Closed turbomam closed 3 weeks ago
especially in support of NMDC ECO-Fab collaboration @mslarae13
Here's the proposed output illustrated with MiscellaneousNaturalOrArtificialEnvironment
and PlantAssociated
MiscellaneousNaturalOrArtificialEnvironment_only:
- alkalinity
- alt
- ammonium
- biomass
- bromide
- calcium
- chloride
- chlorophyll
- density
- diether_lipids
- diss_carb_dioxide
- diss_hydrogen
- diss_inorg_carb
- diss_org_nitro
- diss_oxygen
- nitrate
- nitrite
- nitro
- org_carb
- org_matter
- org_nitro
- ph
- phosphate
- phosplipid_fatt_acid
- potassium
- pressure
- silicate
- sodium
- sulfate
- sulfide
- water_current
PlantAssociated_only:
- air_temp_regm
- ances_data
- antibiotic_regm
- biol_stat
- biotic_regm
- chem_mutagen
- climate_environment
- cult_root_med
- fertilizer_regm
- fungicide_regm
- gaseous_environment
- genetic_mod
- gravity
- growth_facil
- growth_habit
- growth_hormone_regm
- herbicide_regm
- host_age
- host_common_name
- host_disease_stat
- host_dry_mass
- host_genotype
- host_height
- host_length
- host_life_stage
- host_phenotype
- host_subspecf_genlin
- host_symbiont
- host_taxid
- host_tot_mass
- host_wet_mass
- humidity_regm
- light_regm
- mechanical_damage
- mineral_nutr_regm
- non_min_nutr_regm
- pesticide_regm
- ph_regm
- plant_growth_med
- plant_product
- plant_sex
- plant_struc
- radiation_regm
- rainfall_regm
- root_cond
- root_med_carbon
- root_med_macronutr
- root_med_micronutr
- root_med_ph
- root_med_regl
- root_med_solid
- root_med_suppl
- salt_regm
- samp_capt_status
- samp_dis_stage
- season_environment
- standing_water_regm
- tiss_cult_growth_med
- water_temp_regm
- watering_regm
intersection:
- chem_administration
- depth
- elev
- misc_param
- organism_count
- oxy_stat_samp
- perturbation
- project_name
- salinity
- samp_name
- samp_store_dur
- samp_store_loc
- samp_store_temp
- samp_vol_we_dna_ext
- temp
poetry run extension-differences \
--schema src/mixs/schema/mixs.yaml \
--ext1 MiscellaneousNaturalOrArtificialEnvironment \
--ext2 PlantAssociated > soil-vs-water-slot-usage.yaml
This sounds similar to our previous work to define profiles for specific use cases.I fully support mix and matching terms to be included in a new profile.Is that what this ticket is about?Or is this a suggestion of what terms should be included in a particular extension?It is good to keep in mind that the MIxS content does not get changed for specific use cases. That kind of work is not part of the CIG/TWG.Rather, the MIXS terms can be used ‘mix and match’ for projects.If this is for a non GSC project, perhaps the conversation needs to be in that projects GitHub. Cheers,LynnSent from my iPhoneOn Jul 19, 2024, at 2:27 PM, Mark Andrew Miller @.***> wrote: poetry run extension-differences \ --schema src/mixs/schema/mixs.yaml \ --ext1 MiscellaneousNaturalOrArtificialEnvironment \ --ext2 PlantAssociated > soil-vs-water-slot-usage.yaml
—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.***>
extension-differences
is an existing discovery tool in the MIxS repo. It isn't specific to any external project and it was not intended to play any role in profiling.
When @mslarae13 and I were meeting with some EcoFAB scientists recently I was trying to show which slots are available for MiscellaneousNaturalOrArtificialEnvironment
vs PlantAssociated
. I forgot that extension-differences
doesn't currently report the terms that are applicable to both queried Extension
s, so this issue and it's corresponding PR add that functionality in.
The intention here is to help a new MIxS user make a data-driven choice about what Extension they want to use, or whether they will need to take a "mix and match" approach
Currently,
only returns