previously-submitted SRA datasets because it wasn't showing up in the CSV file, but then the SRA admins pointed out that it *does* show up on th…
ressy updated
5 years ago
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_Some of these are confusions about what should be expressed in the nmdc-schema and what should be handled in the submission portal_
- [ ] `Biosample.slot_usage.heavy_metals_meth.multivalued`: imp…