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Class: AgricultureMIMARKSSurvey

Combinatorial checklist Minimal Information about a Marker Specimen: survey with environmental package agriculture

URI: MIXS:AgricultureMIMARKSSurvey

Inheritance

Slots

Name Cardinality and Range Description Inheritance
samp_name 1..1
String		 A local identifier or name that for the material sample used for extracting n... MIMARKSSurvey
samp_taxon_id 1..1
String		 NCBI taxon id of the sample MIMARKSSurvey
project_name 1..1
String		 Name of the project within which the sequencing was organized MIMARKSSurvey
experimental_factor 0..1
String		 Experimental factors are essentially the variable aspects of an experiment de... MIMARKSSurvey
lat_lon 1..1
String		 The geographical origin of the sample as defined by latitude and longitude MIMARKSSurvey, Agriculture
geo_loc_name 1..1
String		 The geographical origin of the sample as defined by the country or sea name f... MIMARKSSurvey, Agriculture
collection_date 1..1
Date		 The time of sampling, either as an instance (single point in time) or interva... MIMARKSSurvey, Agriculture
neg_cont_type 0..1 recommended
NegContTypeEnum		 The substance or equipment used as a negative control in an investigation MIMARKSSurvey
pos_cont_type 0..1 recommended
String		 The substance, mixture, product, or apparatus used to verify that a process w... MIMARKSSurvey
env_broad_scale 1..1
String		 Report the major environmental system the sample or specimen came from MIMARKSSurvey, Agriculture
env_local_scale 1..1
String		 Report the entity or entities which are in the sample or specimen’s local vic... MIMARKSSurvey, Agriculture
env_medium 1..1
String		 Report the environmental material(s) immediately surrounding the sample or sp... MIMARKSSurvey, Agriculture
subspecf_gen_lin 0..1 recommended
String		 Information about the genetic distinctness of the sequenced organism below th... MIMARKSSurvey
extrachrom_elements 0..1
Integer		 Do plasmids exist of significant phenotypic consequence (e MIMARKSSurvey
source_mat_id 0..1 recommended
String		 A unique identifier assigned to a material sample (as defined by http://rs MIMARKSSurvey
biotic_relationship 0..1 recommended
BioticRelationshipEnum		 Description of relationship(s) between the subject organism and other organis... MIMARKSSurvey
trophic_level 0..1 recommended
TrophicLevelEnum		 Trophic levels are the feeding position in a food chain MIMARKSSurvey
rel_to_oxygen 0..1 recommended
RelToOxygenEnum		 Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ... MIMARKSSurvey
isol_growth_condt 1..1
String		 Publication reference in the form of pubmed ID (pmid), digital object identif... MIMARKSSurvey
samp_collec_device 0..1
String		 The device used to collect an environmental sample MIMARKSSurvey
samp_collec_method 0..1
String		 The method employed for collecting the sample MIMARKSSurvey
samp_mat_process 1..1 recommended
String		 A brief description of any processing applied to the sample during or after r... MIMARKSSurvey
samp_size 0..1
QuantityValue		 The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll... MIMARKSSurvey
samp_vol_we_dna_ext 0..1
QuantityValue		 Volume (ml) or mass (g) of total collected sample processed for DNA extractio... MIMARKSSurvey
nucl_acid_ext 1..1 recommended
String		 A link to a literature reference, electronic resource or a standard operating... MIMARKSSurvey
nucl_acid_amp 1..1 recommended
String		 A link to a literature reference, electronic resource or a standard operating... MIMARKSSurvey
target_gene 1..1
String		 Targeted gene or locus name for marker gene studies MIMARKSSurvey
target_subfragment 1..1 recommended
String		 Name of subfragment of a gene or locus MIMARKSSurvey
pcr_primers 1..1 recommended
String		 PCR primers that were used to amplify the sequence of the targeted gene, locu... MIMARKSSurvey
pcr_cond 1..1 recommended
String		 Description of reaction conditions and components of PCR in the form of 'init... MIMARKSSurvey
seq_meth 1..1
String		 Sequencing machine used MIMARKSSurvey
seq_quality_check 0..1 recommended
String		 Indicate if the sequence has been called by automatic systems (none) or under... MIMARKSSurvey
chimera_check 1..1 recommended
String		 Tool(s) used for chimera checking, including version number and parameters, t... MIMARKSSurvey
associated_resource 0..1 recommended
String		 A related resource that is referenced, cited, or otherwise associated to the ... MIMARKSSurvey
sop 0..1 recommended
String		 Standard operating procedures used in assembly and/or annotation of genomes, ... MIMARKSSurvey
depth 0..1
QuantityValue		 The vertical distance below local surface, e Agriculture
alt 0..1
QuantityValue		 Altitude is a term used to identify heights of objects such as airplanes, spa... Agriculture
elev 0..1
QuantityValue		 Elevation of the sampling site is its height above a fixed reference point, m... Agriculture
temp 1..1
QuantityValue		 Temperature of the sample at the time of sampling Agriculture
plant_growth_med 0..1
PlantGrowthMedEnum		 Specification of the media for growing the plants or tissue cultured samples,... Agriculture
soil_horizon 0..1
SoilHorizonEnum		 Specific layer in the land area which measures parallel to the soil surface a... Agriculture
photosynt_activ 0..*
QuantityValue		 Measurement of photosythetic activity (i Agriculture
photosynt_activ_meth 0..*
String		 Reference or method used in measurement of photosythetic activity Agriculture
samp_collect_method 0..1
String		 The method employed for collecting the sample Agriculture
enrichment_protocol 0..1
String		 The microbiological workflow or protocol followed to test for the presence or... Agriculture
library_prep_kit 0..1
String		 Packaged kits (containing adapters, indexes, enzymes, buffers etc Agriculture
sequencing_location 0..1
String		 The location the sequencing run was performed Agriculture
soil_temp 0..*
String		 Temperature of soil at the time of sampling Agriculture
soil_pH 0..1
Double		 The pH of soil at time of sampling Agriculture
soil_conductivity 0..1
QuantityValue		 Conductivity of soil at time of sampling Agriculture
rel_location 0..1
String		 Location of sampled soil to other parts of the farm e Agriculture
soil_cover 0..1
String		 Description of the material covering the sampled soil Agriculture
porosity 0..1
String		 Porosity of deposited sediment is volume of voids divided by the total volume... Agriculture
texture 0..1
QuantityValue		 The relative proportion of different grain sizes of mineral particles in a so... Agriculture
texture_meth 0..1
String		 Reference or method used in determining soil texture Agriculture
host_symbiont 0..*
String		 The taxonomic name of the organism(s) found living in mutualistic, commensali... Agriculture
pres_animal_insect 0..1
String		 The type and number of animals or insects present in the sampling space Agriculture
plant_water_method 0..1
String		 Description of the equipment or method used to distribute water to crops Agriculture
anim_water_method 0..*
String		 Description of the equipment or method used to distribute water to livestock Agriculture
farm_water_source 0..*
FarmWaterSourceEnum		 Source of water used on the farm for irrigation of crops or watering of lives... Agriculture
water_source_shared 0..*
WaterSourceSharedEnum		 Other users sharing access to the same water source Agriculture
water_pH 0..1
Double		 pH measurement of the sample, or liquid portion of sample, or aqueous phase o... Agriculture
season 0..1
String		 The season when sampling occurred Agriculture
solar_irradiance 0..1
QuantityValue		 The amount of solar energy that arrives at a specific area of a surface durin... Agriculture
crop_yield 0..1
String		 Amount of crop produced per unit or area of land Agriculture
season_humidity 0..1
QuantityValue		 Average humidity of the region throughout the growing season Agriculture
humidity 0..1
QuantityValue		 Amount of water vapour in the air, at the time of sampling Agriculture
adjacent_environment 0..*
String		 Description of the environmental system or features that are adjacent to the ... Agriculture
chem_administration 1..*
String		 List of chemical compounds administered to the host or site where sampling oc... Agriculture
food_prod 0..*
String		 Descriptors of the food production system or of the agricultural environment ... Agriculture
lot_number 0..*
String		 A distinctive alpha-numeric identification code assigned by the manufacturer ... Agriculture
fertilizer_admin 0..1
String		 Type of fertilizer or amendment added to the soil or water for the purpose of... Agriculture
samp_stor_temp 0..1
QuantityValue		 Temperature at which sample was stored, e Agriculture
food_trav_mode 0..*
String		 A descriptor for the method of movement of food commodity along the food dist... Agriculture
food_trav_vehic 0..*
String		 A descriptor for the mobile machine which is used to transport food commoditi... Agriculture
farm_equip_san 0..*
String		 Method used to sanitize growing and harvesting equipment Agriculture
farm_equip 0..*
String		 List of equipment used for planting, fertilization, harvesting, irrigation, l... Agriculture
farm_equip_shared 0..*
String		 List of planting, growing or harvesting equipment shared with other farms Agriculture
food_harvest_proc 0..*
String		 A harvesting process is a process which takes in some food material from an i... Agriculture
plant_struc 0..1
String		 Name of plant structure the sample was obtained from; for Plant Ontology (PO)... Agriculture
host_dry_mass 0..1
QuantityValue		 Measurement of dry mass Agriculture
ances_data 0..1
String		 Information about either pedigree or other ancestral information description ... Agriculture
genetic_mod 0..1
String		 Genetic modifications of the genome of an organism, which may occur naturally... Agriculture
Food_Product_type 0..1
String		 new food product categories and food products themselves Agriculture
Food_source 1..1
String		 Type of plant or animal from which the food product or its major ingredient i... Agriculture
spikein_strain 0..*
String		 Taxonomic information about the spike-in organism(s) at the strain level Agriculture
organism_count 0..*
OrganismCountEnum		 Total cell count of any organism (or group of organisms) per gram, volume or ... Agriculture
size_frac_low 0..1
QuantityValue		 Refers to the mesh/pore size used to pre-filter/pre-sort the sample Agriculture
size_frac_up 0..1
QuantityValue		 Refers to the mesh/pore size used to retain the sample Agriculture
cult_isol_date 0..1
Date		 A culture isolation date is a date-time entity marking the end of a process i... Agriculture
samp_pooling 0..*
String		 Physical combination of several instances of like material, e Agriculture
root_med_macronutr 0..1
String		 Measurement of the culture rooting medium macronutrients (N,P, K, Ca, Mg, S);... Agriculture
root_med_carbon 0..1
String		 Source of organic carbon in the culture rooting medium; e Agriculture
root_med_ph 0..1
Double		 pH measurement of the culture rooting medium; e Agriculture
soil_depth 0..1
QuantityValue		 The vertical distance below local surface, e Agriculture
water_temp_regm 0..*
String		 Information about treatment involving an exposure to water with varying degre... Agriculture
watering_regm 0..*
String		 Information about treatment involving an exposure to watering frequencies, tr... Agriculture
standing_water_regm 0..*
String		 Treatment involving an exposure to standing water during a plant's life span,... Agriculture
gaseous_environment 0..*
String		 Use of conditions with differing gaseous environments; should include the nam... Agriculture
fungicide_regm 0..*
String		 Information about treatment involving use of fungicides; should include the n... Agriculture
climate_environment 0..*
String		 Treatment involving an exposure to a particular climate; treatment regimen in... Agriculture
herbicide_regm 0..*
String		 Information about treatment involving use of herbicides; information about tr... Agriculture
non_mineral_nutr_regm 0..*
String		 Information about treatment involving the exposure of plant to non-mineral nu... Agriculture
pesticide_regm 0..*
String		 Information about treatment involving use of insecticides; should include the... Agriculture
ph_regm 0..*
String		 Information about treatment involving exposure of plants to varying levels of... Agriculture
salt_regm 0..*
String		 Information about treatment involving use of salts as supplement to liquid an... Agriculture
season_environment 0..*
String		 Treatment involving an exposure to a particular season (e Agriculture
perturbation 0..*
String		 Type of perturbation, e Agriculture
samp_store_dur 1..1
String		 Duration for which the sample was stored Agriculture
samp_store_loc 1..1
String		 Location at which sample was stored, usually name of a specific freezer/room Agriculture
samp_collect_device 1..1
String		 The device used to collect an environmental sample Agriculture
host_age 1..1
QuantityValue		 Age of host at the time of sampling; relevant scale depends on species and st... Agriculture
host_common_name 1..1
String		 Common name of the host Agriculture
host_genotype 1..1
String		 Observed genotype Agriculture
host_height 1..1
QuantityValue		 The height of subject Agriculture
host_subspecf_genlin 0..*
String		 Information about the genetic distinctness of the host organism below the sub... Agriculture
host_length 1..1
QuantityValue		 The length of subject Agriculture
host_life_stage 1..1
String		 Description of life stage of host Agriculture
host_phenotype 1..1
String		 Phenotype of human or other host Agriculture
host_taxid 1..1
String		 NCBI taxon id of the host, e Agriculture
host_tot_mass 1..1
QuantityValue		 Total mass of the host at collection, the unit depends on host Agriculture
plant_product 0..1
String		 Substance produced by the plant, where the sample was obtained from Agriculture
oxy_stat_samp 0..1
OxyStatSampEnum		 Oxygenation status of sample Agriculture
assembly_quality 0..1
String		 Tool(s) used for assembly, including version number and parameters Agriculture
url 0..*
String		 A related resource that is referenced, cited, or otherwise associated to the ... Agriculture
fao_class 0..1
FaoClassEnum		 Soil classification from the FAO World Reference Database for Soil Resources Agriculture
local_class 0..1
String		 Soil classification based on local soil classification system Agriculture
local_class_meth 0..1
String		 Reference or method used in determining the local soil classification Agriculture
soil_type 1..1
String		 Description of the soil type or classification Agriculture
soil_type_meth 1..1
String		 Reference or method used in determining soil series name or other lower-level... Agriculture
horizon 0..1
HorizonEnum		 Specific layer in the land area which measures parallel to the soil surface a... Agriculture
horizon_meth 0..1
String		 Reference or method used in determining the horizon Agriculture
link_class_info 0..1
String		 Link to digitized soil maps or other soil classification information Agriculture
previous_land_use 0..1
String		 Previous land use and dates Agriculture
previous_land_use_meth 0..1
String		 Reference or method used in determining previous land use and dates Agriculture
crop_rotation 0..1
String		 Whether or not crop is rotated, and if yes, rotation schedule Agriculture
agrochem_addition 0..*
String		 Addition of fertilizers, pesticides, etc Agriculture
tillage 0..*
TillageEnum		 Note method(s) used for tilling Agriculture
fire 0..1
Date		 Historical and/or physical evidence of fire Agriculture
flooding 0..1
Date		 Historical and/or physical evidence of flooding Agriculture
extreme_event 0..1
Date		 Unusual physical events that may have affected microbial populations Agriculture
link_climate_info 0..1
String		 Link to climate resource Agriculture
annual_temp 0..1
QuantityValue		 Mean annual temperature Agriculture
season_temp 0..1
QuantityValue		 Mean seasonal temperature Agriculture
annual_precpt 0..1
QuantityValue		 The average of all annual precipitation values known, or an estimated equival... Agriculture
season_precpt 0..1
QuantityValue		 The average of all seasonal precipitation values known, or an estimated equiv... Agriculture
cur_land_use 0..1
CurLandUseEnum		 Present state of sample site Agriculture
slope_gradient 0..1
QuantityValue		 Commonly called 'slope' Agriculture
slope_aspect 0..1
QuantityValue		 The direction a slope faces Agriculture
profile_position 0..1
ProfilePositionEnum		 Cross-sectional position in the hillslope where sample was collected Agriculture
drainage_class 0..1
DrainageClassEnum		 Drainage classification from a standard system such as the USDA system Agriculture
store_cond 1..1
String		 Explain how and for how long the soil sample was stored before DNA extraction... Agriculture
ph_meth 0..1
String		 Reference or method used in determining ph Agriculture
cur_vegetation 0..1
String		 Vegetation classification from one or more standard classification systems, o... Agriculture
cur_vegetation_meth 0..1
String		 Reference or method used in vegetation classification Agriculture
tot_org_carb 0..1
QuantityValue		 Definition for soil: total organic carbon content of the soil, definition oth... Agriculture
tot_org_c_meth 0..1
String		 Reference or method used in determining total organic carbon Agriculture
tot_nitro 0..1
QuantityValue		 Total nitrogen concentration of water samples, calculated by: total nitrogen ... Agriculture
tot_n_meth 0..1
String		 Reference or method used in determining the total nitrogen Agriculture
microbial_biomass 1..1
QuantityValue		 The part of the organic matter in the soil that constitutes living microorgan... Agriculture
microbial_biomass_meth 1..1
String		 Reference or method used in determining microbial biomass Agriculture
heavy_metals_meth 0..1
String		 Reference or method used in determining heavy metals Agriculture
tot_car 0..1
QuantityValue		 Total carbon content Agriculture
tot_phos 0..1
QuantityValue		 Total amount or concentration of phosphate Agriculture
sieving 1..1
String		 Collection design of pooled samples and/or sieve size and amount of sample si... Agriculture
pool_dna_extracts 1..1
String		 Indicate whether multiple DNA extractions were mixed Agriculture
misc_param 0..*
String		 Any other measurement performed or parameter collected, that is not listed he... Agriculture

Identifier and Mapping Information

Schema Source

  • from schema: http://w3id.org/mixs

Mappings

Mapping Type Mapped Value
self MIXS:AgricultureMIMARKSSurvey
native MIXS:AgricultureMIMARKSSurvey

LinkML Source

Direct

name: agriculture MIMARKS survey
description: 'Combinatorial checklist Minimal Information about a Marker Specimen:
  survey with environmental package agriculture'
from_schema: http://w3id.org/mixs
is_a: agriculture
mixins:
- MIMARKS survey

Induced

name: agriculture MIMARKS survey
description: 'Combinatorial checklist Minimal Information about a Marker Specimen:
  survey with environmental package agriculture'
from_schema: http://w3id.org/mixs
is_a: agriculture
mixins:
- MIMARKS survey
attributes:
  samp_name:
    name: samp_name
    description: A local identifier or name that for the material sample used for
      extracting nucleic acids, and subsequent sequencing. It can refer either to
      the original material collected or to any derived sub-samples. It can have any
      format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. INSDC requires every sample name from
      a single Submitter to be unique. Use of a globally unique identifier for the
      field source_mat_id is recommended in addition to sample_name.
    title: sample name
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text}'
    slot_uri: MIXS:0001107
    multivalued: false
    alias: samp_name
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  samp_taxon_id:
    name: samp_taxon_id
    description: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa
      sample. Use 'synthetic metagenome’ for mock community/positive controls, or
      'blank sample' for negative controls.
    title: Taxonomy ID of DNA sample
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text} [NCBI:txid]'
    slot_uri: MIXS:0001320
    multivalued: false
    alias: samp_taxon_id
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{text}'
    slot_uri: MIXS:0000092
    multivalued: false
    alias: project_name
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  experimental_factor:
    name: experimental_factor
    description: Experimental factors are essentially the variable aspects of an experiment
      design which can be used to describe an experiment, or set of experiments, in
      an increasingly detailed manner. This field accepts ontology terms from Experimental
      Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For
      a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO;
      for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI
    title: experimental factor
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000008
    multivalued: false
    alias: experimental_factor
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  lat_lon:
    name: lat_lon
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees and in WGS84 system
    title: geographic location (latitude and longitude)
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{float} {float}'
    slot_uri: MIXS:0000009
    multivalued: false
    alias: lat_lon
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  geo_loc_name:
    name: geo_loc_name
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name. Country or sea names should be chosen
      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
      (http://purl.bioontology.org/ontology/GAZ)
    title: geographic location (country and/or sea,region)
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{term}: {term}, {text}'
    slot_uri: MIXS:0000010
    multivalued: false
    alias: geo_loc_name
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  collection_date:
    name: collection_date
    description: 'The time of sampling, either as an instance (single point in time)
      or interval. In case no exact time is available, the date/time can be right
      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
    title: collection date
    from_schema: http://w3id.org/mixs
    is_a: environment field
    slot_uri: MIXS:0000011
    multivalued: false
    alias: collection_date
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: date
    required: true
  neg_cont_type:
    name: neg_cont_type
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    slot_uri: MIXS:0001321
    multivalued: false
    alias: neg_cont_type
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: neg_cont_type_enum
    recommended: true
  pos_cont_type:
    name: pos_cont_type
    description: The substance, mixture, product, or apparatus used to verify that
      a process which is part of an investigation delivers a true positive.
    title: positive control type
    from_schema: http://w3id.org/mixs
    is_a: investigation field
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    multivalued: false
    alias: pos_cont_type
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  env_broad_scale:
    name: env_broad_scale
    description: 'Report the major environmental system the sample or specimen came
      from. The system(s) identified should have a coarse spatial grain, to provide
      the general environmental context of where the sampling was done (e.g. in the
      desert or a rainforest). We recommend using subclasses of EnvO’s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.
      EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: broad-scale environmental context
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000012
    multivalued: false
    alias: env_broad_scale
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  env_local_scale:
    name: env_local_scale
    description: 'Report the entity or entities which are in the sample or specimen’s
      local vicinity and which you believe have significant causal influences on your
      sample or specimen. We recommend using EnvO terms which are of smaller spatial
      grain than your entry for env_broad_scale. Terms, such as anatomical sites,
      from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON)
      are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS.'
    title: local environmental context
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000013
    multivalued: false
    alias: env_local_scale
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  env_medium:
    name: env_medium
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top).'
    title: environmental medium
    from_schema: http://w3id.org/mixs
    is_a: environment field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000014
    multivalued: false
    alias: env_medium
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    - built environment
    - air
    - agriculture
    range: string
    required: true
  subspecf_gen_lin:
    name: subspecf_gen_lin
    description: Information about the genetic distinctness of the sequenced organism
      below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any
      relevant genetic typing schemes like Group I plasmid. Subspecies should not
      be recorded in this term, but in the NCBI taxonomy. Supply both the lineage
      name and the lineage rank separated by a colon, e.g., biovar:abc123.
    title: subspecific genetic lineage
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0000020
    multivalued: false
    alias: subspecf_gen_lin
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMARKS survey
    range: string
    recommended: true
  extrachrom_elements:
    name: extrachrom_elements
    description: Do plasmids exist of significant phenotypic consequence (e.g. ones
      that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids
      (borrelia has 15+ plasmids)
    title: extrachromosomal elements
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000023
    multivalued: false
    alias: extrachrom_elements
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS org
    - MIMARKS survey
    range: integer
    required: false
  source_mat_id:
    name: source_mat_id
    description: A unique identifier assigned to a material sample (as defined by
      http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
      digital record of a material sample) used for extracting nucleic acids, and
      subsequent sequencing. The identifier can refer either to the original material
      collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
      /bio_material, or /culture_collection may or may not share the same value as
      the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
      may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
      sampled tissue with the same identifier. However, the /culture_collection qualifier
      may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
      would refer to an identifier from some derived culture from which the nucleic
      acids were extracted (e.g. xatc123 or ark:/2154/R2).
    title: source material identifiers
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000026
    multivalued: false
    alias: source_mat_id
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
    recommended: true
  biotic_relationship:
    name: biotic_relationship
    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
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000028
    multivalued: false
    alias: biotic_relationship
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS virus
    - MIMARKS survey
    - MIUVIG
    range: biotic_relationship_enum
    required: false
    recommended: true
  trophic_level:
    name: trophic_level
    description: Trophic levels are the feeding position in a food chain. Microbes
      can be a range of producers (e.g. chemolithotroph)
    title: trophic level
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000032
    multivalued: false
    alias: trophic_level
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIMARKS survey
    range: trophic_level_enum
    required: false
    recommended: true
  rel_to_oxygen:
    name: rel_to_oxygen
    description: Is this organism an aerobe, anaerobe? Please note that aerobic and
      anaerobic are valid descriptors for microbial environments
    title: relationship to oxygen
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000015
    multivalued: false
    alias: rel_to_oxygen
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS bacteria
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    range: rel_to_oxygen_enum
    recommended: true
  isol_growth_condt:
    name: isol_growth_condt
    description: Publication reference in the form of pubmed ID (pmid), digital object
      identifier (doi) or url for isolation and growth condition specifications of
      the organism/material
    title: isolation and growth condition
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000003
    multivalued: false
    alias: isol_growth_condt
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMARKS survey
    range: string
    required: true
  samp_collec_device:
    name: samp_collec_device
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
    title: sample collection device
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    multivalued: false
    alias: samp_collec_device
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  samp_collec_method:
    name: samp_collec_method
    description: The method employed for collecting the sample.
    title: sample collection method
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001225
    multivalued: false
    alias: samp_collec_method
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
  samp_mat_process:
    name: samp_mat_process
    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
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    string_serialization: '{text}'
    slot_uri: MIXS:0000016
    multivalued: false
    alias: samp_mat_process
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
    recommended: true
  samp_size:
    name: samp_size
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected.
    title: amount or size of sample collected
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000001
    multivalued: false
    alias: samp_size
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: quantity value
    required: false
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    description: 'Volume (ml) or mass (g) of total collected sample processed for
      DNA extraction. Note: total sample collected should be entered under the term
      Sample Size (MIXS:0000001).'
    title: sample volume or weight for DNA extraction
    from_schema: http://w3id.org/mixs
    is_a: nucleic acid sequence source field
    slot_uri: MIXS:0000111
    multivalued: false
    alias: samp_vol_we_dna_ext
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: quantity value
    required: false
  nucl_acid_ext:
    name: nucl_acid_ext
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the material separation to recover
      the nucleic acid fraction from a sample
    title: nucleic acid extraction
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000037
    multivalued: false
    alias: nucl_acid_ext
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
    recommended: true
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000038
    multivalued: false
    alias: nucl_acid_amp
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
    recommended: true
  target_gene:
    name: target_gene
    description: Targeted gene or locus name for marker gene studies
    title: target gene
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000044
    multivalued: false
    alias: target_gene
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    required: true
  target_subfragment:
    name: target_subfragment
    description: Name of subfragment of a gene or locus. Important to e.g. identify
      special regions on marker genes like V6 on 16S rRNA
    title: target subfragment
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{text}'
    slot_uri: MIXS:0000045
    multivalued: false
    alias: target_subfragment
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    required: true
    recommended: true
  pcr_primers:
    name: pcr_primers
    description: PCR primers that were used to amplify the sequence of the targeted
      gene, locus or subfragment. This field should contain all the primers used for
      a single PCR reaction if multiple forward or reverse primers are present in
      a single PCR reaction. The primer sequence should be reported in uppercase letters
    title: pcr primers
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: FWD:{dna};REV:{dna}
    slot_uri: MIXS:0000046
    multivalued: false
    alias: pcr_primers
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    required: true
    recommended: true
  pcr_cond:
    name: pcr_cond
    description: Description of reaction conditions and components of PCR in the form
      of 'initial denaturation:94degC_1.5min; annealing=...'
    title: pcr conditions
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
      elongation:degrees_minutes;total cycles
    slot_uri: MIXS:0000049
    multivalued: false
    alias: pcr_cond
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    required: true
    recommended: true
  seq_meth:
    name: seq_meth
    description: Sequencing machine used. Where possible the term should be taken
      from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).
    title: sequencing method
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000050
    multivalued: false
    alias: seq_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: true
  seq_quality_check:
    name: seq_quality_check
    description: Indicate if the sequence has been called by automatic systems (none)
      or undergone a manual editing procedure (e.g. by inspecting the raw data or
      chromatograms). Applied only for sequences that are not submitted to SRA,ENA
      or DRA
    title: sequence quality check
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '[none|manually edited]'
    slot_uri: MIXS:0000051
    multivalued: false
    alias: seq_quality_check
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    required: false
    recommended: true
  chimera_check:
    name: chimera_check
    description: Tool(s) used for chimera checking, including version number and parameters,
      to discover and remove chimeric sequences. A chimeric sequence is comprised
      of two or more phylogenetically distinct parent sequences.
    title: chimera check software
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{software};{version};{parameters}'
    slot_uri: MIXS:0000052
    multivalued: false
    alias: chimera_check
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIMARKS specimen
    - MIMARKS survey
    range: string
    required: true
    recommended: true
  associated resource:
    name: associated resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence.
    title: relevant electronic resources
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID} | {DOI} | {URL}'
    slot_uri: MIXS:0000091
    multivalued: false
    alias: associated_resource
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    recommended: true
  sop:
    name: sop
    description: Standard operating procedures used in assembly and/or annotation
      of genomes, metagenomes or environmental sequences
    title: relevant standard operating procedures
    from_schema: http://w3id.org/mixs
    is_a: sequencing field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    multivalued: false
    alias: sop
    owner: agriculture MIMARKS survey
    domain_of:
    - core
    - MIGS eukaryote
    - MIGS bacteria
    - MIGS plant
    - MIGS virus
    - MIGS org
    - MIMS
    - MIMARKS specimen
    - MIMARKS survey
    - MISAG
    - MIMAG
    - MIUVIG
    range: string
    required: false
    recommended: true
  depth:
    name: depth
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: The vertical distance below local surface, e.g. for sediment or soil
      samples depth is measured from sediment or soil surface, respectively. Depth
      can be reported as an interval for subsurface samples.
    title: depth
    examples:
    - value: 10 meter
    from_schema: http://w3id.org/mixs
    aliases:
    - depth
    is_a: environment field
    slot_uri: MIXS:0000018
    multivalued: false
    alias: depth
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
  alt:
    name: alt
    annotations:
      expected_value:
        tag: expected_value
        value: measurement value
    description: Altitude is a term used to identify heights of objects such as airplanes,
      space shuttles, rockets, atmospheric balloons and heights of places such as
      atmospheric layers and clouds. It is used to measure the height of an object
      which is above the earth's surface. In this context, the altitude measurement
      is the vertical distance between the earth's surface above sea level and the
      sampled position in the air
    title: altitude
    examples:
    - value: 100 meter
    from_schema: http://w3id.org/mixs
    aliases:
    - altitude
    is_a: environment field
    slot_uri: MIXS:0000094
    multivalued: false
    alias: alt
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
  elev:
    name: elev
    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
    from_schema: http://w3id.org/mixs
    is_a: environment field
    slot_uri: MIXS:0000093
    multivalued: false
    alias: elev
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
    required: false
  temp:
    name: temp
    description: Temperature of the sample at the time of sampling.
    title: temperature
    from_schema: http://w3id.org/mixs
    is_a: environment field
    slot_uri: MIXS:0000113
    multivalued: false
    alias: temp
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - core
    - built environment
    - air
    - agriculture
    range: quantity value
    required: true
  plant_growth_med:
    name: plant_growth_med
    description: Specification of the media for growing the plants or tissue cultured
      samples, e.g. soil, aeroponic, hydroponic, in vitro solid culture medium, in
      vitro liquid culture medium. Recommended value is a specific value from EO:plant
      growth medium (follow this link for terms http://purl.obolibrary.org/obo/EO_0007147)
      or other controlled vocabulary
    title: plant growth medium
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001057
    multivalued: false
    alias: plant_growth_med
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - food-farm environment
    - agriculture
    range: plant_growth_med_enum
    required: false
  soil_horizon:
    name: soil_horizon
    description: Specific layer in the land area which measures parallel to the soil
      surface and possesses physical characteristics which differ from the layers
      above and beneath
    title: soil horizon
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001082
    multivalued: false
    alias: soil_horizon
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: soil_horizon_enum
    required: false
  photosynt_activ:
    name: photosynt_activ
    description: Measurement of photosythetic activity (i.e. leaf gas exchange / chlorophyll
      fluorescence emissions / reflectance / transpiration) Please also include the
      term method term detailing the method of activity measurement.
    title: photosynthetic activity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001296
    multivalued: true
    alias: photosynt_activ
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: quantity value
    required: false
  photosynt_activ_meth:
    name: photosynt_activ_meth
    description: Reference or method used in measurement of photosythetic activity
    title: photosynthetic activity method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001336
    multivalued: true
    alias: photosynt_activ_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: string
    required: false
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample.
    title: sample collection method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001225
    multivalued: false
    alias: samp_collect_method
    owner: agriculture MIMARKS survey
    domain_of:
    - food-food production facility
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  enrichment_protocol:
    name: enrichment_protocol
    description: The microbiological workflow or protocol followed to test for the
      presence or enumeration of the target microbial analyte(s). Please provide a
      PubMed or DOI reference for published protocols.
    title: enrichment protocol
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0001177
    multivalued: false
    alias: enrichment_protocol
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  library_prep_kit:
    name: library_prep_kit
    description: Packaged kits (containing adapters, indexes, enzymes, buffers etc.),
      tailored for specific sequencing workflows, which allow the simplified preparation
      of sequencing-ready libraries for small genomes, amplicons, and plasmids.
    title: library preparation kit
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001145
    multivalued: false
    alias: library_prep_kit
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  sequencing_location:
    name: sequencing_location
    description: The location the sequencing run was performed. Indicate the name
      of the lab or core facility where samples were sequenced.
    title: sequencing location
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001156
    multivalued: false
    alias: sequencing_location
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  soil_temp:
    name: soil_temp
    description: Temperature of soil at the time of sampling.
    title: soil temperature
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{float}{unit}'
    slot_uri: MIXS:0001163
    multivalued: true
    alias: soil_temp
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  soil_pH:
    name: soil_pH
    description: The pH of soil at time of sampling.
    title: soil pH
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001160
    multivalued: false
    alias: soil_pH
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: double
    required: false
  soil_conductivity:
    name: soil_conductivity
    description: Conductivity of soil at time of sampling.
    title: soil conductivity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001158
    multivalued: false
    alias: soil_conductivity
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  rel_location:
    name: rel_location
    description: Location of sampled soil to other parts of the farm e.g. under crop
      plant, near irrigation ditch, from the dirt road.
    title: relative location of sample
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001161
    multivalued: false
    alias: rel_location
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  soil_cover:
    name: soil_cover
    description: Description of the material covering the sampled soil. This field
      accepts terms under ENVO:00010483, environmental material.
    title: soil cover
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001159
    multivalued: false
    alias: soil_cover
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  porosity:
    name: porosity
    description: Porosity of deposited sediment is volume of voids divided by the
      total volume of sample
    title: porosity
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{float} - {float} {unit}'
    slot_uri: MIXS:0000211
    multivalued: false
    alias: porosity
    owner: agriculture MIMARKS survey
    domain_of:
    - sediment
    - hydrocarbon resources-cores
    - agriculture
    range: string
    required: false
  texture:
    name: texture
    description: The relative proportion of different grain sizes of mineral particles
      in a soil, as described using a standard system; express as % sand (50 um to
      2 mm), silt (2 um to 50 um), and clay (<2 um) with textural name (e.g., silty
      clay loam) optional.
    title: texture
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000335
    multivalued: false
    alias: texture
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: quantity value
    required: false
  texture_meth:
    name: texture_meth
    description: Reference or method used in determining soil texture.
    title: texture method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000336
    multivalued: false
    alias: texture_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: string
    required: false
  host_symbiont:
    name: host_symbiont
    description: The taxonomic name of the organism(s) found living in mutualistic,
      commensalistic, or parasitic symbiosis with the specific host.
    title: observed host symbionts
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001298
    multivalued: true
    alias: host_symbiont
    owner: agriculture MIMARKS survey
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - agriculture
    range: string
    required: false
  pres_animal_insect:
    name: pres_animal_insect
    description: The type and number of animals or insects present in the sampling
      space.
    title: presence of pets, animals, or insects
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000819
    multivalued: false
    alias: pres_animal_insect
    owner: agriculture MIMARKS survey
    domain_of:
    - built environment
    - agriculture
    range: string
    required: false
    pattern: ^(cat|dog|rodent|snake|other);\d+$
  plant_water_method:
    name: plant_water_method
    description: Description of the equipment or method used to distribute water to
      crops. This field accepts termed listed under irrigation process (http://purl.obolibrary.org/obo/AGRO_00000006).
      Multiple terms can be separated by pipes.
    title: plant water delivery method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001111
    multivalued: false
    alias: plant_water_method
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  anim_water_method:
    name: anim_water_method
    description: Description of the equipment or method used to distribute water to
      livestock. This field accepts termed listed under water delivery equipment (http://opendata.inra.fr/EOL/EOL_0001653).
      Multiple terms can be separated by pipes.
    title: animal water delivery method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001115
    multivalued: true
    alias: anim_water_method
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  farm_water_source:
    name: farm_water_source
    description: Source of water used on the farm for irrigation of crops or watering
      of livestock.
    title: farm watering water source
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001110
    multivalued: true
    alias: farm_water_source
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: farm_water_source_enum
    required: false
  water_source_shared:
    name: water_source_shared
    description: Other users sharing access to the same water source. Multiple terms
      can be separated by one or more pipes.
    title: water source shared
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001176
    multivalued: true
    alias: water_source_shared
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: water_source_shared_enum
    required: false
  water_pH:
    name: water_pH
    description: pH measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid.
    title: water pH
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001175
    multivalued: false
    alias: water_pH
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: double
    required: false
  season:
    name: season
    description: The season when sampling occurred. Any of the four periods into which
      the year is divided by the equinoxes and solstices. This field accepts terms
      listed under season (http://purl.obolibrary.org/obo/NCIT_C94729).
    title: season
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000829
    multivalued: false
    alias: season
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - built environment
    - agriculture
    range: string
    required: false
  solar_irradiance:
    name: solar_irradiance
    description: The amount of solar energy that arrives at a specific area of a surface
      during a specific time interval
    title: solar irradiance
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000112
    multivalued: false
    alias: solar_irradiance
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - air
    - agriculture
    range: quantity value
    required: false
  crop_yield:
    name: crop_yield
    description: Amount of crop produced per unit or area of land.
    title: crop yield
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{float}{unit}'
    slot_uri: MIXS:0001116
    multivalued: false
    alias: crop_yield
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  season_humidity:
    name: season_humidity
    description: Average humidity of the region throughout the growing season.
    title: mean seasonal humidity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001148
    multivalued: false
    alias: season_humidity
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  humidity:
    name: humidity
    description: Amount of water vapour in the air, at the time of sampling
    title: humidity
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000100
    multivalued: false
    alias: humidity
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - air
    - agriculture
    range: quantity value
    required: false
  adjacent_environment:
    name: adjacent_environment
    description: Description of the environmental system or features that are adjacent
      to the sampling site. This field accepts terms under ecosystem (http://purl.obolibrary.org/obo/ENVO_01001110)
      and human construction (http://purl.obolibrary.org/obo/ENVO_00000070). Multiple
      terms can be separated by pipes.
    title: environment adjacent to site
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel}{[termID]}'
    slot_uri: MIXS:0001121
    multivalued: true
    alias: adjacent_environment
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  chem_administration:
    name: chem_administration
    description: List of chemical compounds administered to the host or site where
      sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
      include multiple compounds. For chemical entities of biological interest ontology
      (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
    title: chemical administration
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]};{timestamp}'
    slot_uri: MIXS:0000751
    multivalued: true
    alias: chem_administration
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - air
    - agriculture
    range: string
    required: true
  food_prod:
    name: food_prod
    description: Descriptors of the food production system or of the agricultural
      environment and growing conditions related to the farm production system, such
      as wild caught, organic, free-range, industrial, dairy, beef,  domestic or cultivated
      food production. This field accepts terms listed under food production (http://purl.obolibrary.org/obo/FOODON_03530206).
      Multiple terms may apply and can be separated by pipes.
    title: food production system characteristics
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001211
    multivalued: true
    alias: food_prod
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  lot_number:
    name: lot_number
    description: 'A distinctive alpha-numeric identification code assigned by the
      manufacturer or distributor to a specific quantity of manufactured material
      or product within a batch. Synonym: Batch Number.  The submitter should provide
      lot number of the item followed by the item name for which the lot number was
      provided.'
    title: lot number
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{integer}, {text}'
    slot_uri: MIXS:0001147
    multivalued: true
    alias: lot_number
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  fertilizer_admin:
    name: fertilizer_admin
    description: Type of fertilizer or amendment added to the soil or water for the
      purpose of improving substrate health and quality for plant growth. This field
      accepts terms listed under agronomic fertilizer (http://purl.obolibrary.org/obo/AGRO_00002062).
      Multiple terms may apply and can be separated by pipes, listing in reverse chronological
      order.
    title: fertilizer administration
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001127
    multivalued: false
    alias: fertilizer_admin
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  samp_stor_temp:
    name: samp_stor_temp
    description: Temperature at which sample was stored, e.g. -80 degree Celsius.
    title: sample storage temperature
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000110
    multivalued: false
    alias: samp_stor_temp
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: quantity value
    required: false
  food_trav_mode:
    name: food_trav_mode
    description: A descriptor for the method of movement of food commodity along the
      food distribution system.  This field accepts terms listed under travel mode
      (http://purl.obolibrary.org/obo/GENEPIO_0001064). If the proper descrptor is
      not listed please use text to describe the mode of travel. Multiple terms can
      be separated by one or more pipes.
    title: food shipping transportation method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001137
    multivalued: true
    alias: food_trav_mode
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  food_trav_vehic:
    name: food_trav_vehic
    description: A descriptor for the mobile machine which is used to transport food
      commodities along the food distribution system.  This field accepts terms listed
      under vehicle (http://purl.obolibrary.org/obo/ENVO_01000604). If the proper
      descrptor is not listed please use text to describe the mode of travel. Multiple
      terms can be separated by one or more pipes.
    title: Food shipping transportation vehicle
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}|{termLabel} {[termID]}'
    slot_uri: MIXS:0001138
    multivalued: true
    alias: food_trav_vehic
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  farm_equip_san:
    name: farm_equip_san
    description: Method used to sanitize growing and harvesting equipment. This can
      including type and concentration of sanitizing solution.  Multiple terms can
      be separated by one or more pipes.
    title: farm equipment sanitization
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text} {float} {unit}'
    slot_uri: MIXS:0001124
    multivalued: true
    alias: farm_equip_san
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  farm_equip:
    name: farm_equip
    description: List of equipment used for planting, fertilization, harvesting, irrigation,
      land levelling, residue management, weeding or transplanting during the growing
      season.  This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416).
      Multiple terms can be separated by pipes.
    title: farm equipment used
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001126
    multivalued: true
    alias: farm_equip
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  farm_equip_shared:
    name: farm_equip_shared
    description: List of planting, growing or harvesting equipment shared with other
      farms. This field accepts terms listed under agricultural implement (http://purl.obolibrary.org/obo/AGRO_00000416).
      Multiple terms can be separated by pipes.
    title: equipment shared with other farms
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001123
    multivalued: true
    alias: farm_equip_shared
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  food_harvest_proc:
    name: food_harvest_proc
    description: A harvesting process is a process which takes in some food material
      from an individual or community of plant or animal organisms in a given context
      and time, and outputs a precursor or consumable food product. This may include
      a part of an organism or the whole, and may involve killing the organism.
    title: Food harvesting process
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001133
    multivalued: true
    alias: food_harvest_proc
    owner: agriculture MIMARKS survey
    domain_of:
    - food-farm environment
    - agriculture
    range: string
    required: false
  plant_struc:
    name: plant_struc
    description: Name of plant structure the sample was obtained from; for Plant Ontology
      (PO) (v releases/2017-12-14) terms, see http://purl.bioontology.org/ontology/PO,
      e.g. petiole epidermis (PO_0000051). If an individual flower is sampled, the
      sex of it can be recorded here.
    title: plant structure
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0001060
    multivalued: false
    alias: plant_struc
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  host_dry_mass:
    name: host_dry_mass
    description: Measurement of dry mass
    title: host dry mass
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000257
    multivalued: false
    alias: host_dry_mass
    owner: agriculture MIMARKS survey
    domain_of:
    - symbiont-associated
    - plant-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  ances_data:
    name: ances_data
    description: Information about either pedigree or other ancestral information
      description (e.g. parental variety in case of mutant or selection), e.g. A/3*B
      (meaning [(A x B) x B] x B)
    title: ancestral data
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000247
    multivalued: false
    alias: ances_data
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: string
    required: false
  genetic_mod:
    name: genetic_mod
    description: Genetic modifications of the genome of an organism, which may occur
      naturally by spontaneous mutation, or be introduced by some experimental means,
      e.g. specification of a transgene or the gene knocked-out or details of transient
      transfection
    title: genetic modification
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}|{text}'
    slot_uri: MIXS:0000859
    multivalued: false
    alias: genetic_mod
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - agriculture
    range: string
    required: false
  Food_Product_type:
    name: Food_Product_type
    description: new food product categories and food products themselves
    title: Foodon product type
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001184
    multivalued: false
    alias: Food_Product_type
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: string
    required: false
  Food_source:
    name: Food_source
    description: Type of plant or animal from which the food product or its major
      ingredient is derived or a chemical food source [FDA CFSAN 1995].
    title: Food source
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001139
    multivalued: false
    alias: Food_source
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: string
    required: true
  spikein_strain:
    name: spikein_strain
    description: Taxonomic information about the spike-in organism(s) at the strain
      level. This field accepts terms under organism (http://purl.obolibrary.org/obo/NCIT_C14250).
      This field also accepts identification numbers from NCBI under https://www.ncbi.nlm.nih.gov/taxonomy.
      Multiple terms can be separated by pipes.
    title: spike-in microbial strain
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}|{integer}'
    slot_uri: MIXS:0001170
    multivalued: true
    alias: spikein_strain
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  organism_count:
    name: organism_count
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000103
    multivalued: true
    alias: organism_count
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - built environment
    - air
    - agriculture
    range: organism_count_enum
    required: false
  size_frac_low:
    name: size_frac_low
    description: Refers to the mesh/pore size used to pre-filter/pre-sort the sample.
      Materials larger than the size threshold are excluded from the sample
    title: size-fraction lower threshold
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000735
    multivalued: false
    alias: size_frac_low
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  size_frac_up:
    name: size_frac_up
    description: Refers to the mesh/pore size used to retain the sample. Materials
      smaller than the size threshold are excluded from the sample
    title: size-fraction upper threshold
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000736
    multivalued: false
    alias: size_frac_up
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  cult_isol_date:
    name: cult_isol_date
    description: A culture isolation date is a date-time entity marking the end of
      a process in which a sample yields a positive result for the target microbial
      analyte(s) in the form of an isolated colony or colonies.
    title: culture isolation date
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001181
    multivalued: false
    alias: cult_isol_date
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: date
    required: false
  samp_pooling:
    name: samp_pooling
    description: Physical combination of several instances of like material, e.g.
      RNA extracted from samples or dishes of cell cultures into one big aliquot of
      cells. Please provide a short description of the samples that were pooled.
    title: sample pooling
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001153
    multivalued: true
    alias: samp_pooling
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: false
  root_med_macronutr:
    name: root_med_macronutr
    description: Measurement of the culture rooting medium macronutrients (N,P, K,
      Ca, Mg, S); e.g. KH2PO4 (170 mg/L).
    title: rooting medium macronutrients
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000578
    multivalued: false
    alias: root_med_macronutr
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - food-farm environment
    - agriculture
    range: string
    required: false
  root_med_carbon:
    name: root_med_carbon
    description: Source of organic carbon in the culture rooting medium; e.g. sucrose.
    title: rooting medium carbon
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000577
    multivalued: false
    alias: root_med_carbon
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - food-farm environment
    - agriculture
    range: string
    required: false
  root_med_ph:
    name: root_med_ph
    description: pH measurement of the culture rooting medium; e.g. 5.5.
    title: rooting medium pH
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001062
    multivalued: false
    alias: root_med_ph
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - food-farm environment
    - agriculture
    range: double
    required: false
  soil_depth:
    name: soil_depth
    description: The vertical distance below local surface, e.g. For sediment or soil
      samples depth is measured from sediment or soil surface, respectively. Depth
      can be reported as an interval for subsurface samples.
    title: soil depth
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000018
    multivalued: false
    alias: soil_depth
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: quantity value
    required: false
  water_temp_regm:
    name: water_temp_regm
    description: Information about treatment involving an exposure to water with varying
      degree of temperature, treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment; can include multiple regimens
    title: water temperature regimen
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000590
    multivalued: true
    alias: water_temp_regm
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  watering_regm:
    name: watering_regm
    description: Information about treatment involving an exposure to watering frequencies,
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple regimens
    title: watering regimen
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000591
    multivalued: true
    alias: watering_regm
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  standing_water_regm:
    name: standing_water_regm
    description: Treatment involving an exposure to standing water during a plant's
      life span, types can be flood water or standing water, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple regimens
    title: standing water regimen
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001069
    multivalued: true
    alias: standing_water_regm
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  gaseous_environment:
    name: gaseous_environment
    description: Use of conditions with differing gaseous environments; should include
      the name of gaseous compound, amount administered, treatment duration, interval
      and total experimental duration; can include multiple gaseous environment regimens
    title: gaseous environment
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000558
    multivalued: true
    alias: gaseous_environment
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  fungicide_regm:
    name: fungicide_regm
    description: Information about treatment involving use of fungicides; should include
      the name of fungicide, amount administered, treatment regimen including how
      many times the treatment was repeated, how long each treatment lasted, and the
      start and end time of the entire treatment; can include multiple fungicide regimens
    title: fungicide regimen
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000557
    multivalued: true
    alias: fungicide_regm
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  climate_environment:
    name: climate_environment
    description: Treatment involving an exposure to a particular climate; treatment
      regimen including how many times the treatment was repeated, how long each treatment
      lasted, and the start and end time of the entire treatment; can include multiple
      climates
    title: climate environment
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001040
    multivalued: true
    alias: climate_environment
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  herbicide_regm:
    name: herbicide_regm
    description: Information about treatment involving use of herbicides; information
      about treatment involving use of growth hormones; should include the name of
      herbicide, amount administered, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include multiple regimens
    title: herbicide regimen
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000561
    multivalued: true
    alias: herbicide_regm
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  non_mineral_nutr_regm:
    name: non_mineral_nutr_regm
    description: Information about treatment involving the exposure of plant to non-mineral
      nutrient such as oxygen, hydrogen or carbon; should include the name of non-mineral
      nutrient, amount administered, treatment regimen including how many times the
      treatment was repeated, how long each treatment lasted, and the start and end
      time of the entire treatment; can include multiple non-mineral nutrient regimens
    title: non-mineral nutrient regimen
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit};{period};{interval};{period}'
    slot_uri: MIXS:0000571
    multivalued: true
    alias: non_mineral_nutr_regm
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: string
    required: false
  pesticide_regm:
    name: pesticide_regm
    description: Information about treatment involving use of insecticides; should
      include the name of pesticide, amount administered, treatment regimen including
      how many times the treatment was repeated, how long each treatment lasted, and
      the start and end time of the entire treatment; can include multiple pesticide
      regimens
    title: pesticide regimen
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000573
    multivalued: true
    alias: pesticide_regm
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  ph_regm:
    name: ph_regm
    description: Information about treatment involving exposure of plants to varying
      levels of ph of the growth media, treatment regimen including how many times
      the treatment was repeated, how long each treatment lasted, and the start and
      end time of the entire treatment; can include multiple regimen
    title: pH regimen
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{float};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001056
    multivalued: true
    alias: ph_regm
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  salt_regm:
    name: salt_regm
    description: Information about treatment involving use of salts as supplement
      to liquid and soil growth media; should include the name of salt, amount administered,
      treatment regimen including how many times the treatment was repeated, how long
      each treatment lasted, and the start and end time of the entire treatment; can
      include multiple salt regimens
    title: salt regimen
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000582
    multivalued: true
    alias: salt_regm
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  season_environment:
    name: season_environment
    description: Treatment involving an exposure to a particular season (e.g. Winter,
      summer, rabi, rainy etc.), treatment regimen including how many times the treatment
      was repeated, how long each treatment lasted, and the start and end time of
      the entire treatment
    title: seasonal environment
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0001068
    multivalued: true
    alias: season_environment
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  perturbation:
    name: perturbation
    description: Type of perturbation, e.g. chemical administration, physical disturbance,
      etc., coupled with perturbation regimen including how many times the perturbation
      was repeated, how long each perturbation lasted, and the start and end time
      of the entire perturbation period; can include multiple perturbation types
    title: perturbation
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    multivalued: true
    alias: perturbation
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-farm environment
    - food-animal and animal feed
    - air
    - agriculture
    range: string
    required: false
  samp_store_dur:
    name: samp_store_dur
    description: Duration for which the sample was stored
    title: sample storage duration
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{duration}'
    slot_uri: MIXS:0000116
    multivalued: false
    alias: samp_store_dur
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - air
    - agriculture
    range: string
    required: true
  samp_store_loc:
    name: samp_store_loc
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000755
    multivalued: false
    alias: samp_store_loc
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - air
    - agriculture
    range: string
    required: true
  samp_collect_device:
    name: samp_collect_device
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).
    title: sample collection device
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}|{text}'
    slot_uri: MIXS:0000002
    multivalued: false
    alias: samp_collect_device
    owner: agriculture MIMARKS survey
    domain_of:
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - agriculture
    range: string
    required: true
  host_age:
    name: host_age
    description: Age of host at the time of sampling; relevant scale depends on species
      and study, e.g. Could be seconds for amoebae or centuries for trees
    title: host age
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000255
    multivalued: false
    alias: host_age
    owner: agriculture MIMARKS survey
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: true
  host_common_name:
    name: host_common_name
    description: Common name of the host.
    title: host common name
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000248
    multivalued: false
    alias: host_common_name
    owner: agriculture MIMARKS survey
    domain_of:
    - symbiont-associated
    - plant-associated
    - host-associated
    - agriculture
    range: string
    required: true
  host_genotype:
    name: host_genotype
    description: Observed genotype
    title: host genotype
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000365
    multivalued: false
    alias: host_genotype
    owner: agriculture MIMARKS survey
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: string
    required: true
  host_height:
    name: host_height
    description: The height of subject
    title: host height
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000264
    multivalued: false
    alias: host_height
    owner: agriculture MIMARKS survey
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: true
  host_subspecf_genlin:
    name: host_subspecf_genlin
    description: Information about the genetic distinctness of the host organism below
      the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar,
      or any relevant genetic typing schemes like Group I plasmid. Subspecies should
      not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage
      name and the lineage rank separated by a colon, e.g., biovar:abc123.
    title: host subspecific genetic lineage
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0001318
    multivalued: true
    alias: host_subspecf_genlin
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: string
    required: false
  host_length:
    name: host_length
    description: The length of subject
    title: host length
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000256
    multivalued: false
    alias: host_length
    owner: agriculture MIMARKS survey
    domain_of:
    - symbiont-associated
    - plant-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: true
  host_life_stage:
    name: host_life_stage
    description: Description of life stage of host
    title: host life stage
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000251
    multivalued: false
    alias: host_life_stage
    owner: agriculture MIMARKS survey
    domain_of:
    - symbiont-associated
    - plant-associated
    - host-associated
    - agriculture
    range: string
    required: true
  host_phenotype:
    name: host_phenotype
    description: Phenotype of human or other host. For phenotypic quality ontology
      (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato.
      For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
    title: host phenotype
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000874
    multivalued: false
    alias: host_phenotype
    owner: agriculture MIMARKS survey
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: string
    required: true
  host_taxid:
    name: host_taxid
    description: NCBI taxon id of the host, e.g. 9606
    title: host taxid
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{NCBI taxid}'
    slot_uri: MIXS:0000250
    multivalued: false
    alias: host_taxid
    owner: agriculture MIMARKS survey
    domain_of:
    - symbiont-associated
    - plant-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: string
    required: true
  host_tot_mass:
    name: host_tot_mass
    description: Total mass of the host at collection, the unit depends on host
    title: host total mass
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000263
    multivalued: false
    alias: host_tot_mass
    owner: agriculture MIMARKS survey
    domain_of:
    - symbiont-associated
    - plant-associated
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-farm environment
    - agriculture
    range: quantity value
    required: true
  plant_product:
    name: plant_product
    description: Substance produced by the plant, where the sample was obtained from
    title: plant product
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0001058
    multivalued: false
    alias: plant_product
    owner: agriculture MIMARKS survey
    domain_of:
    - plant-associated
    - agriculture
    range: string
    required: false
  oxy_stat_samp:
    name: oxy_stat_samp
    description: Oxygenation status of sample
    title: oxygenation status of sample
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000753
    multivalued: false
    alias: oxy_stat_samp
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - air
    - agriculture
    range: oxy_stat_samp_enum
    required: false
  assembly_quality:
    name: assembly_quality
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly quality
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{software};{version};{parameters}'
    slot_uri: MIXS:0000058
    multivalued: false
    alias: assembly_quality
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: string
    required: false
  url:
    name: url
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence.
    title: relevant electronic resources
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{URL}'
    slot_uri: MIXS:0000091
    multivalued: true
    alias: url
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: string
    required: false
  fao_class:
    name: fao_class
    description: Soil classification from the FAO World Reference Database for Soil
      Resources. The list can be found at http://www.fao.org/nr/land/sols/soil/wrb-soil-maps/reference-groups
    title: soil_taxonomic/FAO classification
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001083
    multivalued: false
    alias: fao_class
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: fao_class_enum
    required: false
  local_class:
    name: local_class
    description: Soil classification based on local soil classification system
    title: soil_taxonomic/local classification
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000330
    multivalued: false
    alias: local_class
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: string
    required: false
  local_class_meth:
    name: local_class_meth
    description: Reference or method used in determining the local soil classification
    title: soil_taxonomic/local classification method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000331
    multivalued: false
    alias: local_class_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: string
    required: false
  soil_type:
    name: soil_type
    description: Description of the soil type or classification. This field accepts
      terms under soil (http://purl.obolibrary.org/obo/ENVO_00001998).  Multiple terms
      can be separated by pipes.
    title: soil type
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{termLabel} {[termID]}'
    slot_uri: MIXS:0000332
    multivalued: false
    alias: soil_type
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - food-farm environment
    - agriculture
    range: string
    required: true
  soil_type_meth:
    name: soil_type_meth
    description: Reference or method used in determining soil series name or other
      lower-level classification
    title: soil type method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000334
    multivalued: false
    alias: soil_type_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - food-farm environment
    - agriculture
    range: string
    required: true
  horizon:
    name: horizon
    description: Specific layer in the land area which measures parallel to the soil
      surface and possesses physical characteristics which differ from the layers
      above and beneath
    title: horizon
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001082
    multivalued: false
    alias: horizon
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: horizon_enum
    required: false
  horizon_meth:
    name: horizon_meth
    description: Reference or method used in determining the horizon
    title: soil horizon method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000321
    multivalued: false
    alias: horizon_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: string
    required: false
  link_class_info:
    name: link_class_info
    description: Link to digitized soil maps or other soil classification information
    title: link to classification information
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000329
    multivalued: false
    alias: link_class_info
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: string
    required: false
  previous_land_use:
    name: previous_land_use
    description: Previous land use and dates
    title: history/previous land use
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{timestamp}'
    slot_uri: MIXS:0000315
    multivalued: false
    alias: previous_land_use
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - food-farm environment
    - agriculture
    range: string
    required: false
  previous_land_use_meth:
    name: previous_land_use_meth
    description: Reference or method used in determining previous land use and dates
    title: history/previous land use method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID|DOI|URL}'
    slot_uri: MIXS:0000316
    multivalued: false
    alias: previous_land_use_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: string
    required: false
  crop_rotation:
    name: crop_rotation
    description: Whether or not crop is rotated, and if yes, rotation schedule
    title: history/crop rotation
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{boolean};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000318
    multivalued: false
    alias: crop_rotation
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - food-farm environment
    - agriculture
    range: string
    required: false
  agrochem_addition:
    name: agrochem_addition
    description: Addition of fertilizers, pesticides, etc. - amount and time of applications
    title: history/agrochemical additions
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit};{timestamp}'
    slot_uri: MIXS:0000639
    multivalued: true
    alias: agrochem_addition
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: string
    required: false
  tillage:
    name: tillage
    description: Note method(s) used for tilling
    title: history/tillage
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001081
    multivalued: true
    alias: tillage
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - food-farm environment
    - agriculture
    range: tillage_enum
    required: false
  fire:
    name: fire
    description: Historical and/or physical evidence of fire
    title: history/fire
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001086
    multivalued: false
    alias: fire
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: date
    required: false
  flooding:
    name: flooding
    description: Historical and/or physical evidence of flooding
    title: history/flooding
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000319
    multivalued: false
    alias: flooding
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: date
    required: false
  extreme_event:
    name: extreme_event
    description: Unusual physical events that may have affected microbial populations
    title: history/extreme events
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000320
    multivalued: false
    alias: extreme_event
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: date
    required: false
  link_climate_info:
    name: link_climate_info
    description: Link to climate resource
    title: link to climate information
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000328
    multivalued: false
    alias: link_climate_info
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: string
    required: false
  annual_temp:
    name: annual_temp
    description: Mean annual temperature
    title: mean annual temperature
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000642
    multivalued: false
    alias: annual_temp
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: quantity value
    required: false
  season_temp:
    name: season_temp
    description: Mean seasonal temperature
    title: mean seasonal temperature
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000643
    multivalued: false
    alias: season_temp
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  annual_precpt:
    name: annual_precpt
    description: The average of all annual precipitation values known, or an estimated
      equivalent value derived by such methods as regional indexes or Isohyetal maps.
    title: mean annual precipitation
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000644
    multivalued: false
    alias: annual_precpt
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: quantity value
    required: false
  season_precpt:
    name: season_precpt
    description: The average of all seasonal precipitation values known, or an estimated
      equivalent value derived by such methods as regional indexes or Isohyetal maps.
    title: mean seasonal precipitation
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000645
    multivalued: false
    alias: season_precpt
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  cur_land_use:
    name: cur_land_use
    description: Present state of sample site
    title: current land use
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001080
    multivalued: false
    alias: cur_land_use
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: cur_land_use_enum
    required: false
  slope_gradient:
    name: slope_gradient
    description: Commonly called 'slope'. The angle between ground surface and a horizontal
      line (in percent). This is the direction that overland water would flow. This
      measure is usually taken with a hand level meter or clinometer
    title: slope gradient
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000646
    multivalued: false
    alias: slope_gradient
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: quantity value
    required: false
  slope_aspect:
    name: slope_aspect
    description: The direction a slope faces. While looking down a slope use a compass
      to record the direction you are facing (direction or degrees); e.g., nw or 315
      degrees. This measure provides an indication of sun and wind exposure that will
      influence soil temperature and evapotranspiration.
    title: slope aspect
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000647
    multivalued: false
    alias: slope_aspect
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: quantity value
    required: false
  profile_position:
    name: profile_position
    description: Cross-sectional position in the hillslope where sample was collected.sample
      area position in relation to surrounding areas
    title: profile position
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001084
    multivalued: false
    alias: profile_position
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: profile_position_enum
    required: false
  drainage_class:
    name: drainage_class
    description: Drainage classification from a standard system such as the USDA system
    title: drainage classification
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0001085
    multivalued: false
    alias: drainage_class
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: drainage_class_enum
    required: false
  store_cond:
    name: store_cond
    description: Explain how and for how long the soil sample was stored before DNA
      extraction (fresh/frozen/other).
    title: storage conditions
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{duration}'
    slot_uri: MIXS:0000327
    multivalued: false
    alias: store_cond
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: string
    required: true
  ph_meth:
    name: ph_meth
    description: Reference or method used in determining ph
    title: pH method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0001106
    multivalued: false
    alias: ph_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - food-farm environment
    - agriculture
    range: string
    required: false
  cur_vegetation:
    name: cur_vegetation
    description: Vegetation classification from one or more standard classification
      systems, or agricultural crop
    title: current vegetation
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text}'
    slot_uri: MIXS:0000312
    multivalued: false
    alias: cur_vegetation
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: string
    required: false
  cur_vegetation_meth:
    name: cur_vegetation_meth
    description: Reference or method used in vegetation classification
    title: current vegetation method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000314
    multivalued: false
    alias: cur_vegetation_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: string
    required: false
  tot_org_carb:
    name: tot_org_carb
    description: 'Definition for soil: total organic carbon content of the soil, definition
      otherwise: total organic carbon content'
    title: total organic carbon
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000533
    multivalued: false
    alias: tot_org_carb
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - sediment
    - microbial mat_biofilm
    - food-farm environment
    - agriculture
    range: quantity value
    required: false
  tot_org_c_meth:
    name: tot_org_c_meth
    description: Reference or method used in determining total organic carbon
    title: total organic carbon method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000337
    multivalued: false
    alias: tot_org_c_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - food-farm environment
    - agriculture
    range: string
    required: false
  tot_nitro:
    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'
    title: total nitrogen concentration
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000102
    multivalued: false
    alias: tot_nitro
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - agriculture
    range: quantity value
    required: false
  tot_n_meth:
    name: tot_n_meth
    description: Reference or method used in determining the total nitrogen
    title: total nitrogen method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID|DOI|URL}'
    slot_uri: MIXS:0000338
    multivalued: false
    alias: tot_n_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: string
    required: false
  microbial_biomass:
    name: microbial_biomass
    description: The part of the organic matter in the soil that constitutes living
      microorganisms smaller than 5-10 micrometer. If you keep this, you would need
      to have correction factors used for conversion to the final units
    title: microbial biomass
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000650
    multivalued: false
    alias: microbial_biomass
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: quantity value
    required: true
  microbial_biomass_meth:
    name: microbial_biomass_meth
    description: Reference or method used in determining microbial biomass
    title: microbial biomass method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID|DOI|URL}'
    slot_uri: MIXS:0000339
    multivalued: false
    alias: microbial_biomass_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: string
    required: true
  heavy_metals_meth:
    name: heavy_metals_meth
    description: Reference or method used in determining heavy metals
    title: extreme_unusual_properties/heavy metals method
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000343
    multivalued: false
    alias: heavy_metals_meth
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: string
    required: false
  tot_car:
    name: tot_car
    description: Total carbon content
    title: total carbon
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000525
    multivalued: false
    alias: tot_car
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: quantity value
    required: false
  tot_phos:
    name: tot_phos
    description: Total amount or concentration of phosphate
    title: total phosphorous
    from_schema: http://w3id.org/mixs
    is_a: core field
    slot_uri: MIXS:0000689
    multivalued: false
    alias: tot_phos
    owner: agriculture MIMARKS survey
    domain_of:
    - agriculture
    range: quantity value
    required: false
  sieving:
    name: sieving
    description: Collection design of pooled samples and/or sieve size and amount
      of sample sieved
    title: composite design/sieving
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{{text}|{float} {unit}};{float} {unit}'
    slot_uri: MIXS:0000322
    multivalued: false
    alias: sieving
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - agriculture
    range: string
    required: true
  pool_dna_extracts:
    name: pool_dna_extracts
    description: Indicate whether multiple DNA extractions were mixed. If the answer
      yes, the number of extracts that were pooled should be given
    title: pooling of DNA extracts (if done)
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{boolean};{integer}'
    slot_uri: MIXS:0000325
    multivalued: false
    alias: pool_dna_extracts
    owner: agriculture MIMARKS survey
    domain_of:
    - soil
    - food-human foods
    - food-food production facility
    - food-animal and animal feed
    - agriculture
    range: string
    required: true
  misc_param:
    name: misc_param
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    from_schema: http://w3id.org/mixs
    is_a: core field
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    multivalued: true
    alias: misc_param
    owner: agriculture MIMARKS survey
    domain_of:
    - water
    - wastewater_sludge
    - symbiont-associated
    - soil
    - sediment
    - plant-associated
    - miscellaneous natural or artificial environment
    - microbial mat_biofilm
    - hydrocarbon resources-fluids_swabs
    - hydrocarbon resources-cores
    - human-vaginal
    - human-skin
    - human-oral
    - human-gut
    - human-associated
    - host-associated
    - food-human foods
    - food-food production facility
    - food-farm environment
    - food-animal and animal feed
    - air
    - agriculture
    range: string
    required: false