schema slot updates

[mslarae13]

Collecting all schema slot update issues here for tracking & to determine priority / squad work.
(Addition of tickets is still in progress)

Slot updates

• Determine if and how climate_environment will be used in the submission schema #586
• Determine if and how various soil type/classification/taxonomy terms will be used in the submission schema #585
• Submission Portal- soil template -horizon #584
• Relax certain required: true slots in schema #583
• Submission Portal/ DH: samp_name should be required to be unique #581
• id and samp_name should both be unique keys for Biosamples #588
• Update JGI Plate well description #580
• Issue 382 guidance and examples #571
• Typo in geographic location (latitude and longitude) pattern hint sheets_and_friends#139
• Consolidate "oxygenation status of sample" and "relationship to oxygen" #375
• Add guidance and/or example text to soil template terms #382
• revisit storage and validation of temporal data #384
• DNase not DNAse DataHarmonizer#169
• Could we drop the parenthetical portion of the cur_land_use permissible values? sheets_and_friends#60
• Define ontology for soil treatments nmdc-metadata#166
• Water content validation and structure sheets_and_friends#148
• add explicit units when instantiating biosamples if unit was assumed in DH issues#236
• show but don't require entry of env package nmdc-server#781
• Updated source_mat_id on submission portal sheets_and_friends#157
• Ensure that soil biosamples have two depth values (minimum and maximum) issues#17
• Determine if and how rel_to_oxygen will be used in the submission schema sample-annotator#58
• Elevation should be required in the soil template sheets_and_friends#120
• Soil sample storage temperature help example fails on validation sheets_and_friends#121
• Inconsistent env_broad_scale column sample-annotator#77
• be consistent with underscore, hyphens and whitespace in element names #324
• be consistent with slot ranges #325
• "Structured comment name" and "Package item" lexical rules mixs#25
• Rename or reconstitute "Sample ID" section sheets_and_friends#137
• All MIxS required terms should be required and highlighted yellow DataHarmonizer#150
• All "MIxS required where applicable" terms should be highlighted purple (recommended) DataHarmonizer#151
• Consider if "DNA Collection Site" is redundant and remove DataHarmonizer#156
• Update Elevation help text to include units DataHarmonizer#157
• “DNA Sample ID” should be unique submission-schema#208
• Update validation rules for DNA Well Number DataHarmonizer#160
• Add validation rules for DNA Container Label DataHarmonizer#161
• Provide improved guidance for “experimental factor- other" submission-schema#209
• Rename "NMDC fields esp. GOLD paths" to "NMDC" DataHarmonizer#164
• sample shipped amount: add validation of units submission-schema#210
• Consolidate storage condition terms submission-schema#212
• prepopulate "environmental package" based on previous page selection DataHarmonizer#168
• removed training whitespace in 'sample name ' nmdc-metadata#422
• standardize capitalization of DH column headers/titles DataHarmonizer#109
• section/column annotations should probably go in slot usage DataHarmonizer#115
• include user facility and required units in column headers as appropriate DataHarmonizer#122
• subsurface_depth nmdc-metadata#277
• Sample Metadata "metadata" tab's isotope_exposure treatment not defined in mixs.yaml? nmdc-metadata#388
• NMDC Sample Metadata Template's investigation type and mixs investigation type have almost nothing in common nmdc-metadata#389
• NMDC Sample Metadata Template: currently undefined usage of samp_collect_device nmdc-metadata#390
• Implied but undocumented relationships with size_frac nmdc-metadata#391
• No examples of slots specific to plant package yet nmdc-metadata#393
• remove depth2 and subsurface_depth2 attributes #193
• Define ontology for soil treatments nmdc-metadata#166
• Biosample slot usage for source_mat_id was not migrated to sheets_and_friends #783
• slot altitude is not relevant for soil. Only elevation issues#242

New slots

• Use MIxS samp_taxon_id to model NCBI taxonomy ID from GOLD? #574
• create more subslots of alternative_identifiers #409

DH/Submission portal

• Update process for using display hints directly from the schema nmdc-server#750
• env package or entire template name should be displayed in header of submission portal nmdc-server#780
• Enable EnvO triad dropdowns for soil package sheets_and_friends#118
• remove env_package column from our DH templates. It can be inferred from the selected template sheets_and_friends#136
• Make URLs hyperlinked in the help text DataHarmonizer#149
• Fix broken URL in Sample collection device description DataHarmonizer#153
• Show units for all quantitative values nmdc-server#556
• Display key metadata terms nmdc-server#559
• DH: What determines section and column ordering in DH template from Soil-NMDC-Template_Compiled nmdc-metadata#418
• conflicts between MIxS and NMDC's MIxS namespaces DataHarmonizer#22
• Discuss which NMDC biosample slots to use for NMDC DataHarmonizer #235
• indent DH enums/pulldowns according to subclass hierarchy DataHarmonizer#58
• proofreading Soil-NMDC-Template_Compiled DataHarmonizer#77
• manually entered values in pulldown column do not validate DataHarmonizer#95
• final steps for section composition, section order and column order DataHarmonizer#107

Schema Sheets

• DH: row_ord column in Soil-NMDC-Template_Compiled nmdc-metadata#417
• work on enums sheets_and_friends#6
• standardize multiple examples on one slot sheets_and_friends#42
• no longer MIxS (modified)? sheets_and_friends#69
• ordering of sections and columns in DataHarmonizer templates nmdc-metadata#404
• Add multivalued? column to Soil-NMDC-Template_Compiled nmdc-metadata#419
• MIxS Soil 'extreme_salinity' not mentioned in any Soil-NMDC-Template_Compiled tab nmdc-metadata#423
• MIxS Soil collection_date appears in multiple tabs Soil-NMDC-Template_Compiled nmdc-metadata#424
• move content from bioscales.yaml into nmdc.yaml and delete bioscales Submission Portal template #784

Other

• Extend schema to allow for functional annotations nmdc-metadata#177
• GOLD 'ecosystem' slots at study level #403
• Use MIxS samp_taxon_id to model NCBI taxonomy ID from GOLD? #574
• MIxS sections to exclude? sheets_and_friends#89
• omics type vs omics_type slots #293
• "environmental package" and GOLD ecosystem terms are limited to soil for all 12 MIxS packages sheets_and_friends#123
• Identify strategy to support missing fields in the Submission Portal #318
• Add raw field name back to column description nmdc-server#719
• provide linkml examples of gold paths #240
• remove stray omics_type slot #250
• short term: programmatically tag the origin of MIxS terms when imported into NMDC schema #252
• Awaiting example data in EnvironmentalMetadata tab nmdc-metadata#392
• Include distinct packages in the schema #191
• Repair MIXS environment annotations #197
• Use ENVO hierarchy in search pilot#44
• Use ENVO synonyms in search pilot#45
• Define controlled vocabulary for data object types nmdc-metadata#81
• Align schema with OBI nmdc-metadata#111
• move content from bioscales.yaml into nmdc.yaml and delete bioscales Submission Portal template #784

[mslarae13]

#581
Difficult to accomplish. LinkML only allows for 1 identifier column, and that's the source_mat_id column and also must be unique.
LinkML has unique keys to use, but they aren't checked.
Longer lived issue, backlog.

[mslarae13]

The following should be completed by NMDC SubPort squad

Slot updates

• Determine if and how climate_environment will be used in the submission schema #586
• Determine if and how various soil type/classification/taxonomy terms will be used in the submission schema #585
• Submission Portal- soil template -horizon #584
• Typo in geographic location (latitude and longitude) pattern hint sheets_and_friends#139
• revisit storage and validation of temporal data #384
• Could we drop the parenthetical portion of the cur_land_use permissible values? sheets_and_friends#60
• Water content validation and structure sheets_and_friends#148
• add explicit units when instantiating biosamples if unit was assumed in DH issues#236
• Determine if and how rel_to_oxygen will be used in the submission schema sample-annotator#58
• Soil sample storage temperature help example fails on validation sheets_and_friends#121
• Consider if "DNA Collection Site" is redundant and remove DataHarmonizer#156
• Update validation rules for DNA Well Number DataHarmonizer#160
• Add validation rules for DNA Container Label DataHarmonizer#161
• sample shipped amount: add validation of units submission-schema#210
• Consolidate storage condition terms submission-schema#212
• standardize capitalization of DH column headers/titles DataHarmonizer#109
• section/column annotations should probably go in slot usage DataHarmonizer#115
• include user facility and required units in column headers as appropriate DataHarmonizer#122
• Sample Metadata "metadata" tab's isotope_exposure treatment not defined in mixs.yaml? nmdc-metadata#388
• NMDC Sample Metadata Template: currently undefined usage of samp_collect_device nmdc-metadata#390
• Implied but undocumented relationships with size_frac nmdc-metadata#391
• [ ]
• Relax certain required: true slots in schema #583
• Update JGI Plate well description #580
• Issue 382 guidance and examples #571
• Consolidate "oxygenation status of sample" and "relationship to oxygen" #375
• Add guidance and/or example text to soil template terms #382
• removed training whitespace in 'sample name ' nmdc-metadata#422
• Update Elevation help text to include units DataHarmonizer#157
• be consistent with underscore, hyphens and whitespace in element names #324
• Elevation should be required in the soil template sheets_and_friends#120
• Updated source_mat_id on submission portal sheets_and_friends#157
• DNase not DNAse DataHarmonizer#169

New slots

• Use MIxS samp_taxon_id to model NCBI taxonomy ID from GOLD? #574

DH/Submission portal

• env package or entire template name should be displayed in header of submission portal nmdc-server#780
• Enable EnvO triad dropdowns for soil package sheets_and_friends#118
• Make URLs hyperlinked in the help text DataHarmonizer#149
• Fix broken URL in Sample collection device description DataHarmonizer#153
• Show units for all quantitative values nmdc-server#556

Schema Sheets

• work on enums sheets_and_friends#6
• standardize multiple examples on one slot sheets_and_friends#42
• MIxS Soil 'extreme_salinity' not mentioned in any Soil-NMDC-Template_Compiled tab nmdc-metadata#423
• MIxS Soil collection_date appears in multiple tabs Soil-NMDC-Template_Compiled nmdc-metadata#424

Other

• Use MIxS samp_taxon_id to model NCBI taxonomy ID from GOLD? #574

[turbomam]

de-assinging slot rel_to_oxygen form class Biosample. Will need to remove from sheets_and_friend workflow. There will probably be additional similar changes to reconcile.

[turbomam]

bump

[mslarae13]

@turbomam are you bumping because you'd like to see this prioritized?

[turbomam]

Yeah, sorry about that. No I don't think it needs different prioritization. I just did that selfishly because it makes this appear higher in the list when I sort by "recently up[dated"

I guess a better solution would be for me to make a project of issues I don't want to forget about.