no longer MIxS (modified)?

[turbomam]

For discussion after GSP:

I reviewed the modifications in modifications_long and deleted any rows that were just reiterations of what MIxS already said (one of the disadvantages of SNTC)

I.e. I did make modifications to the Google Sheet and re-ran the generation locally but did not push anything upstream. nmdc_test_data_valid.tsv still imports without any warnings and validates and nmdc_test_data_valid.tsv still imports without any warnings but fails to validate.

I don't think these fields are MIxS (modified) any more. That means that either I did some valuable cleanup or I nuked some legitimate modifications. I've linked the definitions within SNTC.

• biotic_relationship
• elev
• light_regm
• rel_to_oxygen
• samp_mat_process

Here's how they appear in the soil_emls_jgi_mg configuration now. I'll look thought the SNTC definitions above more carefully next week.

- biotic_relationship
  aliases:
  - observed biotic relationship
  annotations:
    expected_value:
      tag: expected_value
      value: enumeration
  description: Description of relationship(s) between the subject organism and other
    organism(s) it is associated with. E.g., parasite on species X; mutualist with species
    Y. The target organism is the subject of the relationship, and the other organism(s)
    is the object
  title: observed biotic relationship
  examples:
  - value: free living
  from_schema: http://w3id.org/mixs/terms
  is_a: nucleic acid sequence source field
  slot_uri: MIXS:0000028
  multivalued: false
  owner: soil MIMS
  range: biotic_relationship_enum

- elev:
  aliases:
  - elevation
  annotations:
    expected_value:
      tag: expected_value
      value: measurement value
  description: Elevation of the sampling site is its height above a fixed reference
    point, most commonly the mean sea level. Elevation is mainly used when referring
    to points on the earth's surface, while altitude is used for points above the surface,
    such as an aircraft in flight or a spacecraft in orbit.
  title: elevation
  examples:
  - value: 100 meter
  from_schema: http://w3id.org/mixs/terms
  is_a: environment field
  slot_uri: MIXS:0000093
  multivalued: false
  owner: soil MIMS
  range: quantity value
  required: true

- light_regm:
  aliases:
  - light regimen
  annotations:
    expected_value:
      tag: expected_value
      value: exposure type;light intensity;light quality
    preferred_unit:
      tag: preferred_unit
      value: lux; micrometer, nanometer, angstrom
    occurrence:
      tag: occurrence
      value: '1'
  description: Information about treatment(s) involving exposure to light, including
    both light intensity and quality.
  title: light regimen
  examples:
  - value: incandescant light;10 lux;450 nanometer
  from_schema: http://w3id.org/mixs/terms
  is_a: core field
  string_serialization: '{text};{float} {unit};{float} {unit}'
  slot_uri: MIXS:0000569
  multivalued: false
  owner: soil MIMS
  range: string

- rel_to_oxygen:
  aliases:
  - relationship to oxygen
  annotations:
    expected_value:
      tag: expected_value
      value: enumeration
  description: Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic
    are valid descriptors for microbial environments
  title: relationship to oxygen
  examples:
  - value: aerobe
  from_schema: http://w3id.org/mixs/terms
  is_a: nucleic acid sequence source field
  slot_uri: MIXS:0000015
  multivalued: false
  owner: soil MIMS
  range: rel_to_oxygen_enum
  required: false

- samp_mat_process:
  aliases:
  - sample material processing
  annotations:
    expected_value:
      tag: expected_value
      value: text
  description: A brief description of any processing applied to the sample during or
    after retrieving the sample from environment, or a link to the relevant protocol(s)
    performed.
  title: sample material processing
  examples:
  - value: filtering of seawater, storing samples in ethanol
  from_schema: http://w3id.org/mixs/terms
  is_a: nucleic acid sequence source field
  string_serialization: '{text}'
  slot_uri: MIXS:0000016
  multivalued: false
  owner: soil MIMS
  range: string
  recommended: true

[mslarae13]

@turbomam What do you need from me on this? Anything?

[turbomam]

@turbomam What do you need from me on this? Anything?

Can I just move slots out of the MIxS (modified) dh_section and into the MIxS section if I find evidence that we are really using the slot as is? I would keep a log of those decisions. (Probably here in this issue.)

See also these notes about building a slot difference detector.

[mslarae13]

@turbomam I believe the answer to this is yes. Let's chat about it tomorrow (02/10)

[mslarae13]

Some MIxS modified slots aren't modified but they're being used outside of the intended extension/package.

We have some slots that we're identifying of modifications, but that might no longer me the case & MIxS is ALSO using it the same way. So it isn't a modification.

Compare mixs.yaml to the modifications in modifications_long in sheets-and-friends. If the modifications are redundant, delete them. (Montana will do this)

biotic_relationship

• This slot if from the agriculture template. We've added it to the soil tempalte.
• Change here is valid and should remain in sheets_and_friends

elev

• Added comments
• Examples should NOT say 'meters' or 'm', since we are requiring meters. Replace examples with only a value
• range changed from QuantityValue to float
• set required = true
• changed title to elevation, meters to clarify required units.
• All changes made here in sheets_and_friends are valid and should remain

light_regm

• This is a plant associated term that may be used in soil experiments. Change is adding it to a different package
• Change here is valid and should remain in sheets_and_friends

rel_to_oxygen

• Decision was made to remove rel_to_oxygen (microbiomedata/nmdc-schema@5b90d88#:~:text=removed%20rel_to_oxygen%20from%20Biosample%3B%20added%20elev%20and%20oxy_stat_samp%20usage) ... and use oxy_stat_sample as a 'merge' of the two.
• Both still appear in sheets and friends... @turbomam can we just delete rel_to_oxygen in sheets and friends from the 'import_slots_regardless' tab?
• oxy_stat_sample has a new range and notes.

samp_mat_process

• samp_mat_process is in MIxS core. We've imported using import_slots_regardless. No contextual changes have been made.
• Are we able to remove this from import_slots_regardless? I think the answer is no, because it's in core? But, it's in mixs.yaml, so will it still appear in the submission portal if we remove it?

Following completing the check of these 5 slots, we need to make a issue to do an automated slot usage check.

[mslarae13]

@turbomam can you please review my above comment. I think this issue can be closed. Do we need to make additional tickets for anything above?

[ssarrafan]

I'm closing this issue based on @mslarae13 last comment. @turbomam if there are additional new issues needed please let me know if I can help.

[turbomam]

I was planning on building a tool that detects which MIxS slots have been modified. I'm not sure how long that would take, or if some of the things @cmungall myself and others are working might make that moot.

In the long run, what is the benefit of making separate sections for MIxS, MiIxS modified and MIxS inspired?