Combination: MimarksS combined with Sediment (MimarksSSediment)

MIxS Data that comply with the MimarksS checklist and the Sediment Extension

Composition

MimarksS [Checklist] + Sediment [Extension]

Terms

MIXS ID	Name	Cardinality and Range	Description
MIXS:0001107	samp_name	1 String	A local identifier or name that for the material sample used for extracting n...
MIXS:0000046	pcr_primers	0..1 recommended String	PCR primers that were used to amplify the sequence of the targeted gene, locu...
MIXS:0000017	size_frac	0..1 String	Filtering pore size used in sample preparation
MIXS:0000043	lib_screen	0..1 recommended String	Specific enrichment or screening methods applied before and/or after creating...
MIXS:0000038	nucl_acid_amp	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...
MIXS:0000039	lib_size	0..1 recommended Integer	Total number of clones in the library prepared for the project
MIXS:0000045	target_subfragment	0..1 recommended String	Name of subfragment of a gene or locus
MIXS:0000047	mid	0..1 recommended String	Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to spe...
MIXS:0000113	temp	0..1 recommended String	Temperature of the sample at the time of sampling
MIXS:0000037	nucl_acid_ext	0..1 recommended String	A link to a literature reference, electronic resource or a standard operating...
MIXS:0000001	samp_size	0..1 recommended String	The total amount or size (volume (ml), mass (g) or area (m2) ) of sample coll...
MIXS:0000094	alt	0..1 recommended String	Heights of objects such as airplanes, space shuttles, rockets, atmospheric ba...
MIXS:0000026	source_mat_id	* recommended String	A unique identifier assigned to a material sample (as defined by http://rs
MIXS:0000111	samp_vol_we_dna_ext	0..1 String	Volume (ml) or mass (g) of total collected sample processed for DNA extractio...
MIXS:0000040	lib_reads_seqd	0..1 recommended Integer	Total number of clones sequenced from the library
MIXS:0000015	rel_to_oxygen	0..1 RelToOxygenEnum	Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic ...
MIXS:0000002	samp_collect_device	0..1 recommended String	The device used to collect an environmental sample
MIXS:0000051	seq_quality_check	0..1 recommended SeqQualityCheckEnum	Indicate if the sequence has been called by automatic systems (none) or under...
MIXS:0000041	lib_layout	0..1 recommended LibLayoutEnum	Specify whether to expect single, paired, or other configuration of reads
MIXS:0000012	env_broad_scale	1 String	Report the major environmental system the sample or specimen came from
MIXS:0000092	project_name	1 String	Name of the project within which the sequencing was organized
MIXS:0000042	lib_vector	0..1 recommended String	Cloning vector type(s) used in construction of libraries
MIXS:0000048	adapters	0..1 recommended String	Adapters provide priming sequences for both amplification and sequencing of t...
MIXS:0001321	neg_cont_type	0..1 recommended NegContTypeEnum	The substance or equipment used as a negative control in an investigation
MIXS:0000058	assembly_software	0..1 recommended String	Tool(s) used for assembly, including version number and parameters
MIXS:0000052	chimera_check	0..1 recommended String	Tool(s) used for chimera checking, including version number and parameters, t...
MIXS:0001322	pos_cont_type	0..1 recommended String	The substance, mixture, product, or apparatus used to verify that a process w...
MIXS:0000013	env_local_scale	1 String	Report the entity or entities which are in the sample or specimen s local vic...
MIXS:0000016	samp_mat_process	0..1 recommended String	A brief description of any processing applied to the sample during or after r...
MIXS:0000018	depth	1 recommended String	The vertical distance below local surface
MIXS:0001225	samp_collect_method	0..1 recommended String	The method employed for collecting the sample
MIXS:0000014	env_medium	1 String	Report the environmental material(s) immediately surrounding the sample or sp...
MIXS:0001320	samp_taxon_id	1 String	NCBI taxon id of the sample
MIXS:0000010	geo_loc_name	1 String	The geographical origin of the sample as defined by the country or sea name f...
MIXS:0000011	collection_date	1 Datetime	The time of sampling, either as an instance (single point in time) or interva...
MIXS:0000050	seq_meth	1 String	Sequencing machine used
MIXS:0000009	lat_lon	1 String	The geographical origin of the sample as defined by latitude and longitude
MIXS:0000093	elev	0..1 recommended String	Elevation of the sampling site is its height above a fixed reference point, m...
MIXS:0000049	pcr_cond	0..1 recommended String	Description of reaction conditions and components of polymerase chain reactio...
MIXS:0000008	experimental_factor	* recommended String	Variable aspects of an experiment design that can be used to describe an expe...
MIXS:0000044	target_gene	1 String	Targeted gene or locus name for marker gene studies
MIXS:0000091	associated_resource	* recommended String	A related resource that is referenced, cited, or otherwise associated to the ...
MIXS:0000090	sop	* recommended String	Standard operating procedures used in assembly and/or annotation of genomes, ...
MIXS:0000421	alkalinity	0..1 String	Alkalinity, the ability of a solution to neutralize acids to the equivalence ...
MIXS:0000490	alkyl_diethers	0..1 String	Concentration of alkyl diethers
MIXS:0000172	aminopept_act	0..1 String	Measurement of aminopeptidase activity
MIXS:0000427	ammonium	0..1 String	Concentration of ammonium in the sample
MIXS:0000173	bacteria_carb_prod	0..1 String	Measurement of bacterial carbon production
MIXS:0000174	biomass	* String	Amount of biomass; should include the name for the part of biomass measured, ...
MIXS:0000175	bishomohopanol	0..1 String	Concentration of bishomohopanol
MIXS:0000176	bromide	0..1 String	Concentration of bromide
MIXS:0000432	calcium	0..1 String	Concentration of calcium in the sample
MIXS:0000310	carb_nitro_ratio	0..1 Float	Ratio of amount or concentrations of carbon to nitrogen
MIXS:0000751	chem_administration	* String	List of chemical compounds administered to the host or site where sampling oc...
MIXS:0000429	chloride	0..1 String	Concentration of chloride in the sample
MIXS:0000177	chlorophyll	0..1 String	Concentration of chlorophyll
MIXS:0000435	density	0..1 String	Density of the sample, which is its mass per unit volume (aka volumetric mass...
MIXS:0000178	diether_lipids	* String	Concentration of diether lipids; can include multiple types of diether lipids
MIXS:0000436	diss_carb_dioxide	0..1 String	Concentration of dissolved carbon dioxide in the sample or liquid portion of ...
MIXS:0000179	diss_hydrogen	0..1 String	Concentration of dissolved hydrogen
MIXS:0000434	diss_inorg_carb	0..1 String	Dissolved inorganic carbon concentration in the sample, typically measured af...
MIXS:0000433	diss_org_carb	0..1 String	Concentration of dissolved organic carbon in the sample, liquid portion of th...
MIXS:0000162	diss_org_nitro	0..1 String	Dissolved organic nitrogen concentration measured as; total dissolved nitroge...
MIXS:0000119	diss_oxygen	0..1 String	Concentration of dissolved oxygen
MIXS:0000137	glucosidase_act	0..1 String	Measurement of glucosidase activity
MIXS:0000431	magnesium	0..1 String	Concentration of magnesium in the sample
MIXS:0000498	mean_frict_vel	0..1 String	Measurement of mean friction velocity
MIXS:0000502	mean_peak_frict_vel	0..1 String	Measurement of mean peak friction velocity
MIXS:0000101	methane	0..1 String	Methane (gas) amount or concentration at the time of sampling
MIXS:0000752	misc_param	* String	Any other measurement performed or parameter collected, that is not listed he...
MIXS:0000503	n_alkanes	* String	Concentration of n-alkanes; can include multiple n-alkanes
MIXS:0000425	nitrate	0..1 String	Concentration of nitrate in the sample
MIXS:0000426	nitrite	0..1 String	Concentration of nitrite in the sample
MIXS:0000504	nitro	0..1 String	Concentration of nitrogen (total)
MIXS:0000508	org_carb	0..1 String	Concentration of organic carbon
MIXS:0000204	org_matter	0..1 String	Concentration of organic matter
MIXS:0000205	org_nitro	0..1 String	Concentration of organic nitrogen
MIXS:0000103	organism_count	* String	Total cell count of any organism (or group of organisms) per gram, volume or ...
MIXS:0000753	oxy_stat_samp	0..1 OxyStatSampEnum	Oxygenation status of sample
MIXS:0001001	ph	0..1 Float	Ph measurement of the sample, or liquid portion of sample, or aqueous phase o...
MIXS:0000206	particle_class	* String	Particles are classified, based on their size, into six general categories:cl...
MIXS:0000515	part_org_carb	0..1 String	Concentration of particulate organic carbon
MIXS:0000754	perturbation	* String	Type of perturbation, e
MIXS:0000516	petroleum_hydrocarb	0..1 String	Concentration of petroleum hydrocarbon
MIXS:0000180	phaeopigments	* String	Concentration of phaeopigments; can include multiple phaeopigments
MIXS:0000505	phosphate	0..1 String	Concentration of phosphate
MIXS:0000181	phosplipid_fatt_acid	* String	Concentration of phospholipid fatty acids; can include multiple values
MIXS:0000211	porosity	0..1 String	Porosity of deposited sediment is volume of voids divided by the total volume...
MIXS:0000430	potassium	0..1 String	Concentration of potassium in the sample
MIXS:0000412	pressure	0..1 String	Pressure to which the sample is subject to, in atmospheres
MIXS:0000182	redox_potential	0..1 String	Redox potential, measured relative to a hydrogen cell, indicating oxidation o...
MIXS:0000183	salinity	0..1 String	The total concentration of all dissolved salts in a liquid or solid sample
MIXS:0000116	samp_store_dur	0..1 String	Duration for which the sample was stored
MIXS:0000755	samp_store_loc	0..1 String	Location at which sample was stored, usually name of a specific freezer/room
MIXS:0000110	samp_store_temp	0..1 String	Temperature at which sample was stored, e
MIXS:0001078	sediment_type	0..1 SedimentTypeEnum	Information about the sediment type based on major constituents
MIXS:0000184	silicate	0..1 String	Concentration of silicate
MIXS:0000428	sodium	0..1 String	Sodium concentration in the sample
MIXS:0000423	sulfate	0..1 String	Concentration of sulfate in the sample
MIXS:0000424	sulfide	0..1 String	Concentration of sulfide in the sample
MIXS:0000750	tidal_stage	0..1 TidalStageEnum	Stage of tide
MIXS:0000525	tot_carb	0..1 String	Total carbon content
MIXS:0000634	tot_depth_water_col	0..1 String	Measurement of total depth of water column
MIXS:0000530	tot_nitro_content	0..1 String	Total nitrogen content of the sample
MIXS:0000533	tot_org_carb	0..1 String	Total organic carbon content
MIXS:0000191	turbidity	0..1 String	Measure of the amount of cloudiness or haziness in water caused by individual...
MIXS:0000185	water_content	0..1 String	Water content measurement

LinkML Source

Direct

name: MimarksSSediment
description: MIxS Data that comply with the MimarksS checklist and the Sediment Extension
title: MimarksS combined with Sediment
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: Sediment
mixins:
- MimarksS
class_uri: MIXS:0010008_0016011

Induced

name: MimarksSSediment
description: MIxS Data that comply with the MimarksS checklist and the Sediment Extension
title: MimarksS combined with Sediment
in_subset:
- combination_classes
from_schema: https://w3id.org/mixs
is_a: Sediment
mixins:
- MimarksS
attributes:
  samp_name:
    name: samp_name
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: ''
    description: A local identifier or name that for the material sample used for
      extracting nucleic acids, and subsequent sequencing. It can refer either to
      the original material collected or to any derived sub-samples. It can have any
      format, but we suggest that you make it concise, unique and consistent within
      your lab, and as informative as possible. INSDC requires every sample name from
      a single Submitter to be unique. Use of a globally unique identifier for the
      field source_mat_id is recommended in addition to sample_name
    title: sample name
    examples:
    - value: ISDsoil1
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    slot_uri: MIXS:0001107
    alias: samp_name
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
  pcr_primers:
    name: pcr_primers
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'FWD: forward primer sequence;REV:reverse primer sequence'
    description: PCR primers that were used to amplify the sequence of the targeted
      gene, locus or subfragment. This field should contain all the primers used for
      a single PCR reaction if multiple forward or reverse primers are present in
      a single PCR reaction. The primer sequence should be reported in uppercase letters
    title: pcr primers
    examples:
    - value: FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - pcr
    string_serialization: FWD:{dna};REV:{dna}
    slot_uri: MIXS:0000046
    alias: pcr_primers
    owner: MimarksSSediment
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  size_frac:
    name: size_frac
    annotations:
      Expected_value:
        tag: Expected_value
        value: filter size value range
    description: Filtering pore size used in sample preparation
    title: size fraction selected
    examples:
    - value: 0-0.22 micrometer
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - fraction
    - size
    string_serialization: '{float}-{float} {unit}'
    slot_uri: MIXS:0000017
    alias: size_frac
    owner: MimarksSSediment
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
  lib_screen:
    name: lib_screen
    annotations:
      Expected_value:
        tag: Expected_value
        value: screening strategy name
    description: Specific enrichment or screening methods applied before and/or after
      creating libraries
    title: library screening strategy
    examples:
    - value: enriched, screened, normalized
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000043
    alias: lib_screen
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  nucl_acid_amp:
    name: nucl_acid_amp
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the enzymatic amplification (PCR,
      TMA, NASBA) of specific nucleic acids
    title: nucleic acid amplification
    examples:
    - value: https://phylogenomics.me/protocols/16s-pcr-protocol/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000038
    alias: nucl_acid_amp
    owner: MimarksSSediment
    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
  lib_size:
    name: lib_size
    description: Total number of clones in the library prepared for the project
    title: library size
    examples:
    - value: '50'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    - size
    slot_uri: MIXS:0000039
    alias: lib_size
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  target_subfragment:
    name: target_subfragment
    description: Name of subfragment of a gene or locus. Important to e.g. identify
      special regions on marker genes like V6 on 16S rRNA
    title: target subfragment
    examples:
    - value: V6, V9, ITS
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - target
    slot_uri: MIXS:0000045
    alias: target_subfragment
    owner: MimarksSSediment
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  mid:
    name: mid
    description: Molecular barcodes, called Multiplex Identifiers (MIDs), that are
      used to specifically tag unique samples in a sequencing run. Sequence should
      be reported in uppercase letters
    title: multiplex identifiers
    examples:
    - value: GTGAATAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    slot_uri: MIXS:0000047
    alias: mid
    owner: MimarksSSediment
    domain_of:
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^[ACGTRKSYMWBHDVN]+$
    structured_pattern:
      syntax: ^{ambiguous_nucleotides}$
      interpolated: true
      partial_match: true
  temp:
    name: temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature of the sample at the time of sampling
    title: temperature
    examples:
    - value: 25 degree Celsius
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - temperature
    slot_uri: MIXS:0000113
    alias: temp
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  nucl_acid_ext:
    name: nucl_acid_ext
    description: A link to a literature reference, electronic resource or a standard
      operating procedure (SOP), that describes the material separation to recover
      the nucleic acid fraction from a sample
    title: nucleic acid extraction
    examples:
    - value: https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000037
    alias: nucl_acid_ext
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    pattern: ^^PMID:\d+$|^doi:10.\d{2,9}/.*$|^https?:\/\/(?:www\.)?[-a-zA-Z0-9@:%._\+~#=]{1,256}\.[a-zA-Z0-9()]{1,6}\b(?:[-a-zA-Z0-9()@:%_\+.~#?&\/=]*)$$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}$
      interpolated: true
      partial_match: true
  samp_size:
    name: samp_size
    description: The total amount or size (volume (ml), mass (g) or area (m2) ) of
      sample collected
    title: amount or size of sample collected
    examples:
    - value: 5 liter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - size
    slot_uri: MIXS:0000001
    alias: samp_size
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    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
  alt:
    name: alt
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Heights of objects such as airplanes, space shuttles, rockets, atmospheric
      balloons and heights of places such as atmospheric layers and clouds. It is
      used to measure the height of an object which is above the earth's surface.
      In this context, the altitude measurement is the vertical distance between the
      earth's surface above sea level and the sampled position in the air
    title: altitude
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000094
    alias: alt
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Air
    - HostAssociated
    - MiscellaneousNaturalOrArtificialEnvironment
    - SymbiontAssociated
    range: string
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  source_mat_id:
    name: source_mat_id
    annotations:
      Expected_value:
        tag: Expected_value
        value: 'for cultures of microorganisms: identifiers for two culture collections;
          for other material a unique arbitrary identifer'
    description: A unique identifier assigned to a material sample (as defined by
      http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular
      digital record of a material sample) used for extracting nucleic acids, and
      subsequent sequencing. The identifier can refer either to the original material
      collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher,
      /bio_material, or /culture_collection may or may not share the same value as
      the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id
      may both contain 'UAM:Herps:14' , referring to both the specimen voucher and
      sampled tissue with the same identifier. However, the /culture_collection qualifier
      may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id
      would refer to an identifier from some derived culture from which the nucleic
      acids were extracted (e.g. xatc123 or ark:/2154/R2)
    title: source material identifiers
    examples:
    - value: MPI012345
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - identifier
    - material
    - source
    slot_uri: MIXS:0000026
    alias: source_mat_id
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - SymbiontAssociated
    range: string
    recommended: true
    multivalued: true
  samp_vol_we_dna_ext:
    name: samp_vol_we_dna_ext
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliliter, gram, milligram, square centimeter
    description: 'Volume (ml) or mass (g) of total collected sample processed for
      DNA extraction. Note: total sample collected should be entered under the term
      Sample Size (MIXS:0000001)'
    title: sample volume or weight for DNA extraction
    examples:
    - value: 1500 milliliter
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - sample
    - volume
    - weight
    slot_uri: MIXS:0000111
    alias: samp_vol_we_dna_ext
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  lib_reads_seqd:
    name: lib_reads_seqd
    description: Total number of clones sequenced from the library
    title: library reads sequenced
    examples:
    - value: '20'
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000040
    alias: lib_reads_seqd
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: integer
    recommended: true
  rel_to_oxygen:
    name: rel_to_oxygen
    description: Is this organism an aerobe, anaerobe? Please note that aerobic and
      anaerobic are valid descriptors for microbial environments
    title: relationship to oxygen
    examples:
    - value: aerobe
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - oxygen
    - relationship
    slot_uri: MIXS:0000015
    alias: rel_to_oxygen
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    range: RelToOxygenEnum
  samp_collect_device:
    name: samp_collect_device
    annotations:
      Expected_value:
        tag: Expected_value
        value: device name
    description: The device used to collect an environmental sample. This field accepts
      terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO).
      This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094)
    title: sample collection device
    examples:
    - value: swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - device
    - sample
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000002
    alias: samp_collect_device
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
  seq_quality_check:
    name: seq_quality_check
    annotations:
      Expected_value:
        tag: Expected_value
        value: none or manually edited
    description: Indicate if the sequence has been called by automatic systems (none)
      or undergone a manual editing procedure (e.g. by inspecting the raw data or
      chromatograms). Applied only for sequences that are not submitted to SRA,ENA
      or DRA
    title: sequence quality check
    examples:
    - value: none
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - quality
    slot_uri: MIXS:0000051
    alias: seq_quality_check
    owner: MimarksSSediment
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: SeqQualityCheckEnum
    recommended: true
  lib_layout:
    name: lib_layout
    description: Specify whether to expect single, paired, or other configuration
      of reads
    title: library layout
    examples:
    - value: paired
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000041
    alias: lib_layout
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: LibLayoutEnum
    recommended: true
  env_broad_scale:
    name: env_broad_scale
    description: 'Report the major environmental system the sample or specimen came
      from. The system(s) identified should have a coarse spatial grain, to provide
      the general environmental context of where the sampling was done (e.g. in the
      desert or a rainforest). We recommend using subclasses of EnvO s biome class:  http://purl.obolibrary.org/obo/ENVO_00000428.
      EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS'
    title: broad-scale environmental context
    examples:
    - value: rangeland biome [ENVO:01000247]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000012
    alias: env_broad_scale
    owner: MimarksSSediment
    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
  project_name:
    name: project_name
    description: Name of the project within which the sequencing was organized
    title: project name
    examples:
    - value: Forest soil metagenome
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - project
    slot_uri: MIXS:0000092
    alias: project_name
    owner: MimarksSSediment
    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
  lib_vector:
    name: lib_vector
    annotations:
      Expected_value:
        tag: Expected_value
        value: vector
    description: Cloning vector type(s) used in construction of libraries
    title: library vector
    examples:
    - value: Bacteriophage P1
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - library
    slot_uri: MIXS:0000042
    alias: lib_vector
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: 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
    examples:
    - value: AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000048
    alias: adapters
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    structured_pattern:
      syntax: ^{adapter_A_DNA_sequence};{adapter_B_DNA_sequence}$
      interpolated: true
      partial_match: true
  neg_cont_type:
    name: neg_cont_type
    annotations:
      Expected_value:
        tag: Expected_value
        value: enumeration or text
    description: The substance or equipment used as a negative control in an investigation
    title: negative control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - type
    slot_uri: MIXS:0001321
    alias: neg_cont_type
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: NegContTypeEnum
    recommended: true
  assembly_software:
    name: assembly_software
    description: Tool(s) used for assembly, including version number and parameters
    title: assembly software
    examples:
    - value: metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    slot_uri: MIXS:0000058
    alias: assembly_software
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  chimera_check:
    name: chimera_check
    description: Tool(s) used for chimera checking, including version number and parameters,
      to discover and remove chimeric sequences. A chimeric sequence is comprised
      of two or more phylogenetically distinct parent sequences
    title: chimera check software
    examples:
    - value: uchime;v4.1;default parameters
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - software
    slot_uri: MIXS:0000052
    alias: chimera_check
    owner: MimarksSSediment
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+);([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{software};{version};{parameters}$
      interpolated: true
      partial_match: true
  pos_cont_type:
    name: pos_cont_type
    description: The substance, mixture, product, or apparatus used to verify that
      a process which is part of an investigation delivers a true positive
    title: positive control type
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - type
    string_serialization: '{term} or {text}'
    slot_uri: MIXS:0001322
    alias: pos_cont_type
    owner: MimarksSSediment
    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
    keywords:
    - context
    - environmental
    slot_uri: MIXS:0000013
    alias: env_local_scale
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  samp_mat_process:
    name: samp_mat_process
    description: A brief description of any processing applied to the sample during
      or after retrieving the sample from environment, or a link to the relevant protocol(s)
      performed
    title: sample material processing
    examples:
    - value: filtering of seawater, storing samples in ethanol
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - material
    - process
    - sample
    slot_uri: MIXS:0000016
    alias: samp_mat_process
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
  depth:
    name: depth
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: The vertical distance below local surface. For sediment or soil samples
      depth is measured from sediment or soil surface, respectively. Depth can be
      reported as an interval for subsurface samples
    title: depth
    examples:
    - value: 10 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - depth
    slot_uri: MIXS:0000018
    alias: depth
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodFarmEnvironment
    - HostAssociated
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    required: true
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_collect_method:
    name: samp_collect_method
    description: The method employed for collecting the sample
    title: sample collection method
    examples:
    - value: swabbing
    in_subset:
    - nucleic acid sequence source
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    - sample
    slot_uri: MIXS:0001225
    alias: samp_collect_method
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - 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()@:%_\+.~#?&\/=]*)$|([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{PMID}|{DOI}|{URL}|{text}$
      interpolated: true
      partial_match: true
  env_medium:
    name: env_medium
    description: 'Report the environmental material(s) immediately surrounding the
      sample or specimen at the time of sampling. We recommend using subclasses of
      ''environmental material'' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO
      documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
      . Terms from other OBO ontologies are permissible as long as they reference
      mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities
      (e.g. a tree, a leaf, a table top)'
    title: environmental medium
    examples:
    - value: bluegrass field soil [ENVO:00005789]
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - environmental
    slot_uri: MIXS:0000014
    alias: env_medium
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\]$
    structured_pattern:
      syntax: ^{termLabel} \[{termID}\]$
      interpolated: true
      partial_match: true
  samp_taxon_id:
    name: samp_taxon_id
    description: NCBI taxon id of the sample.  Maybe be a single taxon or mixed taxa
      sample. Use 'synthetic metagenome  for mock community/positive controls, or
      'blank sample' for negative controls
    title: taxonomy ID of DNA sample
    examples:
    - value: Gut Metagenome [NCBITaxon:749906]
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - dna
    - identifier
    - sample
    - taxon
    slot_uri: MIXS:0001320
    alias: samp_taxon_id
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[NCBITaxon:\d+\]$
    structured_pattern:
      syntax: ^{text} \[{NCBItaxon_id}\]$
      interpolated: true
      partial_match: true
  geo_loc_name:
    name: geo_loc_name
    description: The geographical origin of the sample as defined by the country or
      sea name followed by specific region name. Country or sea names should be chosen
      from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology
      (http://purl.bioontology.org/ontology/GAZ)
    title: geographic location (country and/or sea,region)
    examples:
    - value: 'USA: Maryland, Bethesda'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000010
    alias: geo_loc_name
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: '^([^\s-]{1,2}|[^\s-]+.+[^\s-]+): ([^\s-]{1,2}|[^\s-]+.+[^\s-]+), ([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$'
    structured_pattern:
      syntax: '^{text}: {text}, {text}$'
      interpolated: true
      partial_match: true
  collection_date:
    name: collection_date
    description: 'The time of sampling, either as an instance (single point in time)
      or interval. In case no exact time is available, the date/time can be right
      truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10;
      2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant'
    title: collection date
    examples:
    - value: '2013-03-25T12:42:31+01:00'
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - date
    slot_uri: MIXS:0000011
    alias: collection_date
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: datetime
    required: true
  seq_meth:
    name: seq_meth
    description: Sequencing machine used. Where possible the term should be taken
      from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103)
    title: sequencing method
    examples:
    - value: 454 Genome Sequencer FLX [OBI:0000702]
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - method
    slot_uri: MIXS:0000050
    alias: seq_meth
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    required: true
    pattern: ^([^\s-]{1,2}|[^\s-]+.+[^\s-]+)|(([^\s-]{1,2}|[^\s-]+.+[^\s-]+) \[[a-zA-Z]{2,}:[a-zA-Z0-9]\d+\])$
    structured_pattern:
      syntax: ^{text}|({termLabel} \[{termID}\])$
      interpolated: true
      partial_match: true
  lat_lon:
    name: lat_lon
    description: The geographical origin of the sample as defined by latitude and
      longitude. The values should be reported in decimal degrees, limited to 8 decimal
      points, and in WGS84 system
    title: geographic location (latitude and longitude)
    examples:
    - value: 50.586825 6.408977
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - geographic
    - location
    slot_uri: MIXS:0000009
    alias: lat_lon
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - SymbiontAssociated
    range: string
    required: true
    pattern: ^(-?((?:[0-8]?[0-9](?:\.\d{0,8})?)|90)) -?[0-9]+(?:\.[0-9]{0,8})?$|^-?(1[0-7]{1,2})$
    structured_pattern:
      syntax: ^{lat} {lon}$
      interpolated: true
      partial_match: true
  elev:
    name: elev
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Elevation of the sampling site is its height above a fixed reference
      point, most commonly the mean sea level. Elevation is mainly used when referring
      to points on the earth's surface, while altitude is used for points above the
      surface, such as an aircraft in flight or a spacecraft in orbit
    title: elevation
    examples:
    - value: 100 meter
    in_subset:
    - environment
    from_schema: https://w3id.org/mixs
    keywords:
    - elevation
    slot_uri: MIXS:0000093
    alias: elev
    owner: MimarksSSediment
    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
    recommended: true
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  pcr_cond:
    name: pcr_cond
    annotations:
      Expected_value:
        tag: Expected_value
        value: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
          elongation:degrees_minutes;total cycles
    description: Description of reaction conditions and components of polymerase chain
      reaction performed during library preparation.
    title: pcr conditions
    examples:
    - value: initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35
    - value: initial denaturation:94degC_1.5min
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - condition
    - pcr
    string_serialization: initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final
      elongation:degrees_minutes;total cycles
    slot_uri: MIXS:0000049
    alias: pcr_cond
    owner: MimarksSSediment
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    recommended: true
  experimental_factor:
    name: experimental_factor
    annotations:
      Expected_value:
        tag: Expected_value
        value: text or EFO and/or OBI
    description: Variable aspects of an experiment design that can be used to describe
      an experiment, or set of experiments, in an increasingly detailed manner. This
      field accepts ontology terms from Experimental Factor Ontology (EFO) and/or
      Ontology for Biomedical Investigations (OBI)
    title: experimental factor
    examples:
    - value: time series design [EFO:0001779]
    in_subset:
    - investigation
    from_schema: https://w3id.org/mixs
    keywords:
    - experimental
    - factor
    string_serialization: '{termLabel} [{termID}]|{text}'
    slot_uri: MIXS:0000008
    alias: experimental_factor
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    range: string
    recommended: true
    multivalued: true
    pattern: ^\S+.*\S+ \[[a-zA-Z]{2,}:\d+\]$
  target_gene:
    name: target_gene
    description: Targeted gene or locus name for marker gene studies
    title: target gene
    examples:
    - value: 16S rRNA, 18S rRNA, nif, amoA, rpo
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - target
    slot_uri: MIXS:0000044
    alias: target_gene
    owner: MimarksSSediment
    domain_of:
    - MimarksC
    - MimarksS
    - Agriculture
    range: string
    required: true
  associated_resource:
    name: associated_resource
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to resource
    description: A related resource that is referenced, cited, or otherwise associated
      to the sequence
    title: relevant electronic resources
    examples:
    - value: http://www.earthmicrobiome.org/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - resource
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000091
    alias: associated_resource
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    multivalued: true
  sop:
    name: sop
    annotations:
      Expected_value:
        tag: Expected_value
        value: reference to SOP
    description: Standard operating procedures used in assembly and/or annotation
      of genomes, metagenomes or environmental sequences
    title: relevant standard operating procedures
    examples:
    - value: http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/
    in_subset:
    - sequencing
    from_schema: https://w3id.org/mixs
    keywords:
    - procedures
    string_serialization: '{PMID}|{DOI}|{URL}'
    slot_uri: MIXS:0000090
    alias: sop
    owner: MimarksSSediment
    domain_of:
    - MigsBa
    - MigsEu
    - MigsOrg
    - MigsPl
    - MigsVi
    - Mimag
    - MimarksC
    - MimarksS
    - Mims
    - Misag
    - Miuvig
    - Agriculture
    range: string
    recommended: true
    multivalued: true
  alkalinity:
    name: alkalinity
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milliequivalent per liter, milligram per liter
    description: Alkalinity, the ability of a solution to neutralize acids to the
      equivalence point of carbonate or bicarbonate
    title: alkalinity
    examples:
    - value: 50 milligram per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - alkalinity
    slot_uri: MIXS:0000421
    alias: alkalinity
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  alkyl_diethers:
    name: alkyl_diethers
    description: Concentration of alkyl diethers
    title: alkyl diethers
    examples:
    - value: 0.005 mole per liter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000490
    alias: alkyl_diethers
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  aminopept_act:
    name: aminopept_act
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: mole per liter per hour
    description: Measurement of aminopeptidase activity
    title: aminopeptidase activity
    examples:
    - value: 0.269 mole per liter per hour
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000172
    alias: aminopept_act
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  ammonium:
    name: ammonium
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter, milligram per liter, parts per million
    description: Concentration of ammonium in the sample
    title: ammonium
    examples:
    - value: 1.5 milligram per liter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000427
    alias: ammonium
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  bacteria_carb_prod:
    name: bacteria_carb_prod
    description: Measurement of bacterial carbon production
    title: bacterial carbon production
    examples:
    - value: 2.53 microgram per liter per hour
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - production
    slot_uri: MIXS:0000173
    alias: bacteria_carb_prod
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  biomass:
    name: biomass
    annotations:
      Expected_value:
        tag: Expected_value
        value: biomass type;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: ton, kilogram, gram
    description: Amount of biomass; should include the name for the part of biomass
      measured, e.g. Microbial, total. Can include multiple measurements
    title: biomass
    examples:
    - value: total;20 gram
    from_schema: https://w3id.org/mixs
    keywords:
    - biomass
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000174
    alias: biomass
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    multivalued: true
  bishomohopanol:
    name: bishomohopanol
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: microgram per liter, microgram per gram
    description: Concentration of bishomohopanol
    title: bishomohopanol
    examples:
    - value: 14 microgram per liter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000175
    alias: bishomohopanol
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  bromide:
    name: bromide
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: parts per million
    description: Concentration of bromide
    title: bromide
    examples:
    - value: 0.05 parts per million
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000176
    alias: bromide
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  calcium:
    name: calcium
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter, micromole per liter, parts per million
    description: Concentration of calcium in the sample
    title: calcium
    examples:
    - value: 0.2 micromole per liter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000432
    alias: calcium
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  carb_nitro_ratio:
    name: carb_nitro_ratio
    annotations:
      Expected_value:
        tag: Expected_value
        value: measurement value
    description: Ratio of amount or concentrations of carbon to nitrogen
    title: carbon/nitrogen ratio
    examples:
    - value: '0.417361111'
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - nitrogen
    - ratio
    string_serialization: '{float}:{float}'
    slot_uri: MIXS:0000310
    alias: carb_nitro_ratio
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: float
  chem_administration:
    name: chem_administration
    annotations:
      Expected_value:
        tag: Expected_value
        value: CHEBI;timestamp
    description: List of chemical compounds administered to the host or site where
      sampling occurred, and when (e.g. Antibiotics, n fertilizer, air filter); can
      include multiple compounds. For chemical entities of biological interest ontology
      (chebi) (v 163), http://purl.bioontology.org/ontology/chebi
    title: chemical administration
    examples:
    - value: agar [CHEBI:2509];2018-05-11T20:00Z
    from_schema: https://w3id.org/mixs
    keywords:
    - administration
    string_serialization: '{termLabel} [{termID}];{timestamp}'
    slot_uri: MIXS:0000751
    alias: chem_administration
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  chloride:
    name: chloride
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter, parts per million
    description: Concentration of chloride in the sample
    title: chloride
    examples:
    - value: 5000 milligram per liter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000429
    alias: chloride
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  chlorophyll:
    name: chlorophyll
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per cubic meter, microgram per liter
    description: Concentration of chlorophyll
    title: chlorophyll
    examples:
    - value: 5 milligram per cubic meter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000177
    alias: chlorophyll
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  density:
    name: density
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram per cubic meter, gram per cubic centimeter
    description: Density of the sample, which is its mass per unit volume (aka volumetric
      mass density)
    title: density
    examples:
    - value: 1000 kilogram per cubic meter
    from_schema: https://w3id.org/mixs
    keywords:
    - density
    slot_uri: MIXS:0000435
    alias: density
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  diether_lipids:
    name: diether_lipids
    annotations:
      Expected_value:
        tag: Expected_value
        value: diether lipid name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: nanogram per liter
    description: Concentration of diether lipids; can include multiple types of diether
      lipids
    title: diether lipids
    examples:
    - value: 0.2 nanogram per liter
    from_schema: https://w3id.org/mixs
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000178
    alias: diether_lipids
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    multivalued: true
  diss_carb_dioxide:
    name: diss_carb_dioxide
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter, milligram per liter
    description: Concentration of dissolved carbon dioxide in the sample or liquid
      portion of the sample
    title: dissolved carbon dioxide
    examples:
    - value: 5 milligram per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - dissolved
    slot_uri: MIXS:0000436
    alias: diss_carb_dioxide
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  diss_hydrogen:
    name: diss_hydrogen
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter
    description: Concentration of dissolved hydrogen
    title: dissolved hydrogen
    examples:
    - value: 0.3 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - dissolved
    slot_uri: MIXS:0000179
    alias: diss_hydrogen
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  diss_inorg_carb:
    name: diss_inorg_carb
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: microgram per liter, milligram per liter, parts per million
    description: Dissolved inorganic carbon concentration in the sample, typically
      measured after filtering the sample using a 0.45 micrometer filter
    title: dissolved inorganic carbon
    examples:
    - value: 2059 micromole per kilogram
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - dissolved
    - inorganic
    slot_uri: MIXS:0000434
    alias: diss_inorg_carb
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  diss_org_carb:
    name: diss_org_carb
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter, milligram per liter
    description: Concentration of dissolved organic carbon in the sample, liquid portion
      of the sample, or aqueous phase of the fluid
    title: dissolved organic carbon
    examples:
    - value: 197 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - dissolved
    - organic
    slot_uri: MIXS:0000433
    alias: diss_org_carb
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  diss_org_nitro:
    name: diss_org_nitro
    description: Dissolved organic nitrogen concentration measured as; total dissolved
      nitrogen - NH4 - NO3 - NO2
    title: dissolved organic nitrogen
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - dissolved
    - nitrogen
    - organic
    slot_uri: MIXS:0000162
    alias: diss_org_nitro
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  diss_oxygen:
    name: diss_oxygen
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per kilogram, milligram per liter
    description: Concentration of dissolved oxygen
    title: dissolved oxygen
    examples:
    - value: 175 micromole per kilogram
    from_schema: https://w3id.org/mixs
    keywords:
    - dissolved
    - oxygen
    slot_uri: MIXS:0000119
    alias: diss_oxygen
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  glucosidase_act:
    name: glucosidase_act
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: mol per liter per hour
    description: Measurement of glucosidase activity
    title: glucosidase activity
    examples:
    - value: 5 mol per liter per hour
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000137
    alias: glucosidase_act
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  magnesium:
    name: magnesium
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: mole per liter, milligram per liter, parts per million, micromole per
          kilogram
    description: Concentration of magnesium in the sample
    title: magnesium
    examples:
    - value: 52.8 micromole per kilogram
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000431
    alias: magnesium
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  mean_frict_vel:
    name: mean_frict_vel
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter per second
    description: Measurement of mean friction velocity
    title: mean friction velocity
    examples:
    - value: 0.5 meter per second
    from_schema: https://w3id.org/mixs
    keywords:
    - mean
    - velocity
    slot_uri: MIXS:0000498
    alias: mean_frict_vel
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  mean_peak_frict_vel:
    name: mean_peak_frict_vel
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter per second
    description: Measurement of mean peak friction velocity
    title: mean peak friction velocity
    examples:
    - value: 1 meter per second
    from_schema: https://w3id.org/mixs
    keywords:
    - mean
    - peak
    - velocity
    slot_uri: MIXS:0000502
    alias: mean_peak_frict_vel
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  methane:
    name: methane
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter, parts per billion, parts per million
    description: Methane (gas) amount or concentration at the time of sampling
    title: methane
    examples:
    - value: 0.15 micromole per liter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000101
    alias: methane
    owner: MimarksSSediment
    domain_of:
    - Air
    - MicrobialMatBiofilm
    - Sediment
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  misc_param:
    name: misc_param
    annotations:
      Expected_value:
        tag: Expected_value
        value: parameter name;measurement value
    description: Any other measurement performed or parameter collected, that is not
      listed here
    title: miscellaneous parameter
    examples:
    - value: Bicarbonate ion concentration;2075 micromole per kilogram
    from_schema: https://w3id.org/mixs
    keywords:
    - parameter
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000752
    alias: misc_param
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - Soil
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  n_alkanes:
    name: n_alkanes
    annotations:
      Expected_value:
        tag: Expected_value
        value: n-alkane name;measurement value
    description: Concentration of n-alkanes; can include multiple n-alkanes
    title: n-alkanes
    examples:
    - value: n-hexadecane;100 milligram per liter
    from_schema: https://w3id.org/mixs
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000503
    alias: n_alkanes
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    multivalued: true
  nitrate:
    name: nitrate
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter, milligram per liter, parts per million
    description: Concentration of nitrate in the sample
    title: nitrate
    examples:
    - value: 65 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - nitrate
    slot_uri: MIXS:0000425
    alias: nitrate
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  nitrite:
    name: nitrite
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter, milligram per liter, parts per million
    description: Concentration of nitrite in the sample
    title: nitrite
    examples:
    - value: 0.5 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - nitrite
    slot_uri: MIXS:0000426
    alias: nitrite
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  nitro:
    name: nitro
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter
    description: Concentration of nitrogen (total)
    title: nitrogen
    examples:
    - value: 4.2 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - nitrogen
    slot_uri: MIXS:0000504
    alias: nitro
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  org_carb:
    name: org_carb
    description: Concentration of organic carbon
    title: organic carbon
    examples:
    - value: 1.5 microgram per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - organic
    slot_uri: MIXS:0000508
    alias: org_carb
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  org_matter:
    name: org_matter
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: microgram per liter
    description: Concentration of organic matter
    title: organic matter
    examples:
    - value: 1.75 milligram per cubic meter
    from_schema: https://w3id.org/mixs
    keywords:
    - organic
    slot_uri: MIXS:0000204
    alias: org_matter
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Soil
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  org_nitro:
    name: org_nitro
    description: Concentration of organic nitrogen
    title: organic nitrogen
    examples:
    - value: 4 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - nitrogen
    - organic
    slot_uri: MIXS:0000205
    alias: org_nitro
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Soil
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  organism_count:
    name: organism_count
    annotations:
      Expected_value:
        tag: Expected_value
        value: organism name;measurement value;enumeration
    description: 'Total cell count of any organism (or group of organisms) per gram,
      volume or area of sample, should include name of organism followed by count.
      The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should
      also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)'
    title: organism count
    examples:
    - value: total prokaryotes;3.5e7 cells per milliliter;qPCR
    from_schema: https://w3id.org/mixs
    keywords:
    - count
    - organism
    string_serialization: '{text};{float} {unit};[ATP|MPN|qPCR|other]'
    slot_uri: MIXS:0000103
    alias: organism_count
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - Air
    - BuiltEnvironment
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  oxy_stat_samp:
    name: oxy_stat_samp
    description: Oxygenation status of sample
    title: oxygenation status of sample
    examples:
    - value: aerobic
    from_schema: https://w3id.org/mixs
    keywords:
    - oxygen
    - sample
    - status
    slot_uri: MIXS:0000753
    alias: oxy_stat_samp
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - Air
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: OxyStatSampEnum
  ph:
    name: ph
    description: Ph measurement of the sample, or liquid portion of sample, or aqueous
      phase of the fluid
    title: pH
    examples:
    - value: '7.2'
    from_schema: https://w3id.org/mixs
    keywords:
    - ph
    slot_uri: MIXS:0001001
    alias: ph
    owner: MimarksSSediment
    domain_of:
    - FoodFarmEnvironment
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Soil
    - WastewaterSludge
    - Water
    range: float
  particle_class:
    name: particle_class
    annotations:
      Expected_value:
        tag: Expected_value
        value: particle name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: micrometer
    description: Particles are classified, based on their size, into six general categories:clay,
      silt, sand, gravel, cobbles, and boulders; should include amount of particle
      preceded by the name of the particle type; can include multiple values
    title: particle classification
    from_schema: https://w3id.org/mixs
    keywords:
    - classification
    - particle
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000206
    alias: particle_class
    owner: MimarksSSediment
    domain_of:
    - Sediment
    range: string
    multivalued: true
  part_org_carb:
    name: part_org_carb
    description: Concentration of particulate organic carbon
    title: particulate organic carbon
    examples:
    - value: 1.92 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - organic
    - particle
    - particulate
    slot_uri: MIXS:0000515
    alias: part_org_carb
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  perturbation:
    name: perturbation
    annotations:
      Expected_value:
        tag: Expected_value
        value: perturbation type name;perturbation interval and duration
    description: Type of perturbation, e.g. chemical administration, physical disturbance,
      etc., coupled with perturbation regimen including how many times the perturbation
      was repeated, how long each perturbation lasted, and the start and end time
      of the entire perturbation period; can include multiple perturbation types
    title: perturbation
    examples:
    - value: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M
    from_schema: https://w3id.org/mixs
    keywords:
    - perturbation
    string_serialization: '{text};{Rn/start_time/end_time/duration}'
    slot_uri: MIXS:0000754
    alias: perturbation
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    multivalued: true
  petroleum_hydrocarb:
    name: petroleum_hydrocarb
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter
    description: Concentration of petroleum hydrocarbon
    title: petroleum hydrocarbon
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - hydrocarbon
    - petroleum
    slot_uri: MIXS:0000516
    alias: petroleum_hydrocarb
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  phaeopigments:
    name: phaeopigments
    annotations:
      Expected_value:
        tag: Expected_value
        value: phaeopigment name;measurement value
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per cubic meter
    description: Concentration of phaeopigments; can include multiple phaeopigments
    title: phaeopigments
    examples:
    - value: 2.5 milligram per cubic meter
    from_schema: https://w3id.org/mixs
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000180
    alias: phaeopigments
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    multivalued: true
  phosphate:
    name: phosphate
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter
    description: Concentration of phosphate
    title: phosphate
    examples:
    - value: 0.7 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - phosphate
    slot_uri: MIXS:0000505
    alias: phosphate
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  phosplipid_fatt_acid:
    name: phosplipid_fatt_acid
    annotations:
      Expected_value:
        tag: Expected_value
        value: phospholipid fatty acid name;measurement value
    description: Concentration of phospholipid fatty acids; can include multiple values
    title: phospholipid fatty acid
    examples:
    - value: 2.98 milligram per liter
    from_schema: https://w3id.org/mixs
    string_serialization: '{text};{float} {unit}'
    slot_uri: MIXS:0000181
    alias: phosplipid_fatt_acid
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    multivalued: true
  porosity:
    name: porosity
    annotations:
      Expected_value:
        tag: Expected_value
        value: measurement value or range
      Preferred_unit:
        tag: Preferred_unit
        value: percentage
    description: Porosity of deposited sediment is volume of voids divided by the
      total volume of sample
    title: porosity
    from_schema: https://w3id.org/mixs
    keywords:
    - porosity
    string_serialization: '{float} - {float} {unit}'
    slot_uri: MIXS:0000211
    alias: porosity
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - HydrocarbonResourcesCores
    - Sediment
    range: string
  potassium:
    name: potassium
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter, parts per million
    description: Concentration of potassium in the sample
    title: potassium
    examples:
    - value: 463 milligram per liter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000430
    alias: potassium
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  pressure:
    name: pressure
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: atmosphere
    description: Pressure to which the sample is subject to, in atmospheres
    title: pressure
    examples:
    - value: 50 atmosphere
    from_schema: https://w3id.org/mixs
    keywords:
    - pressure
    slot_uri: MIXS:0000412
    alias: pressure
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  redox_potential:
    name: redox_potential
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: millivolt
    description: Redox potential, measured relative to a hydrogen cell, indicating
      oxidation or reduction potential
    title: redox potential
    examples:
    - value: 300 millivolt
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000182
    alias: redox_potential
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  salinity:
    name: salinity
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: practical salinity unit, percentage
    description: The total concentration of all dissolved salts in a liquid or solid
      sample. While salinity can be measured by a complete chemical analysis, this
      method is difficult and time consuming. More often, it is instead derived from
      the conductivity measurement. This is known as practical salinity. These derivations
      compare the specific conductance of the sample to a salinity standard such as
      seawater
    title: salinity
    examples:
    - value: 25 practical salinity unit
    from_schema: https://w3id.org/mixs
    keywords:
    - salinity
    slot_uri: MIXS:0000183
    alias: salinity
    owner: MimarksSSediment
    domain_of:
    - Air
    - FoodFarmEnvironment
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  samp_store_dur:
    name: samp_store_dur
    description: Duration for which the sample was stored. Indicate the duration for
      which the sample was stored written in ISO 8601 format
    title: sample storage duration
    examples:
    - value: P1Y6M
    from_schema: https://w3id.org/mixs
    keywords:
    - duration
    - period
    - sample
    - storage
    slot_uri: MIXS:0000116
    alias: samp_store_dur
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^P(?:(?:\d+D|\d+M(?:\d+D)?|\d+Y(?:\d+M(?:\d+D)?)?)(?:T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S))?|T(?:\d+H(?:\d+M(?:\d+S)?)?|\d+M(?:\d+S)?|\d+S)|\d+W)$
    structured_pattern:
      syntax: ^{duration}$
      interpolated: true
      partial_match: true
  samp_store_loc:
    name: samp_store_loc
    annotations:
      Expected_value:
        tag: Expected_value
        value: location name
    description: Location at which sample was stored, usually name of a specific freezer/room
    title: sample storage location
    examples:
    - value: Freezer no:5
    from_schema: https://w3id.org/mixs
    keywords:
    - location
    - sample
    - storage
    slot_uri: MIXS:0000755
    alias: samp_store_loc
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
  samp_store_temp:
    name: samp_store_temp
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: degree Celsius
    description: Temperature at which sample was stored, e.g. -80 degree Celsius
    title: sample storage temperature
    examples:
    - value: -80 degree Celsius
    from_schema: https://w3id.org/mixs
    keywords:
    - sample
    - storage
    - temperature
    slot_uri: MIXS:0000110
    alias: samp_store_temp
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - Air
    - FoodAnimalAndAnimalFeed
    - FoodFarmEnvironment
    - FoodFoodProductionFacility
    - FoodHumanFoods
    - HostAssociated
    - HumanAssociated
    - HumanGut
    - HumanOral
    - HumanSkin
    - HumanVaginal
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - PlantAssociated
    - Sediment
    - SymbiontAssociated
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  sediment_type:
    name: sediment_type
    description: Information about the sediment type based on major constituents
    title: sediment type
    examples:
    - value: biogenous
    from_schema: https://w3id.org/mixs
    keywords:
    - sediment
    - type
    slot_uri: MIXS:0001078
    alias: sediment_type
    owner: MimarksSSediment
    domain_of:
    - Sediment
    range: SedimentTypeEnum
  silicate:
    name: silicate
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter
    description: Concentration of silicate
    title: silicate
    examples:
    - value: 0.05 micromole per liter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000184
    alias: silicate
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  sodium:
    name: sodium
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: milligram per liter, parts per million
    description: Sodium concentration in the sample
    title: sodium
    examples:
    - value: 10.5 milligram per liter
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000428
    alias: sodium
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - WastewaterSludge
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  sulfate:
    name: sulfate
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter, milligram per liter, parts per million
    description: Concentration of sulfate in the sample
    title: sulfate
    examples:
    - value: 5 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - sulfate
    slot_uri: MIXS:0000423
    alias: sulfate
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  sulfide:
    name: sulfide
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: micromole per liter, milligram per liter, parts per million
    description: Concentration of sulfide in the sample
    title: sulfide
    examples:
    - value: 2 micromole per liter
    from_schema: https://w3id.org/mixs
    keywords:
    - sulfide
    slot_uri: MIXS:0000424
    alias: sulfide
    owner: MimarksSSediment
    domain_of:
    - HydrocarbonResourcesCores
    - HydrocarbonResourcesFluidsSwabs
    - MicrobialMatBiofilm
    - MiscellaneousNaturalOrArtificialEnvironment
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  tidal_stage:
    name: tidal_stage
    description: Stage of tide
    title: tidal stage
    examples:
    - value: high tide
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000750
    alias: tidal_stage
    owner: MimarksSSediment
    domain_of:
    - Sediment
    - Water
    range: TidalStageEnum
  tot_carb:
    name: tot_carb
    description: Total carbon content
    title: total carbon
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - total
    slot_uri: MIXS:0000525
    alias: tot_carb
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - MicrobialMatBiofilm
    - Sediment
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  tot_depth_water_col:
    name: tot_depth_water_col
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: meter
    description: Measurement of total depth of water column
    title: total depth of water column
    examples:
    - value: 500 meter
    from_schema: https://w3id.org/mixs
    keywords:
    - depth
    - total
    - water
    slot_uri: MIXS:0000634
    alias: tot_depth_water_col
    owner: MimarksSSediment
    domain_of:
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  tot_nitro_content:
    name: tot_nitro_content
    description: Total nitrogen content of the sample
    title: total nitrogen content
    examples:
    - value: 35 milligrams Nitrogen per kilogram of soil
    from_schema: https://w3id.org/mixs
    keywords:
    - content
    - nitrogen
    - total
    slot_uri: MIXS:0000530
    alias: tot_nitro_content
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - MicrobialMatBiofilm
    - Sediment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  tot_org_carb:
    name: tot_org_carb
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram Carbon per kilogram sample material
    description: Total organic carbon content
    title: total organic carbon
    examples:
    - value: '0.02'
    from_schema: https://w3id.org/mixs
    keywords:
    - carbon
    - organic
    - total
    slot_uri: MIXS:0000533
    alias: tot_org_carb
    owner: MimarksSSediment
    domain_of:
    - Agriculture
    - FoodFarmEnvironment
    - MicrobialMatBiofilm
    - Sediment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  turbidity:
    name: turbidity
    description: Measure of the amount of cloudiness or haziness in water caused by
      individual particles
    title: turbidity
    examples:
    - value: 0.3 nephelometric turbidity units
    from_schema: https://w3id.org/mixs
    slot_uri: MIXS:0000191
    alias: turbidity
    owner: MimarksSSediment
    domain_of:
    - FoodFarmEnvironment
    - MicrobialMatBiofilm
    - Sediment
    - Water
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
  water_content:
    name: water_content
    annotations:
      Preferred_unit:
        tag: Preferred_unit
        value: gram per gram or cubic centimeter per cubic centimeter
    description: Water content measurement
    title: water content
    from_schema: https://w3id.org/mixs
    keywords:
    - content
    - water
    string_serialization: '{float} {unit}'
    slot_uri: MIXS:0000185
    alias: water_content
    owner: MimarksSSediment
    domain_of:
    - MicrobialMatBiofilm
    - Sediment
    - Soil
    range: string
    pattern: ^[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?( *- *[-+]?[0-9]*\.?[0-9]+(?:[eE][-+]?[0-9]+)?)?
      *([^\s-]{1,2}|[^\s-]+.+[^\s-]+)$
    structured_pattern:
      syntax: ^{scientific_float}( *- *{scientific_float})? *{text}$
      interpolated: true
      partial_match: true
class_uri: MIXS:0010008_0016011