Expand NMDC to support GLBRC

[mslarae13]

In working with Adina, it's been identified that there are some data as metadata slots that should be added to the NMDC schema to support this project.

Some of the slots below are already in NMDC schema, but aren't in the plant-associated package? need to confirm

In NMDC, add alias

• [x] Wind_Speed_Mean
• atmospheric_data = Measurement of atmospheric data; can include multiple data (example give, wind speed;9 knots
• wind_speed =Speed of wind measured at the time of sampling
• [x] Wind_Direction_Mean (wind_direction)
• Wind direction is the direction from which a wind originates
• north or west, not specific direction
• [ ] Solar_Radiation (?)
• solar_irradiance = The amount of solar energy that arrives at a specific area of a surface during a specific time interval title (kilowatts per square meter per day, ergs per square centimeter per second)
• [ ] Air_temp_mean (season_temp or annual_temp)
• Or average of the day? A: yes, day of sampling
• [ ] RH
• humidity = Amount of water vapour in the air, at the time of sampling
• [ ] AH (abs_air_humidity)
• abs_air_humidity = Actual mass of water vapor - mh20 - present in the air water vapor mixture (gram per gram, kilogram per kilogram, kilogram, pound)
• [ ] nitrogen_percent
• % of ?... Specific form?
• [ ] carbon_percent
• % of ?... Specific form?
• [ ] carbon_per_nitrogen
• Is this microbial biomass? C:N ratio?
• [ ] mass_per_leaf_g (host_dry_mass)
• unclear?
• [ ] PAR = photosynthetic active radiation (photon_flux)
• description needed
• [ ] barometric_pressure, Air_Pressure
• of the day of sampling? A: yes
• barometric_pressure = Force per unit area exerted against a surface by the weight of air above that surface
• [ ] height_mean_cm (host_height)?
• Is this height of the plant? A: average height of plants in the plot

In NMDC, but measurement was on the SOIL. NOT Plant

• [ ] pH
• [ ] P_ppm (tot_phosp)
• Is this total P? A: total P, Bray-Kurtz-P1 phosphorous in plant-associated bulk soil
• [ ] K_ppm (potassium)
• Is this total K? A: total K, Ammonium acetate extractable potassium in plant-associated bulk soil
• [ ] Ca_ppm (calcium)
• Is this total Ca? A: total Ca, Ammonium acetate extractable calcium in plant-associated bulk soil
• [ ] Mg_ppm (magnesium)
• Is this total Mg? A: total Mg, Ammonium acetate extractable magnesium in plant-associated bulk soil
• [ ] organic_matter (org_matter)
• Total organic matter? How is this measured? A: Loss on ignition method, unit is % (combustion)
• [ ] NO3N_ppm (nitrate)
• total nitrate? Or total nitrate N? A: Total soil nitrate-nitrogen (e.g. the nitrogen portion of total nitrate in a sample) , LaChat method. Measured in plant-associated bulk soil
• [ ] NH4_ppm (ammonium)
• total ammonium? total ammonium N? A: Total soil ammonium-nitrogen (e.g. the nitrogen portion of total ammonium in a sample), LaChat method. Measured in plant-associated bulk soil
• [ ] soil_moisture_percent ( water_content?)
• Are these soil or plants? A: soil
• [ ] soil_temp_10cm
• Temperature of the soil at 10cm depth on the day of sampling? A: yes

not in NMDC schema

• [ ] #1221
• [ ] #1222
• mg dry mass / total mass
• leaf dry matter content. Ontology term?
• [ ] #1216
• of the day of sampling? A: yes
• [ ] #1219
• of the day of sampling? A: yes
• [ ] precipitation (annual_precpt or season_precpt)
• precip on the day of sampling. Need a specific slot

Terms that will be added to Biosample, but should discuss putting on Site

• [ ] Agronomic logs and phenology terms need to be at the site level. Some terms added to the plants should be modeled to the site - pending schema refactoring.
• [ ] precipitation (annual_precpt or season_precpt)
• [ ] Wind_Speed_Mean
• [ ] Wind_Direction_Mean (wind_direction)
• [ ] Solar_Radiation (?)
• [ ] Air_temp_mean (season_temp or annual_temp)
• [ ] RH
• [ ] AH (abs_air_humidity)

phenotypic evaluation of plants?

• [ ] date_phenology_assessed
• ?
• [ ] phenology_emergence
• ? true/false?
• [ ] phenology_leaves_full_size
• ? true/false?
• [ ] phenology_herbivore_damage
• ? true/false?
• [ ] phenology_open_flowers
• ? true/false?
• [ ] phenology_ripe_seeds
• ? true/false?
• [ ] phenology_leaf_wilting
• ? true/false?
• [ ] phenology_canopy_closed
• ? true/false?
• [ ] phenology_senescence
• ? true/false?
• [ ] phenology_full_leaf_loss
• ? true/false?

[mslarae13]

@turbomam misx.yaml has no separation of what environmental extension are associated with which slots, correct?

That's only done at the submissions schema, correct?

[turbomam]

Well, there are a couple of mixs.yaml files. The one in the nmdc-schema repo does not make that connection. It's just a collection of terms, which are associated with the monolithic Biosample class and the OmicsProcessing class in nmdc.yaml.

But the previous collection of MIxS YAML files does

And so does the 6.2 release candidate

But you'll see that those two LinkML versions do it in slightly different ways. We could make all of that more transparent if necessary.

[turbomam]

And yes, the submission schema does it too.

[mslarae13]

@turbomam why are some descriptions in ' X ' but some aren't? see tot_phosp

[mslarae13]

why are some descriptions in single quotes but some aren't?

If a phrase has a : in it, Mark writes it in single quotes because : can get messed up.

Need to decide when are single quotes required? Should we just use them all the time? Putting single quotes around is the safer action.

[bmeluch]

Checked the descriptions of all the "In NMDC schema, add to plant-associated" terms for sample type exclusivity. Only "tot_nitro" would exclude plants:

name: tot_nitro
description: 'Total nitrogen concentration of water samples, calculated by: total
  nitrogen = total dissolved nitrogen + particulate nitrogen. Can also be measured
  without filtering, reported as nitrogen'
domain_of:
- HydrocarbonResourcesCores
- HydrocarbonResourcesFluidsSwabs
- WastewaterSludge
- Water 

[turbomam]

@bmeluch @mslarae13 and friends: how would you feel about

• starting a new schema module for this
• attaching the new slots to a new class, like GlbrcSample

We could continue to use GlbrcSample as a mixin, or migrate the slots onto Biosample. But I hope our efforts in December will leave us with a smaller, more modular Biosample overall.

[mslarae13]

@turbomam are you suggesting a GLBRC yaml file that NMDC schema references for these? Like we do with MIXS and EMSL and JGI

[mslarae13]

@turbomam how would you like alias' added to existing slots? They don't need to be curies, right? But I want to be able to attribute that this is what this term is called in GLBRC.

[turbomam]

Yes, I am suggesting that strategy. In the cases you mentioned, we define slots in those separate YAML modules and then assign them to Biosample in nmdc.yaml.

But I have raised the general question to our team: do we want more or fewer YAML modules. At one point, @mslarae13, I think you found the multiple modules difficult to search through. Have you become more comfortable with "find-in-files" in PyCharm or some other tool? I think the PyCharm functionality can be accessed with shift-command-f. @mbthornton-lbl has confirmed that he finds the practice of separate, thematic modules helpful.

I am really concerned about the number of slots we are adding onto Biosample. @mbthornton-lbl has opened an issue to propose a refactoring. I don't know if we can or should work on that before, during or after our December meeting in Berkeley.

[turbomam]

Aliases can be assigned to a schema element with attribution with

• https://linkml.io/linkml-model/latest/docs/structured_aliases/ and https://linkml.io/linkml-model/latest/docs/StructuredAlias/
• https://linkml.io/linkml-model/latest/docs/alt_descriptions/ is kinda related too

[mslarae13]

I'm ok with separate organized files. I can figure it out. I just want to make sure we're making the right decision for the right reasons. We'll make a GLBRC yaml to capture the new slots & can merge it in depending on the decision.

[mslarae13]

Will the BRCs capture this information consistently? Are these slots specific to this study? Do we make mappings and aliases or provide a tool for converting their metadata to the term NMDC would use? For close mappings and more specific mapping, curie required. Can we discuss at the next GLBRC meeting seeing their DH implementation, model, and schema.

[mslarae13]

For now, pull in the submission and pause on mapping & additional/ new metadata fields until we meet. Ingest the mapped metadata & skip schema mapping for now until . Provide a spreadsheet with a column for the GLBRC term and the schema term.