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microbiomedata/nmdc-schema

`StorageProcess`'s `has_input` and `has_output` should have range of `Sample`

Range on this slot (currently NamedThing) does not match the structured_pattern_syntax of {id_nmdc_prefix}:(bsm|procsm)-{id_shoulder}-{id_blade}. Switching to Sample will correct this.

• kheal
·
• Opened 
  3 days ago
·
• #2374

microbiomedata/nmdc-schema

`instrument_used` slot needs `structured_pattern` to match range defined of `Instrument`

This slot does not have a structured_pattern to match its range of Instrument.

• kheal
·
• Opened 
  3 days ago
·
• #2373

microbiomedata/nmdc-schema

`WorkflowExecution` subclasses `was_informed_by` slots should match subclass of appropriate `DataGeneration`

For instance, MagsAnalysis s range is DataGeneration but its structured_syntax refers to the subclass NucleotideSequencing only. Below is the range / structured_pattern to use to guide better ranges. ...

• kheal
·
• Opened 
  3 days ago
·
• #2372

microbiomedata/nmdc-schema

`WorkflowExecution` slots `has_input` and `has_output` range should be `DataObject`

Need to state range on this slot_usage to match structured_syntax

• kheal
·
• Opened 
  3 days ago
·
• #2371

microbiomedata/nmdc-schema

deprecate `Metagenome Bins` permissible value

A while ago we added Metagenome HQMQ Bins Compression File and Metagenome LQ Bins Compression File Existing records have been updated to Metagenome HQMQ Bins Compression File in https://github.com/microbiomedata/issues/issues/1084 ...

• aclum
·
• 1
·
• Opened 
  13 days ago
·
• #2369

microbiomedata/nmdc-schema

404 error to jsonld serialization of nmdc-schema

This doc page: https://microbiomedata.github.io/nmdc-schema/identifiers/ refers to this URL: https://github.com/microbiomedata/nmdc-schema/blob/main/project/jsonschema/nmdc.schema.json which returns 404 ...

• sierra-moxon
·
• Opened 
  13 days ago
·
• #2368

microbiomedata/nmdc-schema

`cur_land_use` multivalued

https://github.com/GenomicsStandardsConsortium/mixs/issues/905 See GSC issue about making this slot multivalued.

• mslarae13
·
• 1
·
• Opened 
  17 days ago
·
• #2367

microbiomedata/nmdc-schema

Add permissible values to `FileTypeEnum` to support LC/MS Metabolomics data

The following permissible values should be added to the FileTypeEnum in anticipation of a new workflow. LC-MS Metabolomics Results LC-MS Metabolomics Processed Data This will block https://github.com/microbiomedata/issues/issues/1090 ...

lcms_metabolomics

• kheal
·
• 2
·
• Opened 
  17 days ago
·
• #2366

microbiomedata/nmdc-schema

Implement migrator for removal of `sample_state_information` slot from `PortionOfSubstance` class

Background In PR https://github.com/microbiomedata/nmdc-schema/pull/2354, the sample_state_information slot is being removed from the PortionOfSubstance class. In the schema docs, I can see that the ...

X SMALL

• eecavanna
·
• Opened 
  20 days ago
·
• #2364

microbiomedata/nmdc-schema

does `DissolvingProcess` also need slot:`mixing_steps`

In Extraction, the mixing I just added is for cell lysis. Dissolving, based on the description, also requires mixing A mixing step where a soluble component is mixed with a liquid component. Should this ...

• mslarae13
·
• Opened 
  20 days ago
·
• #2363

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