Combination: MimarksC combined with Soil (MimarksCSoil)

MIxS Data that comply with the MimarksC checklist and the Soil Extension

Composition

MimarksC [Checklist] + Soil [Extension]

Terms

MIXS ID	Name	Cardinality and Range	Description
MIXS:0001107	samp_name	1 String	A local identifier or name that for the material sample used for extracting n...
MIXS:0000046	pcr_primers	0..1 recommended String	PCR primers that were used to amplify the sequence of the targeted gene, locu...
MIXS:0000038	nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...
MIXS:0000045	target_subfragment	0..1 recommended String	Name of subfragment of a gene or locus
MIXS:0000113	temp	0..1 recommended String	Temperature of the sample at the time of sampling
MIXS:0000049	pcr_cond	0..1 recommended String	Description of reaction conditions and components of polymerase chain reactio...
MIXS:0000037	nucl_acid_ext	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...
MIXS:0000001	samp_size	0..1 String	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...
MIXS:0000003	isol_growth_condt	1 String	Publication reference in the form of pubmed ID (pmid), digital object identif...
MIXS:0000094	alt	0..1 recommended String	Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...
MIXS:0000026	source_mat_id	* recommended String	A unique identifier assigned to a material sample (as defined by http://rs
MIXS:0000023	extrachrom_elements	0..1 Integer	Do plasmids exist of significant phenotypic consequence (e
MIXS:0000111	samp_vol_we_dna_ext	0..1 String	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...
MIXS:0000015	rel_to_oxygen	0..1 recommended RelToOxygenEnum	Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ...
MIXS:0000002	samp_collect_device	0..1 String	The device used to collect an environmental sample
MIXS:0000028	biotic_relationship	0..1 recommended BioticRelationshipEnum	Description of relationship(s) between the subject organism and other organis...
MIXS:0000051	seq_quality_check	0..1 recommended SeqQualityCheckEnum	Indicate if the sequence has been called by automatic systems (none) or under...
MIXS:0000092	project_name	1 String	Name of the project within which the sequencing was organized
MIXS:0001321	neg_cont_type	0..1 recommended NegContTypeEnum	The substance or equipment used as a negative control in an investigation
MIXS:0000052	chimera_check	0..1 recommended String	Tool(s) used for chimera checking, including version number and parameters, t...
MIXS:0000032	trophic_level	0..1 recommended TrophicLevelEnum	Trophic levels are the feeding position in a food chain
MIXS:0001322	pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...
MIXS:0000020	subspecf_gen_lin	0..1 recommended String	Information about the genetic distinctness of the sequenced organism below th...
MIXS:0000013	env_local_scale	1 String	Report the entity or entities which are in the sample or specimen s local vic...
MIXS:0000016	samp_mat_process	0..1 recommended String	A brief description of any processing applied to the sample during or after r...
MIXS:0000018	depth	1 recommended String	The vertical distance below local surface
MIXS:0001225	samp_collect_method	0..1 String	The method employed for collecting the sample
MIXS:0000014	env_medium	1 String	Report the environmental material(s) immediately surrounding the sample or sp...
MIXS:0001320	samp_taxon_id	1 String	NCBI taxon id of the sample
MIXS:0000010	geo_loc_name	1 String	The geographical origin of the sample as defined by the country or sea name f...
MIXS:0000011	collection_date	1 Datetime	The time of sampling, either as an instance (single point in time) or interva...
MIXS:0000050	seq_meth	1 String	Sequencing machine used
MIXS:0000009	lat_lon	1 String	The geographical origin of the sample as defined by latitude and longitude
MIXS:0000093	elev	1 recommended String	Elevation of the sampling site is its height above a fixed reference point, m...
MIXS:0000012	env_broad_scale	1 String	Report the major environmental system the sample or specimen came from
MIXS:0000008	experimental_factor	* String	Variable aspects of an experiment design that can be used to describe an expe...
MIXS:0000044	target_gene	1 String	Targeted gene or locus name for marker gene studies
MIXS:0000091	associated_resource	* recommended String	A related resource that is referenced, cited, or otherwise associated to the ...
MIXS:0000090	sop	* recommended String	Standard operating procedures used in assembly and/or annotation of genomes, ...
MIXS:0001080	cur_land_use	0..1 String	Present state of sample site
MIXS:0000312	cur_vegetation	0..1 String	Vegetation classification from one or more standard classification systems, o...
MIXS:0000314	cur_vegetation_meth	0..1 String	Reference or method used in vegetation classification
MIXS:0000315	previous_land_use	0..1 String	Previous land use and dates
MIXS:0000316	prev_land_use_meth	0..1 String	Reference or method used in determining previous land use and dates
MIXS:0000318	crop_rotation	0..1 String	Whether or not crop is rotated, and if yes, rotation schedule
MIXS:0000639	agrochem_addition	* String	Addition of fertilizers, pesticides, etc
MIXS:0001081	tillage	* TillageEnum	Note method(s) used for tilling
MIXS:0001086	fire	0..1 Datetime	Historical and/or physical evidence of fire
MIXS:0000319	flooding	0..1 Datetime	Historical and/or physical evidence of flooding
MIXS:0000320	extreme_event	0..1 Datetime	Unusual physical events that may have affected microbial populations
MIXS:0001082	soil_horizon	0..1 SoilHorizonEnum	Specific layer in the land area which measures parallel to the soil surface a...
MIXS:0000321	horizon_meth	0..1 String	Reference or method used in determining the horizon
MIXS:0000322	sieving	0..1 String	Collection design of pooled samples and/or sieve size and amount of sample si...
MIXS:0000185	water_content	0..1 String	Water content measurement
MIXS:0000323	water_cont_soil_meth	0..1 String	Reference or method used in determining the water content of soil
MIXS:0000325	pool_dna_extracts	0..1 String	Indicate whether multiple DNA extractions were mixed
MIXS:0000327	store_cond	0..1 String	Explain how and for how long the soil sample was stored before DNA extraction...
MIXS:0000328	link_climate_info	0..1 String	Link to climate resource
MIXS:0000642	annual_temp	0..1 String	Mean annual temperature
MIXS:0000643	season_temp	0..1 String	Mean seasonal temperature
MIXS:0000644	annual_precpt	0..1 String	The average of all annual precipitation values known, or an estimated equival...
MIXS:0000645	season_precpt	0..1 String	The average of all seasonal precipitation values known, or an estimated equiv...
MIXS:0000329	link_class_info	0..1 String	Link to digitized soil maps or other soil classification information
MIXS:0001083	fao_class	0..1 FaoClassEnum	Soil classification from the FAO World soil distribution from International S...
MIXS:0000330	local_class	0..1 String	Soil classification based on local soil classification system
MIXS:0000331	local_class_meth	0..1 String	Reference or method used in determining the local soil classification
MIXS:0000205	org_nitro	0..1 String	Concentration of organic nitrogen
MIXS:0000332	soil_type	0..1 String	Description of the soil type or classification
MIXS:0000334	soil_type_meth	0..1 String	Reference or method used in determining soil series name or other lower-level...
MIXS:0000646	slope_gradient	0..1 String	Commonly called 'slope'
MIXS:0000647	slope_aspect	0..1 String	The direction a slope faces
MIXS:0001084	profile_position	0..1 ProfilePositionEnum	Cross-sectional position in the hillslope where sample was collected
MIXS:0001085	drainage_class	0..1 DrainageClassEnum	Drainage classification from a standard system such as the USDA system
MIXS:0000335	soil_texture	0..1 String	The relative proportion of different grain sizes of mineral particles in a so...
MIXS:0000336	soil_texture_meth	0..1 String	Reference or method used in determining soil texture
MIXS:0001001	ph	0..1 Float	Ph measurement of the sample, or liquid portion of sample, or aqueous phase o...
MIXS:0001106	ph_meth	0..1 String	Reference or method used in determining pH
MIXS:0000204	org_matter	0..1 String	Concentration of organic matter
MIXS:0000533	tot_org_carb	0..1 String	Total organic carbon content
MIXS:0000337	tot_org_c_meth	0..1 String	Reference or method used in determining total organic carbon
MIXS:0000530	tot_nitro_content	0..1 String	Total nitrogen content of the sample
MIXS:0000338	tot_nitro_cont_meth	0..1 String	Reference or method used in determining the total nitrogen
MIXS:0000650	microbial_biomass	0..1 String	The part of the organic matter in the soil that constitutes living microorgan...
MIXS:0000339	micro_biomass_meth	0..1 String	Reference or method used in determining microbial biomass
MIXS:0000340	link_addit_analys	0..1 String	Link to additional analysis results performed on the sample
MIXS:0000652	heavy_metals	* String	Heavy metals present in the sequenced sample and their concentrations
MIXS:0000343	heavy_metals_meth	0..1 String	Reference or method used in determining heavy metals
MIXS:0000607	al_sat	0..1 String	Aluminum saturation (esp
MIXS:0000324	al_sat_meth	0..1 String	Reference or method used in determining Al saturation
MIXS:0000752	misc_param	* String	Any other measurement performed or parameter collected, that is not listed he...

LinkML Source

Direct

name: MimarksCSoil
description: MIxS Data that comply with the MimarksC checklist and the Soil Extension
title: MimarksC combined with Soil
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: Soil
mixins:
- MimarksC
class_uri: MIXS:0010009_0016012

Induced

name: MimarksCSoil
description: MIxS Data that comply with the MimarksC checklist and the Soil Extension
title: MimarksC combined with Soil
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: Soil
mixins:
- MimarksC
attributes:
  samp_name:
    name: samp_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    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
    examples:
    - value: ISDsoil1
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    slot_uri: MIXS:0001107
    alias: samp_name
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
  pcr_primers:
    name: pcr_primers
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'FWD: forward primer sequence;REV:reverse primer sequence'
    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
    examples:
    - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - pcr
    string_serialization: FWD:{dna};REV:{dna}
    slot_uri: MIXS:0000046
    alias: pcr_primers
    owner: MimarksCSoil
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    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
    examples:
    - value: https://phylogenomics.me/protocols/16s-pcr-protocol/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000038
    alias: nucl_acid_amp
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: 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
    examples:
    - value: V6, V9, ITS
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - target
    slot_uri: MIXS:0000045
    alias: target_subfragment
    owner: MimarksCSoil
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  temp:
    name: temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature of the sample at the time of sampling
    title: temperature
    examples:
    - value: 25 degree Celsius
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - temperature
    slot_uri: MIXS:0000113
    alias: temp
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  pcr_cond:
    name: pcr_cond
    annotations:
      Expected_value:
        tag: Expected_value
        value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
          elongation:degrees_minutes;total cycles
    description: Description of reaction conditions and components of polymerase chain
      reaction performed during library preparation.
    title: pcr conditions
    examples:
    - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35
    - value: initial denaturation:94degC_1.5min
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - condition
    - pcr
    string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
      elongation:degrees_minutes;total cycles
    slot_uri: MIXS:0000049
    alias: pcr_cond
    owner: MimarksCSoil
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  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
    examples:
    - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000037
    alias: nucl_acid_ext
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: 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
    examples:
    - value: 5 liter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - size
    slot_uri: MIXS:0000001
    alias: samp_size
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: 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
    examples:
    - value: doi:10.1016/j.syapm.2018.01.009
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - condition
    - growth
    - isolation
    slot_uri: MIXS:0000003
    alias: isol_growth_condt
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - MimarksC
    - Agriculture
    range: string
    required: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  alt:
    name: alt
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: 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
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000094
    alias: alt
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - HostAssociated
    - MiscellaneousNaturalOrArtificialEnvironment
    - SymbiontAssociated
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  source_mat_id:
    name: source_mat_id
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    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
    examples:
    - value: MPI012345
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    - material
    - source
    slot_uri: MIXS:0000026
    alias: source_mat_id
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    recommended: true
    multivalued: 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
    examples:
    - value: '5'
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000023
    alias: extrachrom_elements
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MimarksC
    range: integer
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliliter, gram, milligram, square centimeter
    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
    examples:
    - value: 1500 milliliter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - sample
    - volume
    - weight
    slot_uri: MIXS:0000111
    alias: samp_vol_we_dna_ext
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: 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
    examples:
    - value: aerobe
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - oxygen
    - relationship
    slot_uri: MIXS:0000015
    alias: rel_to_oxygen
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: RelToOxygenEnum
    recommended: true
  samp_collect_device:
    name: samp_collect_device
    annotations:
      Expected_value:
        tag: Expected_value
        value: device name
    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
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - device
    - sample
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000002
    alias: samp_collect_device
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
  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
    examples:
    - value: free living
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - observed
    - relationship
    slot_uri: MIXS:0000028
    alias: biotic_relationship
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - MimarksC
    - Miuvig
    - Agriculture
    range: BioticRelationshipEnum
    recommended: true
  seq_quality_check:
    name: seq_quality_check
    annotations:
      Expected_value:
        tag: Expected_value
        value: none or manually edited
    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
    examples:
    - value: none
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - quality
    slot_uri: MIXS:0000051
    alias: seq_quality_check
    owner: MimarksCSoil
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: SeqQualityCheckEnum
    recommended: true
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    examples:
    - value: Forest soil metagenome
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - project
    slot_uri: MIXS:0000092
    alias: project_name
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
  neg_cont_type:
    name: neg_cont_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration or text
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - type
    slot_uri: MIXS:0001321
    alias: neg_cont_type
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NegContTypeEnum
    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
    examples:
    - value: uchime;v4.1;default parameters
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    slot_uri: MIXS:0000052
    alias: chimera_check
    owner: MimarksCSoil
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: 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
    examples:
    - value: heterotroph
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - level
    slot_uri: MIXS:0000032
    alias: trophic_level
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MimarksC
    - Agriculture
    range: TrophicLevelEnum
    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
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - type
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    alias: pos_cont_type
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    recommended: true
  subspecf_gen_lin:
    name: subspecf_gen_lin
    annotations:
      Expected_value:
        tag: Expected_value
        value: Genetic lineage below lowest rank of NCBI taxonomy, which is subspecies,
          e.g. serovar, biotype, ecotype, variety, cultivar
    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
    examples:
    - value: serovar:Newport
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - lineage
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0000020
    alias: subspecf_gen_lin
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - MimarksC
    - FoodFoodProductionFacility
    range: string
    recommended: true
  env_local_scale:
    name: env_local_scale
    annotations:
      Expected_value:
        tag: Expected_value
        value: Environmental entities having causal influences upon the entity at
          time of sampling
    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
    examples:
    - value: hillside [ENVO:01000333]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000013
    alias: env_local_scale
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  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
    examples:
    - value: filtering of seawater, storing samples in ethanol
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - material
    - process
    - sample
    slot_uri: MIXS:0000016
    alias: samp_mat_process
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  depth:
    name: depth
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: The vertical distance below local surface. 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
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - depth
    slot_uri: MIXS:0000018
    alias: depth
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample
    title: sample collection method
    examples:
    - value: swabbing
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - sample
    slot_uri: MIXS:0001225
    alias: samp_collect_method
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: 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
    examples:
    - value: bluegrass field soil [ENVO:00005789]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - environmental
    slot_uri: MIXS:0000014
    alias: env_medium
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: 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
    examples:
    - value: Gut Metagenome [NCBITaxon:749906]
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - identifier
    - sample
    - taxon
    slot_uri: MIXS:0001320
    alias: samp_taxon_id
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
    structured_pattern:
      syntax: ^{text} \[{NCBItaxon_id}\]$
      interpolated: true
      partial_match: 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)
    examples:
    - value: 'USA: Maryland, Bethesda'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000010
    alias: geo_loc_name
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
    structured_pattern:
      syntax: '^{text}: {text}, {text}$'
      interpolated: true
      partial_match: 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
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - date
    slot_uri: MIXS:0000011
    alias: collection_date
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: datetime
    required: 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
    examples:
    - value: 454 Genome Sequencer FLX [OBI:0000702]
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    slot_uri: MIXS:0000050
    alias: seq_meth
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
    structured_pattern:
      syntax: ^{text}|({termLabel} \[{termID}\])$
      interpolated: true
      partial_match: true
  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, limited to 8 decimal
      points, and in WGS84 system
    title: geographic location (latitude and longitude)
    examples:
    - value: 50.586825 6.408977
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
    structured_pattern:
      syntax: ^{lat} {lon}$
      interpolated: true
      partial_match: true
  elev:
    name: elev
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit
    title: elevation
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - elevation
    slot_uri: MIXS:0000093
    alias: elev
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - HostAssociated
    - HydrocarbonResourcesCores
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - Water
    range: string
    required: true
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: 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
    examples:
    - value: rangeland biome [ENVO:01000247]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000012
    alias: env_broad_scale
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  experimental_factor:
    name: experimental_factor
    annotations:
      Expected_value:
        tag: Expected_value
        value: text or EFO and/or OBI
    description: Variable aspects of an experiment design that 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)
    title: experimental factor
    examples:
    - value: time series design [EFO:0001779]
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - experimental
    - factor
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000008
    alias: experimental_factor
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    multivalued: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  target_gene:
    name: target_gene
    description: Targeted gene or locus name for marker gene studies
    title: target gene
    examples:
    - value: 16S rRNA, 18S rRNA, nif, amoA, rpo
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - target
    slot_uri: MIXS:0000044
    alias: target_gene
    owner: MimarksCSoil
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    required: true
  associated_resource:
    name: associated_resource
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence
    title: relevant electronic resources
    examples:
    - value: http://www.earthmicrobiome.org/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - resource
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    alias: associated_resource
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    multivalued: true
  sop:
    name: sop
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to SOP
    description: Standard operating procedures used in assembly and/or annotation
      of genomes, metagenomes or environmental sequences
    title: relevant standard operating procedures
    examples:
    - value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - procedures
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    alias: sop
    owner: MimarksCSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    multivalued: true
  cur_land_use:
    name: cur_land_use
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration
    description: Present state of sample site
    title: current land use
    examples:
    - value: conifers
    from_schema: https://w3id.org/mixs
    keywords:
    - land
    - use
    string_serialization: '[cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|salt
      flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas|small
      grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands
      (grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands
      used for livestock grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub
      land (e.g. mesquite,sage-brush,creosote bush,shrub oak,eucalyptus)|successional
      shrub land (tree saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub
      crops (blueberries,nursery ornamentals,filberts)|vine crops (grapes)|conifers
      (e.g. pine,spruce,fir,cypress)|hardwoods (e.g. oak,hickory,elm,aspen)|intermixed
      hardwood and conifers|tropical (e.g. mangrove,palms)|rainforest (evergreen forest
      receiving >406 cm annual rainfall)|swamp (permanent or semi-permanent water
      body dominated by woody plants)|crop trees (nuts,fruit,christmas trees,nursery
      trees)]'
    slot_uri: MIXS:0001080
    alias: cur_land_use
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
  cur_vegetation:
    name: cur_vegetation
    annotations:
      Expected_value:
        tag: Expected_value
        value: current vegetation type
    description: Vegetation classification from one or more standard classification
      systems, or agricultural crop
    title: current vegetation
    from_schema: https://w3id.org/mixs
    keywords:
    - vegetation
    slot_uri: MIXS:0000312
    alias: cur_vegetation
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
  cur_vegetation_meth:
    name: cur_vegetation_meth
    description: Reference or method used in vegetation classification
    title: current vegetation method
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - vegetation
    slot_uri: MIXS:0000314
    alias: cur_vegetation_meth
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  previous_land_use:
    name: previous_land_use
    annotations:
      Expected_value:
        tag: Expected_value
        value: land use name;date
    description: Previous land use and dates
    title: history/previous land use
    examples:
    - value: fallow; 2018-05-11:T14:30Z
    from_schema: https://w3id.org/mixs
    keywords:
    - history
    - land
    - use
    string_serialization: '{text};{timestamp}'
    slot_uri: MIXS:0000315
    alias: previous_land_use
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
  prev_land_use_meth:
    name: prev_land_use_meth
    description: Reference or method used in determining previous land use and dates
    title: history/previous land use method
    from_schema: https://w3id.org/mixs
    keywords:
    - history
    - land
    - method
    - use
    slot_uri: MIXS:0000316
    alias: prev_land_use_meth
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  crop_rotation:
    name: crop_rotation
    annotations:
      Expected_value:
        tag: Expected_value
        value: crop rotation status;schedule
    description: Whether or not crop is rotated, and if yes, rotation schedule
    title: history/crop rotation
    examples:
    - value: yes;R2/2017-01-01/2018-12-31/P6M
    from_schema: https://w3id.org/mixs
    keywords:
    - history
    string_serialization: '{boolean};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000318
    alias: crop_rotation
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
  agrochem_addition:
    name: agrochem_addition
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram, mole per liter, milligram per liter
    description: Addition of fertilizers, pesticides, etc. - amount and time of applications
    title: history/agrochemical additions
    examples:
    - value: roundup;5 milligram per liter;2018-06-21
    from_schema: https://w3id.org/mixs
    keywords:
    - history
    slot_uri: MIXS:0000639
    alias: agrochem_addition
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    multivalued: true
    structured_pattern:
      syntax: ^{agrochemical_name};{amount} {unit};{date_time_stamp}$
      interpolated: true
      partial_match: true
  tillage:
    name: tillage
    description: Note method(s) used for tilling
    title: history/tillage
    examples:
    - value: chisel
    from_schema: https://w3id.org/mixs
    keywords:
    - history
    slot_uri: MIXS:0001081
    alias: tillage
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: TillageEnum
    multivalued: true
  fire:
    name: fire
    description: Historical and/or physical evidence of fire
    title: history/fire
    from_schema: https://w3id.org/mixs
    keywords:
    - history
    slot_uri: MIXS:0001086
    alias: fire
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: datetime
  flooding:
    name: flooding
    description: Historical and/or physical evidence of flooding
    title: history/flooding
    from_schema: https://w3id.org/mixs
    keywords:
    - history
    slot_uri: MIXS:0000319
    alias: flooding
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: datetime
  extreme_event:
    name: extreme_event
    description: Unusual physical events that may have affected microbial populations
    title: history/extreme events
    from_schema: https://w3id.org/mixs
    keywords:
    - event
    - history
    slot_uri: MIXS:0000320
    alias: extreme_event
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: datetime
  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
    examples:
    - value: A horizon
    from_schema: https://w3id.org/mixs
    keywords:
    - horizon
    - soil
    slot_uri: MIXS:0001082
    alias: soil_horizon
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: SoilHorizonEnum
  horizon_meth:
    name: horizon_meth
    description: Reference or method used in determining the horizon
    title: horizon method
    from_schema: https://w3id.org/mixs
    keywords:
    - horizon
    - method
    slot_uri: MIXS:0000321
    alias: horizon_meth
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  sieving:
    name: sieving
    annotations:
      Expected_value:
        tag: Expected_value
        value: design name and/or size;amount
    description: Collection design of pooled samples and/or sieve size and amount
      of sample sieved
    title: sieving
    from_schema: https://w3id.org/mixs
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000322
    alias: sieving
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
  water_content:
    name: water_content
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram per gram or cubic centimeter per cubic centimeter
    description: Water content measurement
    title: water content
    from_schema: https://w3id.org/mixs
    keywords:
    - content
    - water
    string_serialization: '{float}'
    slot_uri: MIXS:0000185
    alias: water_content
    owner: MimarksCSoil
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  water_cont_soil_meth:
    name: water_cont_soil_meth
    description: Reference or method used in determining the water content of soil
    title: water content method
    from_schema: https://w3id.org/mixs
    keywords:
    - content
    - method
    - water
    slot_uri: MIXS:0000323
    alias: water_cont_soil_meth
    owner: MimarksCSoil
    domain_of:
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  pool_dna_extracts:
    name: pool_dna_extracts
    annotations:
      Expected_value:
        tag: Expected_value
        value: pooling status;number of pooled extracts
      Preferred_unit:
        tag: Preferred_unit
        value: gram, milliliter, microliter
    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)
    examples:
    - value: yes, 5
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - pooling
    string_serialization: '{boolean};{integer}'
    slot_uri: MIXS:0000325
    alias: pool_dna_extracts
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - Soil
    range: string
  store_cond:
    name: store_cond
    annotations:
      Expected_value:
        tag: Expected_value
        value: storage condition type;duration
    description: Explain how and for how long the soil sample was stored before DNA
      extraction (fresh/frozen/other)
    title: storage conditions
    examples:
    - value: -20 degree Celsius freezer;P2Y10D
    from_schema: https://w3id.org/mixs
    keywords:
    - condition
    - storage
    string_serialization: '{text};{period}'
    slot_uri: MIXS:0000327
    alias: store_cond
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
  link_climate_info:
    name: link_climate_info
    description: Link to climate resource
    title: link to climate information
    from_schema: https://w3id.org/mixs
    keywords:
    - information
    - link
    slot_uri: MIXS:0000328
    alias: link_climate_info
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  annual_temp:
    name: annual_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Mean annual temperature
    title: mean annual temperature
    examples:
    - value: 12.5 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - mean
    - temperature
    slot_uri: MIXS:0000642
    alias: annual_temp
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  season_temp:
    name: season_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Mean seasonal temperature
    title: mean seasonal temperature
    examples:
    - value: 18 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - mean
    - season
    - temperature
    slot_uri: MIXS:0000643
    alias: season_temp
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  annual_precpt:
    name: annual_precpt
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: millimeter
    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: https://w3id.org/mixs
    keywords:
    - mean
    slot_uri: MIXS:0000644
    alias: annual_precpt
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  season_precpt:
    name: season_precpt
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: millimeter
    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
    examples:
    - value: 75 millimeters
    from_schema: https://w3id.org/mixs
    keywords:
    - mean
    - season
    slot_uri: MIXS:0000645
    alias: season_precpt
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  link_class_info:
    name: link_class_info
    annotations:
      Expected_value:
        tag: Expected_value
        value: PMID,DOI or url
    description: Link to digitized soil maps or other soil classification information
    title: link to classification information
    from_schema: https://w3id.org/mixs
    keywords:
    - classification
    - information
    - link
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000329
    alias: link_class_info
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
  fao_class:
    name: fao_class
    description: Soil classification from the FAO World soil distribution from International
      Soil Reference and Information Centre (ISRIC). The list of available soil classifications
      can be found at https://www.isric.org/explore/world-soil-distribution
    title: soil_taxonomic/FAO classification
    examples:
    - value: Luvisols
    from_schema: https://w3id.org/mixs
    keywords:
    - classification
    slot_uri: MIXS:0001083
    alias: fao_class
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: FaoClassEnum
  local_class:
    name: local_class
    annotations:
      Expected_value:
        tag: Expected_value
        value: local classification name
    description: Soil classification based on local soil classification system
    title: soil_taxonomic/local classification
    from_schema: https://w3id.org/mixs
    keywords:
    - classification
    slot_uri: MIXS:0000330
    alias: local_class
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
  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: https://w3id.org/mixs
    keywords:
    - classification
    - method
    slot_uri: MIXS:0000331
    alias: local_class_meth
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  org_nitro:
    name: org_nitro
    description: Concentration of organic nitrogen
    title: organic nitrogen
    examples:
    - value: 4 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - nitrogen
    - organic
    slot_uri: MIXS:0000205
    alias: org_nitro
    owner: MimarksCSoil
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Soil
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  soil_type:
    name: soil_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: ENVO:00001998
    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
    examples:
    - value: plinthosol [ENVO:00002250]
    from_schema: https://w3id.org/mixs
    keywords:
    - soil
    - type
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000332
    alias: soil_type
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
  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
    examples:
    - value: https://www.lrh.usace.army.mil/Portals/38/docs/PR/BluestoneSFEIS/Appendix%20K-Soil%20Descriptions.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - soil
    - type
    slot_uri: MIXS:0000334
    alias: soil_type_meth
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  slope_gradient:
    name: slope_gradient
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: percentage
    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: https://w3id.org/mixs
    keywords:
    - slope
    slot_uri: MIXS:0000646
    alias: slope_gradient
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  slope_aspect:
    name: slope_aspect
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree
    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: https://w3id.org/mixs
    keywords:
    - slope
    slot_uri: MIXS:0000647
    alias: slope_aspect
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  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
    examples:
    - value: summit
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0001084
    alias: profile_position
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: ProfilePositionEnum
  drainage_class:
    name: drainage_class
    description: Drainage classification from a standard system such as the USDA system
    title: drainage classification
    examples:
    - value: well
    from_schema: https://w3id.org/mixs
    keywords:
    - classification
    slot_uri: MIXS:0001085
    alias: drainage_class
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: DrainageClassEnum
  soil_texture:
    name: soil_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: soil texture
    from_schema: https://w3id.org/mixs
    keywords:
    - soil
    - texture
    slot_uri: MIXS:0000335
    alias: soil_texture
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  soil_texture_meth:
    name: soil_texture_meth
    description: Reference or method used in determining soil texture
    title: soil texture method
    examples:
    - value: https://uwlab.soils.wisc.edu/wp-content/uploads/sites/17/2015/09/particle_size.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - soil
    - texture
    slot_uri: MIXS:0000336
    alias: soil_texture_meth
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  ph:
    name: ph
    description: Ph measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid
    title: pH
    examples:
    - value: '7.2'
    from_schema: https://w3id.org/mixs
    keywords:
    - ph
    slot_uri: MIXS:0001001
    alias: ph
    owner: MimarksCSoil
    domain_of:
    - FoodFarmEnvironment
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Soil
    - WastewaterSludge
    - Water
    range: float
  ph_meth:
    name: ph_meth
    description: Reference or method used in determining pH
    title: pH method
    examples:
    - value: https://www.epa.gov/sites/production/files/2015-12/documents/9040c.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - ph
    slot_uri: MIXS:0001106
    alias: ph_meth
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  org_matter:
    name: org_matter
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: microgram per liter
    description: Concentration of organic matter
    title: organic matter
    examples:
    - value: 1.75 milligram per cubic meter
    from_schema: https://w3id.org/mixs
    keywords:
    - organic
    slot_uri: MIXS:0000204
    alias: org_matter
    owner: MimarksCSoil
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Soil
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  tot_org_carb:
    name: tot_org_carb
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram Carbon per kilogram sample material
    description: Total organic carbon content
    title: total organic carbon
    examples:
    - value: '0.02'
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - organic
    - total
    slot_uri: MIXS:0000533
    alias: tot_org_carb
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - MicrobialMatBiofilm
    - Sediment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  tot_org_c_meth:
    name: tot_org_c_meth
    description: Reference or method used in determining total organic carbon
    title: total organic carbon method
    examples:
    - value: https://www.epa.gov/sites/production/files/2015-12/documents/9060a.pdf
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - method
    - organic
    - total
    slot_uri: MIXS:0000337
    alias: tot_org_c_meth
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  tot_nitro_content:
    name: tot_nitro_content
    description: Total nitrogen content of the sample
    title: total nitrogen content
    examples:
    - value: 35 milligrams Nitrogen per kilogram of soil
    from_schema: https://w3id.org/mixs
    keywords:
    - content
    - nitrogen
    - total
    slot_uri: MIXS:0000530
    alias: tot_nitro_content
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - MicrobialMatBiofilm
    - Sediment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  tot_nitro_cont_meth:
    name: tot_nitro_cont_meth
    description: Reference or method used in determining the total nitrogen
    title: total nitrogen content method
    examples:
    - value: https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/0471142913.fab0102s00
    from_schema: https://w3id.org/mixs
    keywords:
    - content
    - method
    - nitrogen
    - total
    slot_uri: MIXS:0000338
    alias: tot_nitro_cont_meth
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  microbial_biomass:
    name: microbial_biomass
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ton, kilogram, gram per kilogram soil
    description: The part of the organic matter in the soil that constitutes living
      microorganisms smaller than 5-10 micrometer. If you keep this, you would need
      to have correction factors used for conversion to the final units
    title: microbial biomass
    from_schema: https://w3id.org/mixs
    keywords:
    - biomass
    - microbial
    slot_uri: MIXS:0000650
    alias: microbial_biomass
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  micro_biomass_meth:
    name: micro_biomass_meth
    description: Reference or method used in determining microbial biomass
    title: microbial biomass method
    comments:
    - slot name/scn was microbial_biomass_meth
    examples:
    - value: http://dx.doi.org/10.1016/j.soilbio.2005.01.021
    from_schema: https://w3id.org/mixs
    keywords:
    - biomass
    - method
    - microbial
    slot_uri: MIXS:0000339
    alias: micro_biomass_meth
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  link_addit_analys:
    name: link_addit_analys
    description: Link to additional analysis results performed on the sample
    title: links to additional analysis
    from_schema: https://w3id.org/mixs
    keywords:
    - link
    slot_uri: MIXS:0000340
    alias: link_addit_analys
    owner: MimarksCSoil
    domain_of:
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  heavy_metals:
    name: heavy_metals
    annotations:
      Expected_value:
        tag: Expected_value
        value: heavy metal name;measurement value unit
      Preferred_unit:
        tag: Preferred_unit
        value: microgram per gram
    description: Heavy metals present in the sequenced sample and their concentrations.
      For multiple heavy metals and concentrations, add multiple copies of this field
    title: extreme_unusual_properties/heavy metals
    examples:
    - value: mercury;0.09 micrograms per gram
    from_schema: https://w3id.org/mixs
    keywords:
    - extreme
    - properties
    - unusual
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000652
    alias: heavy_metals
    owner: MimarksCSoil
    domain_of:
    - Soil
    range: string
    multivalued: true
  heavy_metals_meth:
    name: heavy_metals_meth
    description: Reference or method used in determining heavy metals
    title: extreme_unusual_properties/heavy metals method
    from_schema: https://w3id.org/mixs
    keywords:
    - extreme
    - method
    - properties
    - unusual
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000343
    alias: heavy_metals_meth
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  al_sat:
    name: al_sat
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: percentage
    description: Aluminum saturation (esp. For tropical soils)
    title: extreme_unusual_properties/Al saturation
    from_schema: https://w3id.org/mixs
    keywords:
    - extreme
    - properties
    - saturation
    - unusual
    slot_uri: MIXS:0000607
    alias: al_sat
    owner: MimarksCSoil
    domain_of:
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  al_sat_meth:
    name: al_sat_meth
    description: Reference or method used in determining Al saturation
    title: extreme_unusual_properties/Al saturation method
    from_schema: https://w3id.org/mixs
    keywords:
    - extreme
    - method
    - properties
    - saturation
    - unusual
    slot_uri: MIXS:0000324
    alias: al_sat_meth
    owner: MimarksCSoil
    domain_of:
    - Soil
    range: string
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  misc_param:
    name: misc_param
    annotations:
      Expected_value:
        tag: Expected_value
        value: parameter name;measurement value
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/mixs
    keywords:
    - parameter
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    alias: misc_param
    owner: MimarksCSoil
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
class_uri: MIXS:0010009_0016012