Class: MigsEuSoil

MIxS data that complies with the MigsEu checklist and the Soil environmental package

URI: MIXS:0010002_0016012

Inheritance

• EnvironmentalPackage
  • Soil
    • MigsEuSoil [ MigsEu]

Slots

Name	Cardinality and Range	Description	Inheritance
assembly_qual	1..1 String	The assembly quality category is based on sets of criteria outlined for each ...	MigsEu
samp_name	1..1 String	A local identifier or name that for the material sample used for extracting n...	Soil, MigsEu
estimated_size	0..1 String	The estimated size of the genome prior to sequencing	MigsEu
host_disease_stat	0..1 String	List of diseases with which the host has been diagnosed; can include multiple...	MigsEu
alt	0..1 recommended String	Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...	MigsEu
isol_growth_condt	1..1 String	Publication reference in the form of pubmed ID (pmid), digital object identif...	MigsEu
host_spec_range	0..* String	The range and diversity of host species that an organism is capable of infect...	MigsEu
feat_pred	0..1 String	Method used to predict UViGs features such as ORFs, integration site, etc	MigsEu
compl_software	0..1 String	Tools used for completion estimate, i	MigsEu
neg_cont_type	0..1 recommended NEGCONTTYPEENUM	The substance or equipment used as a negative control in an investigation	MigsEu
elev	1..1 recommended String	Elevation of the sampling site is its height above a fixed reference point, m...	Soil, MigsEu
samp_mat_process	0..1 String	A brief description of any processing applied to the sample during or after r...	MigsEu
assembly_name	0..1 recommended String	Name/version of the assembly provided by the submitter that is used in the ge...	MigsEu
tax_class	0..1 String	Method used for taxonomic classification, along with reference database used,...	MigsEu
specific_host	0..1 String	Report the host's taxonomic name and/or NCBI taxonomy ID	MigsEu
source_mat_id	0..* recommended String	A unique identifier assigned to a material sample (as defined by http://rs	MigsEu
lib_size	0..1 Integer	Total number of clones in the library prepared for the project	MigsEu
samp_collect_device	0..1 String	The device used to collect an environmental sample	MigsEu
assembly_software	1..1 String	Tool(s) used for assembly, including version number and parameters	MigsEu
adapters	0..1 recommended String	Adapters provide priming sequences for both amplification and sequencing of t...	MigsEu
samp_collect_method	0..1 String	The method employed for collecting the sample	MigsEu
biotic_relationship	0..1 BIOTICRELATIONSHIPENUM	Description of relationship(s) between the subject organism and other organis...	MigsEu
annot	0..1 recommended String	Tool used for annotation, or for cases where annotation was provided by a com...	MigsEu
sim_search_meth	0..1 String	Tool used to compare ORFs with database, along with version and cutoffs used	MigsEu
ploidy	0..1 String	The ploidy level of the genome (e	MigsEu
number_contig	1..1 Integer	Total number of contigs in the cleaned/submitted assembly that makes up a giv...	MigsEu
collection_date	1..1 Datetime	The time of sampling, either as an instance (single point in time) or interva...	MigsEu
geo_loc_name	1..1 String	The geographical origin of the sample as defined by the country or sea name f...	MigsEu
ref_biomaterial	0..1 String	Primary publication if isolated before genome publication; otherwise, primary...	MigsEu
nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	MigsEu
samp_taxon_id	1..1 String	NCBI taxon id of the sample	MigsEu
lib_layout	0..1 LIBLAYOUTENUM	Specify whether to expect single, paired, or other configuration of reads	MigsEu
tax_ident	0..1 recommended TAXIDENTENUM	The phylogenetic marker(s) used to assign an organism name to the SAG or MAG	MigsEu
extrachrom_elements	0..1 Integer	Do plasmids exist of significant phenotypic consequence (e	MigsEu
env_medium	1..1 String	Report the environmental material(s) immediately surrounding the sample or sp...	MigsEu
pathogenicity	0..1 recommended String	To what is the entity pathogenic	MigsEu
samp_size	0..1 String	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...	MigsEu
subspecf_gen_lin	0..1 recommended String	Information about the genetic distinctness of the sequenced organism below th...	MigsEu
lib_reads_seqd	0..1 Integer	Total number of clones sequenced from the library	MigsEu
seq_meth	1..1 String	Sequencing machine used	MigsEu
temp	0..1 recommended String	Temperature of the sample at the time of sampling	Soil, MigsEu
experimental_factor	0..* String	Variable aspects of an experiment design that can be used to describe an expe...	MigsEu
lib_vector	0..1 String	Cloning vector type(s) used in construction of libraries	MigsEu
samp_vol_we_dna_ext	0..1 String	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...	Soil, MigsEu
pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...	MigsEu
env_local_scale	1..1 String	Report the entity or entities which are in the sample or specimen s local vic...	MigsEu
env_broad_scale	1..1 String	Report the major environmental system the sample or specimen came from	MigsEu
nucl_acid_ext	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...	MigsEu
compl_score	0..1 String	Completeness score is typically based on either the fraction of markers found...	MigsEu
ref_db	0..1 String	List of database(s) used for ORF annotation, along with version number and re...	MigsEu
lat_lon	1..1 String	The geographical origin of the sample as defined by latitude and longitude	MigsEu
num_replicons	0..1 Integer	Reports the number of replicons in a nuclear genome of eukaryotes, in the gen...	MigsEu
depth	1..1 recommended String	The vertical distance below local surface	Soil, MigsEu
project_name	1..1 String	Name of the project within which the sequencing was organized	Soil, MigsEu
propagation	0..1 recommended String	The type of reproduction from the parent stock	MigsEu
trophic_level	0..1 recommended TROPHICLEVELENUM	Trophic levels are the feeding position in a food chain	MigsEu
lib_screen	0..1 String	Specific enrichment or screening methods applied before and/or after creating...	MigsEu
associated_resource	0..* recommended String	A related resource that is referenced, cited, or otherwise associated to the ...	MigsEu
sop	0..* recommended String	Standard operating procedures used in assembly and/or annotation of genomes, ...	MigsEu
cur_land_use	0..1 String	Present state of sample site	Soil
cur_vegetation	0..1 String	Vegetation classification from one or more standard classification systems, o...	Soil
cur_vegetation_meth	0..1 String	Reference or method used in vegetation classification	Soil
previous_land_use	0..1 String	Previous land use and dates	Soil
prev_land_use_meth	0..1 String	Reference or method used in determining previous land use and dates	Soil
crop_rotation	0..1 String	Whether or not crop is rotated, and if yes, rotation schedule	Soil
agrochem_addition	0..* String	Addition of fertilizers, pesticides, etc	Soil
tillage	0..* TILLAGEENUM	Note method(s) used for tilling	Soil
fire	0..1 Datetime	Historical and/or physical evidence of fire	Soil
flooding	0..1 Datetime	Historical and/or physical evidence of flooding	Soil
extreme_event	0..1 Datetime	Unusual physical events that may have affected microbial populations	Soil
soil_horizon	0..1 SOILHORIZONENUM	Specific layer in the land area which measures parallel to the soil surface a...	Soil
horizon_meth	0..1 String	Reference or method used in determining the horizon	Soil
sieving	0..1 String	Collection design of pooled samples and/or sieve size and amount of sample si...	Soil
water_content	0..1 String	Water content measurement	Soil
water_cont_soil_meth	0..1 String	Reference or method used in determining the water content of soil	Soil
pool_dna_extracts	0..1 String	Indicate whether multiple DNA extractions were mixed	Soil
store_cond	0..1 String	Explain how and for how long the soil sample was stored before DNA extraction...	Soil
link_climate_info	0..1 String	Link to climate resource	Soil
annual_temp	0..1 String	Mean annual temperature	Soil
season_temp	0..1 String	Mean seasonal temperature	Soil
annual_precpt	0..1 String	The average of all annual precipitation values known, or an estimated equival...	Soil
season_precpt	0..1 String	The average of all seasonal precipitation values known, or an estimated equiv...	Soil
link_class_info	0..1 String	Link to digitized soil maps or other soil classification information	Soil
fao_class	0..1 FAOCLASSENUM	Soil classification from the FAO World Reference Database for Soil Resources	Soil
local_class	0..1 String	Soil classification based on local soil classification system	Soil
local_class_meth	0..1 String	Reference or method used in determining the local soil classification	Soil
org_nitro	0..1 String	Concentration of organic nitrogen	Soil
soil_type	0..1 String	Description of the soil type or classification	Soil
soil_type_meth	0..1 String	Reference or method used in determining soil series name or other lower-level...	Soil
slope_gradient	0..1 String	Commonly called 'slope'	Soil
slope_aspect	0..1 String	The direction a slope faces	Soil
profile_position	0..1 PROFILEPOSITIONENUM	Cross-sectional position in the hillslope where sample was collected	Soil
drainage_class	0..1 DRAINAGECLASSENUM	Drainage classification from a standard system such as the USDA system	Soil
soil_texture	0..1 String	The relative proportion of different grain sizes of mineral particles in a so...	Soil
soil_texture_meth	0..1 String	Reference or method used in determining soil texture	Soil
ph	0..1 Float	Ph measurement of the sample, or liquid portion of sample, or aqueous phase o...	Soil
ph_meth	0..1 String	Reference or method used in determining pH	Soil
org_matter	0..1 String	Concentration of organic matter	Soil
tot_org_carb	0..1 String	Total organic carbon content	Soil
tot_org_c_meth	0..1 String	Reference or method used in determining total organic carbon	Soil
tot_nitro_content	0..1 String	Total nitrogen content of the sample	Soil
tot_nitro_cont_meth	0..1 String	Reference or method used in determining the total nitrogen	Soil
microbial_biomass	0..1 String	The part of the organic matter in the soil that constitutes living microorgan...	Soil
micro_biomass_meth	0..1 String	Reference or method used in determining microbial biomass	Soil
link_addit_analys	0..1 String	Link to additional analysis results performed on the sample	Soil
heavy_metals	0..* String	Heavy metals present in the sequenced sample and their concentrations	Soil
heavy_metals_meth	0..1 String	Reference or method used in determining heavy metals	Soil
al_sat	0..1 String	Aluminum saturation (esp	Soil
al_sat_meth	0..1 String	Reference or method used in determining Al saturation	Soil
misc_param	0..* String	Any other measurement performed or parameter collected, that is not listed he...	Soil

Usages

used by	used in	type	used
MixsCompliantData	migs_eu_soil_data	range	MigsEuSoil

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc

Mappings

Mapping Type	Mapped Value
self	MIXS:0010002_0016012
native	mixs_6_2_rc:MigsEuSoil

LinkML Source

Direct

name: MigsEuSoil
description: MIxS data that complies with the MigsEu checklist and the Soil environmental
  package
title: MigsEu combined with Soil
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
is_a: Soil
mixins:
- MigsEu
class_uri: MIXS:0010002_0016012

Induced

name: MigsEuSoil
description: MIxS data that complies with the MigsEu checklist and the Soil environmental
  package
title: MigsEu combined with Soil
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
is_a: Soil
mixins:
- MigsEu
attributes:
  assembly_qual:
    name: assembly_qual
    description: 'The assembly quality category is based on sets of criteria outlined
      for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated,
      contiguous sequence per replicon without gaps or ambiguities with a consensus
      error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments
      where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes
      and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no
      review of assembly other than reporting of standard assembly statistics. Low
      Quality Draft:Many fragments with little to no review of assembly other than
      reporting of standard assembly statistics. Assembly statistics include, but
      are not limited to total assembly size, number of contigs, contig N50/L50, and
      maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence
      per replicon without gaps or ambiguities, with extensive manual review and editing
      to annotate putative gene functions and transcriptional units. High-quality
      draft genome: One or multiple fragments, totaling   90% of the expected genome
      or replicon sequence or predicted complete. Genome fragment(s): One or multiple
      fragments, totalling < 90% of the expected genome or replicon sequence, or for
      which no genome size could be estimated'
    title: assembly quality
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '[Finished genome|High-quality draft genome|Medium-quality
      draft genome|Low-quality draft genome|Genome fragment(s)]'
    slot_uri: MIXS:0000056
    multivalued: false
    alias: assembly_qual
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: true
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001107
    multivalued: false
    alias: samp_name
    owner: MigsEuSoil
    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
  estimated_size:
    name: estimated_size
    description: The estimated size of the genome prior to sequencing. Of particular
      importance in the sequencing of (eukaryotic) genome which could remain in draft
      form for a long or unspecified period
    title: estimated size
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{integer} bp'
    slot_uri: MIXS:0000024
    multivalued: false
    alias: estimated_size
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Miuvig
    range: string
    required: false
    recommended: false
  host_disease_stat:
    name: host_disease_stat
    description: List of diseases with which the host has been diagnosed; can include
      multiple diagnoses. The value of the field depends on host; for humans the terms
      should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org,
      non-human host diseases are free text
    title: host disease status
    examples:
    - value: rabies [DOID:11260]
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000031
    multivalued: false
    alias: host_disease_stat
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - PlantAssociated
    range: string
    required: false
    recommended: false
  alt:
    name: alt
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000094
    multivalued: false
    alias: alt
    owner: MigsEuSoil
    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
  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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000003
    multivalued: false
    alias: isol_growth_condt
    owner: MigsEuSoil
    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
  host_spec_range:
    name: host_spec_range
    description: The range and diversity of host species that an organism is capable
      of infecting, defined by NCBI taxonomy identifier
    title: host specificity or range
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{integer}'
    slot_uri: MIXS:0000030
    multivalued: true
    alias: host_spec_range
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsPl
    - MigsVi
    - Miuvig
    - Agriculture
    range: string
    required: false
    recommended: false
  feat_pred:
    name: feat_pred
    description: Method used to predict UViGs features such as ORFs, integration site,
      etc
    title: feature prediction
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000061
    multivalued: false
    alias: feat_pred
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
    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
  compl_software:
    name: compl_software
    description: Tools used for completion estimate, i.e. checkm, anvi'o, busco
    title: completeness software
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{software};{version}'
    slot_uri: MIXS:0000070
    multivalued: false
    alias: compl_software
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001321
    multivalued: false
    alias: neg_cont_type
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NEG_CONT_TYPE_ENUM
    recommended: true
  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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000093
    multivalued: false
    alias: elev
    owner: MigsEuSoil
    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
  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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000016
    multivalued: false
    alias: samp_mat_process
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: false
    recommended: false
  assembly_name:
    name: assembly_name
    description: Name/version of the assembly provided by the submitter that is used
      in the genome browsers and in the community
    title: assembly name
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text} {text}'
    slot_uri: MIXS:0000057
    multivalued: false
    alias: assembly_name
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  tax_class:
    name: tax_class
    description: Method used for taxonomic classification, along with reference database
      used, classification rank, and thresholds used to classify new genomes
    title: taxonomic classification
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000064
    multivalued: false
    alias: tax_class
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  specific_host:
    name: specific_host
    description: Report the host's taxonomic name and/or NCBI taxonomy ID
    title: host scientific name
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}|{NCBI taxid}'
    slot_uri: MIXS:0000029
    multivalued: false
    alias: specific_host
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsPl
    - MigsVi
    - Miuvig
    - Agriculture
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000026
    multivalued: true
    alias: source_mat_id
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    recommended: true
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000039
    multivalued: false
    alias: lib_size
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    required: false
    recommended: false
  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
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000002
    multivalued: false
    alias: samp_collect_device
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000058
    multivalued: false
    alias: assembly_software
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: 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
  adapters:
    name: adapters
    description: Adapters provide priming sequences for both amplification and sequencing
      of the sample-library fragments. Both adapters should be reported; in uppercase
      letters
    title: adapters
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{dna};{dna}'
    slot_uri: MIXS:0000048
    multivalued: false
    alias: adapters
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample
    title: sample collection method
    examples:
    - value: swabbing
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001225
    multivalued: false
    alias: samp_collect_method
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    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
  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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000028
    multivalued: false
    alias: biotic_relationship
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - MimarksC
    - Miuvig
    - Agriculture
    range: BIOTIC_RELATIONSHIP_ENUM
    required: false
    recommended: false
  annot:
    name: annot
    description: Tool used for annotation, or for cases where annotation was provided
      by a community jamboree or model organism database rather than by a specific
      submitter
    title: annotation
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000059
    multivalued: false
    alias: annot
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  sim_search_meth:
    name: sim_search_meth
    description: Tool used to compare ORFs with database, along with version and cutoffs
      used
    title: similarity search method
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000063
    multivalued: false
    alias: sim_search_meth
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
    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
  ploidy:
    name: ploidy
    description: The ploidy level of the genome (e.g. allopolyploid, haploid, diploid,
      triploid, tetraploid). It has implications for the downstream study of duplicated
      gene and regions of the genomes (and perhaps for difficulties in assembly).
      For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic
      Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer
      to http://purl.bioontology.org/ontology/PATO
    title: ploidy
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000021
    multivalued: false
    alias: ploidy
    owner: MigsEuSoil
    domain_of:
    - MigsEu
    range: string
    required: false
    recommended: false
    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
  number_contig:
    name: number_contig
    description: Total number of contigs in the cleaned/submitted assembly that makes
      up a given genome, SAG, MAG, or UViG
    title: number of contigs
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000060
    multivalued: false
    alias: number_contig
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: integer
    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
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000011
    multivalued: false
    alias: collection_date
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: datetime
    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)
    examples:
    - value: 'USA: Maryland, Bethesda'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000010
    multivalued: false
    alias: geo_loc_name
    owner: MigsEuSoil
    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
  ref_biomaterial:
    name: ref_biomaterial
    description: Primary publication if isolated before genome publication; otherwise,
      primary genome report
    title: reference for biomaterial
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000025
    multivalued: false
    alias: ref_biomaterial
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
    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()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000038
    multivalued: false
    alias: nucl_acid_amp
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001320
    multivalued: false
    alias: samp_taxon_id
    owner: MigsEuSoil
    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
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000041
    multivalued: false
    alias: lib_layout
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: LIB_LAYOUT_ENUM
    required: false
    recommended: false
  tax_ident:
    name: tax_ident
    description: The phylogenetic marker(s) used to assign an organism name to the
      SAG or MAG
    title: taxonomic identity marker
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000053
    alias: tax_ident
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: TAX_IDENT_ENUM
    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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000023
    multivalued: false
    alias: extrachrom_elements
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MimarksC
    range: integer
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000014
    multivalued: false
    alias: env_medium
    owner: MigsEuSoil
    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
  pathogenicity:
    name: pathogenicity
    description: To what is the entity pathogenic
    title: known pathogenicity
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000027
    multivalued: false
    alias: pathogenicity
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    - Miuvig
    - Agriculture
    range: string
    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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000001
    multivalued: false
    alias: samp_size
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    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
  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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{rank name}:{text}'
    slot_uri: MIXS:0000020
    multivalued: false
    alias: subspecf_gen_lin
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - MimarksC
    - FoodFoodProductionFacility
    range: string
    recommended: true
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000040
    multivalued: false
    alias: lib_reads_seqd
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000050
    multivalued: false
    alias: seq_meth
    owner: MigsEuSoil
    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
  temp:
    name: temp
    description: Temperature of the sample at the time of sampling
    title: temperature
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000113
    multivalued: false
    alias: temp
    owner: MigsEuSoil
    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
    required: false
    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
  experimental_factor:
    name: experimental_factor
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000008
    multivalued: true
    alias: experimental_factor
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: false
    recommended: false
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  lib_vector:
    name: lib_vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000042
    multivalued: false
    alias: lib_vector
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000111
    multivalued: false
    alias: samp_vol_we_dna_ext
    owner: MigsEuSoil
    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
    required: false
    recommended: false
    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
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    multivalued: false
    alias: pos_cont_type
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    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-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000013
    multivalued: false
    alias: env_local_scale
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: 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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000012
    multivalued: false
    alias: env_broad_scale
    owner: MigsEuSoil
    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
  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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000037
    multivalued: false
    alias: nucl_acid_ext
    owner: MigsEuSoil
    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
  compl_score:
    name: compl_score
    description: 'Completeness score is typically based on either the fraction of
      markers found as compared to a database or the percent of a genome found as
      compared to a closely related reference genome. High Quality Draft: >90%, Medium
      Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated
      completeness scores'
    title: completeness score
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '[high|med|low];{percentage}'
    slot_uri: MIXS:0000069
    multivalued: false
    alias: compl_score
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  ref_db:
    name: ref_db
    description: List of database(s) used for ORF annotation, along with version number
      and reference to website or publication
    title: reference database(s)
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{database};{version};{reference}'
    slot_uri: MIXS:0000062
    multivalued: false
    alias: ref_db
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - Mims
    - Misag
    - Miuvig
    range: string
    required: false
    recommended: false
  lat_lon:
    name: lat_lon
    annotations:
      Expected_value:
        tag: Expected_value
        value: decimal degrees,  limit to 8 decimal points
    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)
    examples:
    - value: 50.586825 6.408977
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{float} {float}'
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: MigsEuSoil
    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
  num_replicons:
    name: num_replicons
    description: Reports the number of replicons in a nuclear genome of eukaryotes,
      in the genome of a bacterium or archaea or the number of segments in a segmented
      virus. Always applied to the haploid chromosome count of a eukaryote
    title: number of replicons
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{integer}'
    slot_uri: MIXS:0000022
    alias: num_replicons
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsVi
    range: integer
    required: false
    recommended: false
  depth:
    name: depth
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000018
    multivalued: false
    alias: depth
    owner: MigsEuSoil
    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
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000092
    multivalued: false
    alias: project_name
    owner: MigsEuSoil
    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
  propagation:
    name: propagation
    description: 'The type of reproduction from the parent stock. Values for this
      field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately
      lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual'
    title: propagation
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000033
    multivalued: false
    alias: propagation
    owner: MigsEuSoil
    domain_of:
    - MigsEu
    - MigsPl
    - MigsVi
    range: string
    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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000032
    multivalued: false
    alias: trophic_level
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MimarksC
    - Agriculture
    range: TROPHIC_LEVEL_ENUM
    recommended: true
  lib_screen:
    name: lib_screen
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000043
    multivalued: false
    alias: lib_screen
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    multivalued: true
    alias: associated_resource
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    multivalued: true
    alias: sop
    owner: MigsEuSoil
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: 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-6-2-rc/mixs_6_2_rc
    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
    multivalued: false
    alias: cur_land_use
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
  cur_vegetation:
    name: cur_vegetation
    description: Vegetation classification from one or more standard classification
      systems, or agricultural crop
    title: current vegetation
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000312
    multivalued: false
    alias: cur_vegetation
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000314
    multivalued: false
    alias: cur_vegetation_meth
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    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
    description: Previous land use and dates
    title: history/previous land use
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{timestamp}'
    slot_uri: MIXS:0000315
    multivalued: false
    alias: previous_land_use
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000316
    multivalued: false
    alias: prev_land_use_meth
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    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
    description: Whether or not crop is rotated, and if yes, rotation schedule
    title: history/crop rotation
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{boolean};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000318
    multivalued: false
    alias: crop_rotation
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    required: false
    recommended: false
  agrochem_addition:
    name: agrochem_addition
    annotations:
      Expected_value:
        tag: Expected_value
        value: agrochemical name;agrochemical amount;timestamp
      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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit};{timestamp}'
    slot_uri: MIXS:0000639
    multivalued: true
    alias: agrochem_addition
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
  tillage:
    name: tillage
    description: Note method(s) used for tilling
    title: history/tillage
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001081
    multivalued: true
    alias: tillage
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: TILLAGE_ENUM
    required: false
    recommended: false
  fire:
    name: fire
    description: Historical and/or physical evidence of fire
    title: history/fire
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001086
    multivalued: false
    alias: fire
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: datetime
    required: false
    recommended: false
  flooding:
    name: flooding
    description: Historical and/or physical evidence of flooding
    title: history/flooding
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000319
    multivalued: false
    alias: flooding
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: datetime
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000320
    multivalued: false
    alias: extreme_event
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: datetime
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001082
    multivalued: false
    alias: soil_horizon
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: SOIL_HORIZON_ENUM
    required: false
    recommended: false
  horizon_meth:
    name: horizon_meth
    description: Reference or method used in determining the horizon
    title: horizon method
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000321
    multivalued: false
    alias: horizon_meth
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    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
    description: Collection design of pooled samples and/or sieve size and amount
      of sample sieved
    title: sieving
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000322
    multivalued: false
    alias: sieving
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
  water_content:
    name: water_content
    description: Water content measurement
    title: water content
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{float}'
    slot_uri: MIXS:0000185
    multivalued: false
    alias: water_content
    owner: MigsEuSoil
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Soil
    range: string
    required: false
    recommended: false
    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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000323
    multivalued: false
    alias: water_cont_soil_meth
    owner: MigsEuSoil
    domain_of:
    - Soil
    range: string
    required: false
    recommended: false
    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()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  pool_dna_extracts:
    name: pool_dna_extracts
    description: Indicate whether multiple DNA extractions were mixed. If the answer
      yes, the number of extracts that were pooled should be given
    title: pooling of DNA extracts (if done)
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{boolean};{integer}'
    slot_uri: MIXS:0000325
    multivalued: false
    alias: pool_dna_extracts
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - Soil
    range: string
    required: false
    recommended: false
  store_cond:
    name: store_cond
    description: Explain how and for how long the soil sample was stored before DNA
      extraction (fresh/frozen/other)
    title: storage conditions
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{period}'
    slot_uri: MIXS:0000327
    multivalued: false
    alias: store_cond
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
  link_climate_info:
    name: link_climate_info
    description: Link to climate resource
    title: link to climate information
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000328
    multivalued: false
    alias: link_climate_info
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000642
    multivalued: false
    alias: annual_temp
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000643
    multivalued: false
    alias: season_temp
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    required: false
    recommended: false
    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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000644
    multivalued: false
    alias: annual_precpt
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    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
    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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000645
    multivalued: false
    alias: season_precpt
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    required: false
    recommended: false
    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-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}]'
    slot_uri: MIXS:0000329
    multivalued: false
    alias: link_class_info
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001083
    multivalued: false
    alias: fao_class
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: FAO_CLASS_ENUM
    required: false
    recommended: false
  local_class:
    name: local_class
    description: Soil classification based on local soil classification system
    title: soil_taxonomic/local classification
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text}'
    slot_uri: MIXS:0000330
    multivalued: false
    alias: local_class
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: 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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000331
    multivalued: false
    alias: local_class_meth
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000205
    multivalued: false
    alias: org_nitro
    owner: MigsEuSoil
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Soil
    - Water
    range: string
    required: false
    recommended: false
    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
    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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{termLabel} [{termID}]

      '
    slot_uri: MIXS:0000332
    multivalued: false
    alias: soil_type
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    required: false
    recommended: false
  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: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000334
    multivalued: false
    alias: soil_type_meth
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    required: false
    recommended: false
    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
    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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000646
    multivalued: false
    alias: slope_gradient
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    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
    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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000647
    multivalued: false
    alias: slope_aspect
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001084
    multivalued: false
    alias: profile_position
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: PROFILE_POSITION_ENUM
    required: false
    recommended: false
  drainage_class:
    name: drainage_class
    description: Drainage classification from a standard system such as the USDA system
    title: drainage classification
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001085
    multivalued: false
    alias: drainage_class
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: DRAINAGE_CLASS_ENUM
    required: false
    recommended: false
  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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000335
    multivalued: false
    alias: soil_texture
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000336
    multivalued: false
    alias: soil_texture_meth
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    required: false
    recommended: false
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001001
    multivalued: false
    alias: ph
    owner: MigsEuSoil
    domain_of:
    - FoodFarmEnvironment
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Soil
    - WastewaterSludge
    - Water
    range: float
    required: false
    recommended: false
  ph_meth:
    name: ph_meth
    description: Reference or method used in determining pH
    title: pH method
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0001106
    multivalued: false
    alias: ph_meth
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    required: false
    recommended: false
    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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000204
    multivalued: false
    alias: org_matter
    owner: MigsEuSoil
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Soil
    - Water
    range: string
    required: false
    recommended: false
    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
    description: Total organic carbon content
    title: total organic carbon
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000533
    multivalued: false
    alias: tot_org_carb
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - MicrobialMatBiofilm
    - Sediment
    - Soil
    range: string
    required: false
    recommended: false
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000337
    multivalued: false
    alias: tot_org_c_meth
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    required: false
    recommended: false
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000530
    multivalued: false
    alias: tot_nitro_content
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - MicrobialMatBiofilm
    - Sediment
    - Soil
    range: string
    required: false
    recommended: false
    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
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000338
    multivalued: false
    alias: tot_nitro_cont_meth
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - Soil
    range: string
    required: false
    recommended: false
    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()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  microbial_biomass:
    name: microbial_biomass
    description: The part of the organic matter in the soil that constitutes living
      microorganisms smaller than 5-10 micrometer. If you keep this, you would need
      to have correction factors used for conversion to the final units
    title: microbial biomass
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000650
    multivalued: false
    alias: microbial_biomass
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  micro_biomass_meth:
    name: micro_biomass_meth
    description: Reference or method used in determining microbial biomass
    title: microbial biomass method
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000339
    alias: micro_biomass_meth
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000340
    multivalued: false
    alias: link_addit_analys
    owner: MigsEuSoil
    domain_of:
    - Soil
    range: string
    required: false
    recommended: false
    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()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  heavy_metals:
    name: heavy_metals
    annotations:
      Expected_value:
        tag: Expected_value
        value: heavy metal name;measurement value unit
      Preferred_unit:
        tag: Preferred_unit
        value: microgram per gram
    description: Heavy metals present in the sequenced sample and their concentrations.
      For multiple heavy metals and concentrations, add multiple copies of this field
    title: extreme_unusual_properties/heavy metals
    examples:
    - value: mercury;0.09 micrograms per gram
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000652
    multivalued: true
    alias: heavy_metals
    owner: MigsEuSoil
    domain_of:
    - Soil
    range: string
    required: false
    recommended: false
  heavy_metals_meth:
    name: heavy_metals_meth
    description: Reference or method used in determining heavy metals
    title: extreme_unusual_properties/heavy metals method
    from_schema: https://w3id.org/mixs-6-2-rc/mixs_6_2_rc
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000343
    multivalued: false
    alias: heavy_metals_meth
    owner: MigsEuSoil
    domain_of:
    - Agriculture
    - Soil
    range: string
    required: false
    recommended: false
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000607
    multivalued: false
    alias: al_sat
    owner: MigsEuSoil
    domain_of:
    - Soil
    range: string
    required: false
    recommended: false
    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-6-2-rc/mixs_6_2_rc
    slot_uri: MIXS:0000324
    multivalued: false
    alias: al_sat_meth
    owner: MigsEuSoil
    domain_of:
    - Soil
    range: string
    required: false
    recommended: false
    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-6-2-rc/mixs_6_2_rc
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    multivalued: true
    alias: misc_param
    owner: MigsEuSoil
    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
    required: false
    recommended: false
class_uri: MIXS:0010002_0016012